Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.

abstract：:Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of po...

journal_title：Genome research

authors： Wang Y,Lu J,Yu J,Gibbs RA,Yu F

更新日期：2013-05-01 00:00:00

abstract：:WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Ea...

journal_title：Genome research

authors： Crooks GE,Hon G,Chandonia JM,Brenner SE

更新日期：2004-06-01 00:00:00

abstract：:Up-frameshift protein 1 (UPF1) is an ATP-dependent RNA helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3' untranslated region (UTR) of target mRNAs via as-yet-unknown sequ...

journal_title：Genome research

authors： Imamachi N,Salam KA,Suzuki Y,Akimitsu N

更新日期：2017-03-01 00:00:00

abstract：:We have developed a new tool to visualize expression data on metabolic pathways and to evaluate which metabolic pathways are most affected by transcriptional changes in whole-genome expression experiments. Using the Fisher Exact Test, the method scores biochemical pathways according to the probability that as many or ...

journal_title：Genome research

authors： Grosu P,Townsend JP,Hartl DL,Cavalieri D

更新日期：2002-07-01 00:00:00

abstract：:We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...

journal_title：Genome research

authors： Edwards YH,Putt W,Lekoape KM,Stott D,Fox M,Hopkinson DA,Sowden J

更新日期：1996-03-01 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：:We report here a new mechanism for allelic discrimination--allele-specific Holliday Junction formation. The Holliday Junction (HJ) is a unique DNA structure that can be formed in a sequence-nonspecific manner by routine PCR. To cause the PCR-based HJ formation to occur in an allele-specific manner, the PCR primers are...

journal_title：Genome research

authors： Yang Q,Lishanski A,Yang W,Hatcher S,Seet H,Gregg JP

更新日期：2003-07-01 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：:Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotation...

journal_title：Genome research

authors： Lunardon A,Johnson NR,Hagerott E,Phifer T,Polydore S,Coruh C,Axtell MJ

更新日期：2020-03-01 00:00:00

abstract：:Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is org...

journal_title：Genome research

authors： Monk D,Wagschal A,Arnaud P,Müller PS,Parker-Katiraee L,Bourc'his D,Scherer SW,Feil R,Stanier P,Moore GE

更新日期：2008-08-01 00:00:00

abstract：:CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in hu...

journal_title：Genome research

authors： Smallwood A,Hon GC,Jin F,Henry RE,Espinosa JM,Ren B

更新日期：2012-08-01 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：:We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biologic...

journal_title：Genome research

authors： Castillo-Davis CI,Kondrashov FA,Hartl DL,Kulathinal RJ

更新日期：2004-05-01 00:00:00

abstract：:Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypot...

journal_title：Genome research

authors： Kelkar YD,Eckert KA,Chiaromonte F,Makova KD

更新日期：2011-12-01 00:00:00

abstract：:Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...

journal_title：Genome research

authors： Feber A,Wilson GA,Zhang L,Presneau N,Idowu B,Down TA,Rakyan VK,Noon LA,Lloyd AC,Stupka E,Schiza V,Teschendorff AE,Schroth GP,Flanagan A,Beck S

更新日期：2011-04-01 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：:Diversity in the antigen-binding receptors of the immune system has long been a primary interest of biologists. Recently it has been suggested that polymorphism in regulatory (noncoding) gene segments is of substantial importance as well. Here, we survey the level of variation in MHC class II gene promoters in man and...

journal_title：Genome research

authors： Cowell LG,Kepler TB,Janitz M,Lauster R,Mitchison NA

更新日期：1998-02-01 00:00:00

abstract：:Here, we report that CRISPR guide RNAs (gRNAs) with a 5'-triphosphate group (5'-ppp gRNAs) produced via in vitro transcription trigger RNA-sensing innate immune responses in human and murine cells, leading to cytotoxicity. 5'-ppp gRNAs in the cytosol are recognized by DDX58, which in turn activates type I interferon r...

journal_title：Genome research

authors： Kim S,Koo T,Jee HG,Cho HY,Lee G,Lim DG,Shin HS,Kim JS

更新日期：2018-02-22 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：:A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perfor...

journal_title：Genome research

authors： Schibler L,Vaiman D,Oustry A,Giraud-Delville C,Cribiu EP

更新日期：1998-09-01 00:00:00

abstract：:The functional classification of genes on a genome-wide scale is now in its infancy, and we make a first attempt to assess existing methods and identify sources of error. To this end, we compared two independent efforts for associating proteins with functions, one implemented by FlyBase and the other by PANTHER at Cel...

journal_title：Genome research

authors： Mi H,Vandergriff J,Campbell M,Narechania A,Majoros W,Lewis S,Thomas PD,Ashburner M

更新日期：2003-09-01 00:00:00

abstract：:Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed...

journal_title：Genome research

authors： Yatsuki H,Joh K,Higashimoto K,Soejima H,Arai Y,Wang Y,Hatada I,Obata Y,Morisaki H,Zhang Z,Nakagawachi T,Satoh Y,Mukai T

更新日期：2002-12-01 00:00:00

abstract：:How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectiv...

journal_title：Genome research

authors： Arimizu Y,Kirino Y,Sato MP,Uno K,Sato T,Gotoh Y,Auvray F,Brugere H,Oswald E,Mainil JG,Anklam KS,Döpfer D,Yoshino S,Ooka T,Tanizawa Y,Nakamura Y,Iguchi A,Morita-Ishihara T,Ohnishi M,Akashi K,Hayashi T,Ogura Y

更新日期：2019-09-01 00:00:00

abstract：:Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey...

journal_title：Genome research

authors： Wilder SP,Bihoreau MT,Argoud K,Watanabe TK,Lathrop M,Gauguier D

更新日期：2004-04-01 00:00:00

abstract：:A large database of copy number profiles from cancer genomes can facilitate the identification of recurrent chromosomal alterations that often contain key cancer-related genes. It can also be used to explore low-prevalence genomic events such as chromothripsis. In this study, we report an analysis of 8227 human cancer...

journal_title：Genome research

authors： Kim TM,Xi R,Luquette LJ,Park RW,Johnson MD,Park PJ

更新日期：2013-02-01 00:00:00

abstract：:Although much is known about genetic variation in human and African great ape (chimpanzee, bonobo, and gorilla) genomes, substantially less is known about variation in gene-expression profiles within and among these species. This information is necessary for defining transcriptional regulatory networks that contribute...

journal_title：Genome research

authors： Karaman MW,Houck ML,Chemnick LG,Nagpal S,Chawannakul D,Sudano D,Pike BL,Ho VV,Ryder OA,Hacia JG

更新日期：2003-07-01 00:00:00

abstract：:Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. Gr...

journal_title：Genome research

authors： Zhou Z,Alikhan NF,Sergeant MJ,Luhmann N,Vaz C,Francisco AP,Carriço JA,Achtman M

更新日期：2018-09-01 00:00:00

abstract：:Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequen...

journal_title：Genome research

authors： Battle A,Mostafavi S,Zhu X,Potash JB,Weissman MM,McCormick C,Haudenschild CD,Beckman KB,Shi J,Mei R,Urban AE,Montgomery SB,Levinson DF,Koller D

更新日期：2014-01-01 00:00:00

abstract：:A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We desc...

journal_title：Genome research

authors： van Opijnen T,Camilli A

更新日期：2012-12-01 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