A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae.

abstract：:In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...

journal_title：Genome research

authors： Kim Y,Jung JP,Pack CG,Huh WK

更新日期：2019-01-01 00:00:00

abstract：:The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipien...

journal_title：Genome research

authors： Aylor DL,Valdar W,Foulds-Mathes W,Buus RJ,Verdugo RA,Baric RS,Ferris MT,Frelinger JA,Heise M,Frieman MB,Gralinski LE,Bell TA,Didion JD,Hua K,Nehrenberg DL,Powell CL,Steigerwalt J,Xie Y,Kelada SN,Collins FS,Yang IV

更新日期：2011-08-01 00:00:00

abstract：:Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of the relative importance of these two forces is the observation that both diversity within species and interspecies diver...

journal_title：Genome research

authors： Hellmann I,Prüfer K,Ji H,Zody MC,Pääbo S,Ptak SE

更新日期：2005-09-01 00:00:00

abstract：:In addition to mediating sister chromatid cohesion during the cell cycle, the cohesin complex associates with CTCF and with active gene regulatory elements to form long-range interactions between its binding sites. Genome-wide chromosome conformation capture had shown that cohesin's main role in interphase genome orga...

journal_title：Genome research

authors： Ing-Simmons E,Seitan VC,Faure AJ,Flicek P,Carroll T,Dekker J,Fisher AG,Lenhard B,Merkenschlager M

更新日期：2015-04-01 00:00:00

abstract：:The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show t...

journal_title：Genome research

authors： Bollenbach T,Vetsigian K,Kishony R

更新日期：2007-04-01 00:00:00

abstract：:Yeasts and filamentous fungi do not have adenosine deaminase acting on RNA (ADAR) orthologs and are believed to lack A-to-I RNA editing, which is the most prevalent editing of mRNA in animals. However, during this study with the PUK1(FGRRES_01058) pseudokinase gene important for sexual reproduction in Fusarium gramine...

journal_title：Genome research

authors： Liu H,Wang Q,He Y,Chen L,Hao C,Jiang C,Li Y,Dai Y,Kang Z,Xu JR

更新日期：2016-04-01 00:00:00

abstract：:WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Ea...

journal_title：Genome research

authors： Crooks GE,Hon G,Chandonia JM,Brenner SE

更新日期：2004-06-01 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：:X-linked Mental Retardation (XLMR) occurs in 1 in 600 males and is highly genetically heterogeneous. We used a novel human X chromosome cDNA microarray (XCA) to survey the expression profile of X-linked genes in lymphoblasts of XLMR males. Genes with altered expression verified by Northern blot and/or quantitative PCR...

journal_title：Genome research

authors： Zhang L,Jie C,Obie C,Abidi F,Schwartz CE,Stevenson RE,Valle D,Wang T

更新日期：2007-05-01 00:00:00

abstract：:Giardia duodenalis is the best-characterized example of the most ancient eukaryotes, which are primitively amitochondrial and anaerobic. The surface of Giardia is coated with cysteine-rich proteins. One family of these proteins, CRP136, varies among isolates and upon environmental stress. A repeat region within the CR...

journal_title：Genome research

authors： Upcroft P,Chen N,Upcroft JA

更新日期：1997-01-01 00:00:00

abstract：:Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence kn...

journal_title：Genome research

authors： Taillon-Miller P,Piernot EE,Kwok PY

更新日期：1999-05-01 00:00:00

abstract：:Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length o...

journal_title：Genome research

authors： Bousios A,Diez CM,Takuno S,Bystry V,Darzentas N,Gaut BS

更新日期：2016-02-01 00:00:00

abstract：:Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced...

journal_title：Genome research

authors： Rasmussen MD,Kellis M

更新日期：2007-12-01 00:00:00

abstract：:Somatic L1 retrotransposition events have been shown to occur in epithelial cancers. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising ...

journal_title：Genome research

authors： Ewing AD,Gacita A,Wood LD,Ma F,Xing D,Kim MS,Manda SS,Abril G,Pereira G,Makohon-Moore A,Looijenga LH,Gillis AJ,Hruban RH,Anders RA,Romans KE,Pandey A,Iacobuzio-Donahue CA,Vogelstein B,Kinzler KW,Kazazian HH Jr,Sol

更新日期：2015-10-01 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：: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：:Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequen...

journal_title：Genome research

authors： Battle A,Mostafavi S,Zhu X,Potash JB,Weissman MM,McCormick C,Haudenschild CD,Beckman KB,Shi J,Mei R,Urban AE,Montgomery SB,Levinson DF,Koller D

更新日期：2014-01-01 00:00:00

abstract：:Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted...

journal_title：Genome research

authors： Court F,Tayama C,Romanelli V,Martin-Trujillo A,Iglesias-Platas I,Okamura K,Sugahara N,Simón C,Moore H,Harness JV,Keirstead H,Sanchez-Mut JV,Kaneki E,Lapunzina P,Soejima H,Wake N,Esteller M,Ogata T,Hata K,Nakabayashi

更新日期：2014-04-01 00:00:00

abstract：:Chromosome 21 represents approximately 1% of the human genome, and its long arm has been estimated to contain 600-1000 genes. A dense linkage map and almost complete physical maps based on yeast artificial chromosomes (YACs) and cosmids have been developed. We have used exon trapping to identify portions of genes from...

journal_title：Genome research

authors： Chen H,Chrast R,Rossier C,Morris MA,Lalioti MD,Antonarakis SE

更新日期：1996-08-01 00:00:00

abstract：:RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here, we present a new method, Smart-3SEQ, that accuratel...

journal_title：Genome research

authors： Foley JW,Zhu C,Jolivet P,Zhu SX,Lu P,Meaney MJ,West RB

更新日期：2019-11-01 00:00:00

abstract：:Despite much research, our understanding of the architecture and cis-regulatory elements of human promoters is still lacking. Here, we devised a high-throughput assay to quantify the activity of approximately 15,000 fully designed sequences that we integrated and expressed from a fixed location within the human genome...

journal_title：Genome research

authors： Weingarten-Gabbay S,Nir R,Lubliner S,Sharon E,Kalma Y,Weinberger A,Segal E

更新日期：2019-02-01 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：: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

abstract：:The recently identified mouse obese (ob) gene apparently encodes a secreted protein that may function in the signaling pathway of adipose tissue. Mutations in the mouse ob gene are associated with the early development of gross obesity. A detailed knowledge concerning the RNA expression pattern and precise genomic loc...

journal_title：Genome research

authors： Green ED,Maffei M,Braden VV,Proenca R,DeSilva U,Zhang Y,Chua SC Jr,Leibel RL,Weissenbach J,Friedman JM

更新日期：1995-08-01 00:00:00

abstract：:The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of metatherians. Here, we compare Monodelphis with Homo sequences from alignments of single nucleotides, genes, and whole chr...

journal_title：Genome research

authors： Goodstadt L,Heger A,Webber C,Ponting CP

更新日期：2007-07-01 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：: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

abstract：:Custom-designed nucleases (CDNs) greatly facilitate genetic engineering by generating a targeted DNA double-strand break (DSB) in the genome. Once a DSB is created, specific modifications can be introduced around the breakage site during its repair by two major DNA damage repair (DDR) mechanisms: the dominant but erro...

journal_title：Genome research

authors： Maresca M,Lin VG,Guo N,Yang Y

更新日期：2013-03-01 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：:Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. el...

journal_title：Genome research

authors： Yoshimura J,Ichikawa K,Shoura MJ,Artiles KL,Gabdank I,Wahba L,Smith CL,Edgley ML,Rougvie AE,Fire AZ,Morishita S,Schwarz EM

更新日期：2019-06-01 00:00:00