Genome Biology via MedWorm.com 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 'Genome Biology' source. Thu, 09 Feb 2012 09:43:37 +0100 SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data http://www.medworm.com/index.php?rid=5654746&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2FR4 A tool that uses a priori information to optimize alternative splicing prediction from RNA-seq data (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654746 Tue, 31 Jan 2012 05:00:00 +0100 5654746 Uberon, an integrative multi-species anatomy ontology http://www.medworm.com/index.php?rid=5654745&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2FR5 A description of the Uberon ontology tool that allows comparisons of genomic information across multiple animal phyla (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654745 Tue, 31 Jan 2012 05:00:00 +0100 5654745 MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis http://www.medworm.com/index.php?rid=5654744&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2FR6 An algorithm that reconciles metabolic network reconstructions into a single model (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654744 Tue, 31 Jan 2012 05:00:00 +0100 5654744 Dissecting the regulatory architecture of gene expression QTLs http://www.medworm.com/index.php?rid=5654743&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2FR7 An analysis of eQTLs located in regulatory elements in the human genome (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654743 Tue, 31 Jan 2012 05:00:00 +0100 5654743 Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes http://www.medworm.com/index.php?rid=5654742&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2F415 An Open Letter describing the project to sequence the genomes of the saltwater crocodile, the American alligator and the Indian gharial (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654742 Tue, 31 Jan 2012 05:00:00 +0100 5654742 Low-cost sequencing opens new insights into diverse plant genomes http://www.medworm.com/index.php?rid=5654750&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2F311 A report on the 2011 ?Plant Genomes and Biotechnology: From Genes to Networks? meeting, held at Cold Spring Harbor Laboratory. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654750 Mon, 30 Jan 2012 05:00:00 +0100 5654750 Dynamic systems http://www.medworm.com/index.php?rid=5654749&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2F312 A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654749 Mon, 30 Jan 2012 05:00:00 +0100 5654749 Co-survival of the fittest few: mosaic amplification of receptor tyrosine kinases in glioblastoma http://www.medworm.com/index.php?rid=5654748&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2F141 Li Ding highlights recent findings suggesting that tumor cells with different driver mutations may coevolve rather than compete during clonal evolution (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654748 Mon, 30 Jan 2012 05:00:00 +0100 5654748 The dog particle http://www.medworm.com/index.php?rid=5654747&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2F142 In a big announcement suspiciously soon before their funding is renewed, canine researchers have news about the Briggs Noson (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5654747 Mon, 30 Jan 2012 05:00:00 +0100 5654747 Whack-an-E. coli with the morbidostat http://www.medworm.com/index.php?rid=5642452&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2Fcontent%2F13%2F1%2F140 Nathalie Balaban and colleagues highlight a landmark study of antibiotic resistance evolutionary trajectories, which is centered on a morbidostat (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5642452 Fri, 27 Jan 2012 05:00:00 +0100 5642452 DNA-protein interactions in high definition http://www.medworm.com/index.php?rid=5633832&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2F139 Mendenhall and Bernstein highlight ChIP-exo, which is an elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5633832 Fri, 27 Jan 2012 05:00:00 +0100 5633832 A genome triplication associated with early diversification of the core eudicots http://www.medworm.com/index.php?rid=5633833&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2FR3 An investigation of when the gamma polyploidization event occurred in relation to speciation events in angiosperm history (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5633833 Thu, 26 Jan 2012 05:00:00 +0100 5633833 Implications for health and disease in the genetic signature of the Ashkenazi Jewish population http://www.medworm.com/index.php?rid=5633834&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2FR2 A population-specific genetic signature, derived from a large genotyping study, helps explain why some diseases are overrepresented in the Ashkenazi population (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5633834 Wed, 25 Jan 2012 05:00:00 +0100 5633834 Transcriptional enhancers in development and disease http://www.medworm.com/index.php?rid=5623741&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2F238 Enhancers positioned far from promoters are important in development and disease, and genome-wide analyses are now giving greater insights into their function. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5623741 Mon, 23 Jan 2012 05:00:00 +0100 5623741 What is complex about complex disorders? http://www.medworm.com/index.php?rid=5623740&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2F237 Complex disorders such as diabetes and schizophrenia are really groups of many distinct genetic disorders, most of which probably result from rare, recent mutations that have strong biological effects. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5623740 Mon, 23 Jan 2012 05:00:00 +0100 5623740 Genetic adaptation to high altitude in the Ethiopian highlands http://www.medworm.com/index.php?rid=5615710&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2012%2F13%2F1%2FR1 The genetics of hypoxia selection in an Ethiopian high-altitude population are distinct from Andean and Tibetan genotypes, suggestive of convergent evolution (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5615710 Fri, 20 Jan 2012 05:00:00 +0100 5615710 MicroRNAs and their isomiRs function cooperatively to target common biological pathways http://www.medworm.com/index.php?rid=5556144&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR126 IsomiRs act cooperatively with canonical miRNAs to regulate gene expression (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5556144 Fri, 30 Dec 2011 05:00:00 +0100 5556144 Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera http://www.medworm.com/index.php?rid=5556143&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR127 A global screen of mutant fitness in Neisseria meningitidis was used to construct a genome-scale metabolic network (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5556143 Fri, 30 Dec 2011 05:00:00 +0100 5556143 Correction: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development http://www.medworm.com/index.php?rid=5556142&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F414 Correction: The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5556142 Fri, 30 Dec 2011 05:00:00 +0100 5556142 Correction: SpeCond: a method to detect condition-specific gene expression http://www.medworm.com/index.php?rid=5556141&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F413 Correction: A method to detect condition-specific gene expression from microarray data (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5556141 Fri, 30 Dec 2011 05:00:00 +0100 5556141 Making enhancers from spare parts of the genome http://www.medworm.com/index.php?rid=5556145&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F138 Boris Lenhard and colleagues on how developmental enhancers form in genomes by the recycling of existing functional elements (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5556145 Thu, 29 Dec 2011 05:00:00 +0100 5556145 Genomics in 2011: challenges and opportunities http://www.medworm.com/index.php?rid=5567125&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F137 Several members of the Genome Biology Editorial Board give their views on the state of play in genomics (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5567125 Wed, 28 Dec 2011 05:00:00 +0100 5567125 Games with a scientific purpose http://www.medworm.com/index.php?rid=5548760&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F135 Potent algorithms and solved "unsolvable" structures: are the 230,000 players of the protein folding game Foldit the scientists of the future? (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5548760 Wed, 28 Dec 2011 05:00:00 +0100 5548760 The Columnist Manifesto http://www.medworm.com/index.php?rid=5548759&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F136 Scientists need to explain to the public what science is and why it needs funding, especially when the economic situation is bad (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5548759 Wed, 28 Dec 2011 05:00:00 +0100 5548759 As we come to the end of 2011, several members of the Genome Biology Editorial Board give their views on the state of play in genomics http://www.medworm.com/index.php?rid=5548758&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F137 . (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5548758 Wed, 28 Dec 2011 05:00:00 +0100 5548758 Alu elements: know the SINEs http://www.medworm.com/index.php?rid=5548757&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F236 Prescott Deininger reviews the contribution of Alu elements to genome evolution, gene regulation and disease. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5548757 Wed, 28 Dec 2011 05:00:00 +0100 5548757 Opening sequence: computational genomics in the era of high-throughput sequencing http://www.medworm.com/index.php?rid=5548756&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2F310 A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, November 2011. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5548756 Wed, 28 Dec 2011 05:00:00 +0100 5548756 Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights http://www.medworm.com/index.php?rid=5531316&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR125 A comprehensive resource of DNA binding specificity data for all characterized Saccharomyces cerevisiae transcription factors (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5531316 Wed, 21 Dec 2011 05:00:00 +0100 5531316 Caenorhabditis elegans Heterochromatin Protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism http://www.medworm.com/index.php?rid=5531318&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR123 HPL-2, the C. elegans homolog of heterochromatin protein 1, helps regulate longevity, dauer diapause and lipid metabolism (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5531318 Tue, 20 Dec 2011 05:00:00 +0100 5531318 Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing http://www.medworm.com/index.php?rid=5531317&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR124 An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5531317 Tue, 20 Dec 2011 05:00:00 +0100 5531317 The relationship between proteome size, structural disorder and organism complexity http://www.medworm.com/index.php?rid=5519572&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR120 Complexity is a multi-parametric trait, determined by interaction potential, alternative splicing capacity, protein disorder and, above all, proteome size (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5519572 Mon, 19 Dec 2011 05:00:00 +0100 5519572 Loss of the Bloom Syndrome helicase increases DNA ligase 4-independent genome rearrangements and tumorigenesis in aging Drosophila http://www.medworm.com/index.php?rid=5519571&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR121 Drosophila blm mutants show an increase in genome rearrangements which, surprisingly, are independent of DNA ligase 4 (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5519571 Mon, 19 Dec 2011 05:00:00 +0100 5519571 Accurate proteome-wide protein quantification from high-resolution 15N mass spectra http://www.medworm.com/index.php?rid=5519570&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR122 A fast, user-friendly bioinformatic tool for accurate quantification of proteins in 15N mass spectrometry data (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5519570 Mon, 19 Dec 2011 05:00:00 +0100 5519570 RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.) http://www.medworm.com/index.php?rid=5472850&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F12%2FR119 Transcriptomics reveals the evolutionary trajectory of polyploidization, with insights into gene networks and genome organization (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5472850 Fri, 02 Dec 2011 05:00:00 +0100 5472850 Dominoes http://www.medworm.com/index.php?rid=5463713&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2F134 If we fund the next big science program, how many smaller research programs will receive no funding as a consequence? (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5463713 Wed, 30 Nov 2011 05:00:00 +0100 5463713 BRD4 jump-starts transcription after mitotic silencing http://www.medworm.com/index.php?rid=5463714&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2F133 Philipp Voigt and Danny Reinberg highlight BRD4's role in gene bookmarking during mitosis, and how this might be exploited in chemotherapy (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5463714 Tue, 29 Nov 2011 05:00:00 +0100 5463714 Hundreds of putatively functional small open reading frames in Drosophila http://www.medworm.com/index.php?rid=5446427&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2FR118 The Drosophila genome contains hundreds of small open reading frames with putative functionality (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5446427 Fri, 25 Nov 2011 05:00:00 +0100 5446427 Human genetics in full resolution http://www.medworm.com/index.php?rid=5446428&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2F309 A report on the 12th International Congress of Human Genetics, and the annual American Society of Human Genetics conference, October 2011 (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5446428 Thu, 24 Nov 2011 05:00:00 +0100 5446428 Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine http://www.medworm.com/index.php?rid=5446430&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2FR116 The genome and transcriptome sequences of Cordyceps militaris, a fungal pathogen of insects that is used in traditional Chinese medicine (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5446430 Wed, 23 Nov 2011 05:00:00 +0100 5446430 HSF binding in Alu repeats expands its involvement in stress through an antisense mechanism http://www.medworm.com/index.php?rid=5446429&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2FR117 HSF binding to conserved sites in Alu repeats initiates an antisense transcript-mediated response to heat shock (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5446429 Wed, 23 Nov 2011 05:00:00 +0100 5446429 Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor) http://www.medworm.com/index.php?rid=5436185&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2FR114 Genomes from three strains of Sorghum bicolor (one grain and two sweet) have been sequenced and compared with the reference genome (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5436185 Mon, 21 Nov 2011 05:00:00 +0100 5436185 A world in a grain of sand: human history from genetic data http://www.medworm.com/index.php?rid=5436184&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F11%2F6%2FR60 Genome-wide genotypes and sequences are enriching our understanding of the past 50,000 years of human history, according to Chris Tyler-Smith (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5436184 Mon, 21 Nov 2011 05:00:00 +0100 5436184 Wrangling for microRNAs provokes much crosstalk http://www.medworm.com/index.php?rid=5436183&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F11%2F6%2FR60 Chris Ponting highlights recent articles on competitive endogenous RNAs that illustrate how miRNA response elements enable crosstalk between transcripts (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5436183 Mon, 21 Nov 2011 05:00:00 +0100 5436183 Discovery of active enhancers through bidirectional expression of short transcripts http://www.medworm.com/index.php?rid=5415636&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2FR113 Regions showing bidirectional expression of short transcripts can be used to identify active enhancers (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5415636 Mon, 14 Nov 2011 05:00:00 +0100 5415636 Tissue inhibitors of metalloproteinases http://www.medworm.com/index.php?rid=5404034&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2F233 As metalloproteinase-independent functions are discovered for TIMPs, future work will focus on identifying receptors and downstream signaling mechanisms (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5404034 Fri, 11 Nov 2011 05:00:00 +0100 5404034 Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems http://www.medworm.com/index.php?rid=5394526&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2FR112 Error rates are compared in data from Illumina's HiSeq and GAIIx systems (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5394526 Tue, 08 Nov 2011 05:00:00 +0100 5394526 Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors http://www.medworm.com/index.php?rid=5394527&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2FR111 A method that uses both chromatin features and motif identification to predict transcription factor binding sites (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5394527 Mon, 07 Nov 2011 05:00:00 +0100 5394527 Composite effects of gene determinants on the translation speed and density of ribosomes http://www.medworm.com/index.php?rid=5372236&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F11%2FR110 Codon usage, amino acid charge and mRNA folding energy all correlate with translation speed and ribosome density (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5372236 Thu, 03 Nov 2011 04:00:00 +0100 5372236 Bailing out http://www.medworm.com/index.php?rid=5372237&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F131 Let us shout to the public and private sectors, this is not the time to be bailing out (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5372237 Sat, 29 Oct 2011 04:00:00 +0100 5372237 Genome-wide association studies in plants: the missing heritability is in the field http://www.medworm.com/index.php?rid=5394528&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F232 Justin Borevitz on how high-power association mapping is going back 'into the field' through the combination of genomics and population biology (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5394528 Fri, 28 Oct 2011 04:00:00 +0100 5394528 1, 2, 3: Counting the fingers on a chicken wing http://www.medworm.com/index.php?rid=5372239&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F130 Malcolm Logan on an RNA-seq approach to clarifying a long-standing dispute between paleontologists and embryologists (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5372239 Fri, 28 Oct 2011 04:00:00 +0100 5372239 Genome wide association studies in plants: the missing heritability is in the field. http://www.medworm.com/index.php?rid=5372238&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F232 Justin Borevitz on how high-power association mapping is going back 'into the field' through the combination of genomics and population biology (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5372238 Fri, 28 Oct 2011 04:00:00 +0100 5372238 Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles http://www.medworm.com/index.php?rid=5372240&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR109 Application of a new method to prokaryotic genomes reveals an association between lifestyle and codon bias (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5372240 Thu, 27 Oct 2011 04:00:00 +0100 5372240 The rhomboid protease family: a decade of progress on function and mechanism http://www.medworm.com/index.php?rid=5353731&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F231 The rhomboid family of membrane-immersed proteases are found in all domains of life and have been implicated in several human diseases. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5353731 Thu, 27 Oct 2011 04:00:00 +0100 5353731 The draft genome of the carcinogenic human liver fluke Clonorchis sinensis http://www.medworm.com/index.php?rid=5353735&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR107 A draft genome sequence of the liver fluke Clonorchis sinensis, which is a leading cause of liver cancer in Asia (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5353735 Mon, 24 Oct 2011 04:00:00 +0100 5353735 Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity http://www.medworm.com/index.php?rid=5353734&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR108 TAPS is a method for identifying allele-specific copy number changes in tumor samples (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5353734 Mon, 24 Oct 2011 04:00:00 +0100 5353734 Moving beyond genome sequencing into personalized genomic medicine: biological and computing challenges http://www.medworm.com/index.php?rid=5353733&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F308 A report of the Beyond the Genome meeting, the Universities at Shady Grove, Rockville, Maryland, USA, 19-22 September 2011 (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5353733 Mon, 24 Oct 2011 04:00:00 +0100 5353733 Bacterial epidemiology and biology - lessons from genome sequencing http://www.medworm.com/index.php?rid=5353732&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F230 Brendan Wren and Julian Parkhill on how a new era in microbial genomics has solved ancient controversies and promises to revolutionize our understanding of bacterial pathogens (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5353732 Mon, 24 Oct 2011 04:00:00 +0100 5353732 High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing http://www.medworm.com/index.php?rid=5342164&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR104 The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5342164 Fri, 21 Oct 2011 04:00:00 +0100 5342164 Integrating diverse genomic data using gene sets http://www.medworm.com/index.php?rid=5342163&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR105 A method for integrating multiple genomic data types for the identification of enriched gene sets (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5342163 Fri, 21 Oct 2011 04:00:00 +0100 5342163 Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics http://www.medworm.com/index.php?rid=5342162&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR106 Transcription is measured in Rhizobium leguminosarum grown on roots of a host plant, a non-host legume and a non-leguminous plant. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5342162 Fri, 21 Oct 2011 04:00:00 +0100 5342162 The draft genome and transcriptome of Cannabis sativa http://www.medworm.com/index.php?rid=5342167&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR102 The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5342167 Thu, 20 Oct 2011 04:00:00 +0100 5342167 Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer http://www.medworm.com/index.php?rid=5342166&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR103 Chromothripsis is found to be a common mechanism driving structural rearrangement in primary colorectal cancer and metastases (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5342166 Thu, 20 Oct 2011 04:00:00 +0100 5342166 How hemp got high http://www.medworm.com/index.php?rid=5342165&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F409 Senior Assistant Editor Naomi Attar discusses the genome sequence of cannabis (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5342165 Thu, 20 Oct 2011 04:00:00 +0100 5342165 Revealing the molecular signatures of host-pathogen interactions http://www.medworm.com/index.php?rid=5342168&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2F229 Genome-wide association studies and pathogen sequencing are revealing unexpected insights into host-pathogen interactions (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5342168 Wed, 19 Oct 2011 04:00:00 +0100 5342168 SpeCond: a method to detect condition-specific gene expression http://www.medworm.com/index.php?rid=5329140&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR101 A method to detect condition-specific gene expression from microarray data (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5329140 Tue, 18 Oct 2011 04:00:00 +0100 5329140 Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control http://www.medworm.com/index.php?rid=5329141&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR100 The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5329141 Mon, 17 Oct 2011 04:00:00 +0100 5329141 Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium http://www.medworm.com/index.php?rid=5309540&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR99 All response regulators in the genome of Desulfovibrius vulgaris are identified, as are all their target genes (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5309540 Wed, 12 Oct 2011 04:00:00 +0100 5309540 The transcriptional landscape of Chlamydia pneumoniae http://www.medworm.com/index.php?rid=5309541&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F10%2FR98 The life cycle of the obligate intracellular human pathogen C. pneumoniae has a dynamic transcriptional landscape (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5309541 Tue, 11 Oct 2011 04:00:00 +0100 5309541 The one new journal we might actually need http://www.medworm.com/index.php?rid=5266913&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2F129 The one thing that I actually do want for Christmas: another scientific journal (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5266913 Thu, 29 Sep 2011 04:00:00 +0100 5266913 Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis http://www.medworm.com/index.php?rid=5266917&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR93 Two methods are presented, SRFIM and SERVIC4E, for detecting rare variants in pooled exome samples (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5266917 Wed, 28 Sep 2011 04:00:00 +0100 5266917 Comparison of solution-based exome capture methods for next generation sequencing http://www.medworm.com/index.php?rid=5266916&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR94 Roche NimbleGen and Agilent solution-based exome capture kits are compared. NimbleGen kits give more accurate alignments to target regions (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5266916 Wed, 28 Sep 2011 04:00:00 +0100 5266916 Comprehensive comparison of three commercial human whole-exome capture platforms http://www.medworm.com/index.php?rid=5266915&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR95 A comparison of three human exome-capture platforms shows that NimbleGen's SeqCap EZ gives the best efficacy of exome capture and SNP detection (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5266915 Wed, 28 Sep 2011 04:00:00 +0100 5266915 First somatic mutation of E2F1 in a critical DNA binding residue discovered in well- differentiated papillary mesothelioma of the peritoneum http://www.medworm.com/index.php?rid=5266914&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR96 An E2F1 somatic mutation is discovered in a rare form of cancer by exome sequencing (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5266914 Wed, 28 Sep 2011 04:00:00 +0100 5266914 Exome sequencing identifies a novel missense variant in RRM2B associated with autosomal recessive progressive external ophthalmoplegia http://www.medworm.com/index.php?rid=5266918&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR92 Exome sequencing in a single recessive case of progressive external ophthalmoplegia identifies a novel missense variant in RRM2B as a potential causative mutation (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5266918 Tue, 27 Sep 2011 04:00:00 +0100 5266918 Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice http://www.medworm.com/index.php?rid=5244782&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR90 Exome sequencing was used to identify a potentially causative mutation in the Dearish mouse, a model for otitis media (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5244782 Wed, 21 Sep 2011 04:00:00 +0100 5244782 SHROOM3 is a novel candidate for heterotaxy identified by whole exome sequencing http://www.medworm.com/index.php?rid=5244781&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR91 A recessive missense mutation in SHROOM3, which is associated with heterotaxy is identified using exome sequencing (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5244781 Wed, 21 Sep 2011 04:00:00 +0100 5244781 Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in Middle Eastern families http://www.medworm.com/index.php?rid=5244783&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR89 Targeted capture and sequencing of genomic DNA from subjects with inherited hearing loss offers an effective screen for mutations (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5244783 Wed, 14 Sep 2011 04:00:00 +0100 5244783 Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes http://www.medworm.com/index.php?rid=5231343&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR85 A method for performing linkage analysis from exome sequencing variant data is presented (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231343 Wed, 14 Sep 2011 04:00:00 +0100 5231343 Mutation discovery in mice by whole exome sequencing http://www.medworm.com/index.php?rid=5231342&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR86 In solution capture reagents are developed for the mouse exome and demonstrated in multiple inbred strains and novel mutant strains (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231342 Wed, 14 Sep 2011 04:00:00 +0100 5231342 Expanding whole exome resequencing into non-human primates http://www.medworm.com/index.php?rid=5231341&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR87 Human DNA capture tools are used to capture and sequence non-human primate DNA (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231341 Wed, 14 Sep 2011 04:00:00 +0100 5231341 Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome http://www.medworm.com/index.php?rid=5231340&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2FR88 Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231340 Wed, 14 Sep 2011 04:00:00 +0100 5231340 The promise and limitations of population exomics for human evolution studies http://www.medworm.com/index.php?rid=5231339&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2F127 Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231339 Wed, 14 Sep 2011 04:00:00 +0100 5231339 Exome sequencing: the expert view http://www.medworm.com/index.php?rid=5231338&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2F128 Three leaders in the field of exome sequencing discuss why the approach is so popular and how it is contributing to genomics (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231338 Wed, 14 Sep 2011 04:00:00 +0100 5231338 Computational and statistical approaches to analyzing variants identified by exome sequencing http://www.medworm.com/index.php?rid=5231337&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2F227 Many computational and statistical methods are now available to narrow down causal variants in exome sequencing data, for both Mendelian and complex diseases (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231337 Wed, 14 Sep 2011 04:00:00 +0100 5231337 Unlocking Mendelian disease using exome sequencing http://www.medworm.com/index.php?rid=5231336&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2F228 In the past 2 years, exome sequencing has provided significant new insights into the causes of both Mendelian and sporadic genetic diseases (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231336 Wed, 14 Sep 2011 04:00:00 +0100 5231336 The exome factor http://www.medworm.com/index.php?rid=5231335&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F9%2F407 Special Issues Editor, Hannah Stower, introduces Genome Biology's issue on exome sequencing (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231335 Wed, 14 Sep 2011 04:00:00 +0100 5231335 Next-generation human genetics http://www.medworm.com/index.php?rid=5231334&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2Fcontent%2F12%2F9%2F408 Exome and genome sequencing are reshaping the landscape of human genetics; Jay Shendure discusses the lessons learnt and opportunities opened (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5231334 Wed, 14 Sep 2011 04:00:00 +0100 5231334 Nothing to do and all day to do it in http://www.medworm.com/index.php?rid=5189794&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2F126 The perfect end to a perfect vacation day (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5189794 Tue, 30 Aug 2011 23:00:00 +0100 5189794 The real cost of sequencing: higher than you think! http://www.medworm.com/index.php?rid=5167597&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2F125 The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5167597 Wed, 24 Aug 2011 23:00:00 +0100 5167597 Repeated phenotypic changes highlight molecular targets of convergent evolution http://www.medworm.com/index.php?rid=5153462&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2F124 Maggie Wagner and Thomas Mitchell-Olds discuss how selection might preferentially target certain genes that have a strong phenotypic effect (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5153462 Mon, 22 Aug 2011 23:00:00 +0100 5153462 Computational biology: plus c'est la meme chose, plus ca change http://www.medworm.com/index.php?rid=5153461&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2F307 A report on the joint 19th Annual ISMB/10th Annual ECCB and the 7th ISCB Student Council Symposium, Vienna, Austria, 15-19 July 2011 (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5153461 Mon, 22 Aug 2011 23:00:00 +0100 5153461 Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast http://www.medworm.com/index.php?rid=5153464&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR82 A study of marks associated with introns in S. pombe finds distinct patterns of histones, open chromatin and PolII enrichment (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5153464 Sun, 21 Aug 2011 23:00:00 +0100 5153464 Cistrome: an integrative platform for transcriptional regulation studies http://www.medworm.com/index.php?rid=5153463&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR83 A Galaxy-based web application for integrative analysis of ChIP data (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5153463 Sun, 21 Aug 2011 23:00:00 +0100 5153463 Single-cell copy number variation detection http://www.medworm.com/index.php?rid=5216638&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2Fcontent%2F12%2F8%2FR80 A method is presented for detecting copy number variations from array CGH data specifically optimized for use with single cells (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5216638 Fri, 19 Aug 2011 04:00:00 +0100 5216638 Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development http://www.medworm.com/index.php?rid=5153466&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR81 The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5153466 Thu, 18 Aug 2011 23:00:00 +0100 5153466 Sequencing Skippy: the genome sequence of an Australian kangaroo, Macropus eugenii http://www.medworm.com/index.php?rid=5153465&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2F123 The Sanger Institute's David Adams finds our kangaroo genome sequence article to be a fascinating window on mammalian evolution (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5153465 Thu, 18 Aug 2011 23:00:00 +0100 5153465 A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1 http://www.medworm.com/index.php?rid=5153469&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR78 A phospho-proteomics screen identifies many novel Chk1 substrates and a target site consensus motif (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5153469 Wed, 17 Aug 2011 23:00:00 +0100 5153469 PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data http://www.medworm.com/index.php?rid=5153468&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR79 A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5153468 Wed, 17 Aug 2011 23:00:00 +0100 5153468 Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage http://www.medworm.com/index.php?rid=5136782&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR77 Expression profiling in mouse models of mammary tumors identifies miRNA signatures particular to lineages or driver oncogenes (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5136782 Mon, 15 Aug 2011 23:00:00 +0100 5136782 The contrasting roles of PPARdelta and PPARgamma in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue http://www.medworm.com/index.php?rid=5129386&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR75 A specific agonist demonstrates the contrast between PPAR-delta and PPAR-gamma function in lipid metabolism (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5129386 Sun, 14 Aug 2011 23:00:00 +0100 5129386 Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford Progeria syndrome cells http://www.medworm.com/index.php?rid=5123662&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR74 Treating cultured cells from Hutchinson-Gilford progeria patients with farnesyltransferase inhibitors restores wildtype chromosome dynamics (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5123662 Thu, 11 Aug 2011 23:00:00 +0100 5123662 Hybrid selection for sequencing pathogen genomes from clinical samples http://www.medworm.com/index.php?rid=5123663&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR73 Baits generated from Plasmodium DNA are used in solution hybridization to enrich parasite DNA from clinical samples to facilitate sequencing (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5123663 Wed, 10 Aug 2011 23:00:00 +0100 5123663 TopHat-Fusion: an algorithm for discovery of novel fusion transcripts http://www.medworm.com/index.php?rid=5115645&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR72 A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5115645 Wed, 10 Aug 2011 23:00:00 +0100 5115645 Single cell transcriptomics of neighboring hyphae of Aspergillus niger http://www.medworm.com/index.php?rid=5101790&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F8%2FR71 A method for single cell transcriptomics is developed and is demonstrated on single hyphae of Aspergillus niger (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5101790 Wed, 03 Aug 2011 23:00:00 +0100 5101790 Extensive characterization of NF-KappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits http://www.medworm.com/index.php?rid=5075087&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR70 Protein binding microarrays and Electrophoretic Mobility Shift Assay-Sequencing reveal non-canonical NFkappaB binding sites associated with polymorphisms (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5075087 Thu, 28 Jul 2011 23:00:00 +0100 5075087 ExpressionPlot: A web-based framework for analysis of RNA-Seq and microarray gene expression data http://www.medworm.com/index.php?rid=5075089&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR69 A web-based RNA-seq and microarray analysis tool (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5075089 Wed, 27 Jul 2011 23:00:00 +0100 5075089 Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes http://www.medworm.com/index.php?rid=5075088&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2F406 The genome of the Burmese python is being sequenced, providing insights into the unique anatomy, physiology, and evolution of snakes (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5075088 Wed, 27 Jul 2011 23:00:00 +0100 5075088 Atg8: an autophagy-related ubiquitin-like protein family http://www.medworm.com/index.php?rid=5075090&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2F226 The Atg8 family of autophagy-related ubiquitin-like proteins mediate remodeling of intracellular membranes and interact with many proteins to regulate trafficking and autophagy (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5075090 Tue, 26 Jul 2011 23:00:00 +0100 5075090 Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities http://www.medworm.com/index.php?rid=5067597&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR68 Extension of exome capture beyond the commonly targeted regions reveals much higher variant densities in predicted exons (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5067597 Sun, 24 Jul 2011 23:00:00 +0100 5067597 The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology http://www.medworm.com/index.php?rid=5060909&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR66 Comparison of sequenced genomes of Giardia lamblia reveals that it has the fewest number of kinases of any known eukaryote (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5060909 Sun, 24 Jul 2011 23:00:00 +0100 5060909 ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions http://www.medworm.com/index.php?rid=5060908&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR67 ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5060908 Sun, 24 Jul 2011 23:00:00 +0100 5060908 An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data http://www.medworm.com/index.php?rid=5060907&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2F120 Keji Zhao discusses Genome Biology's method article on ZINBA, a novel peak-finding tool developed by Jason Lieb and colleagues (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5060907 Sun, 24 Jul 2011 23:00:00 +0100 5060907 Food of the dogs http://www.medworm.com/index.php?rid=5060906&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2F122 Human evolution and the Paleofood movement (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5060906 Sun, 24 Jul 2011 23:00:00 +0100 5060906 Sex lethal and upstream ORFs: a bait-and-trap system for ribosomes http://www.medworm.com/index.php?rid=5060905&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2F121 Research highlight on a novel mechanism of eukaryotic gene regulation (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5060905 Sun, 24 Jul 2011 23:00:00 +0100 5060905 Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins http://www.medworm.com/index.php?rid=5046612&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR65 Enhanced positive codon selection in the intrinsically disordered regions of yeast proteins (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5046612 Mon, 18 Jul 2011 23:00:00 +0100 5046612 Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis http://www.medworm.com/index.php?rid=5046613&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR64 The miR-30 family of miRNAs is found to regulate adipogenesis by targeting RUNX2 mRNA (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5046613 Sun, 17 Jul 2011 23:00:00 +0100 5046613 A comparative analysis of DNA methylation across human embryonic stem cell lines http://www.medworm.com/index.php?rid=5004716&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR62 Conclusions: These results suggest a possible but as yet unknown functional role for the highly methylated conserved non CG sites in the regulation of HESCs. We also identified a novel set of genes that are likely transcriptionally regulated by methylation in an allele specific manner. The analysis of transcription factor binding sites suggests that the methylation state of cis-regulatory elements impacts the ability of factors to bind and regulate transcription. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5004716 Tue, 05 Jul 2011 23:00:00 +0100 5004716 Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque http://www.medworm.com/index.php?rid=5004715&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F7%2FR63 Conclusions: Genome sequencing and construction of a global sequence variation map in Chinese rhesus macaque with the concomitant database provide applicable resources for evolutionary and biomedical research. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=5004715 Tue, 05 Jul 2011 23:00:00 +0100 5004715 Risky business http://www.medworm.com/index.php?rid=4990384&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2F119 {no abstract} (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4990384 Wed, 29 Jun 2011 23:00:00 +0100 4990384 Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy http://www.medworm.com/index.php?rid=4981280&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR61 Conclusions: The broad generality and the intricate characteristics of the dichotomy of aneuploidy, ranging across numerous tumor classes, are revealed here rigorously for the first time using statistical analyses of large-scale datasets. Our finding suggests that aneuploid cancer cells may use extra chromosome gain or loss events to restore a balance in their altered proteins ratios, needed for maintaining their cellular fitness. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4981280 Tue, 28 Jun 2011 23:00:00 +0100 4981280 The jigsaw puzzle of our African ancestry: unsolved, or unsolvable? http://www.medworm.com/index.php?rid=4973936&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2F118 A revised root for the Y chromosome phylogeny further fragments the picture of modern human origins that can be reconstructed from genetic, linguistic and archaeological data. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4973936 Mon, 27 Jun 2011 23:00:00 +0100 4973936 The tubby family proteins http://www.medworm.com/index.php?rid=4973935&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2F225 The tubby mouse shows a tripartite syndrome characterized by maturity-onset obesity, blindness and deafness. The causative gene Tub is the founding member of a family of related proteins present throughout the animal and plant kingdoms, each characterized by a signature carboxy-terminal tubby domain. This domain consists of a β barrel enclosing a central α helix and binds selectively to specific membrane phosphoinositides. The vertebrate family of tubby-like proteins (TULPs) includes the founding member TUB and the related TULPs, TULP1 to TULP4. Tulp1 is expressed in the retina and mutations in TULP1 cause retinitis pigmentosa in humans; Tulp3 is expressed ubiquitously in the mouse embryo and is important in sonic hedgehog (Shh)-mediated dorso-ventral patterning of the spinal cord. The a... Genome Biology journals http://www.medworm.com/rss/comments.php?id=4973935 Mon, 27 Jun 2011 23:00:00 +0100 4973935 Genomes of uncultured eukaryotes: sorting FACS from fiction http://www.medworm.com/index.php?rid=4973937&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2F117 A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4973937 Sun, 26 Jun 2011 23:00:00 +0100 4973937 Metagenomic biomarker discovery and explanation http://www.medworm.com/index.php?rid=4966387&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR60 This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4966387 Thu, 23 Jun 2011 23:00:00 +0100 4966387 The mouse genetics toolkit: revealing function and mechanism http://www.medworm.com/index.php?rid=4966386&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2F224 Large-scale projects are providing rapid global access to a wealth of mouse genetic resources to help discover disease genes and to manipulate their function. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4966386 Thu, 23 Jun 2011 23:00:00 +0100 4966386 Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study http://www.medworm.com/index.php?rid=4966388&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR59 Conclusions: Our results suggest that the incidence of heteroplasmy may be lower than estimated in some other recent re-sequencing studies, and that mtDNA allelic frequencies differ significantly both between tissues of the same individual and between a mother and her offspring. We designed our study in such a way that the complete analysis can be repeated by anyone either at our Galaxy website or directly on the Amazon Cloud. Our computational pipeline can be easily modified to accommodate other applications, such as viral re-sequencing. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4966388 Wed, 22 Jun 2011 23:00:00 +0100 4966388 Biograph: Unsupervised biomedical knowledge discovery via automated hypothesis generation http://www.medworm.com/index.php?rid=4958475&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR57 We present BioGraph, a data integration and data mining platform for the exploration and discovery of biomedical information. The platform offers prioritizations of putative disease genes, supported by functional hypotheses. We show that BioGraph can retrospectively confirm recently discovered disease genes and identify potential susceptibility genes, outperforming existing technologies, without requiring prior domain knowledge. Additionally, BioGraph allows for generic biomedical applications beyond gene discovery. BioGraph is accessible at http://www.biograph.be. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4958475 Tue, 21 Jun 2011 23:00:00 +0100 4958475 Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content http://www.medworm.com/index.php?rid=4958474&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR58 Conclusions: Our study provides the first direct empirical support for the hypothesis that variation in the level of germ line methylation contributes to substitution rate variation at CpG sites. Moreover, we show that additional genomic features to methylation also impact on CpG substitution rate variation. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4958474 Tue, 21 Jun 2011 23:00:00 +0100 4958474 5-hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells http://www.medworm.com/index.php?rid=4950557&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR54 Conclusions: Our findings suggest that 5hmC may be targeted to certain genomic regions based both on gene expression and sequence composition. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4950557 Sun, 19 Jun 2011 23:00:00 +0100 4950557 Genome-wide mapping of the sixth base http://www.medworm.com/index.php?rid=4950556&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2F116 Mapping of 5-hydroxylmethylcytosine in mammalian genomes has unveiled its unique role in the epigenetic regulation of gene expression.See Research article: http://genomebiology.com/2011/12/6/R54 (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4950556 Sun, 19 Jun 2011 23:00:00 +0100 4950556 Sniper: Improved SNP discovery by multiply mapping deep sequenced reads http://www.medworm.com/index.php?rid=4950555&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR55 SNP (single nucleotide polymorphism) discovery using next-generation sequencing data remains difficult primarily because of redundant genomic regions, such as interspersed repetitive elements and paralogous genes, present in all eukaryotic genomes. To address this problem, we developed Sniper, a novel multi-locus Bayesian probabilistic model and a computationally efficient algorithm that explicitly incorporates sequence reads that map to multiple genomic loci. Our model fully accounts for sequencing error, template bias, and multi-locus SNP combinations, maintaining high sensitivity and specificity under a broad range of conditions. An implementation of Sniper is freely available at http://kim.bio.upenn.edu/software/sniper.shtml. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4950555 Sun, 19 Jun 2011 23:00:00 +0100 4950555 A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs http://www.medworm.com/index.php?rid=4950554&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR56 Conclusions: We have characterized a family of twenty-two telomere-associated lncRNAs in P. falciparum. Homologous lncRNA-TARE loci are coordinately expressed after parasite DNA replication, and are poised to play an important role in P. falciparum telomere maintenance, virulence gene regulation, and potentially other processes of parasite chromosome end biology. Further study of lncRNA-TARE and other promising lncRNA candidates may provide mechanistic insight into P. falciparum transcriptional regulation. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4950554 Sun, 19 Jun 2011 23:00:00 +0100 4950554 Grand network convergence http://www.medworm.com/index.php?rid=4943428&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2F306 A report of the Systems Biology: Networks meeting, Cold Spring Harbor, USA, 22-26 March 2011.The success of the human genome project has provided a model for an analogous interactome project to map how proteins, genes, metabolites and other regulatory components interact to transform a biochemical soup into a living system. These maps promise to serve as a framework for models that predict how a biological system responds to a perturbation or an input, which is relevant to gene mutations and therapeutic treatment in human disease, and as a framework for designing new systems in synthetic biology.Three major themes arose during the 2011 meeting: technological drivers and data generation, algorithmic advances, and convergence on biological applications with context-sensitive networks. (Sourc... Genome Biology journals http://www.medworm.com/rss/comments.php?id=4943428 Thu, 16 Jun 2011 23:00:00 +0100 4943428 Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa http://www.medworm.com/index.php?rid=4930515&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F6%2FR53 Conclusions: Our study, for the first time, revealed the differences in composition and expression profile of miRNAs between developing pollen and sporophytes, and novel and non-conserved known miRNAs would be the main contributors. Our results suggested the important roles of the miRNA pathway in pollen development. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4930515 Wed, 15 Jun 2011 23:00:00 +0100 4930515 The lamin protein family http://www.medworm.com/index.php?rid=4882212&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2F222 SummaryThe lamins are the major architectural proteins of the animal cell nucleus. Lamins line the inside of the nuclear membrane, where they provide a platform for the binding of proteins and chromatin and confer mechanical stability. They have been implicated in a wide range of nuclear functions, including higher-order genome organization, chromatin regulation, transcription, DNA replication and DNA repair. The lamins are members of the intermediate filament (IF) family of proteins, which constitute a major component of the cytoskeleton. Lamins are the only nuclear IFs and are the ancestral founders of the IF protein superfamily. Lamins polymerize into fibers forming a complex protein meshwork in vivo and, like all IF proteins, have a tripartite structure with two globular head and tail ... Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882212 Mon, 30 May 2011 23:00:00 +0100 4882212 Bright days for yeast research http://www.medworm.com/index.php?rid=4882211&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2F305 A report on the British Yeast Group Meeting, Brighton, UK, 23-25 March 2011. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882211 Mon, 30 May 2011 23:00:00 +0100 4882211 Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths http://www.medworm.com/index.php?rid=4882210&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2FR51 Conclusions: Though limited, our data suggest that the two species interbred at some point in their evolutionary histories. One potential explanation is that woolly mammoth haplotypes entered Columbian mammoth populations via introgression at subglacial ecotones, a scenario with compelling parallels in extant elephants and consistent with certain regional paleontological observations. This highlights the need for multi-genomic data to sufficiently characterize mammoth evolutionary history. Our results demonstrate that the use of next-generation sequencing technologies holds promise in obtaining such data, even from non-cave, non-permafrost Pleistocene depositional contexts. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882210 Mon, 30 May 2011 23:00:00 +0100 4882210 Refinement of primate CNV hotspots identifies candidate genomic regions evolving under positive selection http://www.medworm.com/index.php?rid=4882209&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2FR52 Conclusions: These hotspots of primate CNV formation provide a novel perspective on divergence and selective pressures acting on these genomic regions. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882209 Mon, 30 May 2011 23:00:00 +0100 4882209 A mystery unveiled http://www.medworm.com/index.php?rid=4882217&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2F113 A recent phylogenomic study has provided new evidence for two ancient whole genome duplications in plants, with potential importance for the evolution of seed and flowering plants. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882217 Sun, 29 May 2011 23:00:00 +0100 4882217 Mapping of disease-associated variants in admixed populations http://www.medworm.com/index.php?rid=4882216&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2F223 Recent developments in high-throughput genotyping and whole-genome sequencing will enhance the identification of disease loci in admixed populations. We discuss how a more refined estimation of ancestry benefits both admixture mapping and association mapping, making disease loci identification in admixed populations more powerful.High-throughput genotyping and sequencing will enable refined estimation of ancestry, thus enhancing disease loci identification in admixed populations (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882216 Sun, 29 May 2011 23:00:00 +0100 4882216 The volatile microbiome http://www.medworm.com/index.php?rid=4882215&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2F114 The first detailed temporal study of the human microbiome shows that individual body habitats exhibit surprising variation over time yet maintain distinguishable community structures. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882215 Sun, 29 May 2011 23:00:00 +0100 4882215 In praise of model organisms http://www.medworm.com/index.php?rid=4882214&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2F115 {no abstract} (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882214 Sun, 29 May 2011 23:00:00 +0100 4882214 Moving pictures of the human microbiome http://www.medworm.com/index.php?rid=4882213&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2FR50 Conclusions: DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4882213 Sun, 29 May 2011 23:00:00 +0100 4882213 A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure http://www.medworm.com/index.php?rid=4869583&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2FR48 Conclusions: When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4869583 Thu, 26 May 2011 23:00:00 +0100 4869583 Path finding methods accounting for stoichiometry in metabolic networks http://www.medworm.com/index.php?rid=4869582&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2FR49 In this study, we show that reaction stoichiometry can be incorporated into path finding approaches via mixed-integer linear programming. This major advance at the modeling level results in improved prediction of topological and functional properties in metabolic networks. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4869582 Thu, 26 May 2011 23:00:00 +0100 4869582 A high resolution map of a cyanobacterial transcriptome http://www.medworm.com/index.php?rid=4860022&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2FR47 Conclusions: We provide a global analysis of a cyanobacterial transcriptome. Our results uncover insights that reinforce and extend the current views of bacterial transcription. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4860022 Tue, 24 May 2011 23:00:00 +0100 4860022 A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi http://www.medworm.com/index.php?rid=4860023&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2FR45 Conclusion: The existence of mesosynteny between relatively distantly related Ascomycetes could be explained by a high frequency of chromosomal inversions, but translocations must be extremely rare. The mechanism for this phenomenon is not known, but presumably involves generation of frequent inversions during meiosis. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4860023 Mon, 23 May 2011 23:00:00 +0100 4860023 EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data http://www.medworm.com/index.php?rid=4838166&cid=s_34064_50_f&fid=34064&url=http%3A%2F%2Fgenomebiology.com%2F2011%2F12%2F5%2FR44 Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances. We apply the method to natural and simulated microbial communities, and correctly recover community structure from known and previously unreported rRNA gene sequences. An implementation of the method is freely available at https://github.com/csmiller/EMIRGE. (Source: Genome Biology) Genome Biology journals http://www.medworm.com/rss/comments.php?id=4838166 Wed, 18 May 2011 23:00:00 +0100 4838166