abstract：BACKGROUND:Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has b...

journal_title：Genome biology

authors： Gordân R,Murphy KF,McCord RP,Zhu C,Vedenko A,Bulyk ML

更新日期：2011-12-21 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: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：: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：:Rhomboid proteases are the largest family of enzymes that hydrolyze peptide bonds within the cell membrane. Although discovered to be serine proteases only a decade ago, rhomboid proteases are already considered to be the best understood intramembrane proteases. The presence of rhomboid proteins in all domains of life...

journal_title：Genome biology

authors： Urban S,Dickey SW

更新日期：2011-10-27 00:00:00

abstract：:A report of the second annual Beyond the Genome conference held on the 19-22 September 2011 at The Universities at Shady Grove, Rockville, Maryland, USA, where increases in computing that may help make personal genomics a reality were a major focus. ...

journal_title：Genome biology

authors： Kristensen DM

更新日期：2011-10-24 00:00:00

abstract：:We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identificati...

journal_title：Genome biology

authors： Rasmussen M,Sundström M,Göransson Kultima H,Botling J,Micke P,Birgisson H,Glimelius B,Isaksson A

更新日期：2011-10-24 00:00:00

abstract：BACKGROUND:Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental stud...

journal_title：Genome biology

authors： Coyne RS,Hannick L,Shanmugam D,Hostetler JB,Brami D,Joardar VS,Johnson J,Radune D,Singh I,Badger JH,Kumar U,Saier M,Wang Y,Cai H,Gu J,Mather MW,Vaidya AB,Wilkes DE,Rajagopalan V,Asai DJ,Pearson CG,Findly RC,Di

更新日期：2011-10-17 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：:Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality. ...

journal_title：Genome biology

authors： Tennessen JA,O'Connor TD,Bamshad MJ,Akey JM

更新日期：2011-09-14 00:00:00

abstract：:Advances in sequencing technology have led to a sharp decrease in the cost of 'data generation'. But is this sufficient to ensure cost-effective and efficient 'knowledge generation'? ...

journal_title：Genome biology

authors： Sboner A,Mu XJ,Greenbaum D,Auerbach RK,Gerstein MB

更新日期：2011-08-25 00:00:00

abstract：BACKGROUND:The cell-cycle checkpoint kinase Chk1 is essential in mammalian cells due to its roles in controlling processes such as DNA replication, mitosis and DNA-damage responses. Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto...

journal_title：Genome biology

authors： Blasius M,Forment JV,Thakkar N,Wagner SA,Choudhary C,Jackson SP

更新日期：2011-08-18 00:00:00

abstract：:A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities. ...

journal_title：Genome biology

authors： Worden AZ,Dupont C,Allen AE

更新日期：2011-06-27 00:00:00

abstract：:Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously. ...

journal_title：Genome biology

authors： Walhout AJ

更新日期：2011-01-01 00:00:00

abstract：:A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February to 4 March 2011. ...

journal_title：Genome biology

authors： Johansson E,Speck C,Chabes A

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes becau...

journal_title：Genome biology

authors： Zuccolo A,Bowers JE,Estill JC,Xiong Z,Luo M,Sebastian A,Goicoechea JL,Collura K,Yu Y,Jiao Y,Duarte J,Tang H,Ayyampalayam S,Rounsley S,Kudrna D,Paterson AH,Pires JC,Chanderbali A,Soltis DE,Chamala S,Barbazuk B,So

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology...

journal_title：Genome biology

authors： Thomas S,Li XY,Sabo PJ,Sandstrom R,Thurman RE,Canfield TK,Giste E,Fisher W,Hammonds A,Celniker SE,Biggin MD,Stamatoyannopoulos JA

更新日期：2011-01-01 00:00:00

abstract：:Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of seque...

journal_title：Genome biology

authors： Ashelford K,Eriksson ME,Allen CM,D'Amore R,Johansson M,Gould P,Kay S,Millar AJ,Hall N,Hall A

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first ...

journal_title：Genome biology

authors： Burmester A,Shelest E,Glöckner G,Heddergott C,Schindler S,Staib P,Heidel A,Felder M,Petzold A,Szafranski K,Feuermann M,Pedruzzi I,Priebe S,Groth M,Winkler R,Li W,Kniemeyer O,Schroeckh V,Hertweck C,Hube B,White TC

更新日期：2011-01-01 00:00:00

abstract：:A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010. ...

journal_title：Genome biology

authors： Fordyce P,Ingolia N

更新日期：2011-01-01 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：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：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：: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 central goal of biogerontology is to identify robust gene-expression biomarkers of aging. Here we develop a method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. Tested on Caenorhabditis elegans, our algorithm yields better biomar...

journal_title：Genome biology

authors： Fortney K,Kotlyar M,Jurisica I

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. RESULTS:We have construct...

journal_title：Genome biology

authors： Wu G,Feng X,Stein L

更新日期：2010-01-01 00:00:00

abstract：:A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates. ...

journal_title：Genome biology

authors： Weirauch MT,Hughes TR

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:Immunolabeling of metaphase chromosome spreads can map components of the human epigenome at the single cell level. Previously, there has been no systematic attempt to explore the potential of this approach for epigenomic mapping and thereby to complement approaches based on chromatin immunoprecipitation (ChI...

journal_title：Genome biology

authors： Terrenoire E,McRonald F,Halsall JA,Page P,Illingworth RS,Taylor AM,Davison V,O'Neill LP,Turner BM

更新日期：2010-01-01 00:00:00

abstract：:The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions. ...

journal_title：Genome biology

authors： Westhof E

更新日期：2010-01-01 00:00:00

abstract：:We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by

journal_title：Genome biology

authors： Ameur A,Wetterbom A,Feuk L,Gyllensten U

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Hemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms u...

journal_title：Genome biology

authors： Mekouar M,Blanc-Lenfle I,Ozanne C,Da Silva C,Cruaud C,Wincker P,Gaillardin C,Neuvéglise C

更新日期：2010-01-01 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: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：:Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...

journal_title：Genome biology

authors： Plenge R

更新日期：2010-01-01 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：: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：BACKGROUND:The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistanc...

journal_title：Genome biology

authors： Dharia NV,Sidhu AB,Cassera MB,Westenberger SJ,Bopp SE,Eastman RT,Plouffe D,Batalov S,Park DJ,Volkman SK,Wirth DF,Zhou Y,Fidock DA,Winzeler EA

更新日期：2009-02-13 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:The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and expres...

journal_title：Genome biology

authors： Reichwald K,Lauber C,Nanda I,Kirschner J,Hartmann N,Schories S,Gausmann U,Taudien S,Schilhabel MB,Szafranski K,Glöckner G,Schmid M,Cellerino A,Schartl M,Englert C,Platzer M

更新日期：2009-02-11 00:00:00