Organizing knowledge to enable personalization of medicine in cancer.

abstract：:The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify ide...

journal_title：Genome biology

authors： Efroni I,Ip PL,Nawy T,Mello A,Birnbaum KD

更新日期：2015-01-22 00:00:00

abstract：:A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. ...

journal_title：Genome biology

authors： Bakal C

更新日期：2012-01-30 00:00:00

abstract：:Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a si...

journal_title：Genome biology

authors： Davidson NM,Hawkins ADK,Oshlack A

更新日期：2017-08-04 00:00:00

abstract：BACKGROUND:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA pro...

journal_title：Genome biology

authors： Liu Z,Liu Q,Yang X,Zhang Y,Norris M,Chen X,Cheema J,Zhang H,Ding Y

更新日期：2021-01-04 00:00:00

abstract：:The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...

journal_title：Genome biology

authors： Liang S,Tippens ND,Zhou Y,Mort M,Stenson PD,Cooper DN,Yu H

更新日期：2017-01-18 00:00:00

abstract：:The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...

journal_title：Genome biology

authors： Schlueter SD,Wilkerson MD,Dong Q,Brendel V

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Protein domains are protein regions that are shared among different proteins and are frequently functionally and structurally independent from the rest of the protein. Novel domain combinations have a major role in evolutionary innovation. However, the relative contributions of the different molecular mechan...

journal_title：Genome biology

authors： Buljan M,Frankish A,Bateman A

更新日期：2010-01-01 00:00:00

abstract：:Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a central clock. Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks. ...

journal_title：Genome biology

authors： Johnson CH

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...

journal_title：Genome biology

authors： Park G,Park JK,Shin SH,Jeon HJ,Kim NKD,Kim YJ,Shin HT,Lee E,Lee KH,Son DS,Park WY,Park D

更新日期：2017-07-21 00:00:00

abstract：BACKGROUND:The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. RESULTS:Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome...

journal_title：Genome biology

authors： Lemay DG,Lynn DJ,Martin WF,Neville MC,Casey TM,Rincon G,Kriventseva EV,Barris WC,Hinrichs AS,Molenaar AJ,Pollard KS,Maqbool NJ,Singh K,Murney R,Zdobnov EM,Tellam RL,Medrano JF,German JB,Rijnkels M

更新日期：2009-01-01 00:00:00

abstract：:According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends of genomes was presented, and they are important to understand the evolutionary relationship of the differen...

journal_title：Genome biology

authors： Brinkmann A,Souza ARV,Esparza J,Nitsche A,Damaso CR

更新日期：2020-12-04 00:00:00

abstract：:The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sou...

journal_title：Genome biology

authors： Gkoutos GV,Green EC,Mallon AM,Hancock JM,Davidson D

更新日期：2005-01-01 00:00:00

abstract：:Following publication of the original article [1], the authors reported the following errors. ...

journal_title：Genome biology

authors： Lee H,McManus CJ,Cho DY,Eaton M,Renda F,Somma MP,Cherbas L,May G,Powell S,Zhang D,Zhan L,Resch A,Andrews J,Celniker SE,Cherbas P,Przytycka TM,Gatti M,Oliver B,Graveley B,MacAlpine D

更新日期：2019-03-11 00:00:00

abstract：BACKGROUND:Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on tra...

journal_title：Genome biology

authors： Thieme M,Lanciano S,Balzergue S,Daccord N,Mirouze M,Bucher E

更新日期：2017-07-07 00:00:00

abstract：:A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3-STAT6 pathway, which causes dendritic-cell-specific DNA demethylation. ...

journal_title：Genome biology

authors： Lennartsson A

更新日期：2016-02-01 00:00:00

abstract：:The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems. ...

journal_title：Genome biology

authors： Good BM,Su AI

更新日期：2011-12-28 00:00:00

abstract：BACKGROUND:Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched bulk RNA-seq samples. However, these studies generally did not consider the impact of dropouts or isoform ...

journal_title：Genome biology

authors： Westoby J,Artemov P,Hemberg M,Ferguson-Smith A

更新日期：2020-03-23 00:00:00

abstract：UNLABELLED:Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterati...

journal_title：Genome biology

authors： Renaud G,Slon V,Duggan AT,Kelso J

更新日期：2015-10-12 00:00:00

abstract：BACKGROUND:Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known how common this mechanism is. We provide transcriptional evidence of widespread alternate splicing in the Toll-like rece...

journal_title：Genome biology

authors： Wells CA,Chalk AM,Forrest A,Taylor D,Waddell N,Schroder K,Himes SR,Faulkner G,Lo S,Kasukawa T,Kawaji H,Kai C,Kawai J,Katayama S,Carninci P,Hayashizaki Y,Hume DA,Grimmond SM

更新日期：2006-01-01 00:00:00

abstract：:Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or "drop-outs." Here, we extensively analyze diverse UMI data sets to show that clustering should be the foremost step of the workflow. We observe that most drop-outs disappear once ...

journal_title：Genome biology

authors： Kim TH,Zhou X,Chen M

更新日期：2020-08-06 00:00:00

abstract：:We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromat...

journal_title：Genome biology

authors： Fang J,Ma Q,Chu C,Huang B,Li L,Cai P,Batista PJ,Tolentino KEM,Xu J,Li R,Du P,Qu K,Chang HY

更新日期：2019-12-20 00:00:00

abstract：:mtcPTM is an online repository of human and mouse phosphosites in which data are hierarchically organized to preserve biologically relevant experimental information, thus allowing straightforward comparisons of phosphorylation patterns found under different conditions. The database also contains the largest available ...

journal_title：Genome biology

authors： Jiménez JL,Hegemann B,Hutchins JR,Peters JM,Durbin R

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. ...

journal_title：Genome biology

authors： Formey D,Sallet E,Lelandais-Brière C,Ben C,Bustos-Sanmamed P,Niebel A,Frugier F,Combier JP,Debellé F,Hartmann C,Poulain J,Gavory F,Wincker P,Roux C,Gentzbittel L,Gouzy J,Crespi M

更新日期：2014-09-24 00:00:00

abstract：BACKGROUND:The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functio...

journal_title：Genome biology

authors： Chung O,Jin S,Cho YS,Lim J,Kim H,Jho S,Kim HM,Jun J,Lee H,Chon A,Ko J,Edwards J,Weber JA,Han K,O'Brien SJ,Manica A,Bhak J,Paek WK

更新日期：2015-10-21 00:00:00

abstract：:Completion of fungal, plant and human genomes paved the way to the identification of erythrocytic rhesus proteins and their kidney homologs as ammonium transporters. ...

journal_title：Genome biology

authors： Ludewig U,von Wirén N,Rentsch D,Frommer WB

更新日期：2001-01-01 00:00:00

abstract：:ELXR (Exon Locator and Extractor for Resequencing) streamlines the process of determining exon/intron boundaries and designing PCR and sequencing primers for high-throughput resequencing of exons. We have pre-computed ELXR primer sets for all exons identified from the human, mouse, and rat mRNA reference sequence (Ref...

journal_title：Genome biology

authors： Schageman JJ,Horton CJ,Niu S,Garner HR,Pertsemlidis A

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related to sexual yeasts than other Candida species. We show here that the C. glabrata genome contains ma...

journal_title：Genome biology

authors： Wong S,Fares MA,Zimmermann W,Butler G,Wolfe KH

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out func...

journal_title：Genome biology

authors： Whitfield TW,Wang J,Collins PJ,Partridge EC,Aldred SF,Trinklein ND,Myers RM,Weng Z

更新日期：2012-09-26 00:00:00

abstract：:Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...

journal_title：Genome biology

authors： Francki M,Appels R

更新日期：2002-01-01 00:00:00

abstract：:Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method ...

journal_title：Genome biology

authors： Li Z,Schulz MH,Look T,Begemann M,Zenke M,Costa IG

更新日期：2019-02-26 00:00:00