Adenoviral vectors expressing siRNAs for discovery and validation of gene function.

abstract：:Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The 17q24.3 locus harbors the single nucleotide polymorphism (SNP) rs1859962 that is statistically associated with prostate cancer (PCa). It defines a 130-kb linkage disequilibrium (LD) block that lies in an ∼2-Mb gene d...

journal_title：Genome research

authors： Zhang X,Cowper-Sal lari R,Bailey SD,Moore JH,Lupien M

更新日期：2012-08-01 00:00:00

abstract：:The higher-order structural organization and dynamics of the chromosomes play a central role in gene regulation. To explore this structure-function relationship, it is necessary to directly visualize genomic elements in living cells. Genome imaging based on the CRISPR system is a powerful approach but has limited appl...

journal_title：Genome research

authors： Chaudhary N,Nho SH,Cho H,Gantumur N,Ra JS,Myung K,Kim H

更新日期：2020-09-01 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：: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：:Despite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently d...

journal_title：Genome research

authors： Dougherty ML,Underwood JG,Nelson BJ,Tseng E,Munson KM,Penn O,Nowakowski TJ,Pollen AA,Eichler EE

更新日期：2018-10-01 00:00:00

abstract：:In this communication, we describe the use of specialized transposons (Tn5 derivatives) to create deletions in the Escherichia coli K-12 chromosome. These transposons are essentially rearranged composite transposons that have been assembled to promote the use of the internal transposon ends, resulting in intramolecula...

journal_title：Genome research

authors： Goryshin IY,Naumann TA,Apodaca J,Reznikoff WS

更新日期：2003-04-01 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：:DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of approximately 70-mer probes, and used these arrays to analyze gene expression i...

journal_title：Genome research

authors： Barczak A,Rodriguez MW,Hanspers K,Koth LL,Tai YC,Bolstad BM,Speed TP,Erle DJ

更新日期：2003-07-01 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：:Network "guilt by association" (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this approach could account even for nonadditive genetic interactions, which underlie the synergistic combinatio...

journal_title：Genome research

authors： Lee I,Blom UM,Wang PI,Shim JE,Marcotte EM

更新日期：2011-07-01 00:00:00

abstract：:It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood ...

journal_title：Genome research

authors： Liu X,Fu YX,Maxwell TJ,Boerwinkle E

更新日期：2010-01-01 00:00:00

abstract：:Development of composite inflorescences in the plant family Asteraceae has features that cannot be studied in the traditional model plants for flower development. In Gerbera hybrida, inflorescences are composed of morphologically different types of flowers tightly packed into a flower head (capitulum). Individual flor...

journal_title：Genome research

authors： Laitinen RA,Immanen J,Auvinen P,Rudd S,Alatalo E,Paulin L,Ainasoja M,Kotilainen M,Koskela S,Teeri TH,Elomaa P

更新日期：2005-04-01 00:00:00

abstract：:Careful titration of Vent polymerase activity allows efficient amplification of full-length plasmids (12 kb). The high processivity and fidelity of this enzyme made oligonucleotide-directed site-specific mutagenesis of plasmids a straight-forward process. Using only two primers, a mutagenic and a complementary, single...

journal_title：Genome research

authors： Byrappa S,Gavin DK,Gupta KC

更新日期：1995-11-01 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：:Few methods are available for mapping the local structure of DNA throughout a genome. The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA. We report the construction of a relati...

journal_title：Genome research

authors： Greenbaum JA,Pang B,Tullius TD

更新日期：2007-06-01 00:00:00

abstract：:Despite recent progress in genome topology knowledge, the role of repeats, which make up the majority of mammalian genomes, remains elusive. Satellite repeats are highly abundant sequences that cluster around centromeres, attract pericentromeric heterochromatin, and aggregate into nuclear chromocenters. These nuclear ...

journal_title：Genome research

authors： Wijchers PJ,Geeven G,Eyres M,Bergsma AJ,Janssen M,Verstegen M,Zhu Y,Schell Y,Vermeulen C,de Wit E,de Laat W

更新日期：2015-07-01 00:00:00

abstract：:We report the construction of a dense linkage map of the rat genome integrating 767 simple sequence length polymorphism markers, combined over three crosses with high rates of polymorphism. F2 populations from WKY x S (n = 159), BN x S (n = 91), and BN x GK (n = 139) were selected and genotyped for combinations of mic...

journal_title：Genome research

authors： Bihoreau MT,Gauguier D,Kato N,Hyne G,Lindpaintner K,Rapp JP,James MR,Lathrop GM

更新日期：1997-05-01 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：: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：:Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. ...

journal_title：Genome research

authors： Castensson A,Emilsson L,Preece P,Jazin EE

更新日期：2000-08-01 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

abstract：:Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures-including immune responses and therapeutic interventions-shape bacterial genomes. We carri...

journal_title：Genome research

authors： Lee AH,Flibotte S,Sinha S,Paiero A,Ehrlich RL,Balashov S,Ehrlich GD,Zlosnik JE,Mell JC,Nislow C

更新日期：2017-04-01 00:00:00

abstract：:Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey...

journal_title：Genome research

authors： Wilder SP,Bihoreau MT,Argoud K,Watanabe TK,Lathrop M,Gauguier D

更新日期：2004-04-01 00:00:00

abstract：:We have determined the complete sequence of 951,695 bp from the class I region of H2, the mouse major histocompatibility complex (Mhc) from strain 129/Sv (haplotype bc). The sequence contains 26 genes. The sequence spans from the last 50 kb of the H2-T region, including 2 class I genes and 3 class I pseudogenes, and i...

journal_title：Genome research

authors： Takada T,Kumánovics A,Amadou C,Yoshino M,Jones EP,Athanasiou M,Evans GA,Fischer Lindahl K

更新日期：2003-04-01 00:00:00

abstract：:While copy number variation (CNV) is an active area of research, de novo mutation rates within human populations are not well characterized. By focusing on large (>100 kbp) events, we estimate the rate of de novo CNV formation in humans by analyzing 4394 transmissions from human pedigrees with and without neurocogniti...

journal_title：Genome research

authors： Itsara A,Wu H,Smith JD,Nickerson DA,Romieu I,London SJ,Eichler EE

更新日期：2010-11-01 00:00:00

abstract：:Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-base...

journal_title：Genome research

authors： Lv J,Jiao W,Guo H,Liu P,Wang R,Zhang L,Zeng Q,Hu X,Bao Z,Wang S

更新日期：2018-12-01 00:00:00

abstract：:Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to the GART gene. This cluster includes both components of the interferon alpha/beta-receptor (IFNAR1 and IFNAR2) and the second components o...

journal_title：Genome research

authors： Reboul J,Gardiner K,Monneron D,Uzé G,Lutfalla G

更新日期：1999-03-01 00:00:00

abstract：:Double anal fin (Da) is a medaka with an autosomal semidominant mutation that causes mirror image duplication of the ventral region concentrating on the caudal region. The chromosomal location of the Da gene and its sequence have remained unknown. We constructed a medaka linkage map as a first step to approach positio...

journal_title：Genome research

authors： Ohtsuka M,Makino S,Yoda K,Wada H,Naruse K,Mitani H,Shima A,Ozato K,Kimura M,Inoko H

更新日期：1999-12-01 00:00:00

abstract：:Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the z...

journal_title：Genome research

authors： Völker M,Backström N,Skinner BM,Langley EJ,Bunzey SK,Ellegren H,Griffin DK

更新日期：2010-04-01 00:00:00

abstract：:Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have charac...

journal_title：Genome research

authors： Enuameh MS,Asriyan Y,Richards A,Christensen RG,Hall VL,Kazemian M,Zhu C,Pham H,Cheng Q,Blatti C,Brasefield JA,Basciotta MD,Ou J,McNulty JC,Zhu LJ,Celniker SE,Sinha S,Stormo GD,Brodsky MH,Wolfe SA

更新日期：2013-06-01 00:00:00