Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin.

abstract：:Chromosome 21 represents approximately 1% of the human genome, and its long arm has been estimated to contain 600-1000 genes. A dense linkage map and almost complete physical maps based on yeast artificial chromosomes (YACs) and cosmids have been developed. We have used exon trapping to identify portions of genes from...

journal_title：Genome research

authors： Chen H,Chrast R,Rossier C,Morris MA,Lalioti MD,Antonarakis SE

更新日期：1996-08-01 00:00:00

abstract：:As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, an...

journal_title：Genome research

authors： Curwen V,Eyras E,Andrews TD,Clarke L,Mongin E,Searle SM,Clamp M

更新日期：2004-05-01 00:00:00

abstract：:Using AP-PCR-based DNA profiling we examined some structural features of B chromosomes from yellow-necked mice Apodemus flavicollis. Mice harboring one, two, or three or lacking B chromosomes were examined. Chromosomal structure was scanned for variant bands by using a series of arbitrary primers and from these, infor...

journal_title：Genome research

authors： Tanic N,Dedovic N,Vujosevic M,Dimitrijevic B

更新日期：2000-01-01 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：:Chromosome-specific cDNA libraries are new tools for the isolation of genes from specific genomic regions. We have used two YACs than span the approximately 2-Mb cri-du-chat critical region (CDCCR) of chromosome 5p to directly screen a chromosome 5-specific (CH5SP) fetal brain cDNA library. To compare this library wit...

journal_title：Genome research

authors： Simmons AD,Overhauser J,Lovett M

更新日期：1997-02-01 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：:Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. Gr...

journal_title：Genome research

authors： Zhou Z,Alikhan NF,Sergeant MJ,Luhmann N,Vaz C,Francisco AP,Carriço JA,Achtman M

更新日期：2018-09-01 00:00:00

abstract：:Paternal X chromosome inactivation occurs in rodent extraembryonic membranes and in all tissues of marsupials. Methylation of CpG islands occurs on the inactive X in eutherians and is considered to be a stabilizing mechanism. The only previous study of a marsupial X-linked CpG island was of the G6PD gene of the Virgin...

journal_title：Genome research

authors： Loebel DA,Johnston PG

更新日期：1996-02-01 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：:A large database of copy number profiles from cancer genomes can facilitate the identification of recurrent chromosomal alterations that often contain key cancer-related genes. It can also be used to explore low-prevalence genomic events such as chromothripsis. In this study, we report an analysis of 8227 human cancer...

journal_title：Genome research

authors： Kim TM,Xi R,Luquette LJ,Park RW,Johnson MD,Park PJ

更新日期：2013-02-01 00:00:00

abstract：:Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora t...

journal_title：Genome research

authors： Corcoran P,Anderson JL,Jacobson DJ,Sun Y,Ni P,Lascoux M,Johannesson H

更新日期：2016-04-01 00:00:00

abstract：:Detecting rare sequence variants in genomic DNA is central to the analysis of de novo mutation and recombination events and the detection of rare pathological mutations in mixed cell populations. Current PCR techniques suffer from noise that limits detection to variants present at a frequency of at least 10(-4)-10(-5)...

journal_title：Genome research

authors： Jeffreys AJ,May CA

更新日期：2003-10-01 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：:Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important compone...

journal_title：Genome research

authors： Devine SE,Chissoe SL,Eby Y,Wilson RK,Boeke JD

更新日期：1997-05-01 00:00:00

abstract：:X inactivation equalizes the dosage of gene expression between the sexes, but some genes escape silencing and are thus expressed from both alleles in females. To survey X inactivation and escape in mouse, we performed RNA sequencing in Mus musculus x Mus spretus cells with complete skewing of X inactivation, relying o...

journal_title：Genome research

authors： Yang F,Babak T,Shendure J,Disteche CM

更新日期：2010-05-01 00:00:00

abstract：:Telomeres shorten with each cell division and can ultimately become substrates for nonhomologous end-joining repair, leading to large-scale genomic rearrangements of the kind frequently observed in human cancers. We have characterized more than 1400 telomere fusion events at the single-molecule level, using a combinat...

journal_title：Genome research

authors： Liddiard K,Ruis B,Takasugi T,Harvey A,Ashelford KE,Hendrickson EA,Baird DM

更新日期：2016-05-01 00:00:00

abstract：:Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 × 10(-3)). Using three diffe...

journal_title：Genome research

authors： Andrews T,Honti F,Pfundt R,de Leeuw N,Hehir-Kwa J,Vulto-van Silfhout A,de Vries B,Webber C

更新日期：2015-06-01 00:00:00

abstract：:Despite claims that the mammalian Y Chromosome is on a path to extinction, comparative sequence analysis of primate Y Chromosomes has shown the decay of the ancestral single-copy genes has all but ceased in this eutherian lineage. The suite of single-copy Y-linked genes is highly conserved among the majority of euther...

journal_title：Genome research

authors： Brashear WA,Raudsepp T,Murphy WJ

更新日期：2018-12-01 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：: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：:Pollen, the male gametophyte of flowering plants, represents an ideal biological system to study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon hydration, the metabolically quiescent pollen rapidly switches to an active state, exhibiting extremely fast growth. This rapid switch req...

journal_title：Genome research

authors： Grobei MA,Qeli E,Brunner E,Rehrauer H,Zhang R,Roschitzki B,Basler K,Ahrens CH,Grossniklaus U

更新日期：2009-10-01 00:00:00

abstract：:The development of high-throughput sequencing (HTS) technologies has opened the door to novel methods for detecting copy number variants (CNVs) in the human genome. While in the past CNVs have been detected based on array CGH data, recent studies have shown that depth-of-coverage information from HTS technologies can ...

journal_title：Genome research

authors： Medvedev P,Fiume M,Dzamba M,Smith T,Brudno M

更新日期：2010-11-01 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：: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 developed the CADLIVE (Computer-Aided Design of LIVing systEms) Simulator that provided a rule-based automatic way to convert biochemical network maps into dynamic models, which enables simulating their dynamics without going through all of the reactions down to the details of exact kinetic parameters. The sim...

journal_title：Genome research

authors： Kurata H,Masaki K,Sumida Y,Iwasaki R

更新日期：2005-04-01 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：:The primate-specific multisequence family chAB4 is represented with approximately 40 copies within the haploid human genome. Former analyis revealed that unusually long repetition units ( > 35 kb) are distributed to at least eight different chromosomal loci. Remarkably varying copy-numbers within the genomes of closel...

journal_title：Genome research

authors： Wöhr G,Fink T,Assum G

更新日期：1996-04-01 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：: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：: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