Gene regulation and speciation in house mice.

abstract：:Pollen, the male gametophyte of flowering plants, represents an ideal biological system to study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon hydration, the metabolically quiescent pollen rapidly switches to an active state, exhibiting extremely fast growth. This rapid switch req...

journal_title：Genome research

authors： Grobei MA,Qeli E,Brunner E,Rehrauer H,Zhang R,Roschitzki B,Basler K,Ahrens CH,Grossniklaus U

更新日期：2009-10-01 00:00:00

abstract：:Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have asymme...

journal_title：Genome research

authors： Ramachandran S,Zentner GE,Henikoff S

更新日期：2015-03-01 00:00:00

abstract：:The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...

journal_title：Genome research

authors： Xin B,Rohs R

更新日期：2018-01-11 00:00:00

abstract：:We report the validation of a new assay for typing single nucleotide polymorphisms (SNPs) that takes advantage of the 3'-to-5' exonuclease proofreading activity of many DNA polymerases. The assay uses one or more primers labeled on the 3' nucleotide base, and can be implemented in a variety of formats including a one-...

journal_title：Genome research

authors： Cahill P,Bakis M,Hurley J,Kamath V,Nielsen W,Weymouth D,Dupuis J,Doucette-Stamm L,Smith DR

更新日期：2003-05-01 00:00:00

abstract：:Whole-genome sequencing using massively parallel sequencing technologies enables accurate detection of somatic rearrangements in cancer. Pinpointing large numbers of rearrangement breakpoints to base-pair resolution allows analysis of rearrangement microhomology and genomic location for every sample. Here we analyze 9...

journal_title：Genome research

authors： Drier Y,Lawrence MS,Carter SL,Stewart C,Gabriel SB,Lander ES,Meyerson M,Beroukhim R,Getz G

更新日期：2013-02-01 00:00:00

abstract：:The model organism Streptomyces coelicolor represents a genus that produces a vast range of bioactive secondary metabolites. We describe a versatile procedure for systematic and comprehensive mutagenesis of the S. coelicolor genome. The high-throughput process relies on in vitro transposon mutagenesis of an ordered co...

journal_title：Genome research

authors： Bishop A,Fielding S,Dyson P,Herron P

更新日期：2004-05-01 00:00:00

abstract：:DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover <2% of the genome and cannot account...

journal_title：Genome research

authors： Kaplow IM,MacIsaac JL,Mah SM,McEwen LM,Kobor MS,Fraser HB

更新日期：2015-06-01 00:00:00

abstract：:Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional g...

journal_title：Genome research

authors： Kelkar YD,Tyekucheva S,Chiaromonte F,Makova KD

更新日期：2008-01-01 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：:Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously in...

journal_title：Genome research

authors： Hormozdiari F,Penn O,Borenstein E,Eichler EE

更新日期：2015-01-01 00:00:00

abstract：:The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis of 24,398 expressed sequence tags (ESTs) generated from 15 different adult and juvenile Fugu tissues, 74% of which match...

journal_title：Genome research

authors： Clark MS,Edwards YJ,Peterson D,Clifton SW,Thompson AJ,Sasaki M,Suzuki Y,Kikuchi K,Watabe S,Kawakami K,Sugano S,Elgar G,Johnson SL

更新日期：2003-12-01 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：:Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only several operons, primarily those that code for physically interacting proteins, are conserved in all or most of the bacterial and archaeal genomes. Nevertheless, even the limited conservation of operon organization that is obse...

journal_title：Genome research

authors： Wolf YI,Rogozin IB,Kondrashov AS,Koonin EV

更新日期：2001-03-01 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：:Annotation transfer is a principal process in genome annotation. It involves "transferring" structural and functional annotation to uncharacterized open reading frames (ORFs) in a newly completed genome from experimentally characterized proteins similar in sequence. To prevent errors in genome annotation, it is import...

journal_title：Genome research

authors： Hegyi H,Gerstein M

更新日期：2001-10-01 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：: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：:Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of inter...

journal_title：Genome research

authors： Schadt EE,Banerjee O,Fang G,Feng Z,Wong WH,Zhang X,Kislyuk A,Clark TA,Luong K,Keren-Paz A,Chess A,Kumar V,Chen-Plotkin A,Sondheimer N,Korlach J,Kasarskis A

更新日期：2013-01-01 00:00:00

abstract：:As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, an...

journal_title：Genome research

authors： Curwen V,Eyras E,Andrews TD,Clarke L,Mongin E,Searle SM,Clamp M

更新日期：2004-05-01 00:00:00

abstract：:The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we developed a method, termed "GeSNP," to mine the detailed hybridization patterns in oligonucleotide array expression data fo...

journal_title：Genome research

authors： Greenhall JA,Zapala MA,Cáceres M,Libiger O,Barlow C,Schork NJ,Lockhart DJ

更新日期：2007-08-01 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：: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：: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：:Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model t...

journal_title：Genome research

authors： Arnold P,Schöler A,Pachkov M,Balwierz PJ,Jørgensen H,Stadler MB,van Nimwegen E,Schübeler D

更新日期：2013-01-01 00:00:00

abstract：:Recent advances toward the characterization of Alzheimer's disease (AD) have permitted the identification of a dozen of genetic risk factors, although many more remain undiscovered. In parallel, works in the field of network biology have shown a strong link between protein connectivity and disease. In this manuscript,...

journal_title：Genome research

authors： Soler-López M,Zanzoni A,Lluís R,Stelzl U,Aloy P

更新日期：2011-03-01 00:00:00

abstract：:The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of metatherians. Here, we compare Monodelphis with Homo sequences from alignments of single nucleotides, genes, and whole chr...

journal_title：Genome research

authors： Goodstadt L,Heger A,Webber C,Ponting CP

更新日期：2007-07-01 00:00:00

abstract：:A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide...

journal_title：Genome research

authors： Xu Y,Hu B,Choi AJ,Gopalan B,Lee BH,Kalady MF,Church JM,Ting AH

更新日期：2012-02-01 00:00:00

abstract：:It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can exp...

journal_title：Genome research

authors： Blanchette M,Green ED,Miller W,Haussler D

更新日期：2004-12-01 00:00:00

abstract：:Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from evolutionary constraints. We systematically analyzed known human and Saccharomyces cerevisiae regulatory elements and disc...

journal_title：Genome research

authors： Liu Y,Liu XS,Wei L,Altman RB,Batzoglou S

更新日期：2004-03-01 00:00:00

abstract：:Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover rates and how these rates are integrated into cellular decisions. We decided to measure mRNA decay rates in two human ce...

journal_title：Genome research

authors： Yang E,van Nimwegen E,Zavolan M,Rajewsky N,Schroeder M,Magnasco M,Darnell JE Jr

更新日期：2003-08-01 00:00:00