abstract：:MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant inter...

journal_title：Genome research

authors： Lee I,Ajay SS,Yook JI,Kim HS,Hong SH,Kim NH,Dhanasekaran SM,Chinnaiyan AM,Athey BD

更新日期：2009-07-01 00:00:00

abstract：:Sequence-specific DNA-binding transcription factors have widespread biological significance in the regulation of gene expression. However, in lower prokaryotes and eukaryotic metazoans, it is usually difficult to find transcription regulatory factors that recognize specific target promoters. To address this, we have d...

journal_title：Genome research

authors： Guo M,Feng H,Zhang J,Wang W,Wang Y,Li Y,Gao C,Chen H,Feng Y,He ZG

更新日期：2009-07-01 00:00:00

abstract：:Recent studies have revealed that insertions and deletions (indels) are more different in their formation than previously assumed. What remains enigmatic is how the local DNA sequence context contributes to these differences. To investigate the relative impact of various molecular mechanisms to indel formation, we ana...

journal_title：Genome research

authors： Kvikstad EM,Chiaromonte F,Makova KD

更新日期：2009-07-01 00:00:00

abstract：:The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequen...

journal_title：Genome research

authors： Huang X,Feng Q,Qian Q,Zhao Q,Wang L,Wang A,Guan J,Fan D,Weng Q,Huang T,Dong G,Sang T,Han B

更新日期：2009-06-01 00:00:00

abstract：:Human genomic data of many types are readily available, but the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it from a systems level, and apply it to the study of specific pathways or genetic disorders. An investigator could best explore a particular prot...

journal_title：Genome research

authors： Huttenhower C,Haley EM,Hibbs MA,Dumeaux V,Barrett DR,Coller HA,Troyanskaya OG

更新日期：2009-06-01 00:00:00

abstract：:In Drosophila melanogaster, there is an excess of genes duplicated by retroposition from the X chromosome to the autosomes. Most of those retrogenes that originated on the X chromosome have testis expression pattern. These observations could be explained by natural selection favoring genes that avoided spermatogenesis...

journal_title：Genome research

authors： Vibranovski MD,Zhang Y,Long M

更新日期：2009-05-01 00:00:00

abstract：:Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are...

journal_title：Genome research

authors： Norman PJ,Abi-Rached L,Gendzekhadze K,Hammond JA,Moesta AK,Sharma D,Graef T,McQueen KL,Guethlein LA,Carrington CV,Chandanayingyong D,Chang YH,Crespí C,Saruhan-Direskeneli G,Hameed K,Kamkamidze G,Koram KA,Layrisse Z,Ma

更新日期：2009-05-01 00:00:00

abstract：:Chromosomal aberrations have been thought to be random events. However, recent findings introduce a new paradigm in which certain DNA segments have the potential to adopt unusual conformations that lead to genomic instability and nonrandom chromosomal rearrangement. One of the best-studied examples is the palindromic ...

journal_title：Genome research

authors： Inagaki H,Ohye T,Kogo H,Kato T,Bolor H,Taniguchi M,Shaikh TH,Emanuel BS,Kurahashi H

更新日期：2009-02-01 00:00:00

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：:We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on ...

journal_title：Genome research

authors： Gusev A,Lowe JK,Stoffel M,Daly MJ,Altshuler D,Breslow JL,Friedman JM,Pe'er I

更新日期：2009-02-01 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：:Isochromosome 17q, or i(17q), is one of the most frequent nonrandom changes occurring in human neoplasia. Most of the i(17q) breakpoints cluster within a approximately 240-kb interval located in the Smith-Magenis syndrome common deletion region in 17p11.2. The breakpoint cluster region is characterized by a complex ar...

journal_title：Genome research

authors： Carvalho CM,Lupski JR

更新日期：2008-11-01 00:00:00

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：: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：:Alternative splicing (AS) creates multiple mRNA transcripts from a single gene. While AS is known to contribute to gene regulation and proteome diversity in animals, the study of its importance in plants is in its early stages. However, recently available plant genome and transcript sequence data sets are enabling a g...

journal_title：Genome research

authors： Barbazuk WB,Fu Y,McGinnis KM

更新日期：2008-09-01 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：:In comparison to genotypes, knowledge about haplotypes (the combination of alleles present on a single chromosome) is much more useful for whole-genome association studies and for making inferences about human evolutionary history. Haplotypes are typically inferred from population genotype data using computational met...

journal_title：Genome research

authors： Bansal V,Halpern AL,Axelrod N,Bafna V

更新日期：2008-08-01 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：:Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchr...

journal_title：Genome research

authors： Kirsch S,Münch C,Jiang Z,Cheng Z,Chen L,Batz C,Eichler EE,Schempp W

更新日期：2008-07-01 00:00:00

abstract：:Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cepha...

journal_title：Genome research

authors： Holland LZ,Albalat R,Azumi K,Benito-Gutiérrez E,Blow MJ,Bronner-Fraser M,Brunet F,Butts T,Candiani S,Dishaw LJ,Ferrier DE,Garcia-Fernàndez J,Gibson-Brown JJ,Gissi C,Godzik A,Hallböök F,Hirose D,Hosomichi K,Ikuta T,I

更新日期：2008-07-01 00:00:00

abstract：:It is critical to avoid delays in detecting strain manipulations, such as the addition/deletion of a gene or modification of genes for increased virulence or antibiotic resistance, using genome analysis during an epidemic outbreak or a bioterrorist attack. Our objective was to evaluate the efficiency of genome analysi...

journal_title：Genome research

authors： La Scola B,Elkarkouri K,Li W,Wahab T,Fournous G,Rolain JM,Biswas S,Drancourt M,Robert C,Audic S,Löfdahl S,Raoult D

更新日期：2008-05-01 00:00:00

abstract：:DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and H...

journal_title：Genome research

authors： Ray DA,Feschotte C,Pagan HJ,Smith JD,Pritham EJ,Arensburger P,Atkinson PW,Craig NL

更新日期：2008-05-01 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 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：:Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships po...

journal_title：Genome research

authors： Horvath JE,Weisrock DW,Embry SL,Fiorentino I,Balhoff JP,Kappeler P,Wray GA,Willard HF,Yoder AD

更新日期：2008-03-01 00:00:00

abstract：:Recent accumulation of microbial genome data has demonstrated that lateral gene transfers constitute an important and universal evolutionary process in prokaryotes, while those in multicellular eukaryotes are still regarded as unusual, except for endosymbiotic gene transfers from mitochondria and plastids. Here we tho...

journal_title：Genome research

authors： Nikoh N,Tanaka K,Shibata F,Kondo N,Hizume M,Shimada M,Fukatsu T

更新日期：2008-02-01 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：:It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whethe...

journal_title：Genome research

authors： Scannell DR,Wolfe KH

更新日期：2008-01-01 00:00:00

abstract：:Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional g...

journal_title：Genome research

authors： Kelkar YD,Tyekucheva S,Chiaromonte F,Makova KD

更新日期：2008-01-01 00:00:00

abstract：:Facio-scapulo-humeral dystrophy (FSHD), a muscular hereditary disease with a prevalence of 1 in 20,000, is caused by a partial deletion of a subtelomeric repeat array on chromosome 4q. Earlier, we demonstrated the existence in the vicinity of the D4Z4 repeat of a nuclear matrix attachment site, FR-MAR, efficient in no...

journal_title：Genome research

authors： Petrov A,Allinne J,Pirozhkova I,Laoudj D,Lipinski M,Vassetzky YS

更新日期：2008-01-01 00:00:00

abstract：:Disregulation of imprinted genes can be associated with tumorigenesis and altered cell differentiation capacity and so could provide adverse outcomes for stem cell applications. Although the maintenance of mouse and primate embryonic stem cells in a pluripotent state has been reported to disrupt the monoallelic expres...

journal_title：Genome research

authors： Kim KP,Thurston A,Mummery C,Ward-van Oostwaard D,Priddle H,Allegrucci C,Denning C,Young L

更新日期：2007-12-01 00:00:00

abstract：:Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced...

journal_title：Genome research

authors： Rasmussen MD,Kellis M

更新日期：2007-12-01 00:00:00

abstract：:By surveying a filtered, high-quality set of SNPs in the human genome, we have found that SNPs positioned 1, 2, 4, 6, or 8 bp apart are more frequent than SNPs positioned 3, 5, 7, or 9 bp apart. The observed pattern is not restricted to genomic regions that are known to cause sequencing or alignment errors, for exampl...

journal_title：Genome research

authors： Madsen BE,Villesen P,Wiuf C

更新日期：2007-10-01 00:00:00

abstract：:The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoterGFP methodology, we have conducted the largest survey to date on the regulatory regions of annotated C. elegans operons and identified 65, over 25% of those studied, with internal promoters. ...

journal_title：Genome research

authors： Huang P,Pleasance ED,Maydan JS,Hunt-Newbury R,O'Neil NJ,Mah A,Baillie DL,Marra MA,Moerman DG,Jones SJ

更新日期：2007-10-01 00:00:00

abstract：:Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...

journal_title：Genome research

authors： Copley RR,Totrov M,Linnell J,Field S,Ragoussis J,Udalova IA

更新日期：2007-09-01 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：: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：:The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of metatherians. Here, we compare Monodelphis with Homo sequences from alignments of single nucleotides, genes, and whole chr...

journal_title：Genome research

authors： Goodstadt L,Heger A,Webber C,Ponting CP

更新日期：2007-07-01 00:00:00

abstract：:We generated high-resolution maps of histone H3 lysine 9/14 acetylation (H3ac), histone H4 lysine 5/8/12/16 acetylation (H4ac), and histone H3 at lysine 4 mono-, di-, and trimethylation (H3K4me1, H3K4me2, H3K4me3, respectively) across the ENCODE regions. Studying each modification in five human cell lines including th...

journal_title：Genome research

authors： Koch CM,Andrews RM,Flicek P,Dillon SC,Karaöz U,Clelland GK,Wilcox S,Beare DM,Fowler JC,Couttet P,James KD,Lefebvre GC,Bruce AW,Dovey OM,Ellis PD,Dhami P,Langford CF,Weng Z,Birney E,Carter NP,Vetrie D,Dunham I

更新日期：2007-06-01 00:00:00

abstract：:Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of approximately 11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcri...

journal_title：Genome research

authors： Lin JM,Collins PJ,Trinklein ND,Fu Y,Xi H,Myers RM,Weng Z

更新日期：2007-06-01 00:00:00