Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes.

abstract：:We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal change...

journal_title：Genome research

authors： Jaffe DB,Butler J,Gnerre S,Mauceli E,Lindblad-Toh K,Mesirov JP,Zody MC,Lander ES

更新日期：2003-01-01 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：: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：:Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of...

journal_title：Genome research

authors： Visser M,Kayser M,Palstra RJ

更新日期：2012-03-01 00:00:00

abstract：:Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in...

journal_title：Genome research

authors： Neville MDC,Kohze R,Erady C,Meena N,Hayden M,Cooper DN,Mort M,Prabakaran S

更新日期：2021-01-19 00:00:00

abstract：:Drug development efforts against cancer are often hampered by the complex properties of signaling networks. Here we combined the results of an RNAi screen targeting the cellular signaling machinery, with graph theoretical analysis to extract the core modules that process both mitogenic and oncogenic signals to drive c...

journal_title：Genome research

authors： Jailkhani N,Ravichandran S,Hegde SR,Siddiqui Z,Mande SC,Rao KV

更新日期：2011-12-01 00:00:00

abstract：:Large-scale genetic interaction (GI) screens in yeast have been invaluable for our understanding of molecular systems biology and for characterizing novel gene function. Owing in part to the high costs and long experiment times required, a preponderance of GI data has been generated in a single environmental condition...

journal_title：Genome research

authors： Jaffe M,Dziulko A,Smith JD,St Onge RP,Levy SF,Sherlock G

更新日期：2019-04-01 00:00:00

abstract：:The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipien...

journal_title：Genome research

authors： Aylor DL,Valdar W,Foulds-Mathes W,Buus RJ,Verdugo RA,Baric RS,Ferris MT,Frelinger JA,Heise M,Frieman MB,Gralinski LE,Bell TA,Didion JD,Hua K,Nehrenberg DL,Powell CL,Steigerwalt J,Xie Y,Kelada SN,Collins FS,Yang IV

更新日期：2011-08-01 00:00:00

abstract：:Up-frameshift protein 1 (UPF1) is an ATP-dependent RNA helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3' untranslated region (UTR) of target mRNAs via as-yet-unknown sequ...

journal_title：Genome research

authors： Imamachi N,Salam KA,Suzuki Y,Akimitsu N

更新日期：2017-03-01 00:00:00

abstract：:A detailed comparative map of Brassica oleracea and Arabidopsis thaliana has been established based largely on mapping of Arabidopsis ESTs in two Arabidopsis and four Brassica populations. Based on conservative criteria for inferring synteny, "one to one correspondence" between Brassica and Arabidopsis chromosomes acc...

journal_title：Genome research

authors： Lan TH,DelMonte TA,Reischmann KP,Hyman J,Kowalski SP,McFerson J,Kresovich S,Paterson AH

更新日期：2000-06-01 00:00:00

abstract：:Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitati...

journal_title：Genome research

authors： Gao AW,Sterken MG,Uit de Bos J,van Creij J,Kamble R,Snoek BL,Kammenga JE,Houtkooper RH

更新日期：2018-09-01 00:00:00

abstract：:The in vitro cloning of DNA molecules traditionally uses PCR amplification or site-specific restriction endonucleases to generate linear DNA inserts with defined termini and requires DNA ligase to covalently join those inserts to vectors with the corresponding ends. We have used the properties of Vaccinia DNA topoisom...

journal_title：Genome research

authors： Heyman JA,Cornthwaite J,Foncerrada L,Gilmore JR,Gontang E,Hartman KJ,Hernandez CL,Hood R,Hull HM,Lee WY,Marcil R,Marsh EJ,Mudd KM,Patino MJ,Purcell TJ,Rowland JJ,Sindici ML,Hoeffler JP

更新日期：1999-04-01 00:00:00

abstract：:Primate pericentromeric regions recently have been shown to exhibit extraordinary evolutionary plasticity. In this paper we report an additional peculiar feature of these regions that we discovered while analyzing, by FISH, the evolutionary conservation of primate phylogenetic chromosome IX. If the position of the cen...

journal_title：Genome research

authors： Montefalcone G,Tempesta S,Rocchi M,Archidiacono N

更新日期：1999-12-01 00:00:00

abstract：:A DNA mutation detection protocol able to identify and characterize a previously unknown change in a given sequence in a rapid, efficient, sensitive, and inexpensive manner is required to take advantage of the resources now available to researchers through the genome sequencing projects. We have developed a method bas...

journal_title：Genome research

authors： Elso C,Toohey B,Reid GE,Poetter K,Simpson RJ,Foote SJ

更新日期：2002-09-01 00:00:00

abstract：:To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult A. mellifera brains....

journal_title：Genome research

authors： Whitfield CW,Band MR,Bonaldo MF,Kumar CG,Liu L,Pardinas JR,Robertson HM,Soares MB,Robinson GE

更新日期：2002-04-01 00:00:00

abstract：:DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover <2% of the genome and cannot account...

journal_title：Genome research

authors： Kaplow IM,MacIsaac JL,Mah SM,McEwen LM,Kobor MS,Fraser HB

更新日期：2015-06-01 00:00:00

abstract：:Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat S...

journal_title：Genome research

authors： Gymrek M,Golan D,Rosset S,Erlich Y

更新日期：2012-06-01 00:00:00

abstract：:A time course experiment is a widely used design in the study of cellular processes such as differentiation or response to stimuli. In this paper, we propose time course regulatory analysis (TimeReg) as a method for the analysis of gene regulatory networks based on paired gene expression and chromatin accessibility da...

journal_title：Genome research

authors： Duren Z,Chen X,Xin J,Wang Y,Wong WH

更新日期：2020-04-01 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：:Y chromosome haplotypes are particularly useful in deciphering human evolutionary history because they accentuate the effects of drift, migration, and range expansion. Significant acceleration of Y biallelic marker discovery and subsequent typing involving heteroduplex detection has been achieved by implementing an in...

journal_title：Genome research

authors： Underhill PA,Jin L,Lin AA,Mehdi SQ,Jenkins T,Vollrath D,Davis RW,Cavalli-Sforza LL,Oefner PJ

更新日期：1997-10-01 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：:Remnants of more than 3 million transposable elements, primarily retroelements, comprise nearly half of the human genome and have generated much speculation concerning their evolutionary significance. We have exploited the draft human genome sequence to examine the distributions of retroelements on a genome-wide scale...

journal_title：Genome research

authors： Medstrand P,van de Lagemaat LN,Mager DL

更新日期：2002-10-01 00:00:00

abstract：:The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross be...

journal_title：Genome research

authors： Stumpferl SW,Brand SE,Jiang JC,Korona B,Tiwari A,Dai J,Seo JG,Jazwinski SM

更新日期：2012-10-01 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：:In-gel competitive reassociation (IGCR) is a method of differential subtraction to enrich polymorphic DNA restriction fragments between two DNA samples without probes or specific sequence information. Here, we show that by combining IGCR and expressed sequence tags (EST) array hybridization, polymorphic DNA fragments ...

journal_title：Genome research

authors： Gotoh K,Oishi M

更新日期：2003-03-01 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：:Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functi...

journal_title：Genome research

authors： Taher L,McGaughey DM,Maragh S,Aneas I,Bessling SL,Miller W,Nobrega MA,McCallion AS,Ovcharenko I

更新日期：2011-07-01 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：:In an attempt to understand the origin of CpG islands (CGIs) in mammalian genomes, we have studied their location and structure according to the expression pattern of genes and to the G + C content of isochores in which they are embedded. We show that CGIs located over the transcription start site (named start CGIs) a...

journal_title：Genome research

authors： Ponger L,Duret L,Mouchiroud D

更新日期：2001-11-01 00:00:00

abstract：:The expression of most genes is regulated by multiple transcription factors. The interactions between transcription factors produce complex patterns of gene expression that are not always obvious from the arrangement of cis-regulatory elements in a promoter. One critical element of promoters is the TATA box, the docki...

journal_title：Genome research

authors： Mogno I,Vallania F,Mitra RD,Cohen BA

更新日期：2010-10-01 00:00:00