Genome-reconstruction for eukaryotes from complex natural microbial communities.

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

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：:Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted m...

journal_title：Genome research

authors： Wang L,Fan J,Francis JM,Georghiou G,Hergert S,Li S,Gambe R,Zhou CW,Yang C,Xiao S,Cin PD,Bowden M,Kotliar D,Shukla SA,Brown JR,Neuberg D,Alessi DR,Zhang CZ,Kharchenko PV,Livak KJ,Wu CJ

更新日期：2017-08-01 00:00:00

abstract：:High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classi...

journal_title：Genome research

authors： Corvelo A,Clarke WE,Robine N,Zody MC

更新日期：2018-05-01 00:00:00

abstract：:Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of...

journal_title：Genome research

authors： Lay FD,Triche TJ Jr,Tsai YC,Su SF,Martin SE,Daneshmand S,Skinner EC,Liang G,Chihara Y,Jones PA

更新日期：2014-04-01 00:00:00

abstract：:Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the tra...

journal_title：Genome research

authors： Hartl D,Krebs AR,Grand RS,Baubec T,Isbel L,Wirbelauer C,Burger L,Schübeler D

更新日期：2019-04-01 00:00:00

abstract：:To promote the clinical and epidemiological studies that improve our understanding of human genetic susceptibility to environmental exposure, the Environmental Genome Project (EGP) has scanned 213 environmental response genes involved in DNA repair, cell cycle regulation, apoptosis, and metabolism for single nucleotid...

journal_title：Genome research

authors： Livingston RJ,von Niederhausern A,Jegga AG,Crawford DC,Carlson CS,Rieder MJ,Gowrisankar S,Aronow BJ,Weiss RB,Nickerson DA

更新日期：2004-10-01 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：:Histone modifications are now well-established mediators of transcriptional programs that distinguish cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive gene expression changes has been little studied on a genome-wide scale. Vascular endothelial growth facto...

journal_title：Genome research

authors： Zhang B,Day DS,Ho JW,Song L,Cao J,Christodoulou D,Seidman JG,Crawford GE,Park PJ,Pu WT

更新日期：2013-06-01 00:00:00

abstract：:In an attempt to understand the origin of CpG islands (CGIs) in mammalian genomes, we have studied their location and structure according to the expression pattern of genes and to the G + C content of isochores in which they are embedded. We show that CGIs located over the transcription start site (named start CGIs) a...

journal_title：Genome research

authors： Ponger L,Duret L,Mouchiroud D

更新日期：2001-11-01 00:00:00

abstract：:We have developed a simplified method for multiplex PCR based on the use of chimeric primers. Each primer contains a 3' region complementary to sequence-specific recognition sites and a 5' region made up of an unrelated 20-nucleotide sequence. Identical reaction conditions, cycling times, and annealing temperatures ha...

journal_title：Genome research

authors： Shuber AP,Grondin VJ,Klinger KW

更新日期：1995-12-01 00:00:00

abstract：:We compared the genome of the nematode Caenorhabditis elegans to 13% of that of Caenorhabditis briggsae, identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio of translocations to inversions to transpositions being approximately 1:1:2. We estimate that t...

journal_title：Genome research

authors： Coghlan A,Wolfe KH

更新日期：2002-06-01 00:00:00

abstract：:By analyzing 1,780,295 5'-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by m...

journal_title：Genome research

authors： Kimura K,Wakamatsu A,Suzuki Y,Ota T,Nishikawa T,Yamashita R,Yamamoto J,Sekine M,Tsuritani K,Wakaguri H,Ishii S,Sugiyama T,Saito K,Isono Y,Irie R,Kushida N,Yoneyama T,Otsuka R,Kanda K,Yokoi T,Kondo H,Wagatsuma M

更新日期：2006-01-01 00:00:00

abstract：:Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of the relative importance of these two forces is the observation that both diversity within species and interspecies diver...

journal_title：Genome research

authors： Hellmann I,Prüfer K,Ji H,Zody MC,Pääbo S,Ptak SE

更新日期：2005-09-01 00:00:00

abstract：:Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data al...

journal_title：Genome research

authors： Zimin AV,Puiu D,Luo MC,Zhu T,Koren S,Marçais G,Yorke JA,Dvořák J,Salzberg SL

更新日期：2017-05-01 00:00:00

abstract：:DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of approximately 70-mer probes, and used these arrays to analyze gene expression i...

journal_title：Genome research

authors： Barczak A,Rodriguez MW,Hanspers K,Koth LL,Tai YC,Bolstad BM,Speed TP,Erle DJ

更新日期：2003-07-01 00:00:00

abstract：:An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human a...

journal_title：Genome research

authors： Lefébure T,Stanhope MJ

更新日期：2009-07-01 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：:Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using...

journal_title：Genome research

authors： Fungtammasan A,Ananda G,Hile SE,Su MS,Sun C,Harris R,Medvedev P,Eckert K,Makova KD

更新日期：2015-05-01 00:00:00

abstract：:Much of the available human genomic sequence data exist in a fragmentary draft state following the completion of the initial high-volume sequencing performed by the International Human Genome Sequencing Consortium (IHGSC) and Celera Genomics (CG). We compared six draft genome assemblies over a region of chromosome 4p ...

journal_title：Genome research

authors： Semple CA,Morris SW,Porteous DJ,Evans KL

更新日期：2002-03-01 00:00:00

abstract：:Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous pr...

journal_title：Genome research

authors： Zhang W,Qi W,Albert TJ,Motiwala AS,Alland D,Hyytia-Trees EK,Ribot EM,Fields PI,Whittam TS,Swaminathan B

更新日期：2006-06-01 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：:Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat S...

journal_title：Genome research

authors： Gymrek M,Golan D,Rosset S,Erlich Y

更新日期：2012-06-01 00:00:00

abstract：:The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of centromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere ...

journal_title：Genome research

authors： Contreras-Galindo R,Fischer S,Saha AK,Lundy JD,Cervantes PW,Mourad M,Wang C,Qian B,Dai M,Meng F,Chinnaiyan A,Omenn GS,Kaplan MH,Markovitz DM

更新日期：2017-12-01 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

abstract：:Large terminal fragments of human chromosomes 2p, 6p, 8q, 12q, and 18q were cloned using yeast artificial chromosomes (YACs). RecA-assisted restriction endonuclease (RARE) cleavage analysis of genomic DNA samples from II unrelated individuals using YAC-derived probes confirmed the telomeric localizations of the half-Y...

journal_title：Genome research

authors： Macina RA,Morii K,Hu XL,Negorev DG,Spais C,Ruthig LA,Riethman HC

更新日期：1995-10-01 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：: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：:There are numerous examples from the genomes of viruses, mitochondria, and chromosomes that adjacent genes can overlap, sharing at least one nucleotide. Overlaps have been hypothesized to be involved in genome size minimization and as a regulatory mechanism of gene expression. Here we show that overlapping genes are a...

journal_title：Genome research

authors： Johnson ZI,Chisholm SW

更新日期：2004-11-01 00:00:00

abstract：:Mutations in the human AIRE gene (hAIRE) result in the development of an autoimmune disease named APECED (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy; OMIM 240300). Previously, we have cloned hAIRE and shown that it codes for a putative transcription-associated factor. Here we report the cloning and...

journal_title：Genome research

authors： Blechschmidt K,Schweiger M,Wertz K,Poulson R,Christensen HM,Rosenthal A,Lehrach H,Yaspo ML

更新日期：1999-02-01 00:00:00