A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.

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：:One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproduct...

journal_title：Genome research

authors： Mack KL,Campbell P,Nachman MW

更新日期：2016-04-01 00:00:00

abstract：:RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here, we present a new method, Smart-3SEQ, that accuratel...

journal_title：Genome research

authors： Foley JW,Zhu C,Jolivet P,Zhu SX,Lu P,Meaney MJ,West RB

更新日期：2019-11-01 00:00:00

abstract：:We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap bet...

journal_title：Genome research

authors： Baens M,Peeters P,Guo C,Aerssens J,Marynen P

更新日期：1996-05-01 00:00:00

abstract：:High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classi...

journal_title：Genome research

authors： Corvelo A,Clarke WE,Robine N,Zody MC

更新日期：2018-05-01 00:00:00

abstract：:Identifying genes in the genomic context is central to a cell's ability to interpret the genome. Yet, in general, the signals used to define eukaryotic genes are poorly described. Here, we derived simple classifiers that identify where transcription will initiate and terminate using nucleic acid sequence features dete...

journal_title：Genome research

authors： de Boer CG,van Bakel H,Tsui K,Li J,Morris QD,Nislow C,Greenblatt JF,Hughes TR

更新日期：2014-01-01 00:00:00

abstract：:Gene expression can be regulated at multiple levels, but it is not known if and how there is broad coordination between regulation at the transcriptional and post-transcriptional levels. Transcription factors and chromatin regulate gene expression transcriptionally, whereas microRNAs (miRNAs) are small regulatory RNAs...

journal_title：Genome research

authors： Shivram H,Le SV,Iyer VR

更新日期：2019-02-01 00:00:00

abstract：:Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace. The resulting ambiguity sequence is aligned to the genome, identifying one template sequence. A second template se...

journal_title：Genome research

authors： Tenney AE,Wu JQ,Langton L,Klueh P,Quatrano R,Brent MR

更新日期：2007-02-01 00:00:00

abstract：:Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed...

journal_title：Genome research

authors： Yatsuki H,Joh K,Higashimoto K,Soejima H,Arai Y,Wang Y,Hatada I,Obata Y,Morisaki H,Zhang Z,Nakagawachi T,Satoh Y,Mukai T

更新日期：2002-12-01 00:00:00

abstract：:Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcri...

journal_title：Genome research

authors： Liang H,Landweber LF

更新日期：2006-02-01 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：: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：: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：:A rigorous analysis of the Merck-sponsored EST data with respect to known gene sequences increases the utility of the data set and helps refine methods for building a gene index. A highly curated human transcript data base was used as a reference data set of known genes. A detailed analysis of EST sequences derived fr...

journal_title：Genome research

authors： Aaronson JS,Eckman B,Blevins RA,Borkowski JA,Myerson J,Imran S,Elliston KO

更新日期：1996-09-01 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：: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：:All individuals in a finite population are related if traced back long enough and will, therefore, share regions of their genomes identical by descent (IBD). Detection of such regions has several important applications-from answering questions about human evolution to locating regions in the human genome containing di...

journal_title：Genome research

authors： Moltke I,Albrechtsen A,Hansen TV,Nielsen FC,Nielsen R

更新日期：2011-07-01 00:00:00

abstract：:Elucidating the pathophysiology and molecular attributes of common disorders as well as developing targeted and effective treatments hinges on the study of the relevant cell type and tissues. Pancreatic beta cells within the islets of Langerhans are centrally involved in the pathogenesis of both type 1 and type 2 diab...

journal_title：Genome research

authors： Nica AC,Ongen H,Irminger JC,Bosco D,Berney T,Antonarakis SE,Halban PA,Dermitzakis ET

更新日期：2013-09-01 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：:The study of genetic variability within natural populations of pathogens may provide insight into their evolution and pathogenesis. We used a Mycobacterium tuberculosis high-density oligonucleotide microarray to detect small-scale genomic deletions among 19 clinically and epidemiologically well-characterized isolates ...

journal_title：Genome research

authors： Kato-Maeda M,Rhee JT,Gingeras TR,Salamon H,Drenkow J,Smittipat N,Small PM

更新日期：2001-04-01 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

abstract：:Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two set...

journal_title：Genome research

authors： Lu P,Han X,Qi J,Yang J,Wijeratne AJ,Li T,Ma H

更新日期：2012-03-01 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：: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 nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonr...

journal_title：Genome research

authors： Bi X,Cheng YJ,Hu B,Ma X,Wu R,Wang JW,Liu C

更新日期：2017-07-01 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：:Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and co...

journal_title：Genome research

authors： Hoskins RA,Carlson JW,Wan KH,Park S,Mendez I,Galle SE,Booth BW,Pfeiffer BD,George RA,Svirskas R,Krzywinski M,Schein J,Accardo MC,Damia E,Messina G,Méndez-Lago M,de Pablos B,Demakova OV,Andreyeva EN,Boldyreva LV,Ma

更新日期：2015-03-01 00:00:00

abstract：:Despite the availability of dozens of animal genome sequences, two key questions remain unanswered: First, what fraction of any species' genome confers biological function, and second, are apparent differences in organismal complexity reflected in an objective measure of genomic complexity? Here, we address both quest...

journal_title：Genome research

authors： Meader S,Ponting CP,Lunter G

更新日期：2010-10-01 00:00:00

abstract：:We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spannin...

journal_title：Genome research

authors： Sharim H,Grunwald A,Gabrieli T,Michaeli Y,Margalit S,Torchinsky D,Arielly R,Nifker G,Juhasz M,Gularek F,Almalvez M,Dufault B,Chandra SS,Liu A,Bhattacharya S,Chen YW,Vilain E,Wagner KR,Pevsner J,Reifenberger J,Lam

更新日期：2019-04-01 00:00:00

abstract：:Mammalian genomes contain many highly conserved nongenic sequences (CNGs) whose functional significance is poorly understood. Sets of CNGs have previously been identified by selecting the most conserved elements from a chromosome or genome, but in these highly selected samples, conservation may be unrelated to purifyi...

journal_title：Genome research

authors： Keightley PD,Kryukov GV,Sunyaev S,Halligan DL,Gaffney DJ

更新日期：2005-10-01 00:00:00