HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

abstract：:In mammals, genome-wide chromatin maps and immunofluorescence studies show that broad domains of repressive histone modifications are present on pericentromeric and telomeric repeats and on the inactive X chromosome. However, only a few autosomal loci such as silent Hox gene clusters have been shown to lie in broad do...

journal_title：Genome research

authors： Pauler FM,Sloane MA,Huang R,Regha K,Koerner MV,Tamir I,Sommer A,Aszodi A,Jenuwein T,Barlow DP

更新日期：2009-02-01 00:00:00

abstract：:With the genomic sequencing of Arabidopsis nearing completion and rice sequencing very much in its infancy, a key question is whether we can exploit the Arabidopsis sequence to identify candidate genes for traits in cereal crops using a map-based approach. This requires the existence of colinearity between the Arabido...

journal_title：Genome research

authors： Devos KM,Beales J,Nagamura Y,Sasaki T

更新日期：1999-09-01 00:00:00

abstract：:Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to align to reference genomes and to call and annotate genomic variants. This problem is even more pron...

journal_title：Genome research

authors： Ozercan HI,Ileri AM,Ayday E,Alkan C

更新日期：2018-09-01 00:00:00

abstract：:Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at least 14% of disease-causing mutations, thus implicating polymorphisms that affect splicing as likely candidates for dis...

journal_title：Genome research

authors： Goren A,Kim E,Amit M,Bochner R,Lev-Maor G,Ahituv N,Ast G

更新日期：2008-02-01 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：: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：:CRISPR/Cas9-mediated targeted mutagenesis allows efficient generation of loss-of-function alleles in zebrafish. To date, this technology has been primarily used to generate genetic knockout animals. Nevertheless, the study of the function of certain loci might require tight spatiotemporal control of gene inactivation....

journal_title：Genome research

authors： Di Donato V,De Santis F,Auer TO,Testa N,Sánchez-Iranzo H,Mercader N,Concordet JP,Del Bene F

更新日期：2016-05-01 00:00:00

abstract：:The accurate mapping of clones derived from genomic regions containing complex arrangements of repeated elements presents special problems for DNA sequencers. Recent advances in the automation of optical mapping have enabled us to map a set of 16 BAC clones derived from the DAZ locus of the human Y chromosome long arm...

journal_title：Genome research

authors： Giacalone J,Delobette S,Gibaja V,Ni L,Skiadas Y,Qi R,Edington J,Lai Z,Gebauer D,Zhao H,Anantharaman T,Mishra B,Brown LG,Saxena R,Page DC,Schwartz DC

更新日期：2000-09-01 00:00:00

abstract：:The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical m...

journal_title：Genome research

authors： Bankier AT,Spriggs HF,Fartmann B,Konfortov BA,Madera M,Vogel C,Teichmann SA,Ivens A,Dear PH

更新日期：2003-08-01 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：: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：:Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing-based methods for cell lineage analysis depend on low-resolution bulk analysis or rely on extensive single-cell sequencing, which is not scalable and could be biased ...

journal_title：Genome research

authors： Biezuner T,Spiro A,Raz O,Amir S,Milo L,Adar R,Chapal-Ilani N,Berman V,Fried Y,Ainbinder E,Cohen G,Barr HM,Halaban R,Shapiro E

更新日期：2016-11-01 00:00:00

abstract：:As part of an effort to identify the gene responsible for the predominant form of polycystic kidney disease (PKD1), we used a gridded human P1 library for contig assembly. The interval of interest, a 700-kb segment on chromosome 16p13.3, can be physically delineated by the genetic markers D16S125 and D16S84 and chromo...

journal_title：Genome research

authors： Dackowski WR,Connors TD,Bowe AE,Stanton V Jr,Housman D,Doggett NA,Landes GM,Klinger KW

更新日期：1996-06-01 00:00:00

abstract：:While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amp...

journal_title：Genome research

authors： Nurk S,Meleshko D,Korobeynikov A,Pevzner PA

更新日期：2017-05-01 00:00:00

abstract：:During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the t...

journal_title：Genome research

authors： Berchowitz LE,Hanlon SE,Lieb JD,Copenhaver GP

更新日期：2009-12-01 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：:Many missense substitutions are identified in single nucleotide polymorphism (SNP) data and large-scale random mutagenesis projects. Each amino acid substitution potentially affects protein function. We have constructed a tool that uses sequence homology to predict whether a substitution affects protein function. SIFT...

journal_title：Genome research

authors： Ng PC,Henikoff S

更新日期：2001-05-01 00:00:00

abstract：:Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect overlap detection for contig assembly is assumed. Genome-specific and nonrandom effects are neglected. Order of magnitud...

journal_title：Genome research

authors： Wendl MC,Marra MA,Hillier LW,Chinwalla AT,Wilson RK,Waterston RH

更新日期：2001-02-01 00:00:00

abstract：:Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are normally suppressed in somatic tissues mainly due to DNA methylation and antiviral defense. However, the mechanism to suppress L1s may be disrupted in cancers, thus allowing L1s to act as insertional mutagens and cause genomic rearrangement and in...

journal_title：Genome research

authors： Jung H,Choi JK,Lee EA

更新日期：2018-08-01 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：:Memory is a hallmark of adaptive immunity, wherein lymphocytes mount a superior response to a previously encountered antigen. It has been speculated that epigenetic alterations in memory lymphocytes contribute to their functional distinction from their naive counterparts. However, the nature and extent of epigenetic a...

journal_title：Genome research

authors： Lai AY,Mav D,Shah R,Grimm SA,Phadke D,Hatzi K,Melnick A,Geigerman C,Sobol SE,Jaye DL,Wade PA

更新日期：2013-12-01 00:00:00

abstract：:MULTIPROSPECTOR, a multimeric threading algorithm for the prediction of protein-protein interactions, is applied to the genome of Saccharomyces cerevisiae. Each possible pairwise interaction among more than 6000 encoded proteins is evaluated against a dimer database of 768 complex structures by using a confidence esti...

journal_title：Genome research

authors： Lu L,Arakaki AK,Lu H,Skolnick J

更新日期：2003-06-01 00:00:00

abstract：:RNA interference is a powerful tool for studying gene function and for drug target discovery in diverse organisms and cell types. In mammalian systems, small interfering RNAs (siRNAs), or DNA plasmids expressing these siRNAs, have been used to down-modulate gene expression. However, inefficient transfection protocols,...

journal_title：Genome research

authors： Arts GJ,Langemeijer E,Tissingh R,Ma L,Pavliska H,Dokic K,Dooijes R,Mesić E,Clasen R,Michiels F,van der Schueren J,Lambrecht M,Herman S,Brys R,Thys K,Hoffmann M,Tomme P,van Es H

更新日期：2003-10-01 00:00:00

abstract：:Essential genes refer to those whose null mutation leads to lethality or sterility. Theoretical reasoning and empirical data both suggest that the fatal effect of inactivating an essential gene can be attributed to either the loss of indispensable core cellular function (Type I), or the gain of fatal side effects afte...

journal_title：Genome research

authors： Chen P,Wang D,Chen H,Zhou Z,He X

更新日期：2016-10-01 00:00:00

abstract：:Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...

journal_title：Genome research

authors： Grishkevich V,Hashimshony T,Yanai I

更新日期：2011-05-01 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：:Duplication of the genome in mammalian cells occurs in a defined temporal order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400-800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competen...

journal_title：Genome research

authors： Rivera-Mulia JC,Buckley Q,Sasaki T,Zimmerman J,Didier RA,Nazor K,Loring JF,Lian Z,Weissman S,Robins AJ,Schulz TC,Menendez L,Kulik MJ,Dalton S,Gabr H,Kahveci T,Gilbert DM

更新日期：2015-08-01 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：:We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different tran...

journal_title：Genome research

authors： Benos PV,Gatt MK,Murphy L,Harris D,Barrell B,Ferraz C,Vidal S,Brun C,Demaille J,Cadieu E,Dreano S,Gloux S,Lelaure V,Mottier S,Galibert F,Borkova D,Miñana B,Kafatos FC,Bolshakov S,Sidén-Kiamos I,Papagiannakis G,S

更新日期：2001-05-01 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