A predictive model for regulatory sequences directing liver-specific transcription.

abstract：:Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...

journal_title：Genome research

authors： van Dijk D,Sharon E,Lotan-Pompan M,Weinberger A,Segal E,Carey LB

更新日期：2017-01-01 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：: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：:To understand disease mechanisms, a large-scale analysis of human-yeast genetic interactions was performed. Of 1305 human disease genes assayed, 20 genes exhibited strong toxicity in yeast. Human-yeast genetic interactions were identified by en masse transformation of the human disease genes into a pool of 4653 homozy...

journal_title：Genome research

authors： Jo M,Chung AY,Yachie N,Seo M,Jeon H,Nam Y,Seo Y,Kim E,Zhong Q,Vidal M,Park HC,Roth FP,Suk K

更新日期：2017-09-01 00:00:00

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：:Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes cont...

journal_title：Genome research

authors： Fuhrmann DR,Krzywinski MI,Chiu R,Saeedi P,Schein JE,Bosdet IE,Chinwalla A,Hillier LW,Waterston RH,McPherson JD,Jones SJ,Marra MA

更新日期：2003-05-01 00:00:00

abstract：:High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs with various lengths, and GC content covering a 2(20) concentration ra...

journal_title：Genome research

authors： Jiang L,Schlesinger F,Davis CA,Zhang Y,Li R,Salit M,Gingeras TR,Oliver B

更新日期：2011-09-01 00:00:00

abstract：:Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect overlap detection for contig assembly is assumed. Genome-specific and nonrandom effects are neglected. Order of magnitud...

journal_title：Genome research

authors： Wendl MC,Marra MA,Hillier LW,Chinwalla AT,Wilson RK,Waterston RH

更新日期：2001-02-01 00:00:00

abstract：:Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-sequencing (TL-seq), a technique combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast...

journal_title：Genome research

authors： Arribere JA,Gilbert WV

更新日期：2013-06-01 00:00:00

abstract：:We find that the degree of impairment of protein function by missense variants is predictable by comparative sequence analysis alone. The applicable range of impairment is not confined to binary predictions that distinguish normal from deleterious variants, but extends continuously from mild to severe effects. The acc...

journal_title：Genome research

authors： Stone EA,Sidow A

更新日期：2005-07-01 00:00:00

abstract：:The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrat...

journal_title：Genome research

authors： Baldarelli RM,Hill DP,Blake JA,Adachi J,Furuno M,Bradt D,Corbani LE,Cousins S,Frazer KS,Qi D,Yang L,Ramachandran S,Reed D,Zhu Y,Kasukawa T,Ringwald M,King BL,Maltais LJ,McKenzie LM,Schriml LM,Maglott D,Church DM

更新日期：2003-06-01 00:00:00

abstract：:Size sexual dimorphism occurs in almost all mammals. In Portuguese Water Dogs, much of the difference in skeletal size between females and males is due to the interaction between a Quantitative Trait Locus (QTL) on the X-chromosome and a QTL linked to Insulin-like Growth Factor 1 (IGF-1) on the CFA 15 autosome. In fem...

journal_title：Genome research

authors： Chase K,Carrier DR,Adler FR,Ostrander EA,Lark KG

更新日期：2005-12-01 00:00:00

abstract：:Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and...

journal_title：Genome research

authors： Schield DR,Card DC,Hales NR,Perry BW,Pasquesi GM,Blackmon H,Adams RH,Corbin AB,Smith CF,Ramesh B,Demuth JP,Betrán E,Tollis M,Meik JM,Mackessy SP,Castoe TA

更新日期：2019-04-01 00:00:00

abstract：:Analysis procedures are needed to extract useful information from the large amount of gene expression data that is becoming available. This work describes a set of analytical tools and their application to yeast cell cycle data. The components of our approach are (1) a similarity measure that reduces the number of fal...

journal_title：Genome research

authors： Heyer LJ,Kruglyak S,Yooseph S

更新日期：1999-11-01 00:00:00

abstract：:Notwithstanding their biological importance, Y chromosomes remain poorly known in most species. A major obstacle to their study is the identification of Y chromosome sequences; due to its high content of repetitive DNA, in most genome projects, the Y chromosome sequence is fragmented into a large number of small, unma...

journal_title：Genome research

authors： Carvalho AB,Clark AG

更新日期：2013-11-01 00:00:00

abstract：:The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that n...

journal_title：Genome research

authors： Fabbri M,Girnita L,Varani G,Calin GA

更新日期：2019-09-01 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：: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：:The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incred...

journal_title：Genome research

authors： Schatz MC

更新日期：2015-10-01 00:00:00

abstract：:We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal change...

journal_title：Genome research

authors： Jaffe DB,Butler J,Gnerre S,Mauceli E,Lindblad-Toh K,Mesirov JP,Zody MC,Lander ES

更新日期：2003-01-01 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：:Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosa...

journal_title：Genome research

authors： Naqvi S,Bellott DW,Lin KS,Page DC

更新日期：2018-04-01 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：:Large-scale sequencing of human and model organism genomes will have a profound impact on our ability to use sequence data base searching to predict the biochemical functions of sequences of interest. Despite the great value of more sequences in the data bases, a huge increase in data base size will also have adverse ...

journal_title：Genome research

authors： Smith RF

更新日期：1996-08-01 00:00:00

abstract：:Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace. The resulting ambiguity sequence is aligned to the genome, identifying one template sequence. A second template se...

journal_title：Genome research

authors： Tenney AE,Wu JQ,Langton L,Klueh P,Quatrano R,Brent MR

更新日期：2007-02-01 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：:Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chr...

journal_title：Genome research

authors： Kondo M,Hornung U,Nanda I,Imai S,Sasaki T,Shimizu A,Asakawa S,Hori H,Schmid M,Shimizu N,Schartl M

更新日期：2006-07-01 00:00:00

abstract：:Here we describe a high-throughput screen to isolate transcripts with spatially restricted patterns of expression in early embryos. Our approach utilizes robotic automation for rapid analysis of sequence-selected cDNAs in a whole-mount in situ hybridization assay. We determined the spatial distribution of a random col...

journal_title：Genome research

authors： Simin K,Scuderi A,Reamey J,Dunn D,Weiss R,Metherall JE,Letsou A

更新日期：2002-07-01 00:00:00

abstract：:Meiotic DNA double-stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. DSBs can be directly mapped using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Nevertheless, the genome-wide mapping of recombination hotspots in mammals is still ...

journal_title：Genome research

authors： Khil PP,Smagulova F,Brick KM,Camerini-Otero RD,Petukhova GV

更新日期：2012-05-01 00:00:00

abstract：:Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of...

journal_title：Genome research

authors： Visser M,Kayser M,Palstra RJ

更新日期：2012-03-01 00:00:00