Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment.

abstract：:Advances in high-throughput technologies, such as ChIP-chip, and the completion of human and mouse genomic sequences now allow analysis of the mechanisms of gene regulation on a systems level. In this study, we have developed a computational genomics approach (termed ChIPModules), which begins with experimentally dete...

journal_title：Genome research

authors： Jin VX,Rabinovich A,Squazzo SL,Green R,Farnham PJ

更新日期：2006-12-01 00:00:00

abstract：:DNA methylation is found in many eukaryotes, but its function is still controversial. We have studied the methylation of plant and animal genomes using a PCR-based technique amenable for high throughput. Repetitive elements are methylated in both organisms, but whereas most mammalian exons are methylated, plant exons ...

journal_title：Genome research

authors： Rabinowicz PD,Palmer LE,May BP,Hemann MT,Lowe SW,McCombie WR,Martienssen RA

更新日期：2003-12-01 00:00:00

abstract：:We have conducted a phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposons. Analysis of this simple yet highly conserved enzymatic domain from these disparate sources p...

journal_title：Genome research

authors： Malik HS,Eickbush TH

更新日期：2001-07-01 00:00:00

abstract：:Gene duplication and alternative splicing are important sources of proteomic diversity. Despite research indicating that gene duplication and alternative splicing are negatively correlated, the evolutionary relationship between the two remains unclear. One manner in which alternative splicing and gene duplication may ...

journal_title：Genome research

authors： Lambert MJ,Cochran WO,Wilde BM,Olsen KG,Cooper CD

更新日期：2015-05-01 00:00:00

abstract：:Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules,...

journal_title：Genome research

authors： Bundy JG,Papp B,Harmston R,Browne RA,Clayson EM,Burton N,Reece RJ,Oliver SG,Brindle KM

更新日期：2007-04-01 00:00:00

abstract：:Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of...

journal_title：Genome research

authors： Lay FD,Triche TJ Jr,Tsai YC,Su SF,Martin SE,Daneshmand S,Skinner EC,Liang G,Chihara Y,Jones PA

更新日期：2014-04-01 00:00:00

abstract：:Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription facto...

journal_title：Genome research

authors： Satija R,Bradley RK

更新日期：2012-04-01 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：:LSH, a member of the SNF2 family of chromatin remodeling ATPases encoded by the Hells gene, is essential for normal levels of DNA methylation in the mammalian genome. While the role of LSH in the methylation of repetitive DNA sequences is well characterized, its contribution to the regulation of DNA methylation and th...

journal_title：Genome research

authors： Myant K,Termanis A,Sundaram AY,Boe T,Li C,Merusi C,Burrage J,de Las Heras JI,Stancheva I

更新日期：2011-01-01 00:00:00

abstract：:Interactions mediated by cell surface receptors initiate important instructive signaling cues but can be difficult to detect in biochemical assays because they are often highly transient and membrane-embedded receptors are difficult to solubilize in their native conformation. Here, we address these biochemical challen...

journal_title：Genome research

authors： Sharma S,Bartholdson SJ,Couch ACM,Yusa K,Wright GJ

更新日期：2018-09-01 00:00:00

abstract：:CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the...

journal_title：Genome research

authors： Chen R,Sodergren E,Weinstock GM,Gibbs RA

更新日期：2004-04-01 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 have developed a novel quantitative method for rapidly assessing the CpG methylation density of a DNA region in mammalian cells. After bisulfite modification of genomic DNA, the region of interest is PCR amplified with primers containing two dam sites (GATC). The purified PCR products are then incubated with 14C-la...

journal_title：Genome research

authors： Galm O,Rountree MR,Bachman KE,Jair KW,Baylin SB,Herman JG

更新日期：2002-01-01 00:00:00

abstract：:While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amp...

journal_title：Genome research

authors： Nurk S,Meleshko D,Korobeynikov A,Pevzner PA

更新日期：2017-05-01 00:00:00

abstract：:Sequence-specific DNA-binding transcription factors have widespread biological significance in the regulation of gene expression. However, in lower prokaryotes and eukaryotic metazoans, it is usually difficult to find transcription regulatory factors that recognize specific target promoters. To address this, we have d...

journal_title：Genome research

authors： Guo M,Feng H,Zhang J,Wang W,Wang Y,Li Y,Gao C,Chen H,Feng Y,He ZG

更新日期：2009-07-01 00:00:00

abstract：:As part of a recent high-density linkage disequilibrium (LD) study of chromosome 20, we obtained genotypes for approximately 30,000 SNPs at a density of 1 SNP/2 kb on four different population samples (47 CEPH founders; 91 UK unrelateds [unrelated white individuals of western European ancestry]; 97 African Americans; ...

journal_title：Genome research

authors： Lawrence R,Evans DM,Morris AP,Ke X,Hunt S,Paolucci M,Ragoussis J,Deloukas P,Bentley D,Cardon LR

更新日期：2005-11-01 00:00:00

abstract：:The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to carcinogenesis; however, the role of the microbiota is the least well understood. We have characteri...

journal_title：Genome research

authors： Kostic AD,Gevers D,Pedamallu CS,Michaud M,Duke F,Earl AM,Ojesina AI,Jung J,Bass AJ,Tabernero J,Baselga J,Liu C,Shivdasani RA,Ogino S,Birren BW,Huttenhower C,Garrett WS,Meyerson M

更新日期：2012-02-01 00:00:00

abstract：:Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have asymme...

journal_title：Genome research

authors： Ramachandran S,Zentner GE,Henikoff S

更新日期：2015-03-01 00:00:00

abstract：:Mirtrons are intronic hairpin substrates of the dicing machinery that generate functional microRNAs. In this study, we describe experimental assays that defined the essential requirements for entry of introns into the mirtron pathway. These data informed a bioinformatic screen that effectively identified functional mi...

journal_title：Genome research

authors： Chung WJ,Agius P,Westholm JO,Chen M,Okamura K,Robine N,Leslie CS,Lai EC

更新日期：2011-02-01 00:00:00

abstract：:Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger s...

journal_title：Genome research

authors： Huddleston J,Ranade S,Malig M,Antonacci F,Chaisson M,Hon L,Sudmant PH,Graves TA,Alkan C,Dennis MY,Wilson RK,Turner SW,Korlach J,Eichler EE

更新日期：2014-04-01 00:00:00

abstract：:Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and r...

journal_title：Genome research

authors： Marin R,Cortez D,Lamanna F,Pradeepa MM,Leushkin E,Julien P,Liechti A,Halbert J,Brüning T,Mössinger K,Trefzer T,Conrad C,Kerver HN,Wade J,Tschopp P,Kaessmann H

更新日期：2017-12-01 00:00:00

abstract：:Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships po...

journal_title：Genome research

authors： Horvath JE,Weisrock DW,Embry SL,Fiorentino I,Balhoff JP,Kappeler P,Wray GA,Willard HF,Yoder AD

更新日期：2008-03-01 00:00:00

abstract：:UEV proteins are enzymatically inactive variants of the E2 ubiquitin-conjugating enzymes that regulate noncanonical elongation of ubiquitin chains. In Saccharomyces cerevisiae, UEV is part of the RAD6-mediated error-free DNA repair pathway. In mammalian cells, UEV proteins can modulate c-FOS transcription and the G2-M...

journal_title：Genome research

authors： Thomson TM,Lozano JJ,Loukili N,Carrió R,Serras F,Cormand B,Valeri M,Díaz VM,Abril J,Burset M,Merino J,Macaya A,Corominas M,Guigó R

更新日期：2000-11-01 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：:Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force...

journal_title：Genome research

authors： Maggiolini FAM,Sanders AD,Shew CJ,Sulovari A,Mao Y,Puig M,Catacchio CR,Dellino M,Palmisano D,Mercuri L,Bitonto M,Porubský D,Cáceres M,Eichler EE,Ventura M,Dennis MY,Korbel JO,Antonacci F

更新日期：2020-11-01 00:00:00

abstract：:Primate pericentromeric regions recently have been shown to exhibit extraordinary evolutionary plasticity. In this paper we report an additional peculiar feature of these regions that we discovered while analyzing, by FISH, the evolutionary conservation of primate phylogenetic chromosome IX. If the position of the cen...

journal_title：Genome research

authors： Montefalcone G,Tempesta S,Rocchi M,Archidiacono N

更新日期：1999-12-01 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：: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：:The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that n...

journal_title：Genome research

authors： Fabbri M,Girnita L,Varani G,Calin GA

更新日期：2019-09-01 00:00:00

abstract：:Hearing impairment is clinically and genetically heterogeneous. There are >400 disorders in which hearing impairment is a characteristic of the syndrome, and family studies demonstrate that there are at least 30 autosomal loci for nonsyndromic hearing impairment. The genes that have been identified encode diaphanous (...

journal_title：Genome research

authors： Keats BJ,Berlin CI

更新日期：1999-01-01 00:00:00