A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae.

abstract：:Despite the availability of dozens of animal genome sequences, two key questions remain unanswered: First, what fraction of any species' genome confers biological function, and second, are apparent differences in organismal complexity reflected in an objective measure of genomic complexity? Here, we address both quest...

journal_title：Genome research

authors： Meader S,Ponting CP,Lunter G

更新日期：2010-10-01 00:00:00

abstract：:Memory is a hallmark of adaptive immunity, wherein lymphocytes mount a superior response to a previously encountered antigen. It has been speculated that epigenetic alterations in memory lymphocytes contribute to their functional distinction from their naive counterparts. However, the nature and extent of epigenetic a...

journal_title：Genome research

authors： Lai AY,Mav D,Shah R,Grimm SA,Phadke D,Hatzi K,Melnick A,Geigerman C,Sobol SE,Jaye DL,Wade PA

更新日期：2013-12-01 00:00:00

abstract：:We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which a...

journal_title：Genome research

authors： Skinner BM,Sargent CA,Churcher C,Hunt T,Herrero J,Loveland JE,Dunn M,Louzada S,Fu B,Chow W,Gilbert J,Austin-Guest S,Beal K,Carvalho-Silva D,Cheng W,Gordon D,Grafham D,Hardy M,Harley J,Hauser H,Howden P,Howe K,

更新日期：2016-01-01 00:00:00

abstract：:We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal change...

journal_title：Genome research

authors： Jaffe DB,Butler J,Gnerre S,Mauceli E,Lindblad-Toh K,Mesirov JP,Zody MC,Lander ES

更新日期：2003-01-01 00:00:00

abstract：:A detailed comparative map of Brassica oleracea and Arabidopsis thaliana has been established based largely on mapping of Arabidopsis ESTs in two Arabidopsis and four Brassica populations. Based on conservative criteria for inferring synteny, "one to one correspondence" between Brassica and Arabidopsis chromosomes acc...

journal_title：Genome research

authors： Lan TH,DelMonte TA,Reischmann KP,Hyman J,Kowalski SP,McFerson J,Kresovich S,Paterson AH

更新日期：2000-06-01 00:00:00

abstract：:In positional cloning the initial assignment of a gene to a specific chromosomal locus is followed by physical mapping of the critical region. The construction of a high-resolution physical map still involves considerable effort. However, new high-resolution fluorescence in situ hybridization (FISH) techniques have fa...

journal_title：Genome research

authors： Laan M,Isosomppi J,Klockars T,Peltonen L,Palotie A

更新日期：1996-10-01 00:00:00

abstract：:Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functi...

journal_title：Genome research

authors： Taher L,McGaughey DM,Maragh S,Aneas I,Bessling SL,Miller W,Nobrega MA,McCallion AS,Ovcharenko I

更新日期：2011-07-01 00:00:00

abstract：:Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering ...

journal_title：Genome research

authors： Ayele M,Haas BJ,Kumar N,Wu H,Xiao Y,Van Aken S,Utterback TR,Wortman JR,White OR,Town CD

更新日期：2005-04-01 00:00:00

abstract：:We generated high-resolution maps of histone H3 lysine 9/14 acetylation (H3ac), histone H4 lysine 5/8/12/16 acetylation (H4ac), and histone H3 at lysine 4 mono-, di-, and trimethylation (H3K4me1, H3K4me2, H3K4me3, respectively) across the ENCODE regions. Studying each modification in five human cell lines including th...

journal_title：Genome research

authors： Koch CM,Andrews RM,Flicek P,Dillon SC,Karaöz U,Clelland GK,Wilcox S,Beare DM,Fowler JC,Couttet P,James KD,Lefebvre GC,Bruce AW,Dovey OM,Ellis PD,Dhami P,Langford CF,Weng Z,Birney E,Carter NP,Vetrie D,Dunham I

更新日期：2007-06-01 00:00:00

abstract：:In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...

journal_title：Genome research

authors： Kim Y,Jung JP,Pack CG,Huh WK

更新日期：2019-01-01 00:00:00

abstract：:The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis of 24,398 expressed sequence tags (ESTs) generated from 15 different adult and juvenile Fugu tissues, 74% of which match...

journal_title：Genome research

authors： Clark MS,Edwards YJ,Peterson D,Clifton SW,Thompson AJ,Sasaki M,Suzuki Y,Kikuchi K,Watabe S,Kawakami K,Sugano S,Elgar G,Johnson SL

更新日期：2003-12-01 00:00:00

abstract：:Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CAR...

journal_title：Genome research

authors： Mondal T,Rasmussen M,Pandey GK,Isaksson A,Kanduri C

更新日期：2010-07-01 00:00:00

abstract：:It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood ...

journal_title：Genome research

authors： Liu X,Fu YX,Maxwell TJ,Boerwinkle E

更新日期：2010-01-01 00:00:00

abstract：:Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosa...

journal_title：Genome research

authors： Naqvi S,Bellott DW,Lin KS,Page DC

更新日期：2018-04-01 00:00:00

abstract：:The draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromoso...

journal_title：Genome research

authors： Shoguchi E,Kawashima T,Satou Y,Hamaguchi M,Sin-I T,Kohara Y,Putnam N,Rokhsar DS,Satoh N

更新日期：2006-02-01 00:00:00

abstract：:Many missense substitutions are identified in single nucleotide polymorphism (SNP) data and large-scale random mutagenesis projects. Each amino acid substitution potentially affects protein function. We have constructed a tool that uses sequence homology to predict whether a substitution affects protein function. SIFT...

journal_title：Genome research

authors： Ng PC,Henikoff S

更新日期：2001-05-01 00:00:00

abstract：:The in vitro cloning of DNA molecules traditionally uses PCR amplification or site-specific restriction endonucleases to generate linear DNA inserts with defined termini and requires DNA ligase to covalently join those inserts to vectors with the corresponding ends. We have used the properties of Vaccinia DNA topoisom...

journal_title：Genome research

authors： Heyman JA,Cornthwaite J,Foncerrada L,Gilmore JR,Gontang E,Hartman KJ,Hernandez CL,Hood R,Hull HM,Lee WY,Marcil R,Marsh EJ,Mudd KM,Patino MJ,Purcell TJ,Rowland JJ,Sindici ML,Hoeffler JP

更新日期：1999-04-01 00:00:00

abstract：:A time course experiment is a widely used design in the study of cellular processes such as differentiation or response to stimuli. In this paper, we propose time course regulatory analysis (TimeReg) as a method for the analysis of gene regulatory networks based on paired gene expression and chromatin accessibility da...

journal_title：Genome research

authors： Duren Z,Chen X,Xin J,Wang Y,Wong WH

更新日期：2020-04-01 00:00:00

abstract：:We developed a microarray platform for PCR amplification-independent expression profiling of minute samples. A novel scanning system combined with specialized biochips enables detection down to individual fluorescent oligonucleotide molecules specifically hybridized to their complementary sequence over the entire bioc...

journal_title：Genome research

authors： Hesse J,Jacak J,Kasper M,Regl G,Eichberger T,Winklmayr M,Aberger F,Sonnleitner M,Schlapak R,Howorka S,Muresan L,Frischauf AM,Schütz GJ

更新日期：2006-08-01 00:00:00

abstract：:Mammalian genomes contain many highly conserved nongenic sequences (CNGs) whose functional significance is poorly understood. Sets of CNGs have previously been identified by selecting the most conserved elements from a chromosome or genome, but in these highly selected samples, conservation may be unrelated to purifyi...

journal_title：Genome research

authors： Keightley PD,Kryukov GV,Sunyaev S,Halligan DL,Gaffney DJ

更新日期：2005-10-01 00:00:00

abstract：:We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying various publicly available expression data sets we conclude that enrichment of clusters for biological function is, in g...

journal_title：Genome research

authors： Gibbons FD,Roth FP

更新日期：2002-10-01 00:00:00

abstract：:Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. Gr...

journal_title：Genome research

authors： Zhou Z,Alikhan NF,Sergeant MJ,Luhmann N,Vaz C,Francisco AP,Carriço JA,Achtman M

更新日期：2018-09-01 00:00:00

abstract：:Homeotic (Hox) genes are usually clustered and arranged in the same order as they are expressed along the anteroposterior body axis of metazoans. The mechanistic explanation for this colinearity has been elusive, and it may well be that a single and universal cause does not exist. The Hox-gene complex (HOM-C) has been...

journal_title：Genome research

authors： Negre B,Casillas S,Suzanne M,Sánchez-Herrero E,Akam M,Nefedov M,Barbadilla A,de Jong P,Ruiz A

更新日期：2005-05-01 00:00:00

abstract：:Duplication of the genome in mammalian cells occurs in a defined temporal order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400-800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competen...

journal_title：Genome research

authors： Rivera-Mulia JC,Buckley Q,Sasaki T,Zimmerman J,Didier RA,Nazor K,Loring JF,Lian Z,Weissman S,Robins AJ,Schulz TC,Menendez L,Kulik MJ,Dalton S,Gabr H,Kahveci T,Gilbert DM

更新日期：2015-08-01 00:00:00

abstract：:The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution--such as changes in gene expression regulation-remains unknown. A transition...

journal_title：Genome research

authors： Fraser HB,Levy S,Chavan A,Shah HB,Perez JC,Zhou Y,Siegal ML,Sinha H

更新日期：2012-10-01 00:00:00

abstract：:Human genomic data of many types are readily available, but the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it from a systems level, and apply it to the study of specific pathways or genetic disorders. An investigator could best explore a particular prot...

journal_title：Genome research

authors： Huttenhower C,Haley EM,Hibbs MA,Dumeaux V,Barrett DR,Coller HA,Troyanskaya OG

更新日期：2009-06-01 00:00:00

abstract：:CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environ...

journal_title：Genome research

authors： Wang H,Maurano MT,Qu H,Varley KE,Gertz J,Pauli F,Lee K,Canfield T,Weaver M,Sandstrom R,Thurman RE,Kaul R,Myers RM,Stamatoyannopoulos JA

更新日期：2012-09-01 00:00:00

abstract：:Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We presen...

journal_title：Genome research

authors： Florea L,Di Francesco V,Miller J,Turner R,Yao A,Harris M,Walenz B,Mobarry C,Merkulov GV,Charlab R,Dew I,Deng Z,Istrail S,Li P,Sutton G

更新日期：2005-01-01 00:00:00

abstract：:Using AP-PCR-based DNA profiling we examined some structural features of B chromosomes from yellow-necked mice Apodemus flavicollis. Mice harboring one, two, or three or lacking B chromosomes were examined. Chromosomal structure was scanned for variant bands by using a series of arbitrary primers and from these, infor...

journal_title：Genome research

authors： Tanic N,Dedovic N,Vujosevic M,Dimitrijevic B

更新日期：2000-01-01 00:00:00

abstract：:How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectiv...

journal_title：Genome research

authors： Arimizu Y,Kirino Y,Sato MP,Uno K,Sato T,Gotoh Y,Auvray F,Brugere H,Oswald E,Mainil JG,Anklam KS,Döpfer D,Yoshino S,Ooka T,Tanizawa Y,Nakamura Y,Iguchi A,Morita-Ishihara T,Ohnishi M,Akashi K,Hayashi T,Ogura Y

更新日期：2019-09-01 00:00:00