Reconstructing large regions of an ancestral mammalian genome in silico.

abstract：:The expression of most genes is regulated by multiple transcription factors. The interactions between transcription factors produce complex patterns of gene expression that are not always obvious from the arrangement of cis-regulatory elements in a promoter. One critical element of promoters is the TATA box, the docki...

journal_title：Genome research

authors： Mogno I,Vallania F,Mitra RD,Cohen BA

更新日期：2010-10-01 00:00:00

abstract：:Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the z...

journal_title：Genome research

authors： Völker M,Backström N,Skinner BM,Langley EJ,Bunzey SK,Ellegren H,Griffin DK

更新日期：2010-04-01 00:00:00

abstract：:Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of...

journal_title：Genome research

authors： Robbins CM,Tembe WA,Baker A,Sinari S,Moses TY,Beckstrom-Sternberg S,Beckstrom-Sternberg J,Barrett M,Long J,Chinnaiyan A,Lowey J,Suh E,Pearson JV,Craig DW,Agus DB,Pienta KJ,Carpten JD

更新日期：2011-01-01 00:00:00

abstract：:We have developed a computer program that aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing error...

journal_title：Genome research

authors： Wheelan SJ,Church DM,Ostell JM

更新日期：2001-11-01 00:00:00

abstract：:The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 ...

journal_title：Genome research

authors： Veloso A,Kirkconnell KS,Magnuson B,Biewen B,Paulsen MT,Wilson TE,Ljungman M

更新日期：2014-06-01 00:00:00

abstract：:Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have charac...

journal_title：Genome research

authors： Enuameh MS,Asriyan Y,Richards A,Christensen RG,Hall VL,Kazemian M,Zhu C,Pham H,Cheng Q,Blatti C,Brasefield JA,Basciotta MD,Ou J,McNulty JC,Zhu LJ,Celniker SE,Sinha S,Stormo GD,Brodsky MH,Wolfe SA

更新日期：2013-06-01 00:00:00

abstract：:In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylat...

journal_title：Genome research

authors： Court F,Le Boiteux E,Fogli A,Müller-Barthélémy M,Vaurs-Barrière C,Chautard E,Pereira B,Biau J,Kemeny JL,Khalil T,Karayan-Tapon L,Verrelle P,Arnaud P

更新日期：2019-10-01 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：:Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance suggests that their genes may have been subject to adaptive evolution. We have estimated the consequences of selection on ro...

journal_title：Genome research

authors： Emes RD,Beatson SA,Ponting CP,Goodstadt L

更新日期：2004-04-01 00:00:00

abstract：:The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...

journal_title：Genome research

authors： Xin B,Rohs R

更新日期：2018-01-11 00:00:00

abstract：:Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and co...

journal_title：Genome research

authors： Hoskins RA,Carlson JW,Wan KH,Park S,Mendez I,Galle SE,Booth BW,Pfeiffer BD,George RA,Svirskas R,Krzywinski M,Schein J,Accardo MC,Damia E,Messina G,Méndez-Lago M,de Pablos B,Demakova OV,Andreyeva EN,Boldyreva LV,Ma

更新日期：2015-03-01 00:00:00

abstract：:Insertion of the human non-LTR retrotransposon LINE-1 (L1) into chromosomal DNA is thought to be initiated by a mechanism called target-primed reverse transcription (TPRT). This mechanism readily accounts for the attachment of the 3'-end of an L1 copy to the genomic target, but the subsequent integration steps leading...

journal_title：Genome research

authors： Zingler N,Willhoeft U,Brose HP,Schoder V,Jahns T,Hanschmann KM,Morrish TA,Löwer J,Schumann GG

更新日期：2005-06-01 00:00:00

abstract：:Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functi...

journal_title：Genome research

authors： Yu Y,Zhang C,Zhou G,Wu S,Qu X,Wei H,Xing G,Dong C,Zhai Y,Wan J,Ouyang S,Li L,Zhang S,Zhou K,Zhang Y,Wu C,He F

更新日期：2001-08-01 00:00:00

abstract：:Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distan...

journal_title：Genome research

authors： Mortlock DP,Guenther C,Kingsley DM

更新日期：2003-09-01 00:00:00

abstract：:Development of composite inflorescences in the plant family Asteraceae has features that cannot be studied in the traditional model plants for flower development. In Gerbera hybrida, inflorescences are composed of morphologically different types of flowers tightly packed into a flower head (capitulum). Individual flor...

journal_title：Genome research

authors： Laitinen RA,Immanen J,Auvinen P,Rudd S,Alatalo E,Paulin L,Ainasoja M,Kotilainen M,Koskela S,Teeri TH,Elomaa P

更新日期：2005-04-01 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：:A contiguous high-resolution map of 44 loci from a 35-Mb portion of the distal region of the long arm of human chromosome 5, q21-q35, was produced using radiation hybrid (RH) mapping in conjunction with a natural deletion mapping panel. The map includes 30 genes, four sequence-tagged site (STS) loci, and 10 DNA marker...

journal_title：Genome research

authors： Warrington JA,Wasmuth JJ

更新日期：1996-07-01 00:00:00

abstract：:Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data al...

journal_title：Genome research

authors： Zimin AV,Puiu D,Luo MC,Zhu T,Koren S,Marçais G,Yorke JA,Dvořák J,Salzberg SL

更新日期：2017-05-01 00:00:00

abstract：:Despite claims that the mammalian Y Chromosome is on a path to extinction, comparative sequence analysis of primate Y Chromosomes has shown the decay of the ancestral single-copy genes has all but ceased in this eutherian lineage. The suite of single-copy Y-linked genes is highly conserved among the majority of euther...

journal_title：Genome research

authors： Brashear WA,Raudsepp T,Murphy WJ

更新日期：2018-12-01 00:00:00

abstract：:Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels,...

journal_title：Genome research

authors： Krieger G,Lupo O,Levy AA,Barkai N

更新日期：2020-07-01 00:00:00

abstract：:In this study we quantify the features of meiotic recombination on the long arm of human chromosome 21. We constructed a 67. 3-centimorgan (cM) high-resolution, comprehensive, and accurate genetic linkage map of chromosome 21q using 187 highly polymorphic markers covering almost the entire long arm; 46 loci, consistin...

journal_title：Genome research

authors： Lynn A,Kashuk C,Petersen MB,Bailey JA,Cox DR,Antonarakis SE,Chakravarti A

更新日期：2000-09-01 00:00:00

abstract：:Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly un...

journal_title：Genome research

authors： Roy-Engel AM,Salem AH,Oyeniran OO,Deininger L,Hedges DJ,Kilroy GE,Batzer MA,Deininger PL

更新日期：2002-09-01 00:00:00

abstract：:Changes in gene order between the genomes of two related yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum were studied. From the dataset of a previous low coverage sequencing of the S. bayanus var. uvarum genome, 35 different synteny breakpoints between neighboring genes and two cases of l...

journal_title：Genome research

authors： Fischer G,Neuvéglise C,Durrens P,Gaillardin C,Dujon B

更新日期：2001-12-01 00:00:00

abstract：:Chromosomal aberrations have been thought to be random events. However, recent findings introduce a new paradigm in which certain DNA segments have the potential to adopt unusual conformations that lead to genomic instability and nonrandom chromosomal rearrangement. One of the best-studied examples is the palindromic ...

journal_title：Genome research

authors： Inagaki H,Ohye T,Kogo H,Kato T,Bolor H,Taniguchi M,Shaikh TH,Emanuel BS,Kurahashi H

更新日期：2009-02-01 00:00:00

abstract：:Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor bindi...

journal_title：Genome research

authors： Cusack M,King HW,Spingardi P,Kessler BM,Klose RJ,Kriaucionis S

更新日期：2020-10-01 00:00:00

abstract：:Disregulation of imprinted genes can be associated with tumorigenesis and altered cell differentiation capacity and so could provide adverse outcomes for stem cell applications. Although the maintenance of mouse and primate embryonic stem cells in a pluripotent state has been reported to disrupt the monoallelic expres...

journal_title：Genome research

authors： Kim KP,Thurston A,Mummery C,Ward-van Oostwaard D,Priddle H,Allegrucci C,Denning C,Young L

更新日期：2007-12-01 00:00:00

abstract：:Identifying genes in the genomic context is central to a cell's ability to interpret the genome. Yet, in general, the signals used to define eukaryotic genes are poorly described. Here, we derived simple classifiers that identify where transcription will initiate and terminate using nucleic acid sequence features dete...

journal_title：Genome research

authors： de Boer CG,van Bakel H,Tsui K,Li J,Morris QD,Nislow C,Greenblatt JF,Hughes TR

更新日期：2014-01-01 00:00:00

abstract：:Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to align to reference genomes and to call and annotate genomic variants. This problem is even more pron...

journal_title：Genome research

authors： Ozercan HI,Ileri AM,Ayday E,Alkan C

更新日期：2018-09-01 00:00:00

abstract：:X inactivation equalizes the dosage of gene expression between the sexes, but some genes escape silencing and are thus expressed from both alleles in females. To survey X inactivation and escape in mouse, we performed RNA sequencing in Mus musculus x Mus spretus cells with complete skewing of X inactivation, relying o...

journal_title：Genome research

authors： Yang F,Babak T,Shendure J,Disteche CM

更新日期：2010-05-01 00:00:00

abstract：:Diversity in the antigen-binding receptors of the immune system has long been a primary interest of biologists. Recently it has been suggested that polymorphism in regulatory (noncoding) gene segments is of substantial importance as well. Here, we survey the level of variation in MHC class II gene promoters in man and...

journal_title：Genome research

authors： Cowell LG,Kepler TB,Janitz M,Lauster R,Mitchison NA

更新日期：1998-02-01 00:00:00