A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.

abstract：:The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequen...

journal_title：Genome research

authors： Huang X,Feng Q,Qian Q,Zhao Q,Wang L,Wang A,Guan J,Fan D,Weng Q,Huang T,Dong G,Sang T,Han B

更新日期：2009-06-01 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：:To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and compar...

journal_title：Genome research

authors： Churakov G,Zhang F,Grundmann N,Makalowski W,Noll A,Doronina L,Schmitz J

更新日期：2020-10-01 00:00:00

abstract：:We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on ...

journal_title：Genome research

authors： Gusev A,Lowe JK,Stoffel M,Daly MJ,Altshuler D,Breslow JL,Friedman JM,Pe'er I

更新日期：2009-02-01 00:00:00

abstract：:Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which causes Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement in OIS of chromatin reor...

journal_title：Genome research

authors： Lenain C,de Graaf CA,Pagie L,Visser NL,de Haas M,de Vries SS,Peric-Hupkes D,van Steensel B,Peeper DS

更新日期：2017-10-01 00:00:00

abstract：:The sequence of the first plant genome was completed and published at the end of 2000. This spawned a series of large-scale projects aimed at discovering the functions of the 25,000+ genes identified in Arabidopsis thaliana (Arabidopsis). This review summarizes progress made in the past five years and speculates about...

journal_title：Genome research

authors： Bevan M,Walsh S

更新日期：2005-12-01 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：:Coevolution maintains interactions between phenotypic traits through the process of reciprocal natural selection. Detecting molecular coevolution can expose functional interactions between molecules in the cell, generating insights into biological processes, pathways, and the networks of interactions important for cel...

journal_title：Genome research

authors： Tillier ER,Charlebois RL

更新日期：2009-10-01 00:00:00

abstract：:Mycoplasma mycoides subsp. mycoidesSC (MmymySC)is the etiological agent of contagious bovine pleuropneumonia (CBPP), a highly contagious respiratory disease in cattle. The genome of Mmymy SC type strain PG1(T) has been sequenced to map all the genes and to facilitate further studies regarding the cell function of the ...

journal_title：Genome research

authors： Westberg J,Persson A,Holmberg A,Goesmann A,Lundeberg J,Johansson KE,Pettersson B,Uhlén M

更新日期：2004-02-01 00:00:00

abstract：:Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome seque...

journal_title：Genome research

authors： Bourque G,Zdobnov EM,Bork P,Pevzner PA,Tesler G

更新日期：2005-01-01 00:00:00

abstract：:Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using...

journal_title：Genome research

authors： Fungtammasan A,Ananda G,Hile SE,Su MS,Sun C,Harris R,Medvedev P,Eckert K,Makova KD

更新日期：2015-05-01 00:00:00

abstract：:Using both env and long terminal repeat (LTR) sequences, with maximal representation of genetic diversity within primate strains, we revise and expand the unique evolutionary history of human and simian T-cell leukemia/lymphotropic viruses (HTLV/STLV). Based on the robust application of three different phylogenetic al...

journal_title：Genome research

authors： Slattery JP,Franchini G,Gessain A

更新日期：1999-06-01 00:00:00

abstract：:The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we...

journal_title：Genome research

authors： Lee IY,Westaway D,Smit AF,Wang K,Seto J,Chen L,Acharya C,Ankener M,Baskin D,Cooper C,Yao H,Prusiner SB,Hood LE

更新日期：1998-10-01 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：:Comparative gene mapping in mammals typically involves identification of segments of conserved synteny in diverse genomes. The development of maps that permit comparison of gene order within conserved synteny has not advanced beyond the mouse map that takes advantage of linkage analysis in interspecific backcrosses. R...

journal_title：Genome research

authors： Yang YP,Womack JE

更新日期：1998-07-01 00:00:00

abstract：:When transcription is to the right of the promoter, the "top," mRNA-synonymous strand of DNA tends to be purine-rich. When transcription is to the left of the promoter, the top, mRNA-template strand tends to be pyrimidine-rich. This transcription-direction rule suggests that there has been an evolutionary selection pr...

journal_title：Genome research

authors： Lao PJ,Forsdyke DR

更新日期：2000-02-01 00:00:00

abstract：:Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced th...

journal_title：Genome research

authors： Heidel AJ,Lawal HM,Felder M,Schilde C,Helps NR,Tunggal B,Rivero F,John U,Schleicher M,Eichinger L,Platzer M,Noegel AA,Schaap P,Glöckner G

更新日期：2011-11-01 00:00:00

abstract：:The identification and interpretation of the regulatory signals within the human genome remain among the greatest goals and most difficult challenges in genome analysis. The ability to predict the temporal and spatial control of transcription is likely to require a combination of methods to address the contribution of...

journal_title：Genome research

authors： Krivan W,Wasserman WW

更新日期：2001-09-01 00:00:00

abstract：:We developed a high-throughput technique for the generation of cDNA libraries in the yeast Saccharomyces cerevisiae which enables the selection of cloned cDNA inserts containing open reading frames (ORFs). For direct screening of random-primed cDNA libraries, we have constructed a yeast shuttle/expression vector, the ...

journal_title：Genome research

authors： Holz C,Lueking A,Bovekamp L,Gutjahr C,Bolotina N,Lehrach H,Cahill DJ

更新日期：2001-10-01 00:00:00

abstract：:Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover rates and how these rates are integrated into cellular decisions. We decided to measure mRNA decay rates in two human ce...

journal_title：Genome research

authors： Yang E,van Nimwegen E,Zavolan M,Rajewsky N,Schroeder M,Magnasco M,Darnell JE Jr

更新日期：2003-08-01 00:00:00

abstract：:Next-generation sequencing technologies have made it possible to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for ...

journal_title：Genome research

authors： Bansal V,Harismendy O,Tewhey R,Murray SS,Schork NJ,Topol EJ,Frazer KA

更新日期：2010-04-01 00:00:00

abstract：:Disturbance of DNA methylation leading to aberrant gene expression has been implicated in the etiology of many diseases. Whereas variation at the genetic level has been studied extensively, less is known about the extent and function of epigenetic variation. To explore variation and heritability of DNA methylation, we...

journal_title：Genome research

authors： Gervin K,Hammerø M,Akselsen HE,Moe R,Nygård H,Brandt I,Gjessing HK,Harris JR,Undlien DE,Lyle R

更新日期：2011-11-01 00:00:00

abstract：:The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...

journal_title：Genome research

authors： Lazar J,Moreno C,Jacob HJ,Kwitek AE

更新日期：2005-12-01 00:00:00

abstract：:The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this...

journal_title：Genome research

authors： Deeds EJ,Hennessey H,Shakhnovich EI

更新日期：2005-03-01 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：:Chromosome-specific cDNA libraries are new tools for the isolation of genes from specific genomic regions. We have used two YACs than span the approximately 2-Mb cri-du-chat critical region (CDCCR) of chromosome 5p to directly screen a chromosome 5-specific (CH5SP) fetal brain cDNA library. To compare this library wit...

journal_title：Genome research

authors： Simmons AD,Overhauser J,Lovett M

更新日期：1997-02-01 00:00:00

abstract：:Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitati...

journal_title：Genome research

authors： Gao AW,Sterken MG,Uit de Bos J,van Creij J,Kamble R,Snoek BL,Kammenga JE,Houtkooper RH

更新日期：2018-09-01 00:00:00

abstract：:Since complete redundancy between extant duplicates (paralogs) is evolutionarily unfavorable, some degree of functional congruency is eventually lost. However, in budding yeast, experimental evidence collected for duplicated metabolic enzymes and in global physical interaction surveys had suggested widespread function...

journal_title：Genome research

authors： Musso G,Costanzo M,Huangfu M,Smith AM,Paw J,San Luis BJ,Boone C,Giaever G,Nislow C,Emili A,Zhang Z

更新日期：2008-07-01 00:00:00

abstract：:In comparison to genotypes, knowledge about haplotypes (the combination of alleles present on a single chromosome) is much more useful for whole-genome association studies and for making inferences about human evolutionary history. Haplotypes are typically inferred from population genotype data using computational met...

journal_title：Genome research

authors： Bansal V,Halpern AL,Axelrod N,Bafna V

更新日期：2008-08-01 00:00:00

abstract：:We report the validation of a new assay for typing single nucleotide polymorphisms (SNPs) that takes advantage of the 3'-to-5' exonuclease proofreading activity of many DNA polymerases. The assay uses one or more primers labeled on the 3' nucleotide base, and can be implemented in a variety of formats including a one-...

journal_title：Genome research

authors： Cahill P,Bakis M,Hurley J,Kamath V,Nielsen W,Weymouth D,Dupuis J,Doucette-Stamm L,Smith DR

更新日期：2003-05-01 00:00:00