Gene-level differential analysis at transcript-level resolution.

abstract：:Not so fast. The Iqbal et. al. study and the associated Whitelaw commentary highlight the appropriately high standards of study design and interpretation needed to obtain good evidence for or against epigenetic inheritance. Please see related article: www.dx.doi.org/10.1186/s13059-015-0714-1. ...

journal_title：Genome biology

authors： Nadeau JH

更新日期：2015-07-11 00:00:00

abstract：BACKGROUND:Candidate single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) were often selected for validation based on their functional annotation, which was inadequate and biased. We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically p...

journal_title：Genome biology

authors： Chen R,Morgan AA,Dudley J,Deshpande T,Li L,Kodama K,Chiang AP,Butte AJ

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence element...

journal_title：Genome biology

authors： Gama-Carvalho M,Barbosa-Morais NL,Brodsky AS,Silver PA,Carmo-Fonseca M

更新日期：2006-01-01 00:00:00

abstract：:As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold ...

journal_title：Genome biology

authors： Langmead B,Schatz MC,Lin J,Pop M,Salzberg SL

更新日期：2009-01-01 00:00:00

abstract：:A report on the 18th Congress of the European Society for Evolutionary Biology (ESEB), Aarhus, Denmark, 20-25 August, 2001. ...

journal_title：Genome biology

authors： Liberles DA

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...

journal_title：Genome biology

authors： Prakash A,Bateman A

更新日期：2015-04-30 00:00:00

abstract：BACKGROUND:Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations. RESULTS:We propose a new strategy to identify synergistic TFs by fu...

journal_title：Genome biology

authors： Hu Z,Hu B,Collins JF

更新日期：2007-01-01 00:00:00

abstract：:Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. We developed MOABS to increase the speed, accuracy, statistical power and biological relevance of BS-seq data analysis. MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Bino...

journal_title：Genome biology

authors： Sun D,Xi Y,Rodriguez B,Park HJ,Tong P,Meong M,Goodell MA,Li W

更新日期：2014-02-24 00:00:00

abstract：:DNA transposons are efficient tools in transgenesis and have therefore become popular in the analysis of the regulatory genome in vertebrates via enhancer trap screens. Here, I discuss recent progress in this field of research, with a focus on the application of one of these transposons, namely the medaka fish derived...

journal_title：Genome biology

authors： Korzh V

更新日期：2007-01-01 00:00:00

abstract：:In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one a...

journal_title：Genome biology

authors： Obozinski G,Lanckriet G,Grant C,Jordan MI,Noble WS

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Sequencing the genomes of the first few eukaryotes created the impression that gene number shows no correlation with organism complexity, often referred to as the G-value paradox. Several attempts have previously been made to resolve this paradox, citing multifunctionality of proteins, alternative splicing, ...

journal_title：Genome biology

authors： Schad E,Tompa P,Hegyi H

更新日期：2011-12-19 00:00:00

abstract：BACKGROUND:CRISPR-Cas systems have been broadly embraced as effective tools for genome engineering applications, with most studies to date utilizing the Streptococcus pyogenes Cas9. Here we characterize and manipulate the smaller, 1053 amino acid nuclease Staphylococcus aureus Cas9. RESULTS:We find that the S. aureus ...

journal_title：Genome biology

authors： Friedland AE,Baral R,Singhal P,Loveluck K,Shen S,Sanchez M,Marco E,Gotta GM,Maeder ML,Kennedy EM,Kornepati AV,Sousa A,Collins MA,Jayaram H,Cullen BR,Bumcrot D

更新日期：2015-11-24 00:00:00

abstract：BACKGROUND:Epigenetic mechanisms such as chromatin accessibility impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of the male phenotype and prostate cancer pathogenesis, acts primarily through ligand-activated transcription of target genes. Altho...

journal_title：Genome biology

authors： Tewari AK,Yardimci GG,Shibata Y,Sheffield NC,Song L,Taylor BS,Georgiev SG,Coetzee GA,Ohler U,Furey TS,Crawford GE,Febbo PG

更新日期：2012-10-03 00:00:00

abstract：:We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surpris...

journal_title：Genome biology

authors： Waltman P,Kacmarczyk T,Bate AR,Kearns DB,Reiss DJ,Eichenberger P,Bonneau R

更新日期：2010-01-01 00:00:00

abstract：:A method has been developed to identify proteins required for the biogenesis of non-coding RNA in yeast, using a microarray to screen for aberrant patterns of RNA processing in mutant strains, and new proteins involved in the processing of ribosomal and non-coding RNAs have been found. ...

journal_title：Genome biology

authors： Granneman S,Baserga SJ

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...

journal_title：Genome biology

authors： Frankl-Vilches C,Kuhl H,Werber M,Klages S,Kerick M,Bakker A,de Oliveira EH,Reusch C,Capuano F,Vowinckel J,Leitner S,Ralser M,Timmermann B,Gahr M

更新日期：2015-01-29 00:00:00

abstract：BACKGROUND:Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample. RESULTS:Application of decon...

journal_title：Genome biology

authors： Rosenthal R,McGranahan N,Herrero J,Taylor BS,Swanton C

更新日期：2016-02-22 00:00:00

abstract：:We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological O...

journal_title：Genome biology

authors： Bard J,Rhee SY,Ashburner M

更新日期：2005-01-01 00:00:00

abstract：:A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003. ...

journal_title：Genome biology

authors： Quackenbush J

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...

journal_title：Genome biology

authors： Desjardins CA,Gundersen-Rindal DE,Hostetler JB,Tallon LJ,Fadrosh DW,Fuester RW,Pedroni MJ,Haas BJ,Schatz MC,Jones KM,Crabtree J,Forberger H,Nene V

更新日期：2008-01-01 00:00:00

abstract：:The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle.See related Research article: www.dx.doi.org/10.1186/s13059-015-0790-2. ...

journal_title：Genome biology

authors： Orlando L

更新日期：2015-10-26 00:00:00

abstract：BACKGROUND:The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from ...

journal_title：Genome biology

authors： Yu G,Gail MH,Consonni D,Carugno M,Humphrys M,Pesatori AC,Caporaso NE,Goedert JJ,Ravel J,Landi MT

更新日期：2016-07-28 00:00:00

abstract：BACKGROUND:Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging...

journal_title：Genome biology

authors： Vandiver AR,Irizarry RA,Hansen KD,Garza LA,Runarsson A,Li X,Chien AL,Wang TS,Leung SG,Kang S,Feinberg AP

更新日期：2015-04-16 00:00:00

abstract：:Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics. ...

journal_title：Genome biology

authors： Sibley CR,Attig J,Ule J

更新日期：2012-07-17 00:00:00

abstract：BACKGROUND:Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition m...

journal_title：Genome biology

authors： Gao D,Li Y,Kim KD,Abernathy B,Jackson SA

更新日期：2016-01-18 00:00:00

abstract：BACKGROUND:Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symb...

journal_title：Genome biology

authors： González V,Bustos P,Ramírez-Romero MA,Medrano-Soto A,Salgado H,Hernández-González I,Hernández-Celis JC,Quintero V,Moreno-Hagelsieb G,Girard L,Rodríguez O,Flores M,Cevallos MA,Collado-Vides J,Romero D,Dávila G

更新日期：2003-01-01 00:00:00

abstract：:Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples. This result suggests that the lncRNAs might have important functions in specific cell types in the brain. ...

journal_title：Genome biology

authors： Ma Q,Chang HY

更新日期：2016-04-14 00:00:00

abstract：BACKGROUND:As a biomarker of cellular activities, the transcriptome of a specific tissue or cell type during development and disease is of great biomedical interest. We have generated and analyzed 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries: embryonic day 15.5 (M15E) eye, postnatal ...

journal_title：Genome biology

authors： Yu J,Farjo R,MacNee SP,Baehr W,Stambolian DE,Swaroop A

更新日期：2003-01-01 00:00:00

abstract：:The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiativ...

journal_title：Genome biology

authors： Meyer F,Bremges A,Belmann P,Janssen S,McHardy AC,Koslicki D

更新日期：2019-03-04 00:00:00

abstract：:Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the princi...

journal_title：Genome biology

authors： Pertsemlidis A,Fondon JW 3rd

更新日期：2001-01-01 00:00:00