Exo-proofreading, a versatile SNP scoring technology.

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：:Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly un...

journal_title：Genome research

authors： Roy-Engel AM,Salem AH,Oyeniran OO,Deininger L,Hedges DJ,Kilroy GE,Batzer MA,Deininger PL

更新日期：2002-09-01 00:00:00

abstract：:Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted...

journal_title：Genome research

authors： Court F,Tayama C,Romanelli V,Martin-Trujillo A,Iglesias-Platas I,Okamura K,Sugahara N,Simón C,Moore H,Harness JV,Keirstead H,Sanchez-Mut JV,Kaneki E,Lapunzina P,Soejima H,Wake N,Esteller M,Ogata T,Hata K,Nakabayashi

更新日期：2014-04-01 00:00:00

abstract：:Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora t...

journal_title：Genome research

authors： Corcoran P,Anderson JL,Jacobson DJ,Sun Y,Ni P,Lascoux M,Johannesson H

更新日期：2016-04-01 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：: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：:The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the ...

journal_title：Genome research

authors： Kvikstad EM,Makova KD

更新日期：2010-05-01 00:00:00

abstract：:Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We ident...

journal_title：Genome research

authors： Wang J,Zhuang J,Iyer S,Lin X,Whitfield TW,Greven MC,Pierce BG,Dong X,Kundaje A,Cheng Y,Rando OJ,Birney E,Myers RM,Noble WS,Snyder M,Weng Z

更新日期：2012-09-01 00:00:00

abstract：:A large number of cis-regulatory motifs involved in transcriptional control have been identified, but the regulatory context and biological processes in which many of them function are unknown. Here, we computationally identify the sets of human core promoters targeted by motifs, and systematically characterize their ...

journal_title：Genome research

authors： Sinha S,Adler AS,Field Y,Chang HY,Segal E

更新日期：2008-03-01 00:00:00

abstract：:Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessin...

journal_title：Genome research

authors： Yang T,Zhang F,Yardımcı GG,Song F,Hardison RC,Noble WS,Yue F,Li Q

更新日期：2017-11-01 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：: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：:Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Pyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all fou...

journal_title：Genome research

authors： Makarova KS,Aravind L,Galperin MY,Grishin NV,Tatusov RL,Wolf YI,Koonin EV

更新日期：1999-07-01 00:00:00

abstract：:RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and c...

journal_title：Genome research

authors： Cieslik M,Chugh R,Wu YM,Wu M,Brennan C,Lonigro R,Su F,Wang R,Siddiqui J,Mehra R,Cao X,Lucas D,Chinnaiyan AM,Robinson D

更新日期：2015-09-01 00:00:00

abstract：:The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes...

journal_title：Genome research

authors： Ganal MW,Czihal R,Hannappel U,Kloos DU,Polley A,Ling HQ

更新日期：1998-08-01 00:00:00

abstract：:The human genome is estimated to contain 23,000 to 33,000 retropseudogenes. To study the properties of genes giving rise to these retroelements, we compared the structure and expression of genes with or without known retropseudogenes. Four main features have emerged from the analysis of 181 genes associated to retrops...

journal_title：Genome research

authors： Gonçalves I,Duret L,Mouchiroud D

更新日期：2000-05-01 00:00:00

abstract：:Using both env and long terminal repeat (LTR) sequences, with maximal representation of genetic diversity within primate strains, we revise and expand the unique evolutionary history of human and simian T-cell leukemia/lymphotropic viruses (HTLV/STLV). Based on the robust application of three different phylogenetic al...

journal_title：Genome research

authors： Slattery JP,Franchini G,Gessain A

更新日期：1999-06-01 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：:RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolki...

journal_title：Genome research

authors： Derr A,Yang C,Zilionis R,Sergushichev A,Blodgett DM,Redick S,Bortell R,Luban J,Harlan DM,Kadener S,Greiner DL,Klein A,Artyomov MN,Garber M

更新日期：2016-10-01 00:00:00

abstract：:GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored ...

journal_title：Genome research

authors： Parra G,Blanco E,Guigó R

更新日期：2000-04-01 00:00:00

abstract：:Retroposed copies (RPCs) of genes are functional (intronless paralogs) or nonfunctional (processed pseudogenes) copies derived from mRNA through a process of retrotransposition. Previous studies found that gene families involved in mRNA translation or nuclear function were more likely to have large numbers of RPCs. He...

journal_title：Genome research

authors： Strichman-Almashanu LZ,Bustin M,Landsman D

更新日期：2003-05-01 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：: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：:The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution--such as changes in gene expression regulation-remains unknown. A transition...

journal_title：Genome research

authors： Fraser HB,Levy S,Chavan A,Shah HB,Perez JC,Zhou Y,Siegal ML,Sinha H

更新日期：2012-10-01 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：:In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylat...

journal_title：Genome research

authors： Court F,Le Boiteux E,Fogli A,Müller-Barthélémy M,Vaurs-Barrière C,Chautard E,Pereira B,Biau J,Kemeny JL,Khalil T,Karayan-Tapon L,Verrelle P,Arnaud P

更新日期：2019-10-01 00:00:00

abstract：:To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and compar...

journal_title：Genome research

authors： Churakov G,Zhang F,Grundmann N,Makalowski W,Noll A,Doronina L,Schmitz J

更新日期：2020-10-01 00:00:00

abstract：:Translocations are known to affect the expression of genes at the breakpoints and, in the case of unbalanced translocations, alter the gene copy number. However, a comprehensive understanding of the functional impact of this class of variation is lacking. Here, we have studied the effect of balanced chromosomal rearra...

journal_title：Genome research

authors： Harewood L,Schütz F,Boyle S,Perry P,Delorenzi M,Bickmore WA,Reymond A

更新日期：2010-05-01 00:00:00

abstract：:LSH, a member of the SNF2 family of chromatin remodeling ATPases encoded by the Hells gene, is essential for normal levels of DNA methylation in the mammalian genome. While the role of LSH in the methylation of repetitive DNA sequences is well characterized, its contribution to the regulation of DNA methylation and th...

journal_title：Genome research

authors： Myant K,Termanis A,Sundaram AY,Boe T,Li C,Merusi C,Burrage J,de Las Heras JI,Stancheva I

更新日期：2011-01-01 00:00:00

abstract：:We have established a landmark framework map over 20-25 Mb of the long arm of the human X chromosome using yeast artificial chromosome (YAC) clones. The map has approximately one landmark per 45 kb of DNA and stretches from DXS7531 in proximal Xq23 to DXS895 in proximal Xq26, connecting to published framework maps on ...

journal_title：Genome research

authors： Steingruber HE,Dunham A,Coffey AJ,Clegg SM,Howell GR,Maslen GL,Scott CE,Gwilliam R,Hunt PJ,Sotheran EC,Huckle EJ,Hunt SE,Dhami P,Soderlund C,Leversha MA,Bentley DR,Ross MT

更新日期：1999-08-01 00:00:00