Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism.

abstract：BACKGROUND:The nature of the protein molecular clock, the protein-specific rate of amino acid substitutions, is among the central questions of molecular evolution. Protein expression level is the dominant determinant of the clock rate in a number of organisms. It has been suggested that highly expressed proteins evolve...

journal_title：Genome biology

authors： Plata G,Gottesman ME,Vitkup D

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, b...

journal_title：Genome biology

authors： Marth GT,Yu F,Indap AR,Garimella K,Gravel S,Leong WF,Tyler-Smith C,Bainbridge M,Blackwell T,Zheng-Bradley X,Chen Y,Challis D,Clarke L,Ball EV,Cibulskis K,Cooper DN,Fulton B,Hartl C,Koboldt D,Muzny D,Smith R,Soug

更新日期：2011-09-14 00:00:00

abstract：:A subset of X-linked genes escapes silencing by X inactivation and is expressed from both X chromosomes in mammalian females. Species-specific differences in the identity of these genes have recently been discovered, suggesting a role in the evolution of sex differences. Chromatin analyses have aimed to discover how g...

journal_title：Genome biology

authors： Berletch JB,Yang F,Disteche CM

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. RESULTS:Here, we show that KDM5B, which demethylates lysine 4 of histone H3...

journal_title：Genome biology

authors： Kidder BL,Hu G,Zhao K

更新日期：2014-02-04 00:00:00

abstract：BACKGROUND:Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying me...

journal_title：Genome biology

authors： Prins BP,Mead TJ,Brody JA,Sveinbjornsson G,Ntalla I,Bihlmeyer NA,van den Berg M,Bork-Jensen J,Cappellani S,Van Duijvenboden S,Klena NT,Gabriel GC,Liu X,Gulec C,Grarup N,Haessler J,Hall LM,Iorio A,Isaacs A,Li-Gao R,

更新日期：2018-07-17 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：: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：BACKGROUND:During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole...

journal_title：Genome biology

authors： Siddiqui NU,Li X,Luo H,Karaiskakis A,Hou H,Kislinger T,Westwood JT,Morris Q,Lipshitz HD

更新日期：2012-02-20 00:00:00

abstract：BACKGROUND:The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the converging pathways depen...

journal_title：Genome biology

authors： Notebaart RA,Kensche PR,Huynen MA,Dutilh BE

更新日期：2009-02-12 00:00:00

abstract：BACKGROUND:Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processe...

journal_title：Genome biology

authors： Oh Y,Donofrio N,Pan H,Coughlan S,Brown DE,Meng S,Mitchell T,Dean RA

更新日期：2008-01-01 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: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: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:Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all ly...

journal_title：Genome biology

authors： Bakker B,Taudt A,Belderbos ME,Porubsky D,Spierings DC,de Jong TV,Halsema N,Kazemier HG,Hoekstra-Wakker K,Bradley A,de Bont ES,van den Berg A,Guryev V,Lansdorp PM,Colomé-Tatché M,Foijer F

更新日期：2016-05-31 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：: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：: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：BACKGROUND:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in...

journal_title：Genome biology

authors： Yang R,Zheng Z,Chen Q,Yang L,Huang H,Miki D,Wu W,Zeng L,Liu J,Zhou JX,Ogas J,Zhu JK,He XJ,Zhang H

更新日期：2017-05-31 00:00:00

abstract：:Recent work has identified the human NOD-like receptor NLRX1 as a negative regulator of intracellular signaling leading to type I interferon production. Here we discuss these findings and the questions and implications they raise regarding the function of NOD-like receptors in the antiviral response. ...

journal_title：Genome biology

authors： Pietras EM,Cheng G

更新日期：2008-04-25 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：:Many essential transcription factors have conserved roles in regulating biological programs, yet their genomic occupancy can diverge significantly. A new study demonstrates that such variations are primarily due to cis-regulatory sequences, rather than differences between the regulators or nuclear environments. ...

journal_title：Genome biology

authors： Zinzen RP,Furlong EE

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and oc...

journal_title：Genome biology

authors： Al Nadaf S,Waters PD,Koina E,Deakin JE,Jordan KS,Graves JA

更新日期：2010-01-01 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：:A report on the Cold Spring Harbor Asia conference on Genome Assisted Biology of Crops and Model Plant Systems Meeting, held in Suzhou, China, April 21-25, 2014. ...

journal_title：Genome biology

authors： Lee I

更新日期：2014-05-23 00:00:00

abstract：:Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method c...

journal_title：Genome biology

authors： Nilsson B,Johansson M,Heyden A,Nelander S,Fioretos T

更新日期：2008-01-21 00:00:00

abstract：BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...

journal_title：Genome biology

authors： Bergman CM,Quesneville H,Anxolabéhère D,Ashburner M

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of...

journal_title：Genome biology

authors： Liu Z,Ran Y,Tao C,Li S,Chen J,Yang E

更新日期：2019-05-20 00:00:00

abstract：:A genomic analysis of heterogeneous colorectal tumor samples has uncovered interactions between immunophenotype and various aspects of tumor biology, with implications for informing the choice of immunotherapies for specific patients and guiding the design of personalized neoantigen-based vaccines. ...

journal_title：Genome biology

authors： Havel JJ,Chan TA

更新日期：2015-03-31 00:00:00

abstract：:Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomolo...

journal_title：Genome biology

authors： Gerdes P,Richardson SR,Mager DL,Faulkner GJ

更新日期：2016-05-09 00:00:00

abstract：BACKGROUND:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual...

journal_title：Genome biology

authors： Huang M,Ding S,Wang H,Zhu X

更新日期：2008-01-01 00:00:00