Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q telomeres.

abstract：:Giardia duodenalis is the best-characterized example of the most ancient eukaryotes, which are primitively amitochondrial and anaerobic. The surface of Giardia is coated with cysteine-rich proteins. One family of these proteins, CRP136, varies among isolates and upon environmental stress. A repeat region within the CR...

journal_title：Genome research

authors： Upcroft P,Chen N,Upcroft JA

更新日期：1997-01-01 00:00:00

abstract：:Large-scale genetic interaction (GI) screens in yeast have been invaluable for our understanding of molecular systems biology and for characterizing novel gene function. Owing in part to the high costs and long experiment times required, a preponderance of GI data has been generated in a single environmental condition...

journal_title：Genome research

authors： Jaffe M,Dziulko A,Smith JD,St Onge RP,Levy SF,Sherlock G

更新日期：2019-04-01 00:00:00

abstract：:We describe a new method, Tag-seq, which employs ultra high-throughput sequencing of 21 base pair cDNA tags for sensitive and cost-effective gene expression profiling. We compared Tag-seq data to LongSAGE data and observed improved representation of several classes of rare transcripts, including transcription factors,...

journal_title：Genome research

authors： Morrissy AS,Morin RD,Delaney A,Zeng T,McDonald H,Jones S,Zhao Y,Hirst M,Marra MA

更新日期：2009-10-01 00:00:00

abstract：:Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For t...

journal_title：Genome research

authors： Jaffe JD,Stange-Thomann N,Smith C,DeCaprio D,Fisher S,Butler J,Calvo S,Elkins T,FitzGerald MG,Hafez N,Kodira CD,Major J,Wang S,Wilkinson J,Nicol R,Nusbaum C,Birren B,Berg HC,Church GM

更新日期：2004-08-01 00:00:00

abstract：:Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functi...

journal_title：Genome research

authors： Yu Y,Zhang C,Zhou G,Wu S,Qu X,Wei H,Xing G,Dong C,Zhai Y,Wan J,Ouyang S,Li L,Zhang S,Zhou K,Zhang Y,Wu C,He F

更新日期：2001-08-01 00:00:00

abstract：:A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. ...

journal_title：Genome research

authors： Goldstein B,Agranat-Tamir L,Light D,Ben-Naim Zgayer O,Fishman A,Lamm AT

更新日期：2017-03-01 00:00:00

abstract：:The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are establish...

journal_title：Genome research

authors： Hanna CW,Peñaherrera MS,Saadeh H,Andrews S,McFadden DE,Kelsey G,Robinson WP

更新日期：2016-06-01 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：:When transcription is to the right of the promoter, the "top," mRNA-synonymous strand of DNA tends to be purine-rich. When transcription is to the left of the promoter, the top, mRNA-template strand tends to be pyrimidine-rich. This transcription-direction rule suggests that there has been an evolutionary selection pr...

journal_title：Genome research

authors： Lao PJ,Forsdyke DR

更新日期：2000-02-01 00:00:00

abstract：:Most new genes arise by duplication of existing gene structures, after which relaxed selection on the new copy frequently leads to mutational inactivation of the duplicate; only rarely will a new gene with modified function emerge. Here we describe a unique mechanism of gene creation, whereby new combinations of funct...

journal_title：Genome research

authors： Babushok DV,Ohshima K,Ostertag EM,Chen X,Wang Y,Mandal PK,Okada N,Abrams CS,Kazazian HH Jr

更新日期：2007-08-01 00:00:00

abstract：:CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environ...

journal_title：Genome research

authors： Wang H,Maurano MT,Qu H,Varley KE,Gertz J,Pauli F,Lee K,Canfield T,Weaver M,Sandstrom R,Thurman RE,Kaul R,Myers RM,Stamatoyannopoulos JA

更新日期：2012-09-01 00:00:00

abstract：:MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species tha...

journal_title：Genome research

authors： Meunier J,Lemoine F,Soumillon M,Liechti A,Weier M,Guschanski K,Hu H,Khaitovich P,Kaessmann H

更新日期：2013-01-01 00:00:00

abstract：:Advances in high-throughput technologies, such as ChIP-chip, and the completion of human and mouse genomic sequences now allow analysis of the mechanisms of gene regulation on a systems level. In this study, we have developed a computational genomics approach (termed ChIPModules), which begins with experimentally dete...

journal_title：Genome research

authors： Jin VX,Rabinovich A,Squazzo SL,Green R,Farnham PJ

更新日期：2006-12-01 00:00:00

abstract：:We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying various publicly available expression data sets we conclude that enrichment of clusters for biological function is, in g...

journal_title：Genome research

authors： Gibbons FD,Roth FP

更新日期：2002-10-01 00:00:00

abstract：:The human Y chromosome, because it is enriched in repetitive DNA, has been very intractable to genetic and molecular analyses. There is no previous evidence for developmental stage- and testis-specific transcription from the male-specific region of the Y (MSY). Here, we present evidence for the first time for a develo...

journal_title：Genome research

authors： Jehan Z,Vallinayagam S,Tiwari S,Pradhan S,Singh L,Suresh A,Reddy HM,Ahuja YR,Jesudasan RA

更新日期：2007-04-01 00:00:00

abstract：:The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we...

journal_title：Genome research

authors： Lee IY,Westaway D,Smit AF,Wang K,Seto J,Chen L,Acharya C,Ankener M,Baskin D,Cooper C,Yao H,Prusiner SB,Hood LE

更新日期：1998-10-01 00:00:00

abstract：:The primate-specific multisequence family chAB4 is represented with approximately 40 copies within the haploid human genome. Former analyis revealed that unusually long repetition units ( > 35 kb) are distributed to at least eight different chromosomal loci. Remarkably varying copy-numbers within the genomes of closel...

journal_title：Genome research

authors： Wöhr G,Fink T,Assum G

更新日期：1996-04-01 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：:Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CAR...

journal_title：Genome research

authors： Mondal T,Rasmussen M,Pandey GK,Isaksson A,Kanduri C

更新日期：2010-07-01 00:00:00

abstract：:While copy number variation (CNV) is an active area of research, de novo mutation rates within human populations are not well characterized. By focusing on large (>100 kbp) events, we estimate the rate of de novo CNV formation in humans by analyzing 4394 transmissions from human pedigrees with and without neurocogniti...

journal_title：Genome research

authors： Itsara A,Wu H,Smith JD,Nickerson DA,Romieu I,London SJ,Eichler EE

更新日期：2010-11-01 00:00:00

abstract：:Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance suggests that their genes may have been subject to adaptive evolution. We have estimated the consequences of selection on ro...

journal_title：Genome research

authors： Emes RD,Beatson SA,Ponting CP,Goodstadt L

更新日期：2004-04-01 00:00:00

abstract：:We have identified previously a putative tumor suppressor gene (TSG) locus at human chromosome (hchr) 7q31 showing that it is altered in a variety of human epithelial tumors. To determine whether this TSG is conserved in mice, we studied loss of heterozygosity (LOH) in chemically induced mouse liver adenomas. The LOH ...

journal_title：Genome research

authors： Zenklusen JC,Rodriguez LV,LaCava M,Wang Z,Goldstein LS,Conti CJ

更新日期：1996-11-01 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：: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：:Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functi...

journal_title：Genome research

authors： Taher L,McGaughey DM,Maragh S,Aneas I,Bessling SL,Miller W,Nobrega MA,McCallion AS,Ovcharenko I

更新日期：2011-07-01 00:00:00

abstract：:We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization...

journal_title：Genome research

authors： Wu ZJ,Meyer CA,Choudhury S,Shipitsin M,Maruyama R,Bessarabova M,Nikolskaya T,Sukumar S,Schwartzman A,Liu JS,Polyak K,Liu XS

更新日期：2010-12-01 00:00:00

abstract：:A time course experiment is a widely used design in the study of cellular processes such as differentiation or response to stimuli. In this paper, we propose time course regulatory analysis (TimeReg) as a method for the analysis of gene regulatory networks based on paired gene expression and chromatin accessibility da...

journal_title：Genome research

authors： Duren Z,Chen X,Xin J,Wang Y,Wong WH

更新日期：2020-04-01 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：: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：: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