Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II.

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：:The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...

journal_title：Genome research

authors： Lazar J,Moreno C,Jacob HJ,Kwitek AE

更新日期：2005-12-01 00:00:00

abstract：:Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the p...

journal_title：Genome research

authors： Blanchette M,Tompa M

更新日期：2002-05-01 00:00:00

abstract：:It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood ...

journal_title：Genome research

authors： Liu X,Fu YX,Maxwell TJ,Boerwinkle E

更新日期：2010-01-01 00:00:00

abstract：:The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of in...

journal_title：Genome research

authors： Lin B,Wang Z,Vora GJ,Thornton JA,Schnur JM,Thach DC,Blaney KM,Ligler AG,Malanoski AP,Santiago J,Walter EA,Agan BK,Metzgar D,Seto D,Daum LT,Kruzelock R,Rowley RK,Hanson EH,Tibbetts C,Stenger DA

更新日期：2006-04-01 00:00:00

abstract：:Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of...

journal_title：Genome research

authors： Robbins CM,Tembe WA,Baker A,Sinari S,Moses TY,Beckstrom-Sternberg S,Beckstrom-Sternberg J,Barrett M,Long J,Chinnaiyan A,Lowey J,Suh E,Pearson JV,Craig DW,Agus DB,Pienta KJ,Carpten JD

更新日期：2011-01-01 00:00:00

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：:Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these hu...

journal_title：Genome research

authors： Peyrégne S,Boyle MJ,Dannemann M,Prüfer K

更新日期：2017-09-01 00:00:00

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：:The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonr...

journal_title：Genome research

authors： Bi X,Cheng YJ,Hu B,Ma X,Wu R,Wang JW,Liu C

更新日期：2017-07-01 00:00:00

abstract：:Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Pyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all fou...

journal_title：Genome research

authors： Makarova KS,Aravind L,Galperin MY,Grishin NV,Tatusov RL,Wolf YI,Koonin EV

更新日期：1999-07-01 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：:A new algorithm, WABA, was developed for doing large-scale alignments between genomic DNA of different species. WABA was used to align 8 million bases of Caenorhabditis briggsae genomic DNA against the entire 97-million-base Caenorhabditis elegans genome. The alignment, including C. briggsae homologs of 154 geneticall...

journal_title：Genome research

authors： Kent WJ,Zahler AM

更新日期：2000-08-01 00:00:00

abstract：:Isochromosome 17q, or i(17q), is one of the most frequent nonrandom changes occurring in human neoplasia. Most of the i(17q) breakpoints cluster within a approximately 240-kb interval located in the Smith-Magenis syndrome common deletion region in 17p11.2. The breakpoint cluster region is characterized by a complex ar...

journal_title：Genome research

authors： Carvalho CM,Lupski JR

更新日期：2008-11-01 00:00:00

abstract：:Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities...

journal_title：Genome research

authors： Robinson MD,Strbenac D,Stirzaker C,Statham AL,Song J,Speed TP,Clark SJ

更新日期：2012-12-01 00:00:00

abstract：:We assessed the content, structure, and distribution of segmental duplications (> or =90% sequence identity, > or =5 kb length) within the published version of the Rattus norvegicus genome assembly (v.3.1). The overall fraction of duplicated sequence within the rat assembly (2.92%) is greater than that of the mouse (1...

journal_title：Genome research

authors： Tuzun E,Bailey JA,Eichler EE

更新日期：2004-04-01 00:00:00

abstract：:It is critical to avoid delays in detecting strain manipulations, such as the addition/deletion of a gene or modification of genes for increased virulence or antibiotic resistance, using genome analysis during an epidemic outbreak or a bioterrorist attack. Our objective was to evaluate the efficiency of genome analysi...

journal_title：Genome research

authors： La Scola B,Elkarkouri K,Li W,Wahab T,Fournous G,Rolain JM,Biswas S,Drancourt M,Robert C,Audic S,Löfdahl S,Raoult D

更新日期：2008-05-01 00:00:00

abstract：:Dual channel imaging and warping of two-dimensional (2D) protein gels were used to visualize global changes of the gene expression patterns in growing Bacillus subtilis cells during entry into the stationary phase as triggered by glucose exhaustion. The 2D gels only depict single moments during the cells' growth cycle...

journal_title：Genome research

authors： Bernhardt J,Weibezahn J,Scharf C,Hecker M

更新日期：2003-02-01 00:00:00

abstract：:Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...

journal_title：Genome research

authors： Grishkevich V,Hashimshony T,Yanai I

更新日期：2011-05-01 00:00:00

abstract：:Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at least 14% of disease-causing mutations, thus implicating polymorphisms that affect splicing as likely candidates for dis...

journal_title：Genome research

authors： Goren A,Kim E,Amit M,Bochner R,Lev-Maor G,Ahituv N,Ast G

更新日期：2008-02-01 00:00:00

abstract：:The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. Here, we present...

journal_title：Genome research

authors： Mudge JM,Jungreis I,Hunt T,Gonzalez JM,Wright JC,Kay M,Davidson C,Fitzgerald S,Seal R,Tweedie S,He L,Waterhouse RM,Li Y,Bruford E,Choudhary JS,Frankish A,Kellis M

更新日期：2019-12-01 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：:Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward thi...

journal_title：Genome research

authors： Tranchevent LC,Aubé F,Dulaurier L,Benoit-Pilven C,Rey A,Poret A,Chautard E,Mortada H,Desmet FO,Chakrama FZ,Moreno-Garcia MA,Goillot E,Janczarski S,Mortreux F,Bourgeois CF,Auboeuf D

更新日期：2017-06-01 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：:Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor bindi...

journal_title：Genome research

authors： Cusack M,King HW,Spingardi P,Kessler BM,Klose RJ,Kriaucionis S

更新日期：2020-10-01 00:00:00

abstract：:Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which causes Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement in OIS of chromatin reor...

journal_title：Genome research

authors： Lenain C,de Graaf CA,Pagie L,Visser NL,de Haas M,de Vries SS,Peric-Hupkes D,van Steensel B,Peeper DS

更新日期：2017-10-01 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：:Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The 17q24.3 locus harbors the single nucleotide polymorphism (SNP) rs1859962 that is statistically associated with prostate cancer (PCa). It defines a 130-kb linkage disequilibrium (LD) block that lies in an ∼2-Mb gene d...

journal_title：Genome research

authors： Zhang X,Cowper-Sal lari R,Bailey SD,Moore JH,Lupien M

更新日期：2012-08-01 00:00:00

abstract：:Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model...

journal_title：Genome research

authors： Storlazzi CT,Lonoce A,Guastadisegni MC,Trombetta D,D'Addabbo P,Daniele G,L'Abbate A,Macchia G,Surace C,Kok K,Ullmann R,Purgato S,Palumbo O,Carella M,Ambros PF,Rocchi M

更新日期：2010-09-01 00:00:00

abstract：:We report the development of a simplified cap analysis of gene expression (CAGE) protocol adapted for single-molecule sequencers that avoids second strand synthesis, ligation, digestion, and PCR. HeliScopeCAGE directly sequences the 3' end of cap trapped first-strand cDNAs. As with previous versions of CAGE, we better...

journal_title：Genome research

authors： Kanamori-Katayama M,Itoh M,Kawaji H,Lassmann T,Katayama S,Kojima M,Bertin N,Kaiho A,Ninomiya N,Daub CO,Carninci P,Forrest AR,Hayashizaki Y

更新日期：2011-07-01 00:00:00