Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors.

abstract：:A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. ...

journal_title：Genome research

authors： Goldstein B,Agranat-Tamir L,Light D,Ben-Naim Zgayer O,Fishman A,Lamm AT

更新日期：2017-03-01 00:00:00

abstract：:In the attempt to understand human variation and the genetic basis of complex disease, a tremendous number of single nucleotide polymorphisms (SNPs) have been discovered and deposited into NCBI's dbSNP public database. More than 2.7 million SNPs in the database have genotype information. This data provides an invaluab...

journal_title：Genome research

authors： Zaitlen NA,Kang HM,Feolo ML,Sherry ST,Halperin E,Eskin E

更新日期：2005-11-01 00:00:00

abstract：:Identity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographi...

journal_title：Genome research

authors： Rodriguez JM,Bercovici S,Huang L,Frostig R,Batzoglou S

更新日期：2015-02-01 00:00:00

abstract：:Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires' disease. Just five sequence types (ST), from more than 2000 currently described, cause nearly half of disease cases in northwest Europe. Here, we report the sequence and analyses of 364 L. pneumophila genomes, including 337 fro...

journal_title：Genome research

authors： David S,Rusniok C,Mentasti M,Gomez-Valero L,Harris SR,Lechat P,Lees J,Ginevra C,Glaser P,Ma L,Bouchier C,Underwood A,Jarraud S,Harrison TG,Parkhill J,Buchrieser C

更新日期：2016-11-01 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：: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：:The phenotypic variation of living organisms is shaped by genetics, environment, and their interaction. Understanding phenotypic plasticity under natural conditions is hindered by the apparently complex environment and the interacting genes and pathways. Herein, we report findings from the dissection of rice flowering...

journal_title：Genome research

authors： Guo T,Mu Q,Wang J,Vanous AE,Onogi A,Iwata H,Li X,Yu J

更新日期：2020-05-01 00:00:00

abstract：:CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the...

journal_title：Genome research

authors： Chen R,Sodergren E,Weinstock GM,Gibbs RA

更新日期：2004-04-01 00:00:00

abstract：:Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using populati...

journal_title：Genome research

authors： Khodursky S,Svetec N,Durkin SM,Zhao L

更新日期：2020-06-01 00:00:00

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：:A small set of core transcription factors (TFs) dominates control of the gene expression program in embryonic stem cells and other well-studied cellular models. These core TFs collectively regulate their own gene expression, thus forming an interconnected auto-regulatory loop that can be considered the core transcript...

journal_title：Genome research

authors： Saint-André V,Federation AJ,Lin CY,Abraham BJ,Reddy J,Lee TI,Bradner JE,Young RA

更新日期：2016-03-01 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：: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：:Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model...

journal_title：Genome research

authors： Storlazzi CT,Lonoce A,Guastadisegni MC,Trombetta D,D'Addabbo P,Daniele G,L'Abbate A,Macchia G,Surace C,Kok K,Ullmann R,Purgato S,Palumbo O,Carella M,Ambros PF,Rocchi M

更新日期：2010-09-01 00:00:00

abstract：:Histone modifications are now well-established mediators of transcriptional programs that distinguish cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive gene expression changes has been little studied on a genome-wide scale. Vascular endothelial growth facto...

journal_title：Genome research

authors： Zhang B,Day DS,Ho JW,Song L,Cao J,Christodoulou D,Seidman JG,Crawford GE,Park PJ,Pu WT

更新日期：2013-06-01 00:00:00

abstract：:Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...

journal_title：Genome research

authors： Copley RR,Totrov M,Linnell J,Field S,Ragoussis J,Udalova IA

更新日期：2007-09-01 00:00:00

abstract：:Low-copy repeats, or segmental duplications, are highly dynamic regions in the genome. The low-copy repeats on chromosome 22q11.2 (LCR22) are a complex mosaic of genes and pseudogenes formed by duplication processes; they mediate chromosome rearrangements associated with velo-cardio-facial syndrome/DiGeorge syndrome, ...

journal_title：Genome research

authors： Babcock M,Pavlicek A,Spiteri E,Kashork CD,Ioshikhes I,Shaffer LG,Jurka J,Morrow BE

更新日期：2003-12-01 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：:The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of centromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere ...

journal_title：Genome research

authors： Contreras-Galindo R,Fischer S,Saha AK,Lundy JD,Cervantes PW,Mourad M,Wang C,Qian B,Dai M,Meng F,Chinnaiyan A,Omenn GS,Kaplan MH,Markovitz DM

更新日期：2017-12-01 00:00:00

abstract：:Gene duplication and alternative splicing are important sources of proteomic diversity. Despite research indicating that gene duplication and alternative splicing are negatively correlated, the evolutionary relationship between the two remains unclear. One manner in which alternative splicing and gene duplication may ...

journal_title：Genome research

authors： Lambert MJ,Cochran WO,Wilde BM,Olsen KG,Cooper CD

更新日期：2015-05-01 00:00:00

abstract：:Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and lit...

journal_title：Genome research

authors： Ma L,Zhao B,Chen K,Thomas A,Tuteja JH,He X,He C,White KP

更新日期：2017-03-01 00:00:00

abstract：:Isochromosome 17q, or i(17q), is one of the most frequent nonrandom changes occurring in human neoplasia. Most of the i(17q) breakpoints cluster within a approximately 240-kb interval located in the Smith-Magenis syndrome common deletion region in 17p11.2. The breakpoint cluster region is characterized by a complex ar...

journal_title：Genome research

authors： Carvalho CM,Lupski JR

更新日期：2008-11-01 00:00:00

abstract：:Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target ...

journal_title：Genome research

authors： Bozek M,Cortini R,Storti AE,Unnerstall U,Gaul U,Gompel N

更新日期：2019-05-01 00:00:00

abstract：:Biological products of importance in food (e.g., milk) and medical (e.g., donor blood-derived products) sciences often correspond to mixtures of samples contributed by multiple individuals. Identifying which individuals contributed to the mixture and in what proportions may be of interest in several circumstances. We ...

journal_title：Genome research

authors： Coppieters W,Karim L,Georges M

更新日期：2020-08-01 00:00:00

abstract：:Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of...

journal_title：Genome research

authors： Robbins CM,Tembe WA,Baker A,Sinari S,Moses TY,Beckstrom-Sternberg S,Beckstrom-Sternberg J,Barrett M,Long J,Chinnaiyan A,Lowey J,Suh E,Pearson JV,Craig DW,Agus DB,Pienta KJ,Carpten JD

更新日期：2011-01-01 00:00:00

abstract：:Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than seq...

journal_title：Genome research

authors： Seemann SE,Mirza AH,Hansen C,Bang-Berthelsen CH,Garde C,Christensen-Dalsgaard M,Torarinsson E,Yao Z,Workman CT,Pociot F,Nielsen H,Tommerup N,Ruzzo WL,Gorodkin J

更新日期：2017-08-01 00:00:00

abstract：:Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosa...

journal_title：Genome research

authors： Naqvi S,Bellott DW,Lin KS,Page DC

更新日期：2018-04-01 00:00:00

abstract：:We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different tran...

journal_title：Genome research

authors： Benos PV,Gatt MK,Murphy L,Harris D,Barrell B,Ferraz C,Vidal S,Brun C,Demaille J,Cadieu E,Dreano S,Gloux S,Lelaure V,Mottier S,Galibert F,Borkova D,Miñana B,Kafatos FC,Bolshakov S,Sidén-Kiamos I,Papagiannakis G,S

更新日期：2001-05-01 00:00:00

abstract：:The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. Despite MBD proteins being associated with silencing, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD. We functionally ...

journal_title：Genome research

authors： de Mendoza A,Pflueger J,Lister R

更新日期：2019-08-01 00:00:00

abstract：:Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP ass...

journal_title：Genome research

authors： Hardenbol P,Yu F,Belmont J,Mackenzie J,Bruckner C,Brundage T,Boudreau A,Chow S,Eberle J,Erbilgin A,Falkowski M,Fitzgerald R,Ghose S,Iartchouk O,Jain M,Karlin-Neumann G,Lu X,Miao X,Moore B,Moorhead M,Namsaraev E,

更新日期：2005-02-01 00:00:00