General gene movement off the X chromosome in the Drosophila genus.

abstract：:Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumula...

journal_title：Genome research

authors： Keith N,Tucker AE,Jackson CE,Sung W,Lucas Lledó JI,Schrider DR,Schaack S,Dudycha JL,Ackerman M,Younge AJ,Shaw JR,Lynch M

更新日期：2016-01-01 00:00:00

abstract：:Previously, we have described novel families of genes, warthog (wrt) and groundhog (grd), in Caenorhabditis elegans. They are related to Hedgehog (Hh) through the carboxy-terminal autoprocessing domain (called Hog or Hint). A comprehensive survey revealed 10 genes with Hog/Hint modules in C. elegans. Five of these are...

journal_title：Genome research

authors： Aspöck G,Kagoshima H,Niklaus G,Bürglin TR

更新日期：1999-10-01 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：: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：:Gene amplification occurs in most solid tumors and is associated with poor prognosis. Amplification of 20q13.2 is common to several tumor types including breast cancer. The 1 Mb of sequence spanning the 20q13.2 breast cancer amplicon is one of the most exhaustively studied segments of the human genome. These studies h...

journal_title：Genome research

authors： Collins C,Volik S,Kowbel D,Ginzinger D,Ylstra B,Cloutier T,Hawkins T,Predki P,Martin C,Wernick M,Kuo WL,Alberts A,Gray JW

更新日期：2001-06-01 00:00:00

abstract：:We have determined the complete sequence of 951,695 bp from the class I region of H2, the mouse major histocompatibility complex (Mhc) from strain 129/Sv (haplotype bc). The sequence contains 26 genes. The sequence spans from the last 50 kb of the H2-T region, including 2 class I genes and 3 class I pseudogenes, and i...

journal_title：Genome research

authors： Takada T,Kumánovics A,Amadou C,Yoshino M,Jones EP,Athanasiou M,Evans GA,Fischer Lindahl K

更新日期：2003-04-01 00:00:00

abstract：:Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in...

journal_title：Genome research

authors： Neville MDC,Kohze R,Erady C,Meena N,Hayden M,Cooper DN,Mort M,Prabakaran S

更新日期：2021-01-19 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：:Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates e...

journal_title：Genome research

authors： Roy S,Wapinski I,Pfiffner J,French C,Socha A,Konieczka J,Habib N,Kellis M,Thompson D,Regev A

更新日期：2013-06-01 00:00:00

abstract：:The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial comm...

journal_title：Genome research

authors： Sharon I,Morowitz MJ,Thomas BC,Costello EK,Relman DA,Banfield JF

更新日期：2013-01-01 00:00:00

abstract：:Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from...

journal_title：Genome research

authors： West PT,Probst AJ,Grigoriev IV,Thomas BC,Banfield JF

更新日期：2018-04-01 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：:Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important compone...

journal_title：Genome research

authors： Devine SE,Chissoe SL,Eby Y,Wilson RK,Boeke JD

更新日期：1997-05-01 00:00:00

abstract：:Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and lit...

journal_title：Genome research

authors： Ma L,Zhao B,Chen K,Thomas A,Tuteja JH,He X,He C,White KP

更新日期：2017-03-01 00:00:00

abstract：:Eukaryotic DNA replication initiates from multiple discrete sites in the genome, termed origins of replication (origins). Prior to S phase, multiple origins are poised to initiate replication by recruitment of the pre-replicative complex (pre-RC). For proper replication to occur, origin activation must be tightly regu...

journal_title：Genome research

authors： Rodriguez J,Lee L,Lynch B,Tsukiyama T

更新日期：2017-02-01 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：:We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which a...

journal_title：Genome research

authors： Skinner BM,Sargent CA,Churcher C,Hunt T,Herrero J,Loveland JE,Dunn M,Louzada S,Fu B,Chow W,Gilbert J,Austin-Guest S,Beal K,Carvalho-Silva D,Cheng W,Gordon D,Grafham D,Hardy M,Harley J,Hauser H,Howden P,Howe K,

更新日期：2016-01-01 00:00:00

abstract：:Network "guilt by association" (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this approach could account even for nonadditive genetic interactions, which underlie the synergistic combinatio...

journal_title：Genome research

authors： Lee I,Blom UM,Wang PI,Shim JE,Marcotte EM

更新日期：2011-07-01 00:00:00

abstract：:We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...

journal_title：Genome research

authors： Edwards YH,Putt W,Lekoape KM,Stott D,Fox M,Hopkinson DA,Sowden J

更新日期：1996-03-01 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：:A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic l...

journal_title：Genome research

authors： Doerks T,Copley RR,Schultz J,Ponting CP,Bork P

更新日期：2002-01-01 00:00:00

abstract：:Pre-mRNA processing often occurs in coordination with transcription thereby coupling these two key regulatory events. As such, many proteins involved in mRNA processing associate with the transcriptional machinery and are in proximity to DNA. This proximity allows for the mapping of the genomic associations of RNA bin...

journal_title：Genome research

authors： Swinburne IA,Meyer CA,Liu XS,Silver PA,Brodsky AS

更新日期：2006-07-01 00:00:00

abstract：:ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicin...

journal_title：Genome research

authors： Biesecker LG,Mullikin JC,Facio FM,Turner C,Cherukuri PF,Blakesley RW,Bouffard GG,Chines PS,Cruz P,Hansen NF,Teer JK,Maskeri B,Young AC,NISC Comparative Sequencing Program.,Manolio TA,Wilson AF,Finkel T,Hwang P,Arai A

更新日期：2009-09-01 00:00:00

abstract：:Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotation...

journal_title：Genome research

authors： Lunardon A,Johnson NR,Hagerott E,Phifer T,Polydore S,Coruh C,Axtell MJ

更新日期：2020-03-01 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：:The phenotypic variation of living organisms is shaped by genetics, environment, and their interaction. Understanding phenotypic plasticity under natural conditions is hindered by the apparently complex environment and the interacting genes and pathways. Herein, we report findings from the dissection of rice flowering...

journal_title：Genome research

authors： Guo T,Mu Q,Wang J,Vanous AE,Onogi A,Iwata H,Li X,Yu J

更新日期：2020-05-01 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：:Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced th...

journal_title：Genome research

authors： Heidel AJ,Lawal HM,Felder M,Schilde C,Helps NR,Tunggal B,Rivero F,John U,Schleicher M,Eichinger L,Platzer M,Noegel AA,Schaap P,Glöckner G

更新日期：2011-11-01 00:00:00

abstract：:Homeotic (Hox) genes are usually clustered and arranged in the same order as they are expressed along the anteroposterior body axis of metazoans. The mechanistic explanation for this colinearity has been elusive, and it may well be that a single and universal cause does not exist. The Hox-gene complex (HOM-C) has been...

journal_title：Genome research

authors： Negre B,Casillas S,Suzanne M,Sánchez-Herrero E,Akam M,Nefedov M,Barbadilla A,de Jong P,Ruiz A

更新日期：2005-05-01 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