Genomics Proteomics ...This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

This page shows you the latest items in this publication.

Pages: 1 2 3 4 5

218 records returned

Biomarkers for early and late stage chronic allograft nephropathy by proteogenomic profiling of peripheral blood.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - November 12, 2009 Category: Genetics & Stem Cells Authors: Kurian SM, Heilman R, Mondala TS, Nakorchevsky A, Hewel JA, Campbell D, Robison EH, Wang L, Lin W, Gaber L, Solez K, Shidban H, Mendez R, Schaffer RL, Fisher JS, Flechner SM, Head SR, Horvath S, Yates JR, Marsh CL, Salomon DR Tags: PLoS One Source Type: journals

Cellunomics: the interaction analysis of cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 a...
Source: Genomics Proteomics ... - November 6, 2009 Category: Genetics & Stem Cells Authors: Gomase VS, Tripathi AK, Tagore S Tags: Int J Bioinform Res Appl Source Type: journals

Leading applications and technologies in bioinformatics. Proceedings of the European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Martina Franca, Italy. September 18-20, 2008.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: PMID: 19882766 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - November 5, 2009 Category: Genetics & Stem Cells Tags: BMC Bioinformatics Source Type: journals

Top-Down Identification of Protein Biomarkers in Bacteria with Unsequenced Genomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 recogni...
Source: Genomics Proteomics ... - November 2, 2009 Category: Genetics & Stem Cells Authors: Wynne C, Fenselau C, Demirev PA, Edwards N Tags: Anal Chem Source Type: journals

Expression and molecular characterization of the Mycobacterium tuberculosis PII protein.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-ketogluta...
Source: Genomics Proteomics ... - November 2, 2009 Category: Genetics & Stem Cells Authors: Bandyopadhyay A, Arora A, Jain S, Laskar A, Mandal C, Ivanisenko VA, Fomin ES, Pintus SS, Kolchanov NA, Maiti S, Ramachandran S Tags: J Biochem Source Type: journals

Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-...
Source: Genomics Proteomics ... - October 23, 2009 Category: Genetics & Stem Cells Authors: Selesi D, Jehmlich N, von Bergen M, Schmidt F, Rattei T, Tischler P, Lueders T, Meckenstock RU Tags: J Bacteriol Source Type: journals

Qupe - a Rich Internet Application to take a Step Forward in the Analysis of Mass Spectrometry-Based Quantitative Proteomics Experiments.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 mo...
Source: Genomics Proteomics ... - October 5, 2009 Category: Genetics & Stem Cells Authors: Albaum SP, Neuweger H, Fränzel B, Lange S, Mertens D, Trötschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A Tags: Bioinformatics Source Type: journals

Evolving proteins at Darwin's bicentenary.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - September 27, 2009 Category: Genetics & Stem Cells Authors: Pinney JW, Stumpf MP Tags: Genome Biol Source Type: journals

Human protein reference database and human proteinpedia as discovery tools for systems biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 pro...
Source: Genomics Proteomics ... - September 1, 2009 Category: Genetics & Stem Cells Authors: Prasad TS, Kandasamy K, Pandey A Tags: Methods Mol Biol Source Type: journals

Novel insights into adipogenesis from omics data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 co...
Source: Genomics Proteomics ... - August 21, 2009 Category: Genetics & Stem Cells Authors: Prokesch A, Hackl H, Hakim-Weber R, Bornstein SR, Trajanoski Z Tags: Curr Med Chem Source Type: journals

Spectral clustering in peptidomics studies helps to unravel modification profile of biologically active peptides, and enhances peptide identification rate.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Genomics Proteomics ... - August 4, 2009 Category: Genetics & Stem Cells Authors: Menschaert G, Vandekerckhove TT, Landuyt B, Hayakawa E, Schoofs L, Luyten W, Van Criekinge W Tags: Proteomics Source Type: journals

Deconvoluting the 'omics for organ transplantation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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, molec...
Source: Genomics Proteomics ... - July 28, 2009 Category: Genetics & Stem Cells Authors: Sarwal MM Tags: Curr Opin Organ Transplant Source Type: journals

A System for Information Management in BioMedical Studies -SIMBioMS.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 standards and provides data impor...
Source: Genomics Proteomics ... - July 23, 2009 Category: Genetics & Stem Cells 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 Tags: Bioinformatics Source Type: journals

Modern Biotechnology in China.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 th...
Source: Genomics Proteomics ... - July 22, 2009 Category: Genetics & Stem Cells Authors: Wang QZ, Zhao XM Tags: Adv Biochem Eng Biotechnol Source Type: journals

Predicting proteomes of mitochondria and related organelles from genomic and expressed sequence tag data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Genomics Proteomics ... - July 15, 2009 Category: Genetics & Stem Cells Authors: Gaston D, Tsaousis AD, Roger AJ Tags: Methods Enzymol Source Type: journals

Mass spectrometric profiling of (neuro)-peptides in the worker honeybee, Apis mellifera.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 map...
Source: Genomics Proteomics ... - June 30, 2009 Category: Genetics & Stem Cells Authors: Boerjan B, Cardoen D, Bogaerts A, Landuyt B, Schoofs L, Verleyen P Tags: Neuropharmacology Source Type: journals

Applications of signal processing techniques to bioinformatics, genomics, and proteomics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19404479 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - June 28, 2009 Category: Genetics & Stem Cells Authors: Serpedin E, Garcia-Frias J, Huang Y, Braga-Neto U Tags: EURASIP J Bioinform Syst Biol Source Type: journals

The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ne...
Source: Genomics Proteomics ... - June 28, 2009 Category: Genetics & Stem Cells Authors: D'Elia D, Gisel A, Eriksson NE, Kossida S, Mattila K, Klucar L, Bongcam-Rudloff E Tags: BMC Bioinformatics Source Type: journals

SOLpro: accurate sequence-based prediction of protein solubility.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 sequenc...
Source: Genomics Proteomics ... - June 22, 2009 Category: Genetics & Stem Cells Authors: Magnan CN, Randall A, Baldi P Tags: Bioinformatics Source Type: journals

The metabolomics of carotenoids in engineered cell factory.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 caroten...
Source: Genomics Proteomics ... - June 15, 2009 Category: Genetics & Stem Cells Authors: Liu GN, Zhu YH, Jiang JG Tags: Appl Microbiol Biotechnol Source Type: journals

Host cell proteins in biologics development: Identification, quantitation and risk assessment.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 effo...
Source: Genomics Proteomics ... - June 14, 2009 Category: Genetics & Stem Cells Authors: Wang X, Hunter AK, Mozier NM Tags: Biotechnol Bioeng Source Type: journals

Meta-basic estimates the size of druggable human genome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Genomics Proteomics ... - May 31, 2009 Category: Genetics & Stem Cells Authors: Plewczynski D, Rychlewski L Tags: J Mol Model Source Type: journals

FDR made easy in differential feature discovery and correlation analyses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 crit...
Source: Genomics Proteomics ... - May 31, 2009 Category: Genetics & Stem Cells Authors: Ling XB, Cohen H, Jin J, Lau I, Schilling J Tags: Bioinformatics Source Type: journals

Bioinformatics analysis of mass spectrometry-based proteomics data sets.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 proteom...
Source: Genomics Proteomics ... - March 20, 2009 Category: Genetics & Stem Cells Authors: Kumar C, Mann M Tags: FEBS Lett Source Type: journals

FactorY, a bioinformatic resource for genome-wide promoter analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: 192...
Source: Genomics Proteomics ... - March 7, 2009 Category: Genetics & Stem Cells Authors: Guruceaga E, Segura V, Corrales FJ, Rubio A Tags: Comput Biol Med Source Type: journals

Utilizing the Molecular Gateway: The Path to Personalized Cancer Management.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 chemotherape...
Source: Genomics Proteomics ... - February 26, 2009 Category: Genetics & Stem Cells Authors: Overdevest JB, Theodorescu D, Lee JK Tags: Clin Chem Source Type: journals

Global networks of functional coupling in eukaryotes from comprehensive data integration.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 sup...
Source: Genomics Proteomics ... - February 25, 2009 Category: Genetics & Stem Cells Authors: Alexeyenko A, Sonnhammer EL Tags: Genome Res Source Type: journals

A neuromedin-pyrokinin-like neuropeptide signaling system in Caenorhabditis elegans.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Genomics Proteomics ... - February 13, 2009 Category: Genetics & Stem Cells Authors: Lindemans M, Janssen T, Husson SJ, Meelkop E, Temmerman L, Clynen E, Mertens I, Schoofs L Tags: Biochem Biophys Res Commun Source Type: journals

Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. T...
Source: Genomics Proteomics ... - February 11, 2009 Category: Genetics & Stem Cells Authors: Verma A, Yadav VK, Basundra R, Kumar A, Chowdhury S Tags: Nucleic Acids Res Source Type: journals

Wilms' Tumor 1 Gene Expression in Hepatocellular Carcinoma Promotes Cell Dedifferentiation and Resistance to Chemotherapy.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - February 3, 2009 Category: Genetics & Stem Cells Authors: Perugorria MJ, Castillo J, Latasa MU, Goñi S, Segura V, Sangro B, Prieto J, Avila MA, Berasain C Tags: Cancer Res Source Type: journals

Adipokinetic hormone signaling through the gonadotropin-releasing hormone receptor modulates egg-laying in Caenorhabditis elegans.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 s...
Source: Genomics Proteomics ... - January 21, 2009 Category: Genetics & Stem Cells Authors: Lindemans M, Liu F, Janssen T, Husson SJ, Mertens I, Gäde G, Schoofs L Tags: Proc Natl Acad Sci U S A Source Type: journals

Schizophrenia genomics and proteomics: are we any closer to biomarker discovery?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Genomics Proteomics ... - January 7, 2009 Category: Genetics & Stem Cells Authors: Lakhan SE, Kramer A Tags: Behav Brain Funct Source Type: journals

Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - January 6, 2009 Category: Genetics & Stem Cells Authors: Mruk I, Blumenthal RM Tags: Nucleic Acids Res Source Type: journals

Toward theragnostics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 imagi...
Source: Genomics Proteomics ... - January 1, 2009 Category: Genetics & Stem Cells Authors: Pene F, Courtine E, Cariou A, Mira JP Tags: Crit Care Med Source Type: journals

Brazilian genome sequencing projects: state of the art.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 stimula...
Source: Genomics Proteomics ... - December 18, 2008 Category: Genetics & Stem Cells Authors: Xavier ER, Capanema BP, Ruiz JC, Oliveira G, Meyer R, D'Afonseca V, Miyoshi A, Azevedo V Tags: Recent Pat DNA Gene Seq Source Type: journals

Educational Websites - Bioinformatics Tools II.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. ...
Source: Genomics Proteomics ... - December 12, 2008 Category: Genetics & Stem Cells Authors: Lomberk G Tags: Pancreatology Source Type: journals

Candida albicans-macrophage interactions: genomic and proteomic insights.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 comput...
Source: Genomics Proteomics ... - December 1, 2008 Category: Genetics & Stem Cells Authors: Diez-Orejas R, Fernández-Arenas E Tags: Future Microbiol Source Type: journals

MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 - ...
Source: Genomics Proteomics ... - November 12, 2008 Category: Genetics & Stem Cells Authors: Brouwer RW, Hijum SA, Kuipers OP Tags: Bioinformatics Source Type: journals

ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-intro...
Source: Genomics Proteomics ... - November 4, 2008 Category: Genetics & Stem Cells Authors: Bhasi A, Philip P, Manikandan V, Senapathy P Tags: Nucleic Acids Res Source Type: journals

Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 custo...
Source: Genomics Proteomics ... - October 24, 2008 Category: Genetics & Stem Cells Authors: Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M Tags: Plant Physiol Source Type: journals

On the origin of distribution patterns of motifs in biological networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - October 15, 2008 Category: Genetics & Stem Cells Authors: Konagurthu AS, Lesk AM Tags: BMC Syst Biol Source Type: journals

Genomics and proteomics of immune modulatory effects of a butanol fraction of Echinacea purpurea in human dendritic cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - October 13, 2008 Category: Genetics & Stem Cells Authors: Wang CY, Staniforth V, Chiao MT, Hou CC, Wu HM, Yeh KC, Chen CH, Hwang PI, Wen TN, Shyur LF, Yang NS Tags: BMC Genomics Source Type: journals

Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 extens...
Source: Genomics Proteomics ... - October 4, 2008 Category: Genetics & Stem Cells Authors: Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T Tags: Nucleic Acids Res Source Type: journals

ASAS Centennial Paper: Lactation Biology for the 21st Century.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Genomics Proteomics ... - September 26, 2008 Category: Genetics & Stem Cells Authors: Loor JJ, Cohick WS Tags: J Anim Sci Source Type: journals

GabiPD: the GABI primary database--a plant integrative 'omics' database.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 conc...
Source: Genomics Proteomics ... - September 23, 2008 Category: Genetics & Stem Cells Authors: Riaño-Pachón DM, Nagel A, Neigenfind J, Wagner R, Basekow R, Weber E, Mueller-Roeber B, Diehl S, Kersten B Tags: Nucleic Acids Res Source Type: journals

A Toolkit for Capturing and Sharing FuGE Experiments.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - September 17, 2008 Category: Genetics & Stem Cells Authors: Belhajjame K, Jones AR, Paton NW Tags: Bioinformatics Source Type: journals

Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - September 5, 2008 Category: Stem Cells Authors: Bechtel JM, Wittenschlaeger T, Dwyer T, Song J, Arunachalam S, Ramakrishnan SK, Shepard S, Fedorov A Tags: BMC Genomics Source Type: journals

SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...)
Source: Genomics Proteomics ... - September 5, 2008 Category: Stem Cells Authors: Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN Tags: BMC Bioinformatics Source Type: journals

The proteogenomic path towards biomarker discovery.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-b...
Source: Genomics Proteomics ... - August 22, 2008 Category: Stem Cells Authors: Sigdel TK, Sarwal MM Tags: Pediatr Transplant Source Type: journals

Highlighting computations in bioscience and bioinformatics: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB07).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Genomics Proteomics ... - August 2, 2008 Category: Stem Cells Authors: Lu G, Ni J Tags: BMC Bioinformatics Source Type: journals