A comprehensive transcript map of the mouse Gnas imprinted complex.

abstract：:Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for speci...

journal_title：Genome research

authors： Cui L,Wall PK,Leebens-Mack JH,Lindsay BG,Soltis DE,Doyle JJ,Soltis PS,Carlson JE,Arumuganathan K,Barakat A,Albert VA,Ma H,dePamphilis CW

更新日期：2006-06-01 00:00:00

abstract：:Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized th...

journal_title：Genome research

authors： Nolte V,Pandey RV,Kofler R,Schlötterer C

更新日期：2013-01-01 00:00:00

abstract：:Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the ~50% of transcripts without protein-coding potential, including long noncoding RNAs (lncRNAs), has been largely uncharacterized. Activating mutations in the BRAF oncogene are present in >70% of mel...

journal_title：Genome research

authors： Flockhart RJ,Webster DE,Qu K,Mascarenhas N,Kovalski J,Kretz M,Khavari PA

更新日期：2012-06-01 00:00:00

abstract：:A small set of core transcription factors (TFs) dominates control of the gene expression program in embryonic stem cells and other well-studied cellular models. These core TFs collectively regulate their own gene expression, thus forming an interconnected auto-regulatory loop that can be considered the core transcript...

journal_title：Genome research

authors： Saint-André V,Federation AJ,Lin CY,Abraham BJ,Reddy J,Lee TI,Bradner JE,Young RA

更新日期：2016-03-01 00:00:00

abstract：:MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species tha...

journal_title：Genome research

authors： Meunier J,Lemoine F,Soumillon M,Liechti A,Weier M,Guschanski K,Hu H,Khaitovich P,Kaessmann H

更新日期：2013-01-01 00:00:00

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：:In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato frui...

journal_title：Genome research

authors： Moxon S,Jing R,Szittya G,Schwach F,Rusholme Pilcher RL,Moulton V,Dalmay T

更新日期：2008-10-01 00:00:00

abstract：:Phosphotyrosine (pTyr) signaling, which plays a central role in cell-cell and cell-environment interactions, has been considered to be an evolutionary innovation in multicellular metazoans. However, neither the emergence nor the evolution of the human pTyr signaling system is currently understood. Tyrosine kinase (TK)...

journal_title：Genome research

authors： Li L,Tibiche C,Fu C,Kaneko T,Moran MF,Schiller MR,Li SS,Wang E

更新日期：2012-07-01 00:00:00

abstract：:We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, th...

journal_title：Genome research

authors： Buchan DW,Shepherd AJ,Lee D,Pearl FM,Rison SC,Thornton JM,Orengo CA

更新日期：2002-03-01 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：:Loss of heterozygosity (LOH) and copy number alteration (CNA) feature prominently in the somatic genomic landscape of tumors. As such, karyotypic aberrations in cancer genomes have been studied extensively to discover novel oncogenes and tumor-suppressor genes. Advances in sequencing technology have enabled the cost-e...

journal_title：Genome research

authors： Ha G,Roth A,Lai D,Bashashati A,Ding J,Goya R,Giuliany R,Rosner J,Oloumi A,Shumansky K,Chin SF,Turashvili G,Hirst M,Caldas C,Marra MA,Aparicio S,Shah SP

更新日期：2012-10-01 00:00:00

abstract：:A large database of copy number profiles from cancer genomes can facilitate the identification of recurrent chromosomal alterations that often contain key cancer-related genes. It can also be used to explore low-prevalence genomic events such as chromothripsis. In this study, we report an analysis of 8227 human cancer...

journal_title：Genome research

authors： Kim TM,Xi R,Luquette LJ,Park RW,Johnson MD,Park PJ

更新日期：2013-02-01 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：:Thousands of long noncoding RNAs (lncRNAs) have been found in vertebrate animals, a few of which have known biological roles. To better understand the genomics and features of lncRNAs in invertebrates, we used available RNA-seq, poly(A)-site, and ribosome-mapping data to identify lncRNAs of Caenorhabditis elegans. We ...

journal_title：Genome research

authors： Nam JW,Bartel DP

更新日期：2012-12-01 00:00:00

abstract：:Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the tra...

journal_title：Genome research

authors： Hartl D,Krebs AR,Grand RS,Baubec T,Isbel L,Wirbelauer C,Burger L,Schübeler D

更新日期：2019-04-01 00:00:00

abstract：:Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of po...

journal_title：Genome research

authors： Wang Y,Lu J,Yu J,Gibbs RA,Yu F

更新日期：2013-05-01 00:00:00

abstract：:The Saccharomyces cerevisiae genome contains about 35 copies of dispersed retrotransposons called Ty1 elements. Ty1 elements target regions upstream of tRNA genes and other Pol III-transcribed genes when retrotransposing to new sites. We used deep sequencing of Ty1-flanking sequence amplicons to characterize Ty1 integ...

journal_title：Genome research

authors： Mularoni L,Zhou Y,Bowen T,Gangadharan S,Wheelan SJ,Boeke JD

更新日期：2012-04-01 00:00:00

abstract：:The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to approximately 1% of euchromatic regions of the human genome. Gap filling is a lab...

journal_title：Genome research

authors： Leem SH,Kouprina N,Grimwood J,Kim JH,Mullokandov M,Yoon YH,Chae JY,Morgan J,Lucas S,Richardson P,Detter C,Glavina T,Rubin E,Barrett JC,Larionov V

更新日期：2004-02-01 00:00:00

abstract：:Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription...

journal_title：Genome research

authors： Cheng Y,King DC,Dore LC,Zhang X,Zhou Y,Zhang Y,Dorman C,Abebe D,Kumar SA,Chiaromonte F,Miller W,Green RD,Weiss MJ,Hardison RC

更新日期：2008-12-01 00:00:00

abstract：:We have identified previously a putative tumor suppressor gene (TSG) locus at human chromosome (hchr) 7q31 showing that it is altered in a variety of human epithelial tumors. To determine whether this TSG is conserved in mice, we studied loss of heterozygosity (LOH) in chemically induced mouse liver adenomas. The LOH ...

journal_title：Genome research

authors： Zenklusen JC,Rodriguez LV,LaCava M,Wang Z,Goldstein LS,Conti CJ

更新日期：1996-11-01 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：: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：:Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using populati...

journal_title：Genome research

authors： Khodursky S,Svetec N,Durkin SM,Zhao L

更新日期：2020-06-01 00:00:00

abstract：:The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their...

journal_title：Genome research

authors： Yang F,Wang J,GTEx Consortium.,Pierce BL,Chen LS

更新日期：2017-11-01 00:00:00

abstract：:We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and othe...

journal_title：Genome research

authors： MackiewiczP,Gierlik A,Kowalczuk M,Dudek MR,Cebrat S

更新日期：1999-05-01 00:00:00

abstract：:Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host plasma membrane and is involved in protein transport and trafficking. We have identified a novel subtelomeric gene famil...

journal_title：Genome research

authors： Sam-Yellowe TY,Florens L,Johnson JR,Wang T,Drazba JA,Le Roch KG,Zhou Y,Batalov S,Carucci DJ,Winzeler EA,Yates JR 3rd

更新日期：2004-06-01 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：: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：:The str family of genes encoding seven-transmembrane G-protein-coupled or serpentine receptors related to the ODR-10 diacetyl chemoreceptor is very large, with at least 197 members in the Caenorhabditis elegans genome. The closely related stl family has 43 genes, and both families are distantly related to the srd fami...

journal_title：Genome research

authors： Robertson HM

更新日期：1998-05-01 00:00:00

abstract：:CRISPR/Cas9-mediated targeted mutagenesis allows efficient generation of loss-of-function alleles in zebrafish. To date, this technology has been primarily used to generate genetic knockout animals. Nevertheless, the study of the function of certain loci might require tight spatiotemporal control of gene inactivation....

journal_title：Genome research

authors： Di Donato V,De Santis F,Auer TO,Testa N,Sánchez-Iranzo H,Mercader N,Concordet JP,Del Bene F

更新日期：2016-05-01 00:00:00