Genome function and nuclear architecture: from gene expression to nanoscience.

abstract：:Coevolution maintains interactions between phenotypic traits through the process of reciprocal natural selection. Detecting molecular coevolution can expose functional interactions between molecules in the cell, generating insights into biological processes, pathways, and the networks of interactions important for cel...

journal_title：Genome research

authors： Tillier ER,Charlebois RL

更新日期：2009-10-01 00:00:00

abstract：:Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five...

journal_title：Genome research

authors： Navin NE

更新日期：2015-10-01 00:00:00

abstract：:Recent advances toward the characterization of Alzheimer's disease (AD) have permitted the identification of a dozen of genetic risk factors, although many more remain undiscovered. In parallel, works in the field of network biology have shown a strong link between protein connectivity and disease. In this manuscript,...

journal_title：Genome research

authors： Soler-López M,Zanzoni A,Lluís R,Stelzl U,Aloy P

更新日期：2011-03-01 00:00:00

abstract：:We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...

journal_title：Genome research

authors： Edwards YH,Putt W,Lekoape KM,Stott D,Fox M,Hopkinson DA,Sowden J

更新日期：1996-03-01 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：:GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored ...

journal_title：Genome research

authors： Parra G,Blanco E,Guigó R

更新日期：2000-04-01 00:00:00

abstract：:We developed a high-throughput technique for the generation of cDNA libraries in the yeast Saccharomyces cerevisiae which enables the selection of cloned cDNA inserts containing open reading frames (ORFs). For direct screening of random-primed cDNA libraries, we have constructed a yeast shuttle/expression vector, the ...

journal_title：Genome research

authors： Holz C,Lueking A,Bovekamp L,Gutjahr C,Bolotina N,Lehrach H,Cahill DJ

更新日期：2001-10-01 00:00:00

abstract：:Recent advances in genome research have accelerated the process of locating candidate genes and the variable sites within them and have simplified the task of genotype measurement. The development of statistical and computational strategies to utilize information on hundreds -- soon thousands -- of variable loci to in...

journal_title：Genome research

authors： Nelson MR,Kardia SL,Ferrell RE,Sing CF

更新日期：2001-03-01 00:00:00

abstract：:Phosphotyrosine (pTyr) signaling, which plays a central role in cell-cell and cell-environment interactions, has been considered to be an evolutionary innovation in multicellular metazoans. However, neither the emergence nor the evolution of the human pTyr signaling system is currently understood. Tyrosine kinase (TK)...

journal_title：Genome research

authors： Li L,Tibiche C,Fu C,Kaneko T,Moran MF,Schiller MR,Li SS,Wang E

更新日期：2012-07-01 00:00:00

abstract：:RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and c...

journal_title：Genome research

authors： Cieslik M,Chugh R,Wu YM,Wu M,Brennan C,Lonigro R,Su F,Wang R,Siddiqui J,Mehra R,Cao X,Lucas D,Chinnaiyan AM,Robinson D

更新日期：2015-09-01 00:00:00

abstract：:Centromeres pose an evolutionary paradox: strongly conserved in function but rapidly changing in sequence and structure. However, in the absence of damage, centromere locations are usually conserved within a species. We report here that isolates of the pathogenic yeast species Candida parapsilosis show within-species ...

journal_title：Genome research

authors： Ola M,O'Brien CE,Coughlan AY,Ma Q,Donovan PD,Wolfe KH,Butler G

更新日期：2020-05-01 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：: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：:Oncoviral infection is responsible for 12%-15% of cancer in humans. Convergent evidence from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers remain to be discovered. Oncoviral profiles can be obtained from cancer genome sequencing data; however, widespread viral sequence contaminat...

journal_title：Genome research

authors： Chen X,Kost J,Sulovari A,Wong N,Liang WS,Cao J,Li D

更新日期：2019-05-01 00:00:00

abstract：:DNA methylation at the promoter of a gene is presumed to render it silent, yet a sizable fraction of genes with methylated proximal promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a...

journal_title：Genome research

authors： Sarda S,Das A,Vinson C,Hannenhalli S

更新日期：2017-04-01 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 contiguous high-resolution map of 44 loci from a 35-Mb portion of the distal region of the long arm of human chromosome 5, q21-q35, was produced using radiation hybrid (RH) mapping in conjunction with a natural deletion mapping panel. The map includes 30 genes, four sequence-tagged site (STS) loci, and 10 DNA marker...

journal_title：Genome research

authors： Warrington JA,Wasmuth JJ

更新日期：1996-07-01 00:00:00

abstract：:Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules,...

journal_title：Genome research

authors： Bundy JG,Papp B,Harmston R,Browne RA,Clayson EM,Burton N,Reece RJ,Oliver SG,Brindle KM

更新日期：2007-04-01 00:00:00

abstract：:A region-specific ENU mutagenesis screen was conducted to elucidate the functional content of proximal mouse Chr 5. We used the visibly marked, recessive, lethal inversion Rump White (Rw) as a balancer in a three-generation breeding scheme to identify recessive mutations within the approximately 50 megabases spanned b...

journal_title：Genome research

authors： Wilson L,Ching YH,Farias M,Hartford SA,Howell G,Shao H,Bucan M,Schimenti JC

更新日期：2005-08-01 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：: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：:Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. B...

journal_title：Genome research

authors： Kent WJ

更新日期：2002-04-01 00:00:00

abstract：:The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their...

journal_title：Genome research

authors： Yang F,Wang J,GTEx Consortium.,Pierce BL,Chen LS

更新日期：2017-11-01 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：:CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in hu...

journal_title：Genome research

authors： Smallwood A,Hon GC,Jin F,Henry RE,Espinosa JM,Ren B

更新日期：2012-08-01 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：:Eukaryotic DNA replication initiates from multiple discrete sites in the genome, termed origins of replication (origins). Prior to S phase, multiple origins are poised to initiate replication by recruitment of the pre-replicative complex (pre-RC). For proper replication to occur, origin activation must be tightly regu...

journal_title：Genome research

authors： Rodriguez J,Lee L,Lynch B,Tsukiyama T

更新日期：2017-02-01 00:00:00

abstract：:Mutational analysis of large genes with complex genomic structures plays an important role in medical genetics. Technical limitations associated with current mutation screening protocols have placed increased emphasis on the development of new technologies to simplify these procedures. High-density arrays of >90,000-o...

journal_title：Genome research

authors： Hacia JG,Sun B,Hunt N,Edgemon K,Mosbrook D,Robbins C,Fodor SP,Tagle DA,Collins FS

更新日期：1998-12-01 00:00:00

abstract：:Animal microRNA sequences are subject to 3' nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3' adenylation function, we deep-sequenced RNA after k...

journal_title：Genome research

authors： Burroughs AM,Ando Y,de Hoon MJ,Tomaru Y,Nishibu T,Ukekawa R,Funakoshi T,Kurokawa T,Suzuki H,Hayashizaki Y,Daub CO

更新日期：2010-10-01 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