http://genomebiology.com The latest research articles published by Genome Biology 2012-01-31T00:00:00Z The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described. http://genomebiology.com/2012/13/1/415 John St John Edward Braun Sally Isberg Lee Miles Amanda Chong Jaime Gongora Pauline Dalzell Christopher Moran Bertrand Bed'Hom Arkhat Abzhanov Shane Burgess Amanda Cooksey Todd Castoe Nicholas Crawford Llewellyn Densmore Jennifer Drew Scott Edwards Brant Faircloth Matthew Fujita Matthew Greenwold Federico Hoffmann Jonathan Howard Taisen Iguchi Daniel Janes Shahid Yar Khan Satomi Kohno AP Jason de Koning Stacey Lance Fiona McCarthy John McCormack Mark Merchant Daniel Peterson David Pollock Nader Pourmand Brian Raney Kyria Roessler Jeremy Sanford Roger Sawyer Carl Schmidt Eric Triplett Tracey Tuberville Miryam Venegas-Anaya Jason Howard Erich Jarvis Louis Guillette Jr Travis Glenn Richard Green David Ray Genome Biology 2012, null:415 2012-01-31T00:00:00Z doi:10.1186/gb-2012-13-1-415 Crocodilian genome sequencing An Open Letter describing the project to sequence the genomes of the saltwater crocodile, the American alligator and the Indian gharial /content/figures/gb-2012-13-1-415-toc.gif Genome Biology 1465-6906 ${item.volume} 415 2012-01-31T00:00:00Z XML Background: Expression quantitative trait loci (eQTLs) are likely to play an important role in the genetics of complex traits; however their functional basis remains poorly understood. Using the HapMap lymphoblastoid cell lines, we combine 1000 Genomes genotypes and an extensive catalogue of human functional elements to investigate the biological mechanisms that eQTLs perturb. Results: We use a Bayesian hierarchical model to estimate the enrichment of eQTLs in a wide variety of regulatory annotations. We find that ~40% of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions. Analysis of core promoter regions shows that eQTLs also frequently disrupt some known core promoter motifs but, surprisingly, are not enriched in other well-known motifs such as the TATA box. We also show that information from regulatory annotations alone, when weighted by the hierarchical model, can provide a meaningful ranking of the SNPs that are most likely to drive gene expression variation. Conclusions: Our study demonstrates how regulatory annotation and the association signal derived from eQTL-mapping can be combined into a single framework. We used this approach to further our understanding of the biology that drives human gene expression variation, and of the putatively causal SNPs that underlie it. http://genomebiology.com/2012/13/1/R7 Daniel Gaffney Jean-Baptiste Veyrieras Jacob Degner Pique-Regi Roger Athma Pai Gregory Crawford Matthew Stephens Yoav Gilad Jonathan Pritchard Genome Biology 2012, null:R7 2012-01-31T00:00:00Z doi:10.1186/gb-2012-13-1-r7 Regulatory element eQTLs An analysis of eQTLs located in regulatory elements in the human genome /content/figures/gb-2012-13-1-r7-toc.gif Genome Biology 1465-6906 ${item.volume} R7 2012-01-31T00:00:00Z PDF Reconstructed models of metabolic networks are widely used for studying metabolism in various organisms. Many different reconstructions of the same organism often exist concurrently, forcing researchers to choose one of them at the exclusion of the others. We describe MetaMerge, an algorithm for semi-automatically reconciling a pair of existing metabolic network reconstructions into a single metabolic network model. We use MetaMerge to combine two published metabolic networks for Mycobacterium tuberculosis into a single network which allows many reactions that could not be active in the individual models to become active, and predicts essential genes with a higher positive predictive value. http://genomebiology.com/2012/13/1/R6 Leonid Chindelevitch Sarah Stanley Deborah Hung Aviv Regev Bonnie Berger Genome Biology 2012, null:R6 2012-01-31T00:00:00Z doi:10.1186/gb-2012-13-1-r6 MetaMerge An algorithm that reconciles metabolic network reconstructions into a single model /content/figures/gb-2012-13-1-r6-toc.gif Genome Biology 1465-6906 ${item.volume} R6 2012-01-31T00:00:00Z PDF We present Uberon, an integrated cross-species ontology consisting of over 6500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://obo.svn.sourceforge.net/viewvc/obo/uberon/releases/2011-09-25/ http://genomebiology.com/2012/13/1/R5 Christopher Mungall Carlo Torniai Georgios Gkoutos Suzanna Lewis Melissa Haendel Genome Biology 2012, null:R5 2012-01-31T00:00:00Z doi:10.1186/gb-2012-13-1-r5 Uberon multi-species ontology A description of the Uberon ontology tool that allows comparisons of genomic information across multiple animal phyla /content/figures/gb-2012-13-1-r5-toc.gif Genome Biology 1465-6906 ${item.volume} R5 2012-01-31T00:00:00Z PDF We propose a method for predicting splice graphs that enhances curated gene models using evidence from RNA-Seq and EST alignments. Results obtained using RNA-Seq experiments in Arabidopsis thaliana show that predictions made by our SpliceGrapher method are more consistent with current gene models than predictions made by TAU and Cufflinks. Furthermore, analysis of plant and human data indicates that the machine learning approach used by SpliceGrapher is useful for discriminating between real and spurious splice sites, and can improve the reliability of detection of alternative splicing. SpliceGrapher is available for download at http://SpliceGrapher.sf.net. http://genomebiology.com/2012/13/1/R4 Mark Rogers Julie Thomas Anireddy Reddy Asa Ben-Hur Genome Biology 2012, null:R4 2012-01-31T00:00:00Z doi:10.1186/gb-2012-13-1-r4 SpliceGrapher A tool that uses a priori information to optimize alternative splicing prediction from RNA-seq data /content/figures/gb-2012-13-1-r4-toc.gif Genome Biology 1465-6906 ${item.volume} R4 2012-01-31T00:00:00Z PDF {no abstract} http://genomebiology.com/2012/13/1/142 Gregory Petsko Genome Biology 2012, null:142 2012-01-30T00:00:00Z doi:10.1186/gb-2012-13-1-142 The dog particle In a big announcement suspiciously soon before their funding is renewed, canine researchers have news about the Briggs Noson /content/figures/gb-2012-13-1-142-toc.gif Genome Biology 1465-6906 ${item.volume} 142 2012-01-30T00:00:00Z XML Mosaic amplification of receptor tyrosine kinases in glioblastoma suggests that tumor cells with different progression driver mutations may coevolve rather than compete during clonal evolution. http://genomebiology.com/2012/13/1/141 Feng Chen Li Ding Genome Biology 2012, null:141 2012-01-30T00:00:00Z doi:10.1186/gb-2012-13-1-141 RTK mosaic amplification Li Ding highlights recent findings suggesting that tumor cells with different driver mutations may coevolve rather than compete during clonal evolution /content/figures/gb-2012-13-1-141-toc.gif Genome Biology 1465-6906 ${item.volume} 141 2012-01-30T00:00:00Z XML A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. http://genomebiology.com/2012/13/1/312 Chris Bakal Genome Biology 2012, null:312 2012-01-30T00:00:00Z doi:10.1186/gb-2012-13-1-312 Dynamic systems A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. /content/figures/gb-2012-13-1-312-toc.gif Genome Biology 1465-6906 ${item.volume} 312 2012-01-30T00:00:00Z XML A report on the Plant Genomes and Biotechnology: From Genes to Networks meeting, held at Cold Spring Harbor Laboratory, 30 November to 3 December 2011. http://genomebiology.com/2012/13/1/311 Kenneth Birnbaum Genome Biology 2012, null:311 2012-01-30T00:00:00Z doi:10.1186/gb-2012-13-1-311 Low-cost sequencing in plants A report on the 2011 ?Plant Genomes and Biotechnology: From Genes to Networks? meeting, held at Cold Spring Harbor Laboratory. /content/figures/gb-2012-13-1-311-toc.gif Genome Biology 1465-6906 ${item.volume} 311 2012-01-30T00:00:00Z XML An elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors has been developed by Rhee and Pugh. http://genomebiology.com/2012/13/1/139 Eric Mendenhall Bradley Bernstein Genome Biology 2012, null:139 2012-01-27T00:00:00Z doi:10.1186/gb-2012-13-1-139 DNA-protein interactions Mendenhall and Bernstein highlight ChIP-exo, which is an elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors /content/figures/gb-2012-13-1-139-toc.gif Genome Biology 1465-6906 ${item.volume} 139 2012-01-27T00:00:00Z XML