Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining.

abstract：:Translocations are a common class of chromosomal aberrations and can cause disease by physically disrupting genes or altering their regulatory environment. Some translocations, apparently balanced at the microscopic level, include deletions, duplications, insertions, or inversions at the molecular level. Traditionally...

journal_title：Genome research

authors： Sobreira NL,Gnanakkan V,Walsh M,Marosy B,Wohler E,Thomas G,Hoover-Fong JE,Hamosh A,Wheelan SJ,Valle D

更新日期：2011-10-01 00:00:00

abstract：:Despite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently d...

journal_title：Genome research

authors： Dougherty ML,Underwood JG,Nelson BJ,Tseng E,Munson KM,Penn O,Nowakowski TJ,Pollen AA,Eichler EE

更新日期：2018-10-01 00:00:00

abstract：:Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires' disease. Just five sequence types (ST), from more than 2000 currently described, cause nearly half of disease cases in northwest Europe. Here, we report the sequence and analyses of 364 L. pneumophila genomes, including 337 fro...

journal_title：Genome research

authors： David S,Rusniok C,Mentasti M,Gomez-Valero L,Harris SR,Lechat P,Lees J,Ginevra C,Glaser P,Ma L,Bouchier C,Underwood A,Jarraud S,Harrison TG,Parkhill J,Buchrieser C

更新日期：2016-11-01 00:00:00

abstract：:The human genome is estimated to contain 23,000 to 33,000 retropseudogenes. To study the properties of genes giving rise to these retroelements, we compared the structure and expression of genes with or without known retropseudogenes. Four main features have emerged from the analysis of 181 genes associated to retrops...

journal_title：Genome research

authors： Gonçalves I,Duret L,Mouchiroud D

更新日期：2000-05-01 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：:Forty-three yeast artificial chromosomes (YACs) from the X chromosome have been overlapped across the 4-Mb Xq21.3 region, which is homologous to a segment in Yp11.1. The region is formatted to 60-kb resolution with 57 STSs and is merged at its edges with contigs specific for X. This allows a direct comparison of marke...

journal_title：Genome research

authors： Mumm S,Molini B,Terrell J,Srivastava A,Schlessinger D

更新日期：1997-04-01 00:00:00

abstract：:The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a ch...

journal_title：Genome research

authors： Pettersson ME,Rochus CM,Han F,Chen J,Hill J,Wallerman O,Fan G,Hong X,Xu Q,Zhang H,Liu S,Liu X,Haggerty L,Hunt T,Martin FJ,Flicek P,Bunikis I,Folkvord A,Andersson L

更新日期：2019-11-01 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：:The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of m...

journal_title：Genome research

authors： Yandava CN,Gastier JM,Pulido JC,Brody T,Sheffield V,Murray J,Buetow K,Duyk GM

更新日期：1997-07-01 00:00:00

abstract：:PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree ...

journal_title：Genome research

authors： Schwartz S,Zhang Z,Frazer KA,Smit A,Riemer C,Bouck J,Gibbs R,Hardison R,Miller W

更新日期：2000-04-01 00:00:00

abstract：:We used a combination of cDNA selection, exon amplification, and computational prediction from genomic sequence to isolate transcribed sequences from genomic DNA surrounding the familial Mediterranean fever (FMF) locus. Eighty-seven kb of genomic DNA around D16S3370, a marker showing a high degree of linkage disequili...

journal_title：Genome research

authors： Centola M,Chen X,Sood R,Deng Z,Aksentijevich I,Blake T,Ricke DO,Chen X,Wood G,Zaks N,Richards N,Krizman D,Mansfield E,Apostolou S,Liu J,Shafran N,Vedula A,Hamon M,Cercek A,Kahan T,Gumucio D,Callen DF,Richards

更新日期：1998-11-01 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：:We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying various publicly available expression data sets we conclude that enrichment of clusters for biological function is, in g...

journal_title：Genome research

authors： Gibbons FD,Roth FP

更新日期：2002-10-01 00:00:00

abstract：:GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored ...

journal_title：Genome research

authors： Parra G,Blanco E,Guigó R

更新日期：2000-04-01 00:00:00

abstract：:Recent advances in genome research have accelerated the process of locating candidate genes and the variable sites within them and have simplified the task of genotype measurement. The development of statistical and computational strategies to utilize information on hundreds -- soon thousands -- of variable loci to in...

journal_title：Genome research

authors： Nelson MR,Kardia SL,Ferrell RE,Sing CF

更新日期：2001-03-01 00:00:00

abstract：:Large copy number variants (CNVs) have been recently found as structural polymorphisms of the human genome of still unknown biological significance. CNVs are significantly enriched in regions with segmental duplications or low-copy repeats (LCRs). Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused ...

journal_title：Genome research

authors： Cuscó I,Corominas R,Bayés M,Flores R,Rivera-Brugués N,Campuzano V,Pérez-Jurado LA

更新日期：2008-05-01 00:00:00

abstract：:Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. B...

journal_title：Genome research

authors： Kent WJ

更新日期：2002-04-01 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：:A contiguous high-resolution map of 44 loci from a 35-Mb portion of the distal region of the long arm of human chromosome 5, q21-q35, was produced using radiation hybrid (RH) mapping in conjunction with a natural deletion mapping panel. The map includes 30 genes, four sequence-tagged site (STS) loci, and 10 DNA marker...

journal_title：Genome research

authors： Warrington JA,Wasmuth JJ

更新日期：1996-07-01 00:00:00

abstract：:Dystroglycan is a laminin binding protein, which provides a structural link between the subsarcolemmal cytoskeleton and the extracellular matrix. It is also involved in the organization of basement membranes. So far the genomic organization of the dystroglycan gene DAG1 has not been completely investigated. Here we re...

journal_title：Genome research

authors： Leeb T,Neumann S,Deppe A,Breen M,Brenig B

更新日期：2000-03-01 00:00:00

abstract：:Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are...

journal_title：Genome research

authors： Norman PJ,Abi-Rached L,Gendzekhadze K,Hammond JA,Moesta AK,Sharma D,Graef T,McQueen KL,Guethlein LA,Carrington CV,Chandanayingyong D,Chang YH,Crespí C,Saruhan-Direskeneli G,Hameed K,Kamkamidze G,Koram KA,Layrisse Z,Ma

更新日期：2009-05-01 00:00:00

abstract：:Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochro...

journal_title：Genome research

authors： Brönner C,Salvi L,Zocco M,Ugolini I,Halic M

更新日期：2017-07-01 00:00:00

abstract：:An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under wha...

journal_title：Genome research

authors： Dupuy D,Li QR,Deplancke B,Boxem M,Hao T,Lamesch P,Sequerra R,Bosak S,Doucette-Stamm L,Hope IA,Hill DE,Walhout AJ,Vidal M

更新日期：2004-10-01 00:00:00

abstract：:In this study, we propose a system-theoretic approach to the analysis and quantitative modeling of the TNFalpha-mediated NF-kappaB-signaling pathway. Tumor necrosis factor alpha (TNFalpha) is a potent proinflammatory cytokine that plays an important role in immunity and inflammation, in the control of cell proliferati...

journal_title：Genome research

authors： Cho KH,Shin SY,Lee HW,Wolkenhauer O

更新日期：2003-11-01 00:00:00

abstract：:We report the construction of a dense linkage map of the rat genome integrating 767 simple sequence length polymorphism markers, combined over three crosses with high rates of polymorphism. F2 populations from WKY x S (n = 159), BN x S (n = 91), and BN x GK (n = 139) were selected and genotyped for combinations of mic...

journal_title：Genome research

authors： Bihoreau MT,Gauguier D,Kato N,Hyne G,Lindpaintner K,Rapp JP,James MR,Lathrop GM

更新日期：1997-05-01 00:00:00

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：:In mammals, genetic recombination during meiosis is limited to a set of 1- to 2-kb regions termed hotspots. Their locations are predominantly determined by the zinc finger protein PRDM9, which binds to DNA in hotspots and subsequently uses its SET domain to locally trimethylate histone H3 at lysine 4 (H3K4me3). This s...

journal_title：Genome research

authors： Baker CL,Walker M,Kajita S,Petkov PM,Paigen K

更新日期：2014-05-01 00:00:00

abstract：:We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap bet...

journal_title：Genome research

authors： Baens M,Peeters P,Guo C,Aerssens J,Marynen P

更新日期：1996-05-01 00:00:00

abstract：:Recent accumulation of microbial genome data has demonstrated that lateral gene transfers constitute an important and universal evolutionary process in prokaryotes, while those in multicellular eukaryotes are still regarded as unusual, except for endosymbiotic gene transfers from mitochondria and plastids. Here we tho...

journal_title：Genome research

authors： Nikoh N,Tanaka K,Shibata F,Kondo N,Hizume M,Shimada M,Fukatsu T

更新日期：2008-02-01 00:00:00

abstract：:CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occ...

journal_title：Genome research

authors： Beagan JA,Duong MT,Titus KR,Zhou L,Cao Z,Ma J,Lachanski CV,Gillis DR,Phillips-Cremins JE

更新日期：2017-07-01 00:00:00