A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems.

abstract：BACKGROUND:The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of mult...

journal_title：Genome biology

authors： Poets AM,Fang Z,Clegg MT,Morrell PL

更新日期：2015-08-21 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：:Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, in...

journal_title：Genome biology

authors： Clark KJ,Carlson DF,Fahrenkrug SC

更新日期：2007-01-01 00:00:00

abstract：:Next-generation massively parallel sequencing technology provides a powerful new means of assessing rates and regulation of translation across an entire transcriptome. ...

journal_title：Genome biology

authors： Morris DR

更新日期：2009-01-01 00:00:00

abstract：:The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutio...

journal_title：Genome biology

authors： Bock C,Halachev K,Büch J,Lengauer T

更新日期：2009-02-10 00:00:00

abstract：:Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that eluded examination just a few years ago. With the advantages of scRNA-seq come computational challenges that are just beginning to be addressed. In this article, we highlight the computational...

journal_title：Genome biology

authors： Bacher R,Kendziorski C

更新日期：2016-04-07 00:00:00

abstract：:A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012. ...

journal_title：Genome biology

authors： Highnam G,Mittelman D

更新日期：2012-12-19 00:00:00

abstract：:Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare o...

journal_title：Genome biology

authors： Daley TP,Lin Z,Lin X,Liu Y,Wong WH,Qi LS

更新日期：2018-10-08 00:00:00

abstract：:A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generated a candidate set of differentially expressed genes that may regulate limb identity. ...

journal_title：Genome biology

authors： Logan M

更新日期：2002-01-01 00:00:00

abstract：:Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33...

journal_title：Genome biology

authors： Xing S,Chen K,Zhu H,Zhang R,Zhang H,Li B,Gao C

更新日期：2020-09-03 00:00:00

abstract：:Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...

journal_title：Genome biology

authors： Marques AC,Tan J,Ponting CP

更新日期：2011-11-21 00:00:00

abstract：:The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we revie...

journal_title：Genome biology

authors： Zhao Z,Shilatifard A

更新日期：2019-11-20 00:00:00

abstract：BACKGROUND:Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patient...

journal_title：Genome biology

authors： Quick J,Ashton P,Calus S,Chatt C,Gossain S,Hawker J,Nair S,Neal K,Nye K,Peters T,De Pinna E,Robinson E,Struthers K,Webber M,Catto A,Dallman TJ,Hawkey P,Loman NJ

更新日期：2015-05-30 00:00:00

abstract：:The telomeres that cap the ends of eukaryotic chromosomes serve a dual role in protecting the chromosome ends and in intracellular signaling for regulating cell proliferation. A complex of six telomere-associated proteins has been identified--the telosome or shelterin complex--that is crucial for both the maintenance ...

journal_title：Genome biology

authors： Xin H,Liu D,Songyang Z

更新日期：2008-01-01 00:00:00

abstract：:A report on the Genome-Based Pathogen Biology meeting, Hinxton, UK, 7-10 July 2002. ...

journal_title：Genome biology

authors： Simpson AJ

更新日期：2002-08-27 00:00:00

abstract：BACKGROUND:Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that cat...

journal_title：Genome biology

authors： Huse SM,Huber JA,Morrison HG,Sogin ML,Welch DM

更新日期：2007-01-01 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：BACKGROUND:The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. RESULTS:Here,...

journal_title：Genome biology

authors： Najafabadi HS,Garton M,Weirauch MT,Mnaimneh S,Yang A,Kim PM,Hughes TR

更新日期：2017-09-06 00:00:00

abstract：BACKGROUND:The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodologic...

journal_title：Genome biology

authors： Lorente-Galdos B,Bleyhl J,Santpere G,Vives L,Ramírez O,Hernandez J,Anglada R,Cooper GM,Navarro A,Eichler EE,Marques-Bonet T

更新日期：2013-01-29 00:00:00

abstract：BACKGROUND:Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species....

journal_title：Genome biology

authors： Hane JK,Rouxel T,Howlett BJ,Kema GH,Goodwin SB,Oliver RP

更新日期：2011-01-01 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：:Abhay Sharma brings two arguments in favor of transgenerational epigenetic inheritance (TGEI) in mammals when criticizing our work. He uses probability calculations and finds that the probability of obtaining the number of common changes in the in utero-exposed prospermatogonia and the same cells in the next generatio...

journal_title：Genome biology

authors： Szabó PE

更新日期：2016-05-16 00:00:00

abstract：:The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34...

journal_title：Genome biology

authors： Repana D,Nulsen J,Dressler L,Bortolomeazzi M,Venkata SK,Tourna A,Yakovleva A,Palmieri T,Ciccarelli FD

更新日期：2019-01-03 00:00:00

abstract：:DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo....

journal_title：Genome biology

authors： Lausted C,Dahl T,Warren C,King K,Smith K,Johnson M,Saleem R,Aitchison J,Hood L,Lasky SR

更新日期：2004-01-01 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：:Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions. ...

journal_title：Genome biology

authors： Brenner C

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in gr...

journal_title：Genome biology

authors： Dal Santo S,Tornielli GB,Zenoni S,Fasoli M,Farina L,Anesi A,Guzzo F,Delledonne M,Pezzotti M

更新日期：2013-06-07 00:00:00

abstract：BACKGROUND:The distributed genome hypothesis (DGH) posits that chronic bacterial pathogens utilize polyclonal infection and reassortment of genic characters to ensure persistence in the face of adaptive host defenses. Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial s...

journal_title：Genome biology

authors： Hogg JS,Hu FZ,Janto B,Boissy R,Hayes J,Keefe R,Post JC,Ehrlich GD

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:While large-scale cancer genomic projects are comprehensively characterizing the mutational spectrum of various cancers, so far little attention has been devoted to either define the antigenicity of these mutations or to characterize the immune responses they elicit. Here we present a strategy to characteriz...

journal_title：Genome biology

authors： Angelova M,Charoentong P,Hackl H,Fischer ML,Snajder R,Krogsdam AM,Waldner MJ,Bindea G,Mlecnik B,Galon J,Trajanoski Z

更新日期：2015-03-31 00:00:00

abstract：:The genetic and molecular analysis of circadian timekeeping mechanisms has accelerated as a result of the increasing volume of genomic markers and nucleotide sequence information. Completion of whole genome sequences and the use of differential gene expression technology will hasten the discovery of the clock output p...

journal_title：Genome biology

authors： Hardin PE

更新日期：2000-01-01 00:00:00