Gene-specific vulnerability to imprinting variability in human embryonic stem cell lines.

abstract：:Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies of 82 synthetic single-stranded oligonucleotides comprising all tetra- and trinucleotide repeats revealed an inverse co...

journal_title：Genome research

authors： Bacolla A,Larson JE,Collins JR,Li J,Milosavljevic A,Stenson PD,Cooper DN,Wells RD

更新日期：2008-10-01 00:00:00

abstract：:The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incred...

journal_title：Genome research

authors： Schatz MC

更新日期：2015-10-01 00:00:00

abstract：:Annotation transfer is a principal process in genome annotation. It involves "transferring" structural and functional annotation to uncharacterized open reading frames (ORFs) in a newly completed genome from experimentally characterized proteins similar in sequence. To prevent errors in genome annotation, it is import...

journal_title：Genome research

authors： Hegyi H,Gerstein M

更新日期：2001-10-01 00:00:00

abstract：:In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato frui...

journal_title：Genome research

authors： Moxon S,Jing R,Szittya G,Schwach F,Rusholme Pilcher RL,Moulton V,Dalmay T

更新日期：2008-10-01 00:00:00

abstract：:Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward thi...

journal_title：Genome research

authors： Tranchevent LC,Aubé F,Dulaurier L,Benoit-Pilven C,Rey A,Poret A,Chautard E,Mortada H,Desmet FO,Chakrama FZ,Moreno-Garcia MA,Goillot E,Janczarski S,Mortreux F,Bourgeois CF,Auboeuf D

更新日期：2017-06-01 00:00:00

abstract：:Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of post-transcriptional gene regulatory evolution are largely unknown. Here we used ri...

journal_title：Genome research

authors： McManus CJ,May GE,Spealman P,Shteyman A

更新日期：2014-03-01 00:00:00

abstract：:Since complete redundancy between extant duplicates (paralogs) is evolutionarily unfavorable, some degree of functional congruency is eventually lost. However, in budding yeast, experimental evidence collected for duplicated metabolic enzymes and in global physical interaction surveys had suggested widespread function...

journal_title：Genome research

authors： Musso G,Costanzo M,Huangfu M,Smith AM,Paw J,San Luis BJ,Boone C,Giaever G,Nislow C,Emili A,Zhang Z

更新日期：2008-07-01 00:00:00

abstract：:Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and r...

journal_title：Genome research

authors： Marin R,Cortez D,Lamanna F,Pradeepa MM,Leushkin E,Julien P,Liechti A,Halbert J,Brüning T,Mössinger K,Trefzer T,Conrad C,Kerver HN,Wade J,Tschopp P,Kaessmann H

更新日期：2017-12-01 00:00:00

abstract：:Metagenomic projects generate short, overlapping fragments of DNA sequence, each deriving from a different individual. We report a new method for inferring the scaled mutation rate, theta = 2Neu, and the scaled exponential growth rate, R = Ner, from the site-frequency spectrum of these data while accounting for sequen...

journal_title：Genome research

authors： Johnson PL,Slatkin M

更新日期：2006-10-01 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：: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：:Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and lit...

journal_title：Genome research

authors： Ma L,Zhao B,Chen K,Thomas A,Tuteja JH,He X,He C,White KP

更新日期：2017-03-01 00:00:00

abstract：:Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires' disease. Just five sequence types (ST), from more than 2000 currently described, cause nearly half of disease cases in northwest Europe. Here, we report the sequence and analyses of 364 L. pneumophila genomes, including 337 fro...

journal_title：Genome research

authors： David S,Rusniok C,Mentasti M,Gomez-Valero L,Harris SR,Lechat P,Lees J,Ginevra C,Glaser P,Ma L,Bouchier C,Underwood A,Jarraud S,Harrison TG,Parkhill J,Buchrieser C

更新日期：2016-11-01 00:00:00

abstract：:The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...

journal_title：Genome research

authors： Lazar J,Moreno C,Jacob HJ,Kwitek AE

更新日期：2005-12-01 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：:The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of in...

journal_title：Genome research

authors： Lin B,Wang Z,Vora GJ,Thornton JA,Schnur JM,Thach DC,Blaney KM,Ligler AG,Malanoski AP,Santiago J,Walter EA,Agan BK,Metzgar D,Seto D,Daum LT,Kruzelock R,Rowley RK,Hanson EH,Tibbetts C,Stenger DA

更新日期：2006-04-01 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：:Mosaic mutations present in the germline have important implications for reproductive risk and disease transmission. We previously demonstrated a phenomenon occurring in the male germline, whereby specific mutations arising spontaneously in stem cells (spermatogonia) lead to clonal expansion, resulting in elevated mut...

journal_title：Genome research

authors： Maher GJ,Ralph HK,Ding Z,Koelling N,Mlcochova H,Giannoulatou E,Dhami P,Paul DS,Stricker SH,Beck S,McVean G,Wilkie AOM,Goriely A

更新日期：2018-12-01 00:00:00

abstract：:A benchmark problem is described for the reconstruction and analysis of biochemical networks given sampled experimental data. The growth of the organisms is described in a bioreactor in which one substrate is fed into the reactor with a given feed rate and feed concentration. Measurements for some intracellular compon...

journal_title：Genome research

authors： Kremling A,Fischer S,Gadkar K,Doyle FJ,Sauter T,Bullinger E,Allgöwer F,Gilles ED

更新日期：2004-09-01 00:00:00

abstract：:DNA is a universal language encrypted with biological instruction for life. In higher organisms, the genetic information is preserved predominantly in an organized exon/intron structure. When a gene is expressed, the exons are spliced together to form the transcript for protein synthesis. We have developed a complexit...

journal_title：Genome research

authors： Chuang TJ,Lin WC,Lee HC,Wang CW,Hsiao KL,Wang ZH,Shieh D,Lin SC,Ch'ang LY

更新日期：2003-02-01 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：: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：:Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model t...

journal_title：Genome research

authors： Arnold P,Schöler A,Pachkov M,Balwierz PJ,Jørgensen H,Stadler MB,van Nimwegen E,Schübeler D

更新日期：2013-01-01 00:00:00

abstract：:The sequence of the first plant genome was completed and published at the end of 2000. This spawned a series of large-scale projects aimed at discovering the functions of the 25,000+ genes identified in Arabidopsis thaliana (Arabidopsis). This review summarizes progress made in the past five years and speculates about...

journal_title：Genome research

authors： Bevan M,Walsh S

更新日期：2005-12-01 00:00:00

abstract：:Chromosome 21 represents approximately 1% of the human genome, and its long arm has been estimated to contain 600-1000 genes. A dense linkage map and almost complete physical maps based on yeast artificial chromosomes (YACs) and cosmids have been developed. We have used exon trapping to identify portions of genes from...

journal_title：Genome research

authors： Chen H,Chrast R,Rossier C,Morris MA,Lalioti MD,Antonarakis SE

更新日期：1996-08-01 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：: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 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：: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：:Variation in the composition of the human oral microbiome in health and disease has been observed. We have characterized inter- and intra-individual variation of microbial communities of 107 individuals in one of the largest cohorts to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We ex...

journal_title：Genome research

authors： Stahringer SS,Clemente JC,Corley RP,Hewitt J,Knights D,Walters WA,Knight R,Krauter KS

更新日期：2012-11-01 00:00:00