Conserved rules govern genetic interaction degree across species.

abstract：BACKGROUND:Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there...

journal_title：Genome biology

authors： Ying H,Cooke I,Sprungala S,Wang W,Hayward DC,Tang Y,Huttley G,Ball EE,Forêt S,Miller DJ

更新日期：2018-11-02 00:00:00

abstract：BACKGROUND:RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails when considering th...

journal_title：Genome biology

authors： Gonzàlez-Porta M,Frankish A,Rung J,Harrow J,Brazma A

更新日期：2013-07-01 00:00:00

abstract：BACKGROUND:We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models the outcome variable as a sum of the average expression profiles of chosen clusters and their products. It can be applied to many...

journal_title：Genome biology

authors： Hastie T,Tibshirani R,Botstein D,Brown P

更新日期：2001-01-01 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：:Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for comparing automatically derived metabolic reconstructions of sequenced genomes on a large scale. Applying our method to 266 genomes di...

journal_title：Genome biology

authors： Kastenmüller G,Schenk ME,Gasteiger J,Mewes HW

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Heterochromatin protein 1 (HP1) family proteins have a well-characterized role in heterochromatin packaging and gene regulation. Their function in organismal development, however, is less well understood. Here we used genome-wide expression profiling to assess novel functions of the Caenorhabditis elegans HP...

journal_title：Genome biology

authors： Meister P,Schott S,Bedet C,Xiao Y,Rohner S,Bodennec S,Hudry B,Molin L,Solari F,Gasser SM,Palladino F

更新日期：2011-12-20 00:00:00

abstract：BACKGROUND:In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular ...

journal_title：Genome biology

authors： Yeoh LM,Goodman CD,Mollard V,McHugh E,Lee VV,Sturm A,Cozijnsen A,McFadden GI,Ralph SA

更新日期：2019-08-01 00:00:00

abstract：:An intriguing recent study examines the role of miR-1202, a glutamate receptor regulating microRNA, in regulating major depressive disorder. ...

journal_title：Genome biology

authors： Rucker JJ,McGuffin P

更新日期：2014-07-26 00:00:00

abstract：:The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not...

journal_title：Genome biology

authors： An L,Yang T,Yang J,Nuebler J,Xiang G,Hardison RC,Li Q,Zhang Y

更新日期：2019-12-18 00:00:00

abstract：:Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene...

journal_title：Genome biology

authors： Aran D,Hu Z,Butte AJ

更新日期：2017-11-15 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：: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:Malaria is a one of the most important infectious diseases and is caused by parasitic protozoa of the genus Plasmodium. Previously, quantitative characterization of the P. falciparum transcriptome demonstrated that the strictly controlled progression of these parasites through their intra-erythrocytic develo...

journal_title：Genome biology

authors： Foth BJ,Zhang N,Mok S,Preiser PR,Bozdech Z

更新日期：2008-01-01 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

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：BACKGROUND:Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS...

journal_title：Genome biology

authors： Kubicek CP,Herrera-Estrella A,Seidl-Seiboth V,Martinez DA,Druzhinina IS,Thon M,Zeilinger S,Casas-Flores S,Horwitz BA,Mukherjee PK,Mukherjee M,Kredics L,Alcaraz LD,Aerts A,Antal Z,Atanasova L,Cervantes-Badillo MG,Challac

更新日期：2011-01-01 00:00:00

abstract：:Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released ...

journal_title：Genome biology

authors： Eöry L,Gilbert MT,Li C,Li B,Archibald A,Aken BL,Zhang G,Jarvis E,Flicek P,Burt DW

更新日期：2015-01-29 00:00:00

abstract：:Early gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative breast cancers, few are informative for ER negative/HER2 negative an...

journal_title：Genome biology

authors： Haibe-Kains B,Desmedt C,Rothé F,Piccart M,Sotiriou C,Bontempi G

更新日期：2010-01-01 00:00:00

abstract：:A report on the 23rd annual meeting on 'The Biology of Genomes', 11-15 May 2010, Cold Spring Harbor, USA. ...

journal_title：Genome biology

authors： Capra JA,Carbone L,Riesenfeld SJ,Wall JD

更新日期：2010-01-01 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:Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases an...

journal_title：Genome biology

authors： Jansen IE,Ye H,Heetveld S,Lechler MC,Michels H,Seinstra RI,Lubbe SJ,Drouet V,Lesage S,Majounie E,Gibbs JR,Nalls MA,Ryten M,Botia JA,Vandrovcova J,Simon-Sanchez J,Castillo-Lizardo M,Rizzu P,Blauwendraat C,Chouhan AK

更新日期：2017-01-30 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：: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: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：:We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...

journal_title：Genome biology

authors： Peterson LE,Lau K

更新日期：2002-05-29 00:00:00

abstract：BACKGROUND:The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. RESULTS:To investigate the relat...

journal_title：Genome biology

authors： Wen C,Zheng Z,Shao T,Liu L,Xie Z,Le Chatelier E,He Z,Zhong W,Fan Y,Zhang L,Li H,Wu C,Hu C,Xu Q,Zhou J,Cai S,Wang D,Huang Y,Breban M,Qin N,Ehrlich SD

更新日期：2017-07-27 00:00:00

abstract：:Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-p...

journal_title：Genome biology

authors： Hosur R,Peng J,Vinayagam A,Stelzl U,Xu J,Perrimon N,Bienkowska J,Berger B

更新日期：2012-08-31 00:00:00

abstract：:In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggr...

journal_title：Genome biology

authors： Kessler MD,O'Connor TD

更新日期：2017-02-27 00:00:00

abstract：:The 3.5-day-old blastocyst-stage mouse embryo consists of two tissues and contains approximately 60 cells. This tiny structure has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome. ...

journal_title：Genome biology

authors： Eakin GS,Hadjantonakis AK

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key component of Hedgehog signaling, remains largely unknown. RESULTS:In this study, we describe a novel p...

journal_title：Genome biology

authors： Wu X,Xiao S,Zhang M,Yang L,Zhong J,Li B,Li F,Xia X,Li X,Zhou H,Liu D,Huang N,Yang X,Xiao F,Zhang N

更新日期：2021-01-14 00:00:00