Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.

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：:Eukaryotic translation initiation involves preinitiation ribosomal complex 5'-to-3' directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak ...

journal_title：Genome research

authors： Benitez-Cantos MS,Yordanova MM,O'Connor PBF,Zhdanov AV,Kovalchuk SI,Papkovsky DB,Andreev DE,Baranov PV

更新日期：2020-07-01 00:00:00

abstract：:Spatially distinct gene expression profiles in neural stem cells (NSCs) are a prerequisite to the formation of neuronal diversity, but how these arise from the regulatory interactions between chromatin accessibility and transcription factor activity has remained unclear. Here, we demonstrate that, despite their distin...

journal_title：Genome research

authors： Hagey DW,Zaouter C,Combeau G,Lendahl MA,Andersson O,Huss M,Muhr J

更新日期：2016-07-01 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：: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：:CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in hu...

journal_title：Genome research

authors： Smallwood A,Hon GC,Jin F,Henry RE,Espinosa JM,Ren B

更新日期：2012-08-01 00:00:00

abstract：:Detecting and estimating DNA sample contamination are important steps to ensure high-quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each indi...

journal_title：Genome research

authors： Zhang F,Flickinger M,Taliun SAG,InPSYght Psychiatric Genetics Consortium.,Abecasis GR,Scott LJ,McCaroll SA,Pato CN,Boehnke M,Kang HM

更新日期：2020-02-01 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：: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

abstract：:In mammals, genome-wide chromatin maps and immunofluorescence studies show that broad domains of repressive histone modifications are present on pericentromeric and telomeric repeats and on the inactive X chromosome. However, only a few autosomal loci such as silent Hox gene clusters have been shown to lie in broad do...

journal_title：Genome research

authors： Pauler FM,Sloane MA,Huang R,Regha K,Koerner MV,Tamir I,Sommer A,Aszodi A,Jenuwein T,Barlow DP

更新日期：2009-02-01 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：:The Mammalian Gene Collection (MGC) consortium (http://mgc.nci.nih.gov) seeks to establish publicly available collections of full-ORF cDNAs for several organisms of significance to biomedical research, including human. To date over 15,200 human cDNA clones containing full-length open reading frames (ORFs) have been id...

journal_title：Genome research

authors： Baross A,Butterfield YS,Coughlin SM,Zeng T,Griffith M,Griffith OL,Petrescu AS,Smailus DE,Khattra J,McDonald HL,McKay SJ,Moksa M,Holt RA,Marra MA

更新日期：2004-10-01 00:00:00

abstract：:Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-...

journal_title：Genome research

authors： Martinez JM,Breidenbach HH,Cawthon R

更新日期：1996-01-01 00:00:00

abstract：:Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey...

journal_title：Genome research

authors： Wilder SP,Bihoreau MT,Argoud K,Watanabe TK,Lathrop M,Gauguier D

更新日期：2004-04-01 00:00:00

abstract：:The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incred...

journal_title：Genome research

authors： Schatz MC

更新日期：2015-10-01 00:00:00

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：:Elucidating the pathophysiology and molecular attributes of common disorders as well as developing targeted and effective treatments hinges on the study of the relevant cell type and tissues. Pancreatic beta cells within the islets of Langerhans are centrally involved in the pathogenesis of both type 1 and type 2 diab...

journal_title：Genome research

authors： Nica AC,Ongen H,Irminger JC,Bosco D,Berney T,Antonarakis SE,Halban PA,Dermitzakis ET

更新日期：2013-09-01 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：:Random spontaneous genome rearrangements are difficult to detect in vivo, especially in postmitotic tissues. Using a lacZ-plasmid reporter mouse model, we have previously presented evidence for the accumulation of large genome rearrangements in various tissues, including postmitotic tissues, during aging. These rearra...

journal_title：Genome research

authors： Dollé ME,Vijg J

更新日期：2002-11-01 00:00:00

abstract：:Mammalian genomes are partitioned into domains that replicate in a defined temporal order. These domains can replicate at similar times in all cell types (constitutive) or at cell type-specific times (developmental). Genome-wide chromatin conformation capture (Hi-C) has revealed sub-megabase topologically associating ...

journal_title：Genome research

authors： Dileep V,Ay F,Sima J,Vera DL,Noble WS,Gilbert DM

更新日期：2015-08-01 00:00:00

abstract：:We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel se...

journal_title：Genome research

authors： Dellino GI,Cittaro D,Piccioni R,Luzi L,Banfi S,Segalla S,Cesaroni M,Mendoza-Maldonado R,Giacca M,Pelicci PG

更新日期：2013-01-01 00:00:00

abstract：:Live-cell imaging allows detailed dynamic cellular phenotyping for cell biology and, in combination with small molecule or drug libraries, for high-content screening. Fully automated analysis of live cell movies has been hampered by the lack of computational approaches that allow tracking and recognition of individual...

journal_title：Genome research

authors： Harder N,Mora-Bermúdez F,Godinez WJ,Wünsche A,Eils R,Ellenberg J,Rohr K

更新日期：2009-11-01 00:00:00

abstract：:We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biologic...

journal_title：Genome research

authors： Castillo-Davis CI,Kondrashov FA,Hartl DL,Kulathinal RJ

更新日期：2004-05-01 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：:Animal microRNA sequences are subject to 3' nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3' adenylation function, we deep-sequenced RNA after k...

journal_title：Genome research

authors： Burroughs AM,Ando Y,de Hoon MJ,Tomaru Y,Nishibu T,Ukekawa R,Funakoshi T,Kurokawa T,Suzuki H,Hayashizaki Y,Daub CO

更新日期：2010-10-01 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：:Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures-including immune responses and therapeutic interventions-shape bacterial genomes. We carri...

journal_title：Genome research

authors： Lee AH,Flibotte S,Sinha S,Paiero A,Ehrlich RL,Balashov S,Ehrlich GD,Zlosnik JE,Mell JC,Nislow C

更新日期：2017-04-01 00:00:00

abstract：:Most new genes arise by duplication of existing gene structures, after which relaxed selection on the new copy frequently leads to mutational inactivation of the duplicate; only rarely will a new gene with modified function emerge. Here we describe a unique mechanism of gene creation, whereby new combinations of funct...

journal_title：Genome research

authors： Babushok DV,Ohshima K,Ostertag EM,Chen X,Wang Y,Mandal PK,Okada N,Abrams CS,Kazazian HH Jr

更新日期：2007-08-01 00:00:00

abstract：:Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)-related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of...

journal_title：Genome research

authors： Watanabe Y,Yamamoto H,Oikawa R,Toyota M,Yamamoto M,Kokudo N,Tanaka S,Arii S,Yotsuyanagi H,Koike K,Itoh F

更新日期：2015-03-01 00:00:00

abstract：:Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uni...

journal_title：Genome research

authors： Daubin V,Ochman H

更新日期：2004-06-01 00:00:00