Recent segmental duplications in the working draft assembly of the brown Norway rat.

abstract：:A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic l...

journal_title：Genome research

authors： Doerks T,Copley RR,Schultz J,Ponting CP,Bork P

更新日期：2002-01-01 00:00:00

abstract：:Large terminal fragments of human chromosomes 2p, 6p, 8q, 12q, and 18q were cloned using yeast artificial chromosomes (YACs). RecA-assisted restriction endonuclease (RARE) cleavage analysis of genomic DNA samples from II unrelated individuals using YAC-derived probes confirmed the telomeric localizations of the half-Y...

journal_title：Genome research

authors： Macina RA,Morii K,Hu XL,Negorev DG,Spais C,Ruthig LA,Riethman HC

更新日期：1995-10-01 00:00:00

abstract：:Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to the GART gene. This cluster includes both components of the interferon alpha/beta-receptor (IFNAR1 and IFNAR2) and the second components o...

journal_title：Genome research

authors： Reboul J,Gardiner K,Monneron D,Uzé G,Lutfalla G

更新日期：1999-03-01 00:00:00

abstract：:A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We desc...

journal_title：Genome research

authors： van Opijnen T,Camilli A

更新日期：2012-12-01 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：:Large-scale genetic interaction (GI) screens in yeast have been invaluable for our understanding of molecular systems biology and for characterizing novel gene function. Owing in part to the high costs and long experiment times required, a preponderance of GI data has been generated in a single environmental condition...

journal_title：Genome research

authors： Jaffe M,Dziulko A,Smith JD,St Onge RP,Levy SF,Sherlock G

更新日期：2019-04-01 00:00:00

abstract：:We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...

journal_title：Genome research

authors： Edwards YH,Putt W,Lekoape KM,Stott D,Fox M,Hopkinson DA,Sowden J

更新日期：1996-03-01 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：:The alignment of full-length human cDNA sequences to the finished sequence of the human genome provides a unique opportunity to study the distribution of genes throughout the genome. By analyzing the distances between 23,752 genes, we identified a class of divergently transcribed gene pairs, representing more than 10%...

journal_title：Genome research

authors： Trinklein ND,Aldred SF,Hartman SJ,Schroeder DI,Otillar RP,Myers RM

更新日期：2004-01-01 00:00:00

abstract：:Recent computational and experimental work suggests that functional modules underlie much of cellular physiology and are a useful unit of cellular organization from the perspective of systems biology. Because interactions among modules can give rise to higher-level properties that are essential to cellular function, a...

journal_title：Genome research

authors： Petti AA,Church GM

更新日期：2005-09-01 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：:A genome-wide search for multiple loci influencing salt-loaded systolic blood pressure (NaSBP) variation among 188 F2 progeny from a cross between the Brown-Norway and spontaneously hypertensive rat strains was pursued in an effort to gain insight into the polygenic basis of blood pressure regulation. The results sugg...

journal_title：Genome research

authors： Schork NJ,Krieger JE,Trolliet MR,Franchini KG,Koike G,Krieger EM,Lander ES,Dzau VJ,Jacob HJ

更新日期：1995-09-01 00:00:00

abstract：:Organisms with large genomes contain vast amounts of repetitive DNA sequences, much of which is composed of retrotransposons. Amplification of retrotransposons has been postulated to be a major mechanism increasing genome size and leading to "genomic obesity." To gain insights into the relation between retrotransposon...

journal_title：Genome research

authors： Shirasu K,Schulman AH,Lahaye T,Schulze-Lefert P

更新日期：2000-07-01 00:00:00

abstract：:Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which...

journal_title：Genome research

authors： Li G,Davis BW,Raudsepp T,Pearks Wilkerson AJ,Mason VC,Ferguson-Smith M,O'Brien PC,Waters PD,Murphy WJ

更新日期：2013-09-01 00:00:00

abstract：:Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed ampli...

journal_title：Genome research

authors： Nabilsi NH,Deleyrolle LP,Darst RP,Riva A,Reynolds BA,Kladde MP

更新日期：2014-02-01 00:00:00

abstract：:The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross be...

journal_title：Genome research

authors： Stumpferl SW,Brand SE,Jiang JC,Korona B,Tiwari A,Dai J,Seo JG,Jazwinski SM

更新日期：2012-10-01 00:00:00

abstract：:Eukaryotic DNA replication initiates from multiple discrete sites in the genome, termed origins of replication (origins). Prior to S phase, multiple origins are poised to initiate replication by recruitment of the pre-replicative complex (pre-RC). For proper replication to occur, origin activation must be tightly regu...

journal_title：Genome research

authors： Rodriguez J,Lee L,Lynch B,Tsukiyama T

更新日期：2017-02-01 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：:Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around n...

journal_title：Genome research

authors： Schep AN,Buenrostro JD,Denny SK,Schwartz K,Sherlock G,Greenleaf WJ

更新日期：2015-11-01 00:00:00

abstract：:Recent studies have analyzed large-scale data sets of gene expression to identify genes associated with interindividual variation in phenotypes ranging from cancer subtypes to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to ...

journal_title：Genome research

authors： Hanson C,Cairns J,Wang L,Sinha S

更新日期：2018-08-01 00:00:00

abstract：:Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted m...

journal_title：Genome research

authors： Wang L,Fan J,Francis JM,Georghiou G,Hergert S,Li S,Gambe R,Zhou CW,Yang C,Xiao S,Cin PD,Bowden M,Kotliar D,Shukla SA,Brown JR,Neuberg D,Alessi DR,Zhang CZ,Kharchenko PV,Livak KJ,Wu CJ

更新日期：2017-08-01 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：:We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap bet...

journal_title：Genome research

authors： Baens M,Peeters P,Guo C,Aerssens J,Marynen P

更新日期：1996-05-01 00:00:00

abstract：:Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries representing the high, middle, an...

journal_title：Genome research

authors： Wicker T,Robertson JS,Schulze SR,Feltus FA,Magrini V,Morrison JA,Mardis ER,Wilson RK,Peterson DG,Paterson AH,Ivarie R

更新日期：2005-01-01 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：:Careful titration of Vent polymerase activity allows efficient amplification of full-length plasmids (12 kb). The high processivity and fidelity of this enzyme made oligonucleotide-directed site-specific mutagenesis of plasmids a straight-forward process. Using only two primers, a mutagenic and a complementary, single...

journal_title：Genome research

authors： Byrappa S,Gavin DK,Gupta KC

更新日期：1995-11-01 00:00:00

abstract：:An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human a...

journal_title：Genome research

authors： Lefébure T,Stanhope MJ

更新日期：2009-07-01 00:00:00

abstract：:The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the ...

journal_title：Genome research

authors： Kvikstad EM,Makova KD

更新日期：2010-05-01 00:00:00

abstract：:We have assembled a first-generation anchor map of the mouse genome using a panel of 94 whole-genome-radiation hybrids (WG-RHs) and 271 sequence-tagged sites (STSs). This is the first genome-wide RH anchor map of a model organism. All of the STSs have been previously localized on the genetic map and are located 8.8 Mb...

journal_title：Genome research

authors： McCarthy LC,Terrett J,Davis ME,Knights CJ,Smith AL,Critcher R,Schmitt K,Hudson J,Spurr NK,Goodfellow PN

更新日期：1997-12-01 00:00:00

abstract：:Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g., granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs)...

journal_title：Genome research

authors： Fehniger TA,Wylie T,Germino E,Leong JW,Magrini VJ,Koul S,Keppel CR,Schneider SE,Koboldt DC,Sullivan RP,Heinz ME,Crosby SD,Nagarajan R,Ramsingh G,Link DC,Ley TJ,Mardis ER

更新日期：2010-11-01 00:00:00