MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Genomics Proteomics ...' source. Thu, 09 Feb 2012 09:43:38 +0100 http://www.medworm.com/index.php?rid=5594048&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22237267%26dopt%3DAbstract Authors: Li XH, Li JJ, Liu YY, Chen JX Abstract Some researchers focus on research of the nature of syndromes. The methods of combining traditional Chinese medicine syndrome and diseases and the correspondence between formulas and syndromes may be used in research of the nature of syndromes. According to combined theories of zang-organ state and seven emotions in traditional Chinese medicine with stress theory in modern medicine, the authors applied the methods of chronic immobilization stress to induce liver depression and spleen deficiency syndrome in rats based on the thinking of relativity on formula and syndrome. The research showed that the central neurobiology mechanism of liver depression and spleen deficiency syndrome closely correlates to the hypothalamic-pituitary-adrena... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5594048 Sun, 01 Jan 2012 05:00:00 +0100 5594048 http://www.medworm.com/index.php?rid=5594049&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22227401%26dopt%3DAbstract This article is part of a Special Issue entitled: Genome regulations and Genetic diversity. PMID: 22227401 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5594049 Fri, 30 Dec 2011 05:00:00 +0100 5594049 http://www.medworm.com/index.php?rid=5504080&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21843342%26dopt%3DAbstract CONCLUSIONS: The pathways generated with IL-4R highlight possible important intracellular signaling cascades implicating, for instance, NFκB. Furthermore, the proposed interaction between SOCS5 and IL-4R could explain how different genes can lead to identical clinical RAO phenotypes, as observed in two Swiss Warmblood half sibling families because these proteins interact upstream of an important cascade where they may act as a functional unit. PMID: 21843342 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5504080 Thu, 15 Dec 2011 23:06:02 +0100 5504080 http://www.medworm.com/index.php?rid=5450244&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22114102%26dopt%3DAbstract Authors: Barbhuiya MA, Sahasrabuddhe NA, Pinto SM, Muthusamy B, Singh TD, Nanjappa V, Keerthikumar S, Delanghe B, Harsha HC, Chaerkady R, Jalaj V, Gupta S, Shrivastav BR, Tiwari PK, Pandey A Abstract Bile serves diverse functions from metabolism to transport. In addition to acids and salts, bile is composed of proteins secreted or shed by the hepatobiliary system. Although there have been previous efforts to catalog biliary proteins, an in-depth analysis of the bile proteome has not yet been reported. We carried out fractionation of non-cancerous bile samples using a multipronged approach (SDS-PAGE, SCX and OFFGEL) followed by MS analysis on an LTQ-Orbitrap Velos mass spectrometer using high resolution at both MS and MS/MS levels. We identified 2552 proteins - the largest number of... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5450244 Mon, 28 Nov 2011 13:30:12 +0100 5450244 http://www.medworm.com/index.php?rid=5433470&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22090146%26dopt%3DAbstract Authors: Puri A, Neelamegham S Abstract Following the footsteps of genomics and proteomics, recent years have witnessed the growth of large-scale experimental methods in the field of glycomics. In parallel, there has also been growing interest in developing Systems Biology based methods to study the glycome. The combined goals of these endeavors is to identify glycosylation-dependent mechanisms regulating human physiology, check points that can control the progression of pathophysiology, and modifications to reaction pathways that can result in more uniform biopharmaceutical processes. In these efforts, mathematical models of N- and O-linked glycosylation have emerged as paradigms for the field. While these are relatively few in number, nevertheless, the existing models provide a b... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5433470 Thu, 17 Nov 2011 05:00:00 +0100 5433470 http://www.medworm.com/index.php?rid=5372925&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21992029%26dopt%3DAbstract CONCLUSIONS: With AASsites single SNPs can be checked for those causing splice modifications. Screening 80,000 known human SNPs we detected about 1,200 SNPs which probably modify splicing. AASsites is available at http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar using any web browser. PMID: 21992029 [PubMed - in process] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5372925 Fri, 04 Nov 2011 14:30:03 +0100 5372925 http://www.medworm.com/index.php?rid=5372922&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22046025%26dopt%3DAbstract Authors: Turteltaub KW, Davis MA, Burns-Naas LA, Lawton MP, Clark AM, Reynolds JA Abstract There has been an explosion of technology-enabled scientific insight into the basic biology of the causes of adverse events. This has been driven, in part, by the development of the various "omics" tools (e.g., genomics, proteomics, and metabolomics) and associated bioinformatics platforms. Meanwhile, for decades, changes in preclinical testing protocols and guidelines have been limited. Preclinical safety testing currently relies heavily on the use of outdated animal models. Application of systems biology methods to evaluation of toxicities in oncology treatments can accelerate the introduction of safe, effective drugs. Systems biology adds insights regarding the causes and mechanisms of adv... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5372922 Tue, 01 Nov 2011 04:00:00 +0100 5372922 http://www.medworm.com/index.php?rid=5372923&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22034500%26dopt%3DAbstract In this study, using a combination of detergent-free Blue Native Gel Electrophoresis, proteomics and in vitro testing of pre-tRNA maturation, we reveal the physical association of these plus other mitochondrial activities in a large, stable complex of 136 proteins. It contains a total of seven proteins involved in RNA processing including RNase P and RNase Z, five out of six subunits of the mitochondrial RNA degradosome, components of the fatty acid synthesis pathway, translation, metabolism and protein folding. At the RNA level, there are the small and large rRNA subunits and RNase P RNA. Surprisingly, this complex is absent in an oar1Δ deletion mutant of the type II fatty acid synthesis pathway, supporting a recently published functional link between pre-tRNA processing and the FAS II p... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5372923 Thu, 27 Oct 2011 04:00:00 +0100 5372923 http://www.medworm.com/index.php?rid=5372924&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22024468%26dopt%3DAbstract Authors: Wang X Abstract ABSTRACT: Network biomarker as a new type of biomarkers with protein-protein interactions was initiated and investigated with the integration of knowledge on protein annotations, interaction, and signaling pathway. A number of methodologies and computational programs have been developed to integrate selected proteins into the knowledge-based networks via the combination of genomics, proteomics and bioinformatics. Alterations of network biomarkers can be monitored and evaluated at different stages and time points during the development of diseases, named dynamic network biomarkers. Dynamic network biomarkers should be furthermore correlated with clinical informatics, including patient complaints, history, therapies, clinical symptoms and signs, physician's e... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5372924 Mon, 24 Oct 2011 04:00:00 +0100 5372924 http://www.medworm.com/index.php?rid=5372926&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22011341%26dopt%3DAbstract Authors: Daszkowska-Golec A Abstract Abstract Different abiotic stresses inhibit or delay the development and growth of plants. The most crucial step of plant life cycle, which ensures the survival of the next generation, is seed germination. Plants are sessile organisms that need to integrate internal and external signals in order to produce the correct response. Plants have evolved mechanisms that enable seed germination to be arrested under stress conditions and then resumed when conditions are favorable. The complexity of this mechanism was explored in Arabidopsis thaliana using mutants that had defects in their phytohormone metabolism and signaling pathways. These analyses led to the identification of many important components that are involved in these pathways and shed ligh... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5372926 Wed, 19 Oct 2011 04:00:00 +0100 5372926 http://www.medworm.com/index.php?rid=5272300&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21496229%26dopt%3DAbstract CONCLUSION: FungalRV webserver facilitating the discovery process for novel human pathogenic fungal adhesin vaccine has been developed. PMID: 21496229 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5272300 Sun, 02 Oct 2011 11:05:02 +0100 5272300 http://www.medworm.com/index.php?rid=5237917&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21931718%26dopt%3DAbstract In this study, we identified proteins that are removed along with the targeted high abundant proteins. Three plasma samples were depleted using each of the three MARS (Hu-6, Hu-14 and Proteoprep 20) cartridges. The affinity bound fractions were subjected to gelC-MS using an LTQ-Orbitrap instrument. Using four database search algorithms including MassWiz (developed in house), we selected the peptides identified at <1% FDR. Peptides identified by at least two algorithms were selected for protein identification. After this rigorous bioinformatics analysis, we identified 101 proteins with high confidence. Thus, we believe that for biomarker discovery and proper quantitation of proteins, it might be better to study both bound and depleted fractions from any MARS depleted plasma sample. P... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5237917 Thu, 22 Sep 2011 07:32:02 +0100 5237917 http://www.medworm.com/index.php?rid=5213481&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21575182%26dopt%3DAbstract CONCLUSION: Although the impact of AS on the functional properties of the proteome remains to be uncovered, the results of this study indicate that AS-induced diversity at the transcriptome level is also expressed at the proteome level. PMID: 21575182 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5213481 Tue, 13 Sep 2011 11:08:02 +0100 5213481 http://www.medworm.com/index.php?rid=5213480&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21575196%26dopt%3DAbstract CONCLUSIONS: PRIN is the first well annotated protein interaction database for the important model plant Oryza sativa. It has greatly extended the current available protein-protein interaction data of rice with a computational approach, which will certainly provide further insights into rice functional genomics and systems biology. PRIN is available online at http://bis.zju.edu.cn/prin/. PMID: 21575196 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5213480 Tue, 13 Sep 2011 11:08:02 +0100 5213480 http://www.medworm.com/index.php?rid=5213478&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21908202%26dopt%3DAbstract Authors: Sarwal MM, Sigdel TK, Salomon DR Abstract The evolving era of functional genomics in organ transplantation is supported by advances in gene profiling, sequencing, proteomics, antibody profiling and bioinformatics, thus heralding a new era of intelligent and customized monitoring and therapy. These advances will serve to meet the critical unmet needs of improving graft survival, limiting graft injury from under-immunosuppression and reducing patient morbidity from over-immunosuppression. This review is a summary of current status of potentially useful technologies available for genomics and proteomics applications in transplantation with the emphasis on addressing the complexities of cellular immunology at the molecular level and the clinical challenges of transplantation t... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5213478 Fri, 09 Sep 2011 04:00:00 +0100 5213478 http://www.medworm.com/index.php?rid=5213479&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21893519%26dopt%3DAbstract Authors: Kamburov A, Cavill R, Ebbels TM, Herwig R, Keun HC Abstract SUMMARY: Pathway-level analysis is a powerful approach enabling interpretation of post-genomic data at a higher level than that of individual biomolecules. Yet, it is currently hard to integrate more than one type of omics data in such an approach. Here, we present a web tool 'IMPaLA' for the joint pathway analysis of transcriptomics or proteomics and metabolomics data. It performs over-representation or enrichment analysis with user-specified lists of metabolites and genes using over 3,000 pre-annotated pathways from 11 databases. As a result, pathways can be identified that may be disregulated on the transcriptional level, the metabolic level or both. Evidence of pathway disregulation is combined, allowing for t... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5213479 Sun, 04 Sep 2011 04:00:00 +0100 5213479 http://www.medworm.com/index.php?rid=5132959&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21029773%26dopt%3DAbstract This article is part of a Special Issue entitled: Translating nuclear receptors from health to disease. PMID: 21029773 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5132959 Sun, 31 Jul 2011 23:00:00 +0100 5132959 http://www.medworm.com/index.php?rid=5132958&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21831800%26dopt%3DAbstract Authors: Yang X, Jiao R, Yang L, Wu LP, Li YR, Wang J In recent years, new-generation high-throughput technologies, including next-generation sequencing technology and mass spectrometry method, have been widely applied in solving biological problems, especially in human diseases field. This data driven, large-scale and industrialized research model enables the omnidirectional and multi-level study of human diseases from the perspectives of genomics, transcriptomics and proteomics levels, etc. In this paper, the latest development of the high-throughput technologies that applied in DNA, RNA, epigenomics, metagenomics including proteomics and some applications in translational medicine are reviewed. At genomics level, exome sequencing has been the hot spot of the recent research. However... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5132958 Sun, 31 Jul 2011 23:00:00 +0100 5132958 http://www.medworm.com/index.php?rid=5086606&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21773993%26dopt%3DAbstract In conclusion, the present integrative evidences from DNA, RNA, and protein levels supported SOD2 as a susceptibility gene for osteoporosis. © 2011 American Society for Bone and Mineral Research. PMID: 21773993 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5086606 Mon, 18 Jul 2011 23:00:00 +0100 5086606 http://www.medworm.com/index.php?rid=5037271&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21729868%26dopt%3DAbstract Authors: Kumar P, Yadav VK, Baral A, Kumar P, Saha D, Chowdhury S Function of non-B DNA structures are poorly understood though several bioinformatics studies predict role of the G-quadruplex DNA structure in transcription. Earlier, using transcriptome profiling we found evidence of widespread G-quadruplex-mediated gene regulation. Herein, we asked whether potential G-quadruplex (PG4) motifs associate with transcription factors (TF). This was analyzed using 220 position weight matrices [designated as transcription factor binding sites (TFBS)], representing 187 unique TF, in >75 000 genes in human, chimpanzee, mouse and rat. Results show binding sites of nine TFs, including that of AP-2, SP1, MAZ and VDR, occurred significantly within 100 bases of the PG4 motif (P < 1.24E-10... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=5037271 Sun, 03 Jul 2011 23:00:00 +0100 5037271 http://www.medworm.com/index.php?rid=4993284&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21685100%26dopt%3DAbstract This article introduces a mathematically rigorous algorithm to delineate protein structure using the elegant statistical and inductive inference framework of minimum message length (MML). Our method generates consistent and statistically robust piecewise linear explanations of protein coordinate data, resulting in a powerful and concise representation of the structure. The delineation is completely independent of the approaches of using hydrogen-bonding patterns or inspecting local substructural geometry that the current methods use. Indeed, as is common with applications of the MML criterion, this method is free of parameters and thresholds, in striking contrast to the existing programs which are often beset by them. The analysis of results over a large number of proteins suggests that th... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4993284 Thu, 30 Jun 2011 23:00:00 +0100 4993284 http://www.medworm.com/index.php?rid=4993283&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21709402%26dopt%3DAbstract Authors: Ghidoni R, Benussi L, Paterlini A, Albertini V, Binetti G, Emanuele E Alzheimer's disease (AD) is the major cause of dementia in the elderly. The biochemical changes that precede AD may be present up to 20 years before the clinical manifestation of the disease. The translational development of AD biomarkers may be theoretically achieved via two different strategies: the first strategy can be defined as 'knowledge-based' (deductive method), while the second one is a hypothesis-generating 'unbiased' approach (inductive strategy). The 'knowledge-based' approach relies on a direct understanding of the neuropathological processes that underlie the development of AD. In contrast, the 'unbiased' approach involves the use of modern techniques including proteomics and bioinformatics th... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4993283 Fri, 24 Jun 2011 23:00:00 +0100 4993283 http://www.medworm.com/index.php?rid=4943693&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21679186%26dopt%3DAbstract Conclusion:  The data generated by the use of 'omic technologies have huge potential to inform paradigm shifts in our understanding of periodontal diseases, but data management, analysis and interpretation require a thoughtful and systematic bioinformatics approach, to ensure meaningful conclusions can be made. PMID: 21679186 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4943693 Thu, 16 Jun 2011 23:00:00 +0100 4943693 http://www.medworm.com/index.php?rid=4794150&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21535262%26dopt%3DAbstract Conclusion:  Random loss of cell survival/replication genes was calculated to be low enough for colon stem cells with APC gene mutations to 'select' LOH and derivative chromosome combinations favouring tumour cell proliferation. However, cell survival/replication gene loss was calculated to be too high for colonic stem cells lacking MMR genes to survive chromosomal instability, explaining why MMR mutations only produce tumours with diploid chromosome cells. PMID: 21535262 [PubMed - in process] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4794150 Sat, 07 May 2011 08:30:21 +0100 4794150 http://www.medworm.com/index.php?rid=4794151&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21517945%26dopt%3DAbstract Authors: Doyle S Some fungi cause disease in humans and plants, while others have demonstrable potential for the control of insect pests. In addition, fungi are also a rich reservoir of therapeutic metabolites and industrially-useful enzymes. Detailed analysis of fungal biochemistry is now enabled by multiple technologies including protein mass spectrometry, genome and transcriptome sequencing and advances in bioinformatics. Yet, the assignment of function to fungal proteins, encoded either by in silico annotated, or unannotated genes, remains problematic. The purpose of this review is to describe the strategies used by many researchers to reveal protein function in fungi, and more importantly, to consolidate the nomenclature of 'unknown function protein', or UFP, as opposed to 'hypoth... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4794151 Sun, 24 Apr 2011 23:00:00 +0100 4794151 http://www.medworm.com/index.php?rid=4742229&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21470146%26dopt%3DAbstract Authors: Pirogova E, Istivan T, Gan E, Cosic I Drug discovery and development are intense, lengthy and interdisciplinary processes. Traditionally, drugs were discovered by synthesizing compounds in time-consuming multi-step experimental investigations followed by in vitro and in vivo biological screening. Promising candidates were then further studied for their pharmacokinetic properties, metabolism and potential toxicity. Today, the process of drug discovery has been revolutionized due to the advances in genomics, proteomics, and bioinformatics. Efficient technologies such as combinatorial chemistry, high throughput screening (HTS), virtual screening, de novo design and structure-based drug design contribute greatly to drug discovery. Peptides are emerging as a novel class of drugs fo... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4742229 Tue, 05 Apr 2011 23:00:00 +0100 4742229 http://www.medworm.com/index.php?rid=4684864&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21466243%26dopt%3DAbstract Authors: Anagnostopoulos A, Dimas K, Papathanasiou C, Braoudaki M, Anastasiadou E, Vougas K, Kontos H, Karamolegou K, Prodromou N, Tzortzatou F, Tsangaris GT Childhood pilocytic astrocytoma is the most frequent brain tumor affecting children. Proteomics analysis is currently considered a powerful tool for global evaluation of protein expression, and has been widely applied in the field of cancer research. In the present study a series of proteomics, genomics and bioinformatics approaches were employed in order to identify, classify and characterize the proteome content of low grade brain tumors as it appears in early childhood. Through bioinformatics database construction, protein profiles generated from pathological tissues samples were compared against profiles of normal brain tissue... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4684864 Tue, 05 Apr 2011 23:00:00 +0100 4684864 http://www.medworm.com/index.php?rid=4566403&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21370077%26dopt%3DAbstract Authors: Schneider MV, Orchard S We provide an overview on the state of the art for the Omics technologies, the types of omics data and the bioinformatics resources relevant and related to Omics. We also illustrate the bioinformatics challenges of dealing with high-throughput data. This overview touches several fundamental aspects of Omics and bioinformatics: data standardisation, data sharing, storing Omics data appropriately and exploring Omics data in bioinformatics. Though the principles and concepts presented are true for the various different technological fields, we concentrate in three main Omics fields namely: genomics, transcriptomics and proteomics. Finally we address the integration of Omics data, and provide several useful links for bioinformatics and Omics. PMID: 2137... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4566403 Thu, 10 Mar 2011 07:00:08 +0100 4566403 http://www.medworm.com/index.php?rid=4566404&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21349866%26dopt%3DAbstract Authors: Ahmad I, Suits F, Hoekman B, Swertz MA, Byelas H, Dijkstra M, Hooft R, Katsubo D, van Breukelen B, Bischoff R, Horvatovich P SUMMARY: Warp2D is a novel time alignment approach, which uses the overlapping peak volume of the reference and sample peak lists to correct misleading peak shifts. Here we present an easy-to-use web interface for high-throughput Warp2D batch processing time alignment service using the Dutch Life Science Grid reducing processing time from days to hours. This service provides the warping function, the sample chromatogram peak list with adjusted retention times, and normalized quality scores based on the sum of over-lapping peak volume of all peaks. Heat maps before and after time alignment are created from the arithmetic mean of the sum of over-lapping pe... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4566404 Wed, 23 Feb 2011 00:00:00 +0100 4566404 http://www.medworm.com/index.php?rid=4511724&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21330406%26dopt%3DAbstract We examined the importance of AR binding to DNA in prostate cancer cells in which proliferation in the absence of hormone was profoundly (~90%) dependent on endogenous AR and where the receptor was not up-regulated or mutated but was predominantly nuclear. Here, ARE-mediated promoter activation and the binding of AR to a known ARE in the chromatin remained entirely androgen dependent, and the cells showed an androgen-responsive gene expression profile with an unaltered sensitivity to androgen dose. In the same cells, a different set of genes primarily enriched for cell division functions was activated by AR independently of hormone and significantly overlapped the signature gene overexpression profile of hormone ablation-insensitive clinical tumors. After knockdown of endogenous AR, hormon... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4511724 Thu, 17 Feb 2011 00:00:00 +0100 4511724 http://www.medworm.com/index.php?rid=4454111&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21255096%26dopt%3DAbstract Authors: Kalantari-Dehaghi M, Molina DM, Farhadieh M, John Morrow W, Liang X, Felgner PL, Grando SA We performed partial evaluation of pemphigus vulgaris (PV) autoantibody profile using the protein array technology. The sera from seven patients with acute PV and five healthy donors were probed for the presence of autoantibodies characteristic of the organ-non-specific autoimmune disorders rheumatoid arthritis, lupus erythematosus, scleroderma, diabetes and some other autoimmune disorders, but not to desmosomal proteins. The array targeted 785 human genes amplified using Mammalian Gene Clone Collection with gene-specific primers containing 20-bp nucleotide extension complementary to ends of linear pXT7 vector. The array identified PV antibodies significantly (P < 0.05) differen... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4454111 Tue, 01 Feb 2011 00:00:00 +0100 4454111 http://www.medworm.com/index.php?rid=4388539&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21253555%26dopt%3DAbstract Authors: Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4388539 Sun, 23 Jan 2011 23:30:02 +0100 4388539 http://www.medworm.com/index.php?rid=4297866&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21166477%26dopt%3DAbstract Authors: Tran BQ, Hernandez C, Waridel P, Potts A, Barblan J, Lisacek F, Quadroni M In the vast majority of bottom-up proteomics studies, protein digestion is performed using only mammalian trypsin. Although it is clearly the best enzyme available, the sole use of trypsin rarely leads to complete sequence coverage, even for abundant proteins. It is commonly assumed that this is because many tryptic peptides are either too short or too long to be identified by RPLC-MS/MS. We show through in silico analysis that 20-30% of the total sequence of three proteomes (Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Homo sapiens) is expected to be covered by Large post-Trypsin Peptides (LpTPs) with M(r) above 3000 Da. We then established size exclusion chromatography to fractionate compl... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4297866 Mon, 20 Dec 2010 00:00:00 +0100 4297866 http://www.medworm.com/index.php?rid=4266572&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21151453%26dopt%3DAbstract Authors: Muñoz B, Albores A Exposure to different substances in an occupational environment is of utmost concern to global agencies such as the World Health Organization and the International Labour Organization. Interest in improving work health conditions, particularly of those employees exposed to noxious chemicals, has increased considerably and has stimulated the search for new, more specific and selective tests. Recently, the field of molecular biology has been indicated as an alternative technique for monitoring personnel while evaluating work-related pathologies. Originally, occupational exposure to environmental toxicants was assessed using biochemical techniques to determine the presence of higher concentrations of toxic compounds in blood, urine, or other fluids or tissues;... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4266572 Sun, 19 Dec 2010 08:40:06 +0100 4266572 http://www.medworm.com/index.php?rid=4266571&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21164131%26dopt%3DAbstract CONCLUSIONS: Screening of simplified cell culture systems may aid the discovery of novel biomarkers in clinical neurovascular injury. Further collaborative efforts are warranted to discover and validate more candidates of interest. PMID: 21164131 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4266571 Thu, 16 Dec 2010 00:00:00 +0100 4266571 http://www.medworm.com/index.php?rid=4266573&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21145989%26dopt%3DAbstract INCORPORATING BIOINFORMATICS INTO BIOLOGICAL SCIENCE EDUCATION IN NIGERIA: PROSPECTS AND CHALLENGES. Infect Genet Evol. 2010 Dec 8; Authors: Ojo OO, Maxwell O The urgency to process and analyze the deluge of data created by proteomics and genomics studies worldwide has caused bioinformatics to gain prominence and importance. However, its multidisciplinary nature has created a unique demand for specialist trained in both biology and computing. Several countries, in response to this challenge, have developed a number of manpower training programmes. This review presents a description of the meaning, scope, history and development of bioinformatics with focus on prospects and challenges facing bioinformatics education worldwide. The paper also provides an overview of attempts at t... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4266573 Wed, 08 Dec 2010 00:00:00 +0100 4266573 http://www.medworm.com/index.php?rid=4211701&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21109216%26dopt%3DAbstract Authors: Brewis IA, Brennan P This review provides an introduction for the nonspecialist to proteomics and in particular the major approaches available for global protein identification and quantification. Proteomics technologies offer considerable opportunities for improved biological understanding and biomarker discovery. The central platform for proteomics is tandem mass spectrometry (MS) but a number of other technologies, resources, and expertise are absolutely required to perform meaningful experiments. These include protein separation science (and protein biochemistry in general), genomics, and bioinformatics. There are a range of workflows available for protein (or peptide) separation prior to tandem MS and subsequent bioinformatics analysis to achieve protein identifications. ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4211701 Tue, 30 Nov 2010 22:15:25 +0100 4211701 http://www.medworm.com/index.php?rid=4211694&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21109531%26dopt%3DAbstract Authors: Mewes HW, Ruepp A, Theis F, Rattei T, Walter M, Frishman D, Suhre K, Spannagl M, Mayer KF, Stümpflen V, Antonov A The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are Phenom... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4211694 Wed, 24 Nov 2010 00:00:00 +0100 4211694 http://www.medworm.com/index.php?rid=4211706&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21098431%26dopt%3DAbstract Authors: García-Alcalde F, García-Lopez F, Dopazo J, Conesa A MOTIVATION: The development of the omics technologies such as transcriptomics, proteomics and metabolomics has made possible the realization of systems biology studies where biological systems are interrogated at different levels of biochemical activity (gene expression, protein activity and/or metabolite concentration). An effective approach to the analysis of these complex data-sets is the joined visualization of the disparate biomolecular data on the framework of known biological pathways. RESULTS: We have developed the Paintomics web server as an easy-to- use bioinformatics resource that facilitates the integrated visual analysis of experiments where transcriptomics and metabolomics data have been measured on different... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4211706 Tue, 23 Nov 2010 00:00:00 +0100 4211706 http://www.medworm.com/index.php?rid=4163622&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21071396%26dopt%3DAbstract This study, along with the following discussion, details the association of thousands of ncRNAs-snoRNA, miRNA, siRNA, piRNA and long ncRNA-within human introns. We propose that such an association between human introns and ncRNAs has a pronounced synergistic effect with important implications for fine-tuning gene expression patterns across the entire genome. PMID: 21071396 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4163622 Wed, 10 Nov 2010 00:00:00 +0100 4163622 http://www.medworm.com/index.php?rid=4106530&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20967315%26dopt%3DAbstract Authors: Krug K, Nahnsen S, Macek B With the onset of modern DNA sequencing technologies, genomics is experiencing a revolution in terms of quantity and quality of sequencing data. Rapidly growing numbers of sequenced genomes and metagenomes present a tremendous challenge for bioinformatics tools that predict protein-coding regions. Experimental evidence of expressed genomic regions, both at the RNA and protein level, is becoming invaluable for genome annotation and training of gene prediction algorithms. Evidence of gene expression at the protein level using mass spectrometry-based proteomics is increasingly used in refinement of raw genome sequencing data. In a typical "proteogenomics" experiment, the whole proteome of an organism is extracted, digested into peptides and measured by ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4106530 Wed, 20 Oct 2010 23:00:00 +0100 4106530 http://www.medworm.com/index.php?rid=4057421&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20927658%26dopt%3DAbstract Authors: Goel R, Muthusamy B, Pandey A, Prasad TS In the recent years, research in molecular biotechnology has transformed from being small scale studies targeted at a single or a small set of molecule(s) into a combination of high throughput discovery platforms and extensive validations. Such a discovery platform provided an unbiased approach which resulted in the identification of several novel genetic and protein biomarkers. High throughput nature of these investigations coupled with higher sensitivity and specificity of Next Generation technologies provided qualitatively and quantitatively richer biological data. These developments have also revolutionized biological research and speed of data generation. However, it is becoming difficult for individual investigators to directly be... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4057421 Wed, 06 Oct 2010 23:00:00 +0100 4057421 http://www.medworm.com/index.php?rid=4057420&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20934990%26dopt%3DAbstract Authors: Magnan CN, Zeller M, Kayala MA, Vigil A, Randall A, Felgner PL, Baldi P MOTIVATION: Discovery of novel protective antigens is fundamental to the development of vaccines for existing and emerging pathogens. Most computational methods for predicting protein antigenicity rely directly on homology with previously characterized protective antigens; however, homology-based methods will fail to discover truly novel protective antigens. Thus, there is a significant need for homology-free methods capable of screening entire proteomes for the antigens most likely to generate a protective humoral immune response. RESULTS: Here we begin by curating two types of positive data: (1) antigens which elicit a strong antibody response in protected individuals but not in unprotected individuals, ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4057420 Wed, 06 Oct 2010 23:00:00 +0100 4057420 http://www.medworm.com/index.php?rid=4024168&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20871759%26dopt%3DAbstract Authors: Giacomelli L, Covani U Genomics and proteomics have promised to change the practice of dentistry and oral pathology, allowing the identification and the characterization of risk factors and therapeutic targets at a molecular level. However, mass-scale molecular genomics and proteomics suffer from some pitfalls: gene/protein expression are significant only if inserted in a detailed network of molecular pathways and gene/gene, gene/protein and protein/protein interactions. The proper analysis of these complex pictures requires the contribution of theoretical disciplines, like bioinformatics and data mining. In particular, data-mining of existing information could become a strong starting point to formulate new targeted hypotheses and to plan ad hoc experimentation.In this review... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4024168 Sat, 02 Oct 2010 19:05:03 +0100 4024168 http://www.medworm.com/index.php?rid=4024169&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20864444%26dopt%3DAbstract Authors: Bazykin GA, Kochetov AV Alternative start AUG codons within a single transcript can contribute to diversity of the proteome; however, their functional significance remains controversial. Here, we provide comparative genomics evidence that alternative start codons are under negative selection in vertebrates, insects and yeast. In genes where the annotated start codon (sAUG) resides within the suboptimal nucleotide context, the downstream in-frame AUG codons (dAUG) among the first ∼30 codon sites are significantly more conserved between species than in genes where the sAUG resides within the optimal context. Proteomics data show that this difference is not an annotation artifact and that dAUGs are in fact under selection as alternative start sites. The key optimal, and some... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=4024169 Tue, 21 Sep 2010 23:00:00 +0100 4024169 http://www.medworm.com/index.php?rid=3981182&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20841405%26dopt%3DAbstract Authors: Galinkin JL, Demmer L, Yaster M Molecular genetics is the study, at the molecular level, of how genetic information is stored, inherited, and expressed and of how it influences the structure and function of cells in health and in disease. Although molecular approaches have been used for decades in the laboratory and are at the core of modern medical education, they are only now beginning to influence clinical practice. A variety of sophisticated techniques permit rapid and affordable DNA sequencing, gene expression profiling, gene cloning, gene manipulation, gene transfer, recombinant protein production, and other technologies of enormous biomedical importance. Success in genomics has spawned additional ambitious endeavors, including proteomics, pharmacogenomics, and bioinform... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3981182 Mon, 13 Sep 2010 23:00:00 +0100 3981182 http://www.medworm.com/index.php?rid=3908493&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20738858%26dopt%3DAbstract Authors: Shastry BS ABSTRACT: Retinopathy of prematurity (ROP) is a vascular vitreoretinopathy that affects infants with short gestational age and low birth-weight. The condition is a multifactorial disease and is clinically similar to familial exudative vitreoretinopathy (FEVR), which is a bilateral hereditary eye disorder affecting full-term infants. Both of them are characterized by the abnormal vessel growth in the vitreous that can lead to vitreoretinal traction, retinal detachment and other complications resulting in blindness. Despite the recent advances in diagnosis and treatment, ROP remains a major cause of childhood blindness in developed countries. The etiology of pathogenesis of advanced ROP is currently unknown. In the past, many causative factors such as length of time e... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3908493 Tue, 24 Aug 2010 23:00:00 +0100 3908493 http://www.medworm.com/index.php?rid=3908494&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20736923%26dopt%3DAbstract Authors: Naesens M, Sarwal MM The past few decades are characterized by an explosive evolution of genetics and molecular cell biology. Advances in chemistry and engineering have enabled increased data throughput, permitting the study of complete sets of molecules with increasing speed and accuracy using techniques such as genomics, transcriptomics, proteomics, and metabolomics. Prediction of long-term outcomes in transplantation is hampered by the absence of sufficiently robust biomarkers and a lack of adequate insight into the mechanisms of acute and chronic alloimmune injury and the adaptive mechanisms of immunological quiescence that may support transplantation tolerance. Here, we discuss some of the great opportunities that molecular diagnostic tools have to offer both basic scient... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3908494 Mon, 23 Aug 2010 23:00:00 +0100 3908494 http://www.medworm.com/index.php?rid=3881265&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20700709%26dopt%3DAbstract Authors: Bross P, Palmfeldt J, Hansen J, Vang S, Gregersen N The ambition to measure all or at least a significant fraction of relevant molecules in a cell culture or tissue sample has reached possible realization with the development of the so-called OMICS technologies. We will here briefly review current technologies and give examples of their applications in investigations related to protein misfolding diseases. We will primarily cover the classical OMICS categories GENOMICS, TRANSCRIPTOMICS, METABOLOMICS, and with some more detail PROTEOMICS. These techniques are in most cases performed by dedicated core facilities or commercial services. We will give an assessment of uses as well as limitations of these technologies supported by examples of their application in research related to... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3881265 Thu, 19 Aug 2010 12:48:03 +0100 3881265 http://www.medworm.com/index.php?rid=3881264&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20704270%26dopt%3DAbstract Authors: Ibeagha-Awemu EM, Ibeagha AE, Messier S, Zhao X Gram-negative and -positive bacteria elicit different response patterns by the host. The proteomic profiles of milk whey samples from cows naturally infected with Escherichia coli or Staphyloccocus aureus as compared to whey from healthy cows were determined by one-dimensional, liquid chromatography-tandem mass spectrometry (LC-MS/MS), bioinformatics processing, and pathway analyses. Since mammary epithelial cells contribute to immune responses in mammary glands, the genes of selected proteins were measured in MAC-T cells by real time quantitative PCR (qPCR) after stimulation with heat inactivated E. coli strain P4 and S. aureus strain Smith CP bacteria. A total of 173 proteins were identified including 73 proteins differentially... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3881264 Wed, 11 Aug 2010 23:00:00 +0100 3881264 http://www.medworm.com/index.php?rid=3881263&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20708669%26dopt%3DAbstract Authors: Everley PA, Dillman JF Medical research on the effects of chemical warfare agents (CWAs) has been ongoing for nearly 100 years, yet these agents continue to pose a serious threat to deployed military forces and civilian populations. CWAs are extremely toxic, relatively inexpensive, and easy to produce, making them a legitimate weapon of choice for terrorist organizations. While the mechanisms of action for many CWAs have been known for years, questions about their molecular effects following acute and chronic exposure remain largely unanswered. Global approaches that can pinpoint which cellular pathways are altered in response to CWAs and characterize long-term toxicity have not been widely used. Fortunately, innovations in genomics and proteomics technologies now allow for th... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3881263 Tue, 10 Aug 2010 23:00:00 +0100 3881263 http://www.medworm.com/index.php?rid=3700107&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20573251%26dopt%3DAbstract Authors: Xia XQ, McClelland M, Wang Y ABSTRACT: With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. Ta... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3700107 Tue, 22 Jun 2010 23:00:00 +0100 3700107 http://www.medworm.com/index.php?rid=3659319&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20535543%26dopt%3DAbstract In conclusion, our findings indicate a new regulatory mechanism of let-7 miRNAs in ER-alpha mediated cellular malignant growth of breast cancer. PMID: 20535543 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3659319 Wed, 09 Jun 2010 23:00:00 +0100 3659319 http://www.medworm.com/index.php?rid=3614744&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20508300%26dopt%3DAbstract Authors: Thiele H, Glandorf J, Hufnagel P With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScapeTM bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists; current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specif... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3614744 Mon, 31 May 2010 17:03:02 +0100 3614744 http://www.medworm.com/index.php?rid=3589296&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491070%26dopt%3DAbstract We present examples of a variety of data-integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long-term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include 1) an approach for addressing discrepancies between experiment results and interpreted results, and 2) expanding the range of data-integration techniques to include usability engineering at the presentation level. PMID: 20491070 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3589296 Wed, 19 May 2010 23:00:00 +0100 3589296 http://www.medworm.com/index.php?rid=3578188&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20478823%26dopt%3DAbstract Authors: Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls and TDTs, and allows population stratification analysis and correction). All these genomic data... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3578188 Sat, 15 May 2010 23:00:00 +0100 3578188 http://www.medworm.com/index.php?rid=3553181&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20455215%26dopt%3DAbstract Authors: Ubaida Mohien C, Hartler J, Breitwieser F, Rix U, Remsing Rix L, Winter GE, Thallinger GG, Bennett KL, Superti-Furga G, Trajanoski Z, Colinge J MASPECTRAS 2 is a freely available platform for integrating MS protein identifications with information from major bioinformatics databases (ontologies, domains, literature, etc.). It assists researchers in understanding their data and publishing through sample comparisons, targeted queries, summaries, and exports in multiple formats such as PRIDE XML (Jones, et al., 2008). MASPECTRAS 2 also comprises mechanisms to facilitate its integration in a high-throughput infrastructure. We illustrate application of MASPECTRAS 2 with unpublished tyrosine kinase inhibitor drug proteomics profiles in cancerous cells. PMID: 20455215 [PubMed - a... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3553181 Thu, 06 May 2010 23:00:00 +0100 3553181 http://www.medworm.com/index.php?rid=3497968&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20407944%26dopt%3DAbstract Authors: Parnell LD, Schueller CM Proteomics-based biomarker discovery studies usually entail the isolation of peptide fragments from candidate biomarkers of interest. Detection of such peptides from biological or clinical samples and identification of the corresponding full-length protein and the gene encoding that protein provide the means to gather a wealth of information. This information, termed annotation because it is attached to the gene or protein sequence under study, describes relationships to human disease, cytogenetic map position, protein domains, protein-protein and small molecule interactions, tissues or cell types in which the gene is expressed, as well as several other aspects of gene and protein function. Bioinformatics tools are employed and genome databases are min... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3497968 Fri, 23 Apr 2010 15:06:03 +0100 3497968 http://www.medworm.com/index.php?rid=3447331&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20158872%26dopt%3DAbstract CONCLUSIONS: This work identifies parameter settings and thresholds for a selection of disorder predictors to produce comparable results at a desired level of specificity over a newly derived benchmark dataset that accounts equally for ordered and disordered regions of different lengths. PMID: 20158872 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3447331 Thu, 08 Apr 2010 15:08:03 +0100 3447331 http://www.medworm.com/index.php?rid=3447330&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20195258%26dopt%3DAbstract Authors: Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have many visualization methods and tools to choose from. The challenge is to create clear, meaningful and integrated visualizations that give biological insight, without being overwhelmed by the intrinsic complexity of the data. In this review, we discuss how visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data, and we highlight emerging new directions. PMID: 20195258 [PubMed - ind... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3447330 Mon, 01 Mar 2010 00:00:00 +0100 3447330 http://www.medworm.com/index.php?rid=3200786&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20093627%26dopt%3DAbstract Conclusions: Taken together, these findings reveal Myozap as a previously unrecognized component of a Rho-dependent signaling pathway that links the intercalated disc to cardiac gene regulation. Moreover, its subcellular localization and the observation of a severe cardiac phenotype in zebrafish, implicate Myozap in the pathogenesis of cardiomyopathy. PMID: 20093627 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3200786 Thu, 21 Jan 2010 00:00:00 +0100 3200786 http://www.medworm.com/index.php?rid=3102541&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20013210%26dopt%3DAbstract Authors: Boonen K, Husson SJ, Landuyt B, Baggerman G, Hayakawa E, Luyten WH, Schoofs L Endocrine tissues like the pituitary, hypothalamus and islets of Langerhans are rich in bioactive peptides. These are used for intercellular signalling and are involved in regulation of almost all physiological processes. Peptidomics is the comprehensive analysis of peptides in tissues, fluids and cells. Peptidomics applied to (neuro-)endocrine tissues aims therefore to identify as many bioactive peptides as possible. Peptidomics of (neuro-)endocrine tissues requires an integrated approach that consists of careful sample handling, peptide separation techniques, mass spectrometry and bioinformatics. Here we describe the methods for isolation and dissection of endocrine tissues, the extraction of bioac... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3102541 Sat, 19 Dec 2009 13:10:16 +0100 3102541 http://www.medworm.com/index.php?rid=3102540&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20014923%26dopt%3DAbstract Authors: Yang S Y, Adelstein J, Kassis AI Prostate cancer is the most common cancer among men worldwide and is the second leading cause of death among those over 50 years of age in the USA. However, many men who develop a prostate tumor never exhibit symptoms in the early stage of the disease or even before it spreads to other parts of the body, such as bones and lymph nodes. Therefore, the successful prevention and treatment of prostate cancer relies on the early and accurate detection of the disease. Although prostate-specific antigen has been extensively used as a serum biomarker to detect prostate tumors in the past 20 years, this screening method has suffered from a lack of specificities and sensitivities, despite its wide use. Furthermore, fluorine-18-labeled fluorodeoxyglucose, ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3102540 Sat, 19 Dec 2009 13:10:13 +0100 3102540 http://www.medworm.com/index.php?rid=3102539&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20018595%26dopt%3DAbstract Authors: Baginsky S, Hennig L, Zimmermann P, Gruissem W Technological advances in biological experimentation are now enabling researchers to investigate living systems on an unprecedented scale by studying genomes, proteomes or molecular networks in their entirety. Genomics technologies have led to a paradigm shift in biological experimentation because they measure ("profile") most or even all components of one class (e.g. transcripts, proteins etc.) in a highly parallel way. Whether gene expression analysis using microarrays, proteome and metabolome analysis using mass-spectrometry or large-scale screens for genetic interactions, high-throughput profiling technologies provide a rich source of quantitative biological information that allows researchers to move beyond a reductionist app... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3102539 Fri, 11 Dec 2009 00:00:00 +0100 3102539 http://www.medworm.com/index.php?rid=3102542&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20005547%26dopt%3DAbstract Authors: Quirino BF, Candido ES, Campos PF, Franco OL, Krüger RH The analysis of plant proteomes has drastically expanded in the last few years. Mass spectrometry technology, stains, software and progress in bioinformatics have made identification of proteins relatively easy. The assignment of proteins to particular organelles and the development of better algorithms to predict sub-cellular localization are examples of how proteomic studies are contributing to plant biology. Protein phosphorylation and degradation are also known to occur during plant defense signaling cascades. Despite the great potential to give contributions to the study of plant-pathogen interactions, only recently has the proteomic approach begun to be applied to this field. Biological variation and complexity... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3102542 Thu, 10 Dec 2009 00:00:00 +0100 3102542 http://www.medworm.com/index.php?rid=3102538&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20019791%26dopt%3DAbstract We present several case studies, including both well-studied examples (GRIN1) and novel examples (EXOC7). These data also show that RSPR strongly outperforms other approaches such as standard sequence conservation (which fails to distinguish amino acid selection pressure from RNA selection pressure), or pairwise genome comparison (which lacks adequate statistical power for predicting individual exons). PMID: 20019791 [PubMed - in process] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=3102538 Tue, 01 Dec 2009 00:00:00 +0100 3102538 http://www.medworm.com/index.php?rid=2982165&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19593431%26dopt%3DAbstract CONCLUSIONS: This study identifies several unique signatures of transcript and protein biomarkers with high predictive accuracies for mild and moderate/severe CAN, the most common cause of late allograft failure. These biomarkers are the necessary first step to a proteogenomic classification of CAN based on peripheral blood profiling and will be the targets of a prospective clinical validation study. PMID: 19593431 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2982165 Thu, 12 Nov 2009 12:00:03 +0100 2982165 http://www.medworm.com/index.php?rid=2967895&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19887340%26dopt%3DAbstract Authors: Gomase VS, Tripathi AK, Tagore S Cellunomics envisions the new branch of cell, which integrates genomics and proteomics with a new knowledge base built from temporal and spatial data on the chemical and molecular interrelationships of cellular components, i.e., cellome. Cellunomics helps in finding cell-specific protein and protein-protein interaction using cell-specific mRNA and protein repository. A flexible statistical-model-based clustering approach is introduced for identifying cell populations and the data revealed by the cellome is informational as well as physical. Cellunomics aids the automated, high-content platforms, to increase the scope and scale of experiments traditionally executed through interactive microscopy. PMID: 19887340 [PubMed - in process] (Source:... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2967895 Fri, 06 Nov 2009 22:32:03 +0100 2967895 http://www.medworm.com/index.php?rid=2959565&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19882766%26dopt%3DAbstract Authors: PMID: 19882766 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2959565 Thu, 05 Nov 2009 01:58:02 +0100 2959565 http://www.medworm.com/index.php?rid=2959564&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19883058%26dopt%3DAbstract Authors: Wynne C, Fenselau C, Demirev PA, Edwards N MALDI mass spectrometry-based systems for rapid characterization of microorganisms in biodefense or medical diagnostics usually detect intact proteins in the 5000-20,000 Da range. To evaluate the reliability of species discrimination, and also for forensic applications, it is important that these biomarker proteins be identified. In the present study we apply high resolution tandem mass analysis on an Orbitrap and top-down bioinformatics to identify major biomarker proteins observed in MALDI spectra of intact bacteria for which little genomic or protein sequence information is available. The strategy depends on recognition of proteins with very high homology in related (sequenced) species, making it possible to place unsequenced organ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2959564 Mon, 02 Nov 2009 00:00:00 +0100 2959564 http://www.medworm.com/index.php?rid=2959563&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19884192%26dopt%3DAbstract Authors: Bandyopadhyay A, Arora A, Jain S, Laskar A, Mandal C, Ivanisenko VA, Fomin ES, Pintus SS, Kolchanov NA, Maiti S, Ramachandran S The signal transduction protein PII plays an important role in cellular nitrogen assimilation and regulation. The molecular characteristics of the M. tuberculosis PII (Mtb PII) were investigated using biophysical experiments. The Mtb PII coding ORF Rv2919c was cloned and expressed in Escherichia coli. The binding characteristics of the purified protein with ATP and ADP were investigated using Surface Plasmon Resonance (SPR) and Isothermal Titration Calorimetry (ITC). Mtb PII binds to ATP strongly with K(d) in the range 1.93-6.44 microM. This binding strength was not significantly affected by the presence of 2-ketoglutarate even in molar concentrations... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2959563 Mon, 02 Nov 2009 00:00:00 +0100 2959563 http://www.medworm.com/index.php?rid=2934601&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19854898%26dopt%3DAbstract Authors: Selesi D, Jehmlich N, von Bergen M, Schmidt F, Rattei T, Tischler P, Lueders T, Meckenstock RU The highly enriched deltaproteobacterial culture N47 anaerobically oxidizes the polycyclic aromatic hydrocarbons naphthalene and 2-methylnaphthalene with sulfate as electron acceptor. Combined genome sequencing and LC-MS/MS-based shotgun proteome analysis were performed to identify genes and proteins involved in anaerobic aromatic catabolism. Proteome analysis from 2-methylnaphthalene-grown N47 cells resulted in the identification of putative enzymes catalyzing the anaerobic conversion of 2-methylnaphthalene to 2-naphthoyl-CoA as well as the reductive ring cleavage of 2-naphthoyl-CoA leading to the formation of acetyl-CoA and CO2. The glycyl radical-catalyzed fumarate addition to the... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2934601 Fri, 23 Oct 2009 00:00:00 +0100 2934601 http://www.medworm.com/index.php?rid=2876918&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19808875%26dopt%3DAbstract Authors: Albaum SP, Neuweger H, Fränzel B, Lange S, Mertens D, Trötschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A MOTIVATION: The goal of present -omics sciences is to understand biological systems as a whole in terms of interactions of the individual cellular components. One of the main building blocks in this field of study is proteomics where tandem mass spectrometry (LC-MS/MS) in combination with isotopic labelling techniques provides a common way to obtain a direct insight into regulation at the protein level. Methods to identify and quantify the peptides contained in a sample are well-established, and their output usually results in lists of identified proteins and calculated relative abundance values. The next step is to move ahead from these abstract list... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2876918 Mon, 05 Oct 2009 23:00:00 +0100 2876918 http://www.medworm.com/index.php?rid=2834728&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19435482%26dopt%3DAbstract Authors: Pinney JW, Stumpf MP A report of the Biochemical Society/Wellcome Trust meeting 'Protein Evolution - Sequences, Structures and Systems', Hinxton, UK, 26-27 January 2009. PMID: 19435482 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2834728 Sun, 27 Sep 2009 03:28:03 +0100 2834728 http://www.medworm.com/index.php?rid=2748495&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19718509%26dopt%3DAbstract Authors: Prasad TS, Kandasamy K, Pandey A Although high-throughput technologies used in biology have resulted in the accumulation of vast amounts of data in the literature, it is becoming difficult for individual investigators to directly benefit from this data because they are not easily accessible. Databases have assumed a crucial role in assimilating and storing information that could enable future discoveries. To this end, our group has developed two resources - Human Protein Reference Database (HPRD) and Human Proteinpedia - that provide integrated information pertaining to human proteins. These databases contain information on a number of features of proteins that have been discovered using various experimental methods. Human Proteinpedia was developed as a portal for community p... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2748495 Tue, 01 Sep 2009 10:04:02 +0100 2748495 http://www.medworm.com/index.php?rid=2717223&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19689276%26dopt%3DAbstract Authors: Prokesch A, Hackl H, Hakim-Weber R, Bornstein SR, Trajanoski Z Obesity, the excess accumulation of adipose tissue, is one of the most pressing health problems in both the Western world and in developing countries. Adipose tissue growth results from two processes: the increase in number of adipocytes (hyperplasia) that develop from precursor cells, and the growth of individual fat cells (hypertrophy) due to incorporation of triglycerides. Adipogenesis, the process of fat cell development, has been extensively studied using various cell and animal models. While these studies pointed out a number of key factors involved in adipogenesis, the list of molecular components is far from complete. The advance of high-throughput technologies has sparked many experimental studies aimed at... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2717223 Fri, 21 Aug 2009 09:40:03 +0100 2717223 http://www.medworm.com/index.php?rid=2680768&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19658089%26dopt%3DAbstract Authors: Menschaert G, Vandekerckhove TT, Landuyt B, Hayakawa E, Schoofs L, Luyten W, Van Criekinge W When studying the set of biologically active peptides (the so-called peptidome) of a cell type, organ, or entire organism, the identification of peptides is mostly attempted by mass spectrometry. However, identification rates are often dismally unsatisfactory. A great deal of failed or missed identifications may be attributable to the wealth of modifications on peptides, some of which may originate from in vivo post-translational processes to activate the molecule, whereas others could be introduced during the tissue preparation procedures. Preliminary knowledge of the modification profile of specific peptidome samples would greatly improve identification rates.To this end we developed... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2680768 Tue, 04 Aug 2009 23:00:00 +0100 2680768 http://www.medworm.com/index.php?rid=2662809&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19644370%26dopt%3DAbstract This article reviews some recent applications of the many evolving 'omic technologies to organ transplantation. RECENT FINDINGS: With the advancement of many high-throughput 'omic techniques such as genomics, metabolomics, antibiomics, peptidomics, and proteomics, efforts have been made to understand potential mechanisms of specific graft injuries and develop novel biomarkers for acute rejection, chronic rejection, and operational tolerance. SUMMARY: The translation of potential biomarkers from the laboratory bench to the clinical bedside is not an easy task and will require the concerted effort of the immunologists, molecular biologists, transplantation specialists, geneticists, and experts in bioinformatics. Rigorous prospective validation studies will be needed using large sets of indep... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2662809 Tue, 28 Jul 2009 23:00:00 +0100 2662809 http://www.medworm.com/index.php?rid=2650372&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19633095%26dopt%3DAbstract Authors: Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A SUMMARY: SIMBioMS is a web based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customised and has proven to be successful in several large scale multi-site collaborative projects. It is compatible with emerging functional genomics data stan... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2650372 Thu, 23 Jul 2009 23:00:00 +0100 2650372 http://www.medworm.com/index.php?rid=2639790&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19626302%26dopt%3DAbstract Authors: Wang QZ, Zhao XM In recent years, with the booming economy, the Chinese government has increased its financial input to biotechnology research, which has led to remarkable achievements by China in modern biotechnology. As one of the key parts of modern biotechnology, industrial biotechnology will be crucial for China's sustainable development in this century. This review presents an overview of Chinese industrial biotechnology in last 10 years. Modern biotechnology had been classified into metabolic engineering and systems biology framework. Metabolic engineering is a field of broad fundamental and practical concept so we integrated the related technology achievements into the real practices of many metabolic engineering cases, such as biobased products production, environment... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2639790 Wed, 22 Jul 2009 23:00:00 +0100 2639790 http://www.medworm.com/index.php?rid=2601359&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19426860%26dopt%3DAbstract Authors: Gaston D, Tsaousis AD, Roger AJ In eukaryotes, determination of the subcellular location of a novel protein encoded in genomic or transcriptomic data provides useful clues as to its possible function. However, experimental localization studies are expensive and time-consuming. As a result, accurate in silico prediction of subcellular localization from sequence data alone is an extremely important field of study in bioinformatics. This is especially so as genomic studies expand beyond model system organisms to encompass the full diversity of eukaryotes. Here we review some of the more commonly used programs for prediction of proteins that function in mitochondria, or mitochondrion-related organelles in diverse eukaryotic lineages and provide recommendations on how to apply thes... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2601359 Wed, 15 Jul 2009 12:04:03 +0100 2601359 http://www.medworm.com/index.php?rid=2577478&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19576913%26dopt%3DAbstract Authors: Boerjan B, Cardoen D, Bogaerts A, Landuyt B, Schoofs L, Verleyen P The honeybee is the economically most important beneficial insect and a model for studying immunity, development and social behavior. Hence, this species was selected for genome sequencing and annotation. An intensive interplay between bioinformatics and mass spectrometry (MS) resulted in the annotation of 36 neuropeptide genes (Hummon et al., 2006). Exactly 100 peptides were demonstrated by a variety of MS techniques. In this follow-up study we dissected and analysed separately all ganglia of the central nervous system (CNS) of adult worker bees in three repeats. The combined MALDI-TOF spectra enabled the accurate mapping of 67 peptides, encoded by 20 precursors. We also demonstrated the expression of an addit... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2577478 Tue, 30 Jun 2009 23:00:00 +0100 2577478 http://www.medworm.com/index.php?rid=2543596&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19404479%26dopt%3DAbstract Authors: Serpedin E, Garcia-Frias J, Huang Y, Braga-Neto U PMID: 19404479 [PubMed - in process] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2543596 Sun, 28 Jun 2009 01:43:03 +0100 2543596 http://www.medworm.com/index.php?rid=2543590&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19534734%26dopt%3DAbstract Authors: D'Elia D, Gisel A, Eriksson NE, Kossida S, Mattila K, Klucar L, Bongcam-Rudloff E The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its foundation in 1988, EMBnet has been working to promote collaborative development of bioinformatics services and tools to serve the European community of molecular biology laboratories. This conference was the first meeting organized by the network that was open to the international scientific community outside EMBnet. The conference covered a broad range of research topics in bioinformatics with a main focus on new achievements and trends in emerging technologies supporting genomics, transcr... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2543590 Sun, 28 Jun 2009 01:43:03 +0100 2543590 http://www.medworm.com/index.php?rid=2543592&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19549632%26dopt%3DAbstract Authors: Magnan CN, Randall A, Baldi P MOTIVATION: Protein insolubility is a major obstacle for many experimental studies. A sequence-based prediction method able to accurately predict the propensity of a protein to be soluble on overexpression could be used, for instance, to prioritize targets in large-scale proteomics projects and to identify mutations likely to increase the solubility of insoluble proteins. RESULTS: Here we first curate a large, non-redundant, and balanced training set of more than 17,000 proteins. Next, we extract and study twenty three groups of features computed directly or predicted (e.g. secondary structure) from the primary sequence. The data and the features are used to train a two-stage SVM architecture. The resulting predictor, SOLpro, is compared directly ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2543592 Mon, 22 Jun 2009 23:00:00 +0100 2543592 http://www.medworm.com/index.php?rid=2543594&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19529930%26dopt%3DAbstract Authors: Liu GN, Zhu YH, Jiang JG Carotenoids such as beta-carotene, lycopene, and antheraxanthin have plenty of scientific and commercial value. The comprehensive investigation of carotenoids drives people to improve and develop all kinds of analytical techniques to approach or even achieve "versatile" analysis. The metabolic engineering efforts in plants and algae have progressed rapidly, aiming to enable the use of plants and algae as "cell factories" for producing specific or novel carotenoids, such as beta-carotene (provitamin A) in Gold rice, while the emerging technologies of metabolomics support it by providing comprehensive analysis of carotenoids biochemical characterizations. This review describes metabolomics as a high-throughput platform to study carotenoids, including the... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2543594 Mon, 15 Jun 2009 23:00:00 +0100 2543594 http://www.medworm.com/index.php?rid=2543598&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19388135%26dopt%3DAbstract Authors: Wang X, Hunter AK, Mozier NM Host cell proteins (HCPs) are those produced or encoded by the organisms and unrelated to the intended recombinant product. Some are necessary for growth, survival, and normal cellular processing whereas others may be non-essential, simply carried along as baggage. Like the recombinant product, HCPs may also be modified by the host with a number of post-translational modifications. Regardless of the utility, or lack thereof, HCPs are undesirable in the final drug substance. Though commonly present in small quantities (parts per million expressed as nanograms per milligrams of the intended recombinant protein) much effort and cost is expended by industry to remove them. The purpose of this review is to summarize what is of relevance in regards to th... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2543598 Sun, 14 Jun 2009 23:00:00 +0100 2543598 http://www.medworm.com/index.php?rid=2543603&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18663489%26dopt%3DAbstract We present here the estimation of the upper limit of the number of molecular targets in the human genome that represent an opportunity for further therapeutic treatment. We select around approximately 6300 human proteins that are similar to sequences of known protein targets collected from DrugBank database. Our bioinformatics study estimates the size of 'druggable' human genome to be around 20% of human proteome, i.e. the number of the possible protein targets for small-molecule drug design in medicinal chemistry. We do not take into account any toxicity prediction, the three-dimensional characteristics of the active site in the predicted 'druggable' protein families, or detailed chemical analysis of known inhibitors/drugs. Instead we rely on remote homology detection method Meta-BASIC, w... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2543603 Sun, 31 May 2009 23:00:00 +0100 2543603 http://www.medworm.com/index.php?rid=2543600&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19376824%26dopt%3DAbstract Authors: Ling XB, Cohen H, Jin J, Lau I, Schilling J SUMMARY: Rapid progress in technology, particularly in high-throughput biology, allows the analysis of thousands of genes or proteins simultaneously, where the multiple comparison problems occurs. Global false discovery rate (gFDR) analysis statistically controls this error, computing the ratio of the number of false positives over the total number of rejections. Local FDR (lFDR) method can associate the corrected significance measure with each hypothesis testing for its feature-by-feature interpretation. Given the large feature number and sample size in any genomics or proteomics analysis, FDR computation, albeit critical, is both beyond the regular biologists' specialty and computationally expensive, easily exceeding the capacity o... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2543600 Sun, 31 May 2009 23:00:00 +0100 2543600 http://www.medworm.com/index.php?rid=2294301&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19306877%26dopt%3DAbstract Authors: Kumar C, Mann M Proteomics has made tremendous progress, attaining throughput and comprehensiveness so far only seen in genomics technologies. The consequent avalanche of proteome level data poses great analytical challenges for downstream interpretation. We review bioinformatic analysis of qualitative and quantitative proteomic data, focusing on current and emerging paradigms employed for functional analysis, data mining and knowledge discovery from high resolution quantitative mass spectrometric data. Many bioinformatics tools developed for microarrays can be reused in proteomics, however, the uniquely quantitative nature of proteomics data also offers entirely novel analysis possibilities, which directly suggest and illuminate biological mechanisms. PMID: 19306877 [PubM... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2294301 Fri, 20 Mar 2009 04:00:00 +0100 2294301 http://www.medworm.com/index.php?rid=2255780&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19272592%26dopt%3DAbstract Authors: Guruceaga E, Segura V, Corrales FJ, Rubio A The interpretation of the complex molecular descriptions generated by high-throughput gene expression technologies is still challenging. The development of new tools to identify common regulatory mechanisms involved in the control of the expression of a set of co-expressed genes, might enhance our capacity to extract functional information from genomic data sets. Here we present FactorY, a website that allows identification of enriched transcription factor binding sites (TFBSs) in the proximal promoter of a cluster of genes, as well as functional interpretation, and intuitive visualization of the results. PMID: 19272592 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2255780 Sat, 07 Mar 2009 05:00:00 +0100 2255780 http://www.medworm.com/index.php?rid=2221046&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19246616%26dopt%3DAbstract Authors: Overdevest JB, Theodorescu D, Lee JK BACKGROUND: Personalized medicine is the provision of focused prevention, detection, prognostic, and therapeutic efforts according to an individual's genetic composition. The actualization of personalized medicine will require combining a patient's conventional clinical data with bioinformatics-based molecular-assessment profiles. This synergistic approach offers tangible benefits, such as heightened specificity in the molecular classification of cancer subtypes, improved prognostic accuracy, targeted development of new therapies, novel applications for old therapies, and tailored selection and delivery of chemotherapeutics. CONTENT: Our ability to personalize cancer management is rapidly expanding through biotechnological advances in the p... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2221046 Thu, 26 Feb 2009 05:00:00 +0100 2221046 http://www.medworm.com/index.php?rid=2221047&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19246318%26dopt%3DAbstract Authors: Alexeyenko A, Sonnhammer EL No single experimental method can discover all connections in the interactome. A computational approach can help by integrating data from multiple, often unrelated, proteomics and genomics pipelines. Reconstructing global networks of functional coupling (FC) faces the challenges of scale and heterogeneity - how to efficiently integrate huge amounts of diverse data from multiple organisms, yet ensuring high accuracy? We developed FunCoup, an optimized Bayesian framework, to resolve these issues. Because interactomes comprise functional coupling of many types, FunCoup annotates network edges with confidence scores in support of different kinds of interactions: physical interaction, protein complex member, metabolic or signaling link. This capability b... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2221047 Wed, 25 Feb 2009 05:00:00 +0100 2221047 http://www.medworm.com/index.php?rid=2221048&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19133232%26dopt%3DAbstract Authors: Lindemans M, Janssen T, Husson SJ, Meelkop E, Temmerman L, Clynen E, Mertens I, Schoofs L Neuromedin U (NMU) in vertebrates is a structurally highly conserved neuropeptide of which highest levels are found in the pituitary and gastrointestinal tract. In Drosophila, two neuropeptide genes encoding pyrokinins (PKs), capability (capa) and hugin, are possible insect homologs of vertebrate NMU. Here, the ligand for an orphan G protein-coupled receptor in the nematode Caenorhabditis elegans (Ce-PK-R) was found using a bioinformatics approach. After cloning and expressing Ce-PK-R in HEK293T cells, we found that it was activated by a neuropeptide from the C. elegans NLP-44 precursor (EC(50)=18nM). This neuropeptide precursor is reminiscent of insect CAPA precursors since it encodes a ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2221048 Fri, 13 Feb 2009 05:00:00 +0100 2221048 http://www.medworm.com/index.php?rid=2186529&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19211664%26dopt%3DAbstract Authors: Verma A, Yadav VK, Basundra R, Kumar A, Chowdhury S Guanine-rich DNA of a particular sequence adopts four-stranded structural forms known as G-quadruplex or G4 DNA. Though in vitro formation of G4 DNA is known for several years, in vivo presence of G4 DNA was only recently noted in eukaryote telomeres. Recent bioinformatics analyses showing prevalence of G4 DNA within promoters of human and related species seems to implicate G4 DNA in a genome-wide cis-regulatory role. Herein we demonstrate that G4 DNA may present regulatory sites on a genome-wide scale by showing widespread effect on gene expression in response to the established intracellular G4 DNA-binding ligands. This is particularly relevant to genes that harbor conserved potential G4 DNA (PG4 DNA) forming sequence acros... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2186529 Wed, 11 Feb 2009 05:00:00 +0100 2186529 http://www.medworm.com/index.php?rid=2162938&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19190340%26dopt%3DAbstract In conclusion, WT1 is expressed in a substantial proportion of HCC contributing to tumor progression and resistance to chemotherapy, suggesting that WT1 may be an important target for HCC treatment. [Cancer Res 2009;69(4):1358-67]. PMID: 19190340 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2162938 Tue, 03 Feb 2009 05:00:00 +0100 2162938 http://www.medworm.com/index.php?rid=2130756&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19164555%26dopt%3DAbstract In this study, the ligand for the GnRH receptor in the nematode Caenorhabditis elegans (Ce-GnRHR) was found using a bioinformatics approach. The peptide and its precursor are reminiscent of both insect adipokinetic hormones and GnRH-preprohormone precursors from tunicates and higher vertebrates. We cloned the AKH-GnRH-like preprohormone and the Ce-GnRHR and expressed the GPCR in HEK293T cells. The GnRHR was activated by the C. elegans AKH-GnRH-like peptide (EC(50) = 150 nM) and by Drosophila AKH and other nematode AKH-GnRHs that we found in EST databases. Analogous to both insect AKH receptor and vertebrate GnRH receptor signaling, Ce-AKH-GnRH activated its receptor through a Galpha(q) protein with Ca(2+) as a second messenger. Gene silencing of Ce-GnRHR, Ce-AKH-GnRH, or both resulted in a... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2130756 Wed, 21 Jan 2009 05:00:00 +0100 2130756 http://www.medworm.com/index.php?rid=2091934&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19128481%26dopt%3DAbstract Authors: Lakhan SE, Kramer A ABSTRACT: The field of proteomics has made leaps and bounds in the last 10 years particularly in the fields of oncology and cardiovascular medicine. In comparison, neuroproteomics is still playing catch up mainly due to the relative complexity of neurological disorders. Schizophrenia is one such disorder, believed to be the results of multiple factors both genetic and environmental. Affecting over 2 million people in the US alone, it has become a major clinical and public health concern worldwide. This paper gives an update of schizophrenia biomarker research as reviewed by Lakhan in 2006 and gives us a rundown of the progress made during the last two years. Several studies demonstrate the potential of cerebrospinal fluid as a source of neuro-specific bioma... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2091934 Wed, 07 Jan 2009 05:00:00 +0100 2091934 http://www.medworm.com/index.php?rid=2089229&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19126580%26dopt%3DAbstract In this study, the intra-operator spacers are shown to modulate relative C.PvuII affinity. In light of a recently reported C.Esp1396I-DNA co-crystal structure, in vitro and in vivo effects of altering O(L) and O(R) spacers were determined. The results suggest that the GACTnnnAGTC consensus is the primary determinant of C.PvuII binding affinity, with intra-operator spacers playing a fine-tuning role that affects mobility of this R-M system. PMID: 19126580 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2089229 Tue, 06 Jan 2009 05:00:00 +0100 2089229 http://www.medworm.com/index.php?rid=2083291&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19104225%26dopt%3DAbstract Authors: Pene F, Courtine E, Cariou A, Mira JP Theragnostics is a treatment strategy that combines therapeutics with diagnostics. It associates both a diagnostic test that identifies patients most likely to be helped or harmed by a new medication, and targeted drug therapy based on the test results. Bioinformatics, genomics, proteomics, and functional genomics are molecular biology tools essential for the progress of molecular theragnostics. These tools generate the genetic and protein information required for the development of diagnostic assays. Theragnostics includes a wide range of subjects, including personalized medicine, pharmacogenomics, and molecular imaging to develop efficient new targeted therapies with adequate benefit/risk to patients and a better molecular understanding ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2083291 Thu, 01 Jan 2009 05:00:00 +0100 2083291 http://www.medworm.com/index.php?rid=2045098&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19075951%26dopt%3DAbstract Authors: Xavier ER, Capanema BP, Ruiz JC, Oliveira G, Meyer R, D'Afonseca V, Miyoshi A, Azevedo V This review covers all Brazilian Genome, EST and Metagenome Projects, Sequencing Networks' history and structure, and patents related to Brazilian Genome Projects, beginning with the first genome sequenced in this country, i.e. the 9a5c strain of Xylella fastidiosa CVC, up till the recently sequenced 1002 strain of Corynebacterium pseudotuberculosis, which was done with a mixed strategy that included both traditional Sanger methodology and Avant Garde 454 Life Sciences pyrosequencing technology. Almost 90% of all genomic research that has been done in Latin America is a product of Brazil's effort to support and stimulate OMICs in our country. Consequently, we gave special attention to pate... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2045098 Thu, 18 Dec 2008 06:02:03 +0100 2045098 http://www.medworm.com/index.php?rid=2045097&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19077448%26dopt%3DAbstract Authors: Lomberk G In this issue, the highlighted websites are a continuation of a series of educational websites; this one in particular from a couple of years ago, Bioinformatics Tools [Pancreatology 2005;5:314-315]. These include sites that are valuable resources for many research needs in genomics and proteomics. Bioinformatics has become a laboratory tool to map sequences to databases, develop models of molecular interactions, evaluate structural compatibilities, describe differences between normal and disease-associated DNA, identify conserved motifs within proteins, and chart extensive signaling networks, all in silico. and IAP. PMID: 19077448 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2045097 Fri, 12 Dec 2008 05:00:00 +0100 2045097 http://www.medworm.com/index.php?rid=2045099&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19072183%26dopt%3DAbstract Authors: Diez-Orejas R, Fernández-Arenas E Candida albicans infection is a significant cause of morbidity and mortality in immunocompromised patients. In vivo and in vitro models have been developed to study both the fungal and the mammalian immune responses. Phagocytic cells (i.e., macrophages) play a key role in innate immunity against C. albicans by capturing, killing and processing the pathogen for presentation to T cells. The use of microarray technology to study global fungal transcriptional changes after interaction with different host cells has revealed how C. albicans adapts to its environment. Proteomic tools complement molecular approaches and computational methods enable the formulation of relevant biological hypotheses. Therefore, the combination of genomics, proteomi... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=2045099 Mon, 01 Dec 2008 05:00:00 +0100 2045099 http://www.medworm.com/index.php?rid=1963521&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19008250%26dopt%3DAbstract Authors: Brouwer RW, Hijum SA, Kuipers OP SUMMARY: We have developed MINOMICS, a tool that allows facile and in-depth visualization of prokaryotic transcriptomic and proteomic data in conjunction with genomics data. MINOMICS generates interactive linear genome maps in which multiple experimental datasets are displayed together with operon, regulatory motif, transcriptional promoter, and transcriptional terminator information. AVAILABILITY: MINOMICS is freely accessible at http://www.minomics.nl CONTACT: o.p.kuipers@rug.nl or sacha.vanhijum@nizo.nl SUPPLEMENTARY INFORMATION: http://bioinformatics.biol.rug.nl/supplementary/minomics/ PMID: 19008250 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1963521 Wed, 12 Nov 2008 05:00:00 +0100 1963521 http://www.medworm.com/index.php?rid=1937586&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18984624%26dopt%3DAbstract Authors: Bhasi A, Philip P, Manikandan V, Senapathy P We have developed ExDom, a unique database for the comparative analysis of the exon-intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon-intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1937586 Tue, 04 Nov 2008 05:00:00 +0100 1937586 http://www.medworm.com/index.php?rid=1913937&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18952863%26dopt%3DAbstract Authors: Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M In addition to the genomes of Arabidopsis thaliana and poplar (Populus trichocarpa), two near-complete rosid genome sequences, grape (Vitis vinifera) and papaya (Carica papaya), have been recently released. The phylogenetic relationship among these four genomes, and the placement of their three independent, fractionated tetraploidies, sums to a powerful comparative genomic system. CoGe, a platform of multiple whole or near-complete genome sequences, provides an integrative web-based system to find and align syntenic chromosomal regions and visualize the output in an intuitive and interactive manner. CoGe has been customized to specifically support comparisons among the rosids... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1913937 Fri, 24 Oct 2008 04:00:00 +0100 1913937 http://www.medworm.com/index.php?rid=1875410&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18700017%26dopt%3DAbstract CONCLUSION: Indeed, certain topological features of biological networks give rise naturally to the common appearance of the motifs. We therefore question whether frequencies of occurrences are reasonable evidence that the structures of motifs have been selected for their functional contribution to the operation of networks. PMID: 18700017 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1875410 Wed, 15 Oct 2008 09:15:05 +0100 1875410 http://www.medworm.com/index.php?rid=1875409&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18847511%26dopt%3DAbstract CONCLUSION: This study provides information on candidate target molecules and molecular signaling mechanisms for future systematic research into the immune-modulatory activities of an important traditional medicinal herb and its derived phytocompounds. PMID: 18847511 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1875409 Mon, 13 Oct 2008 04:00:00 +0100 1875409 http://www.medworm.com/index.php?rid=1858830&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18836191%26dopt%3DAbstract Authors: Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T The function of a protein is intimately tied to its subcellular localization. Although localizations have been measured for many yeast proteins through systematic GFP fusions, similar studies in other branches of life are still forthcoming. In the interim, various machine-learning methods have been proposed to predict localization using physical characteristics of a protein, such as amino acid content, hydrophobicity, side-chain mass and domain composition. However, there has been comparatively little work on predicting localization using protein networks. Here, we predict protein localizations by integrating an extensive set of protein physical characteristics over a protein's extended protein-protein interaction nei... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1858830 Sat, 04 Oct 2008 04:00:00 +0100 1858830 http://www.medworm.com/index.php?rid=1840231&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18820152%26dopt%3DAbstract Authors: Loor JJ, Cohick WS Knowledge of general aspects of mammary gland function, including metabolic pathways and hormonal regulation of mammary gland development and lactation, in livestock species was obtained several decades ago. As basic biological information of growth factor action, apoptotic mechanisms, and signal transduction events has exploded, the mouse became the model of choice for studying fundamental mechanisms regulating mammary function. A complete sequenced genome also has made the mouse amenable for studies of mammary gene network expression. Advances in molecular biology techniques currently allow researchers to genetically modify mice to either over express or completely lack specific genes, thereby studying their function in an in vivo setting. Furthermore, the... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1840231 Fri, 26 Sep 2008 04:00:00 +0100 1840231 http://www.medworm.com/index.php?rid=1828660&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18812395%26dopt%3DAbstract Authors: Riaño-Pachón DM, Nagel A, Neigenfind J, Wagner R, Basekow R, Weber E, Mueller-Roeber B, Diehl S, Kersten B The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different 'omics' fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text-based retrieval o... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1828660 Tue, 23 Sep 2008 04:00:00 +0100 1828660 http://www.medworm.com/index.php?rid=1810941&cid=s_33035_50_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18801749%26dopt%3DAbstract We describe a toolkit that supports data capture, storage and web-based search of FuGE experiment models; the toolkit can be used directly on FuGE compliant models or configured for use with FuGE extensions. The toolkit is illustrated using a FuGE extension standardised by the Proteomics Standards Initiative, namely GelML. AVAILABILITY: The toolkit and a demonstration are available at http://code.google.com/p/fugetoolkit CONTACT: Khalid.Belhajjame@manchester.ac.uk. PMID: 18801749 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1810941 Wed, 17 Sep 2008 04:00:00 +0100 1810941 http://www.medworm.com/index.php?rid=1763126&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18549495%26dopt%3DAbstract CONCLUSION: We demonstrate that the excess of strong local SS in pre-mRNAs is linked to the little explored phenomenon of genomic mid-range inhomogeneity (MRI). MRI is an interdependence between nucleotide choice and base composition over a distance of 20-1000 nt. Additionally, we have created a public computational resource to support further study of genomic MRI. PMID: 18549495 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1763126 Fri, 05 Sep 2008 09:03:55 +0100 1763126 http://www.medworm.com/index.php?rid=1763125&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18638396%26dopt%3DAbstract CONCLUSION: SpliceCenter http://discover.nci.nih.gov/splicecenter provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists. PMID: 18638396 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1763125 Fri, 05 Sep 2008 09:03:55 +0100 1763125 http://www.medworm.com/index.php?rid=1763124&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18764911%26dopt%3DAbstract Authors: Sigdel TK, Sarwal MM The desire for biomarkers for diagnosis and prognosis of diseases has never been greater. With the availability of genome data and an increased availability of proteome data, the discovery of biomarkers has become increasingly feasible. However, the task is daunting and requires collaborations among researchers working in the fields of transplantation, immunology, genetics, molecular biology, biostatistics and bioinformatics. With the advancement of high throughput omic techniques such as genomics and proteomics (collectively known as proteogenomics), efforts have been made to develop diagnostic tools from new and to-be discovered biomarkers. Yet biomarker validation, particularly in organ transplantation, remains challenging because of the lack of a true ... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1763124 Fri, 22 Aug 2008 04:00:00 +0100 1763124 http://www.medworm.com/index.php?rid=1673924&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18541044%26dopt%3DAbstract Authors: Lu G, Ni J The Second Symposium on Computations in Bioinformatics and Bioscience (SCBB07) was held in Iowa City, Iowa, USA, on August 13-15, 2007. This annual event attracted dozens of bioinformatics professionals and students, who are interested in solving emerging computational problems in bioscience, from China, Japan, Taiwan and the United States. The Scientific Committee of the symposium selected 18 peer-reviewed papers for publication in this supplemental issue of BMC Bioinformatics. These papers cover a broad spectrum of topics in computational biology and bioinformatics, including DNA, protein and genome sequence analysis, gene expression and microarray analysis, computational proteomics and protein structure classification, systems biology and machine learning. PM... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1673924 Sat, 02 Aug 2008 10:14:50 +0100 1673924 http://www.medworm.com/index.php?rid=1663318&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18656912%26dopt%3DAbstract Authors: Othman R, Kiat TS, Khalid N, Yusof R, Irene Newhouse E, Newhouse JS, Alam M, Rahman NA A group of flavanones and their chalcones, isolated from Boesenbergia rotunda L., were previously reported to show varying degrees of noncompetitive inhibitory activities toward Dengue virus type 2 (Den2) protease. Results obtained from automated docking studies are in agreement with experimental data in which the ligands were shown to bind to sites other than the active site of the protease. The calculated K i values are very small, indicating that the ligands bind quite well to the allosteric binding site. Greater inhibition by pinostrobin, compared to the other compounds, can be explained by H-bonding interaction with the backbone carbonyl of Lys74, which is bonded to Asp75 (one of the ca... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1663318 Sat, 26 Jul 2008 04:00:00 +0100 1663318 http://www.medworm.com/index.php?rid=1651720&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18649350%26dopt%3DAbstract Authors: Stein GS, Davie JR, Knowlton JR, Zaidi SK Nucleic acids and regulatory proteins are architecturally organized in nuclear microenvironments. The compartmentalization of regulatory machinery for gene expression, replication and repair, is obligatory for fidelity of biological control. Perturbations in the organization, assembly and integration of regulatory machinery have been functionally linked to the onset and progression of tumorigenesis. The combined application of cellular, molecular, biochemical and in vivo genetic approaches, together with structural biology, genomics, proteomics and bioinformatics, will likely lead to new approaches in cancer diagnostics and therapy. J. Cell. Biochem. 104: 1949-1952, 2008. (c) 2008 Wiley-Liss, Inc. PMID: 18649350 [PubMed - as suppli... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1651720 Tue, 22 Jul 2008 04:00:00 +0100 1651720 http://www.medworm.com/index.php?rid=1638790&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18636545%26dopt%3DAbstract Authors: Feng X, Liu X, Luo Q, Liu BF As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1638790 Thu, 17 Jul 2008 04:00:00 +0100 1638790 http://www.medworm.com/index.php?rid=1605036&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18611286%26dopt%3DAbstract CONCLUSION : The current data set demonstrates that mutations affecting splicing are located throughout exons and might be enriched within local RNA secondary structures. Exons from the ASMD have below average splicing junction strength scores, but the difference is small and is judged not to be significant. PMID: 18611286 [PubMed - in process] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1605036 Fri, 11 Jul 2008 08:41:16 +0100 1605036 http://www.medworm.com/index.php?rid=1605035&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18611287%26dopt%3DAbstract CONCLUSION : We show that a vast majority of known exonic splicing enhancers have highly positive cumulative SP values, while known splicing silencers have core motifs with strongly negative cumulative SP values. Our approach allows for computation of the cumulative SP value of any sequence segment and, thus, gives researchers the ability to measure the possible contribution of any sequence to the pattern of splicing. PMID: 18611287 [PubMed - in process] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1605035 Fri, 11 Jul 2008 08:41:16 +0100 1605035 http://www.medworm.com/index.php?rid=1563092&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18592192%26dopt%3DAbstract Authors: Plewniak F With genome sequencing projects producing huge amounts of sequence data, database sequence similarity search has become a central tool in bioinformatics to identify potentially homologous sequences. It is thus widely used as an initial step for sequence characterization and annotation, phylogeny, genomics, transcriptomics, and proteomics studies. Database similarity search is based upon sequence alignment methods also used in pairwise sequence comparison. Sequence alignment can be global (whole sequence alignment) or local (partial sequence alignment) and there are algorithms to find the optimal alignment given particular comparison criteria. However, as database searches require the comparison of the query sequence with every single sequence in the database, heuris... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1563092 Thu, 03 Jul 2008 07:03:05 +0100 1563092 http://www.medworm.com/index.php?rid=1559573&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18588376%26dopt%3DAbstract Authors: M Ardekani A, Akhondi MM, Sadeghi MR Advances in molecular biology over the past decade have helped to enhance understanding of the complex interplay between genetic, transcriptional, and translational alterations in human cancers. These molecular changes are the basis for an evolving field of high-throughput cancer discovery techniques using microscopic amounts of patient-based materials. Laser capture microdissection allows pure populations of cells to be isolated from both the tumor and stroma in order to identify subtle differences in RNA and protein expression. Comparative analysis of these alterations between normal, preinvasive, and invasive tissue using powerful bioinformatics programs has allowed us to identify novel tumor markers, profile complex protein pathways, an... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1559573 Tue, 01 Jul 2008 04:00:00 +0100 1559573 http://www.medworm.com/index.php?rid=1534561&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18566765%26dopt%3DAbstract Authors: Kim N, Lee C In recent years, genome-wide detection of alternative splicing based on Expressed Sequence Tag (EST) sequence alignments with mRNA and genomic sequences has dramatically expanded our understanding of the role of alternative splicing in functional regulation. This chapter reviews the data, methodology, and technical challenges of these genome-wide analyses of alternative splicing, and briefly surveys some of the uses to which such alternative splicing databases have been put. For example, with proper alternative splicing database schema design, it is possible to query genome-wide for alternative splicing patterns that are specific to particular tissues, disease states (e.g., cancer), gender, or developmental stages. EST alignments can be used to estimate exon inclu... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1534561 Sat, 21 Jun 2008 20:45:41 +0100 1534561 http://www.medworm.com/index.php?rid=1468846&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18358782%26dopt%3DAbstract Authors: Sangar V, Lesk VI, Lesk AM In designing an algorithm to find pairs of points that are within Euclidean distance d it is effective to use a screening procedure to reject most pairs of points that are far apart. A procedure based on multiple, overlapping lattices can efficiently identify close points and exclude distant ones. PMID: 18358782 [PubMed - in process] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468846 Tue, 27 May 2008 15:10:42 +0100 1468846 http://www.medworm.com/index.php?rid=1468844&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18387208%26dopt%3DAbstract CONCLUSIONS: Our method improves the quality of the prediction of the free energy change due to single point protein mutations by adopting a hypothesis of thermodynamic reversibility of the existing experimental data. By this we both recast the thermodynamic symmetry of the problem and balance the distribution of the available experimental measurements of free energy changes. This eliminates possible overestimations of the previously described methods trained on an unbalanced data set comprising a number of destabilizing mutations higher than stabilizing ones. PMID: 18387208 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468844 Tue, 27 May 2008 15:10:13 +0100 1468844 http://www.medworm.com/index.php?rid=1468841&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18453553%26dopt%3DAbstract Authors: Bogdan I, Rivers J, Beynon RJ, Coca D MOTIVATION: Peptide Mass Fingerprinting (PMF) is a method for protein identification in which a protein is fragmented by a defined cleavage protocol (usually proteolysis with trypsin), and the masses of these products constitute a 'fingerprint' that can be searched against theoretical fingerprints of all known proteins. In the first stage of PMF, the raw mass spectrometric data are processed to generate a peptide mass list. In the second stage this protein fingerprint is used to search a database of known proteins for the best protein match. Although current software solutions can typically deliver a match in a relatively short time, a system that can find a match in real-time could change the way in which PMF is deployed and presented. In... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468841 Sat, 03 May 2008 04:00:00 +0100 1468841 http://www.medworm.com/index.php?rid=1468842&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18447634%26dopt%3DAbstract This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468842 Wed, 30 Apr 2008 04:00:00 +0100 1468842 http://www.medworm.com/index.php?rid=1468843&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18433061%26dopt%3DAbstract Authors: Konagurthu AS, Lesk AM Interactions between transcription factors and target genes form regulatory networks that control target gene expression. Regulatory networks contain canonical motifs, including the feed forward loop (FFL), single input module (SIM), and multiple input module (MIM) (Fig. 1). A challenge for network analysis is to identify and enumerate the motifs, required to illuminate their biological significance. Although there is consensus about the definition of the FFL, published definitions of the SIM and MIM are unclear and often used inconsistently. Here, we provide, for the first time, a complete and consistent definition of SIM and MIM, and algorithms for enumerating SIMs and MIMs in any network. From the algorithmic point of view, enumeration of SIMs and MIM... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468843 Wed, 23 Apr 2008 04:00:00 +0100 1468843 http://www.medworm.com/index.php?rid=1468851&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18290608%26dopt%3DAbstract Authors: Chen ST, Pan TL, Juan HF, Chen TY, Lin YS, Huang CM Tumor secreted substances (secretome), including extracellular matrix (ECM) components, act as mediators of tumor-host communication in the breast tumor microenvironment. Proteomic analysis has emphasized the value of the secretome as a source of prospective markers and drug targets for the treatment of breast cancers. Utilizing bioinformatics, our recent studies revealed global changes in protein expression after the activation of ECM-mediated signaling in breast cancer cells. A newly designed technique integrating a capillary ultrafiltration (CUF) probe with mass spectrometry was demonstrated to dynamically sample and identify in vivo and pure secretome from the tumor microenvironment. Such in vivo profiling of breast cance... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468851 Tue, 01 Apr 2008 04:00:00 +0100 1468851 http://www.medworm.com/index.php?rid=1468850&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18336222%26dopt%3DAbstract Authors: Gomase VS, Tagore S, Kale KV, Bhiwgade DA The rapid developments in the field of genomics and proteomics are expected to lead to a further increase in the potential for early diagnosis, the fine-tuning of prognostic features of specific tumors and the detection of cancer predisposition. Oncogenomics has identified new drug targets for genotype-specific treatments and provided strategies to validate these targets and to develop drugs. With the potential need to stratify patients by genotype, clinical testing of targeted drugs has become more complicated while expectations of patients, investors, and funding agencies have become accelerated. Oncogenomics has progressed logically from molecular profiling to model systems, cancer pharmacology and clinical trials. Oncogenomics cove... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468850 Sat, 01 Mar 2008 05:00:00 +0100 1468850 http://www.medworm.com/index.php?rid=1468849&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18336229%26dopt%3DAbstract Authors: Gomase VS, Tagore S Transcriptomics, a genome-wide measurement of mRNA expression levels based on DNA microarray technology is one of the prominent fields of study. This is the term given to the set of all transcripts or messenger RNA (mRNA) molecules produced in cells. It can also be applied to the specific subset of transcripts present in a particular cell or the total set of transcripts in a given organism. Transcriptomics has evolved from a variety of already present technologies and areas. These areas include proteomics, genomics, and environmental science. PMID: 18336229 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468849 Sat, 01 Mar 2008 05:00:00 +0100 1468849 http://www.medworm.com/index.php?rid=1468848&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18336230%26dopt%3DAbstract Authors: Gomase VS, Tagore S Toxicogenomics is defined as an integration of genomics (transcriptomics, proteomics and metabolomics) and toxicology. It is a scientific field that studies how the genome is involved in responses to environmental stressors and toxicants. It combines studies of mRNA expression, cell and tissue-wide protein expression and metabonomics to understand the role of gene-environment interactions in disease. One of the important aspects of toxicogenomics research is the development and application of bioinformatics tools and databases in order to facilitate the analysis, mining, visualizing and sharing of the vast amount of biological information being generated in this field. This rapidly growing area promises to have a large impact on many other scientific and me... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468848 Sat, 01 Mar 2008 05:00:00 +0100 1468848 http://www.medworm.com/index.php?rid=1468847&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18336231%26dopt%3DAbstract Authors: Gomase VS, Tagore S Kinomics is derived from the word kinome that is the kinase part of the proteome. Kinomics is a merger between genomics and proteomics. Defining the kinase complement of the human genome, the kinome, has provided an excellent starting point for understanding the scale of the problem. This approach combines the understanding of small molecules and targets, and thereby assists the researcher in finding new targets for existing molecules or understanding selectivity and poly-pharmacology of molecules in related targets. Deciphering the complex network of phosphorylation-based signaling is necessary for a thorough and therapeutically applicable understanding of the functioning of a cell in physiological and pathological states. PMID: 18336231 [PubMed - inde... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468847 Sat, 01 Mar 2008 05:00:00 +0100 1468847 http://www.medworm.com/index.php?rid=1468845&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18401917%26dopt%3DAbstract Authors: Suehara Y PMID: 18401917 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...) Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468845 Sat, 01 Mar 2008 05:00:00 +0100 1468845 http://www.medworm.com/index.php?rid=1468855&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18203265%26dopt%3DAbstract Authors: Meinnel T, Giglione C The vast majority of the proteins encoded in any genome naturally undergo a large number of different N-terminal modifications, hindering their characterization by routine proteomic approaches. These modifications are often irreversible, usually cotranslational and are crucial, as their occurrence may reflect or affect the status, fate and function of the protein. For example, large signal peptide cleavages and N-blocking mechanisms reflect targeting to various cell compartments, whereas N-ligation events tend to be related to protein half-life. N-terminal positional proteomic strategies hold promise as a new generation of approaches to the fine analysis of such modifications. However, further biological investigation is required to resolve problems assoc... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468855 Fri, 01 Feb 2008 05:00:00 +0100 1468855 http://www.medworm.com/index.php?rid=1468853&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18230036%26dopt%3DAbstract Authors: De Paoli P Biobanks are actively contributing to advances in biomedical research by offering opportunities to link laboratory research with clinical applications and by accelerating developments in personalized medicine. Microbiologists have a long tradition of storing microorganisms as part of projects focused on microbial genetics or phenotypic investigations. However, the impressive recent advances of biomedical translational research demand the integration of biobanks with high-level technological infrastructures in genomics, proteomics, bioinformatics, patient information systems and disease registries, where data originating from microorganisms are linked with human clinical information with the ultimate aim of improving healthcare by increasing the quality of biomedical... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468853 Fri, 01 Feb 2008 05:00:00 +0100 1468853 http://www.medworm.com/index.php?rid=1468852&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18266258%26dopt%3DAbstract Authors: Boonen K, Landuyt B, Baggerman G, Husson SJ, Huybrechts J, Schoofs L MS is currently one of the most important analytical techniques in biological and medical research. ESI and MALDI launched the field of MS into biology. The performance of mass spectrometers increased tremendously over the past decades. Other technological advances increased the analytical power of biological MS even more. First, the advent of the genome projects allowed an automated analysis of mass spectrometric data. Second, improved separation techniques, like nanoscale HPLC, are essential for MS analysis of biomolecules. The recent progress in bioinformatics is the third factor that accelerated the biochemical analysis of macromolecules. The first part of this review will introduce the basics of these te... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468852 Fri, 01 Feb 2008 05:00:00 +0100 1468852 http://www.medworm.com/index.php?rid=1468856&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18160232%26dopt%3DAbstract Authors: Bazeley PS, Shepelev V, Talebizadeh Z, Butler MG, Fedorova L, Filatov V, Fedorov A Among thousands of non-protein-coding RNAs which have been found in humans, a significant group represents snoRNA molecules that guide other types of RNAs to specific chemical modifications, cleavages, or proper folding. Yet, hundreds of mammalian snoRNAs have unknown function and are referred to as "orphan" molecules. In 2006, for the first time, it was shown that a particular orphan snoRNA (HBII-52) plays an important role in the regulation of alternative splicing of the serotonin receptor gene in humans and other mammals. In order to facilitate the investigation of possible involvement of snoRNAs in the regulation of pre-mRNA processing, we developed a new computational web resource, snoTARGE... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468856 Thu, 31 Jan 2008 05:00:00 +0100 1468856 http://www.medworm.com/index.php?rid=1468860&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17947323%26dopt%3DAbstract Authors: Kriventseva EV, Rahman N, Espinosa O, Zdobnov EM The concept of orthology is widely used to relate genes across different species using comparative genomics, and it provides the basis for inferring gene function. Here we present the web accessible OrthoDB database that catalogs groups of orthologous genes in a hierarchical manner, at each radiation of the species phylogeny, from more general groups to more fine-grained delineations between closely related species. We used a COG-like and Inparanoid-like ortholog delineation procedure on the basis of all-against-all Smith-Waterman sequence comparisons to analyze 58 eukaryotic genomes, focusing on vertebrates, insects and fungi to facilitate further comparative studies. The database is freely available at http://cegg.unige.ch/ort... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468860 Tue, 01 Jan 2008 05:00:00 +0100 1468860 http://www.medworm.com/index.php?rid=1468858&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17999997%26dopt%3DAbstract Authors: Glasner JD, Plunkett G, Anderson BD, Baumler DJ, Biehl BS, Burland V, Cabot EL, Darling AE, Mau B, Neeno-Eckwall EC, Pot D, Qiu Y, Rissman AI, Worzella S, Zaremba S, Fedorko J, Hampton T, Liss P, Rusch M, Shaker M, Shaull L, Shetty P, Thotakura S, Whitmore J, Blattner FR, Greene JM, Perna NT ERIC, the Enteropathogen Resource Integration Center (www.ericbrc.org), is a new web portal serving as a rich source of information about enterobacteria on the NIAID established list of Select Agents related to biodefense-diarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. More than 30 genomes have been completely sequenced, many more exist in draft form and additional projects are underway. These organisms are increasingly the focus... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468858 Tue, 01 Jan 2008 05:00:00 +0100 1468858 http://www.medworm.com/index.php?rid=1468857&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18003657%26dopt%3DAbstract Authors: Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ, Wang H, Brunk BP ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website. PMID: 18003657 [PubMed - indexed f... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468857 Tue, 01 Jan 2008 05:00:00 +0100 1468857 http://www.medworm.com/index.php?rid=1468854&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18220576%26dopt%3DAbstract Authors: Gomase VS, Changbhale SS, Patil SA, Kale KV Metabolomics is based on the simultaneous analysis of multiple low-molecular-weight metabolites from a given sample. The goals of metabolomics are to catalog and quantify the myriad small molecules found in biological fluids under different conditions. The metabolomics represents the collection of all metabolites in a biological organism, and metabolic profiling can give an instantaneous 'snapshot' of the physiology of that cell. Together with the other more established omics technologies, metabolomics will strengthen its claim to contribute to the detailed understanding of the in vivo function of gene products, biochemical analysis, regulatory networks and more ambitious, the mathematical description and simulation of the whole cell... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468854 Tue, 01 Jan 2008 05:00:00 +0100 1468854 http://www.medworm.com/index.php?rid=1468862&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17907274%26dopt%3DAbstract Authors: Hamacher M, Grünewald P, Rammert K, Bustamante NP, Hardt T, van Hall A, Meyer HE The symposium High Performance Proteomics was held in Dortmund on May 14-16, 2007, to celebrate the opening of the Zentrum für Angewandte Proteomik as well as the 6(th) anniversary of the German Human Brain Proteome Project. It offered an outstanding opportunity to obtain a broad overview about all fields of proteomics and related fields, combining the expertise of biochemists, physicians, bioinformatics, mathematicians and other researchers in Life Sciences. The main topics were the presentation of state-of-the-art proteomics technologies as well as possible transfer models for industrial applications. An accompanying industrial exhibition, as well as a discussion panel, offered the pos... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468862 Mon, 01 Oct 2007 04:00:00 +0100 1468862 http://www.medworm.com/index.php?rid=1468861&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17907277%26dopt%3DAbstract Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France. Proteomics. 2007 Oct;7(19):3436-40 Authors: Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H Over the last five years, the Human Proteome Organisation Proteomics Standards Initiative (HUPO PSI) has produced and released community-accepted XML interchange formats in the fields of mass spectrometry, molecular interactions and gel electrophoresis, have led the field in the discussion of the minimum information with which such data should be annotated and are now in the process of publishing much of this informati... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468861 Mon, 01 Oct 2007 04:00:00 +0100 1468861 http://www.medworm.com/index.php?rid=1468859&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17956938%26dopt%3DAbstract Authors: Hühne R, Koch FT, Sühnel J The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide inform... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1468859 Sat, 01 Sep 2007 04:00:00 +0100 1468859 http://www.medworm.com/index.php?rid=1228668&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18267295%26dopt%3DAbstract Authors: Xiao JF, Yu J It is believed that in the RNA world the operational (ribozymes) and the informational (riboscripts) RNA molecules were created with only three (adenosine, uridine, and guanosine) and two (adenosine and uridine) nucleosides, respectively, so that the genetic code started uncomplicated. Ribozymes subsequently evolved to be able to cut and paste themselves and riboscripts were acceptive to rigorous editing (adenosine to inosine); the intensive diversification of RNA molecules shaped novel cellular machineries that are capable of polymerizing amino acids-a new type of cellular building materials for life. Initially, the genetic code, encoding seven amino acids, was created only to distinguish purine and pyrimidine; it was later expanded in a stepwise way to encode 1... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1228668 Wed, 01 Aug 2007 04:00:00 +0100 1228668 http://www.medworm.com/index.php?rid=1228667&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18267296%26dopt%3DAbstract Authors: Damodaran S, Wood TD, Nagarajan P, Rabin RA Identification of proteins by mass spectrometry (MS) is an essential step in proteomic studies and is typically accomplished by either peptide mass fingerprinting (PMF) or amino acid sequencing of the peptide. Although sequence information from MS/MS analysis can be used to validate PMF-based protein identification, it may not be practical when analyzing a large number of proteins and when high- throughput MS/MS instrumentation is not readily available. At present, a vast majority of proteomic studies employ PMF. However, there are huge disparities in criteria used to identify proteins using PMF. Therefore, to reduce incorrect protein identification using PMF, and also to increase confidence in PMF-based protein identification withou... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1228667 Wed, 01 Aug 2007 04:00:00 +0100 1228667 http://www.medworm.com/index.php?rid=1228666&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18267297%26dopt%3DAbstract Authors: Chen AB, Hamamura K, Wang G, Xing W, Mohan S, Yokota H, Liu Y Understanding the regulatory mechanism that controls the alteration of global gene expression patterns continues to be a challenging task in computational biology. We previously developed an ant algorithm, a biologically-inspired computational technique for microarray data, and predicted putative transcription-factor binding motifs (TFBMs) through mimicking interactive behaviors of natural ants. Here we extended the algorithm into a set of web-based software, Ant Modeler, and applied it to investigate the transcriptional mechanism underlying bone formation. Mechanical loading and administration of bone morphogenic proteins (BMPs) are two known treatments to strengthen bone. We addressed a question: Is there any TFBM... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1228666 Wed, 01 Aug 2007 04:00:00 +0100 1228666 http://www.medworm.com/index.php?rid=1228665&cid=s_33035_176_f&fid=33035&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18267298%26dopt%3DAbstract Authors: Guda P, Guda C, Subramaniam S We have used a bioinformatics approach for the identification and reconstruction of metabolic pathways associated with amino acid metabolism in human mitochondria. Human mitochondrial proteins determined by experimental and computational methods have been superposed on the reference pathways from the KEGG database to identify mitochondrial pathways. Enzymes at the entry and exit points for each reconstructed pathway were identified, and mitochondrial solute carrier proteins were determined where applicable. Intermediate enzymes in the mitochondrial pathways were identified based on the annotations available from public databases, evidence in current literature, or our MITOPRED program, which predicts the mitochondrial localization of proteins. Thr... Genomics Proteomics ... journals http://www.medworm.com/rss/comments.php?id=1228665 Wed, 01 Aug 2007 04:00:00 +0100 1228665