Pattern of sequence variation across 213 environmental response genes.

abstract：:With the genomic sequencing of Arabidopsis nearing completion and rice sequencing very much in its infancy, a key question is whether we can exploit the Arabidopsis sequence to identify candidate genes for traits in cereal crops using a map-based approach. This requires the existence of colinearity between the Arabido...

journal_title：Genome research

authors： Devos KM,Beales J,Nagamura Y,Sasaki T

更新日期：1999-09-01 00:00:00

abstract：:The common genetic variants associated with complex traits typically lie in noncoding DNA and may alter gene regulation in a cell type-specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an expression quantitative trait loci (eQTL) st...

journal_title：Genome research

authors： Grundberg E,Kwan T,Ge B,Lam KC,Koka V,Kindmark A,Mallmin H,Dias J,Verlaan DJ,Ouimet M,Sinnett D,Rivadeneira F,Estrada K,Hofman A,van Meurs JM,Uitterlinden A,Beaulieu P,Graziani A,Harmsen E,Ljunggren O,Ohlsson C,

更新日期：2009-11-01 00:00:00

abstract：:Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of inter...

journal_title：Genome research

authors： Schadt EE,Banerjee O,Fang G,Feng Z,Wong WH,Zhang X,Kislyuk A,Clark TA,Luong K,Keren-Paz A,Chess A,Kumar V,Chen-Plotkin A,Sondheimer N,Korlach J,Kasarskis A

更新日期：2013-01-01 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：:Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 indivi...

journal_title：Genome research

authors： Montgomery SB,Goode DL,Kvikstad E,Albers CA,Zhang ZD,Mu XJ,Ananda G,Howie B,Karczewski KJ,Smith KS,Anaya V,Richardson R,Davis J,1000 Genomes Project Consortium.,MacArthur DG,Sidow A,Duret L,Gerstein M,Makova KD,Marc

更新日期：2013-05-01 00:00:00

abstract：:Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochro...

journal_title：Genome research

authors： Brönner C,Salvi L,Zocco M,Ugolini I,Halic M

更新日期：2017-07-01 00:00:00

abstract：:The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...

journal_title：Genome research

authors： Lazar J,Moreno C,Jacob HJ,Kwitek AE

更新日期：2005-12-01 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：: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：:Large numbers of expressed sequence tags (ESTs) continue to fill public and private databases with partial cDNA sequences. However, using this huge amount of ESTs to facilitate gene finding in genomic sequence imposes a challenge, especially to wet-lab scientists who often have limited computing resources. In an effor...

journal_title：Genome research

authors： Jiang J,Jacob HJ

更新日期：1998-03-01 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：: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：:We find that the degree of impairment of protein function by missense variants is predictable by comparative sequence analysis alone. The applicable range of impairment is not confined to binary predictions that distinguish normal from deleterious variants, but extends continuously from mild to severe effects. The acc...

journal_title：Genome research

authors： Stone EA,Sidow A

更新日期：2005-07-01 00:00:00

abstract：:In Drosophila melanogaster, there is an excess of genes duplicated by retroposition from the X chromosome to the autosomes. Most of those retrogenes that originated on the X chromosome have testis expression pattern. These observations could be explained by natural selection favoring genes that avoided spermatogenesis...

journal_title：Genome research

authors： Vibranovski MD,Zhang Y,Long M

更新日期：2009-05-01 00:00:00

abstract：:The draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromoso...

journal_title：Genome research

authors： Shoguchi E,Kawashima T,Satou Y,Hamaguchi M,Sin-I T,Kohara Y,Putnam N,Rokhsar DS,Satoh N

更新日期：2006-02-01 00:00:00

abstract：:Disregulation of imprinted genes can be associated with tumorigenesis and altered cell differentiation capacity and so could provide adverse outcomes for stem cell applications. Although the maintenance of mouse and primate embryonic stem cells in a pluripotent state has been reported to disrupt the monoallelic expres...

journal_title：Genome research

authors： Kim KP,Thurston A,Mummery C,Ward-van Oostwaard D,Priddle H,Allegrucci C,Denning C,Young L

更新日期：2007-12-01 00:00:00

abstract：:Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels,...

journal_title：Genome research

authors： Krieger G,Lupo O,Levy AA,Barkai N

更新日期：2020-07-01 00:00:00

abstract：:Changes in gene order between the genomes of two related yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum were studied. From the dataset of a previous low coverage sequencing of the S. bayanus var. uvarum genome, 35 different synteny breakpoints between neighboring genes and two cases of l...

journal_title：Genome research

authors： Fischer G,Neuvéglise C,Durrens P,Gaillardin C,Dujon B

更新日期：2001-12-01 00:00:00

abstract：:Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For t...

journal_title：Genome research

authors： Jaffe JD,Stange-Thomann N,Smith C,DeCaprio D,Fisher S,Butler J,Calvo S,Elkins T,FitzGerald MG,Hafez N,Kodira CD,Major J,Wang S,Wilkinson J,Nicol R,Nusbaum C,Birren B,Berg HC,Church GM

更新日期：2004-08-01 00:00:00

abstract：:Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functi...

journal_title：Genome research

authors： Yu Y,Zhang C,Zhou G,Wu S,Qu X,Wei H,Xing G,Dong C,Zhai Y,Wan J,Ouyang S,Li L,Zhang S,Zhou K,Zhang Y,Wu C,He F

更新日期：2001-08-01 00:00:00

abstract：:Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is org...

journal_title：Genome research

authors： Monk D,Wagschal A,Arnaud P,Müller PS,Parker-Katiraee L,Bourc'his D,Scherer SW,Feil R,Stanier P,Moore GE

更新日期：2008-08-01 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：:Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from evolutionary constraints. We systematically analyzed known human and Saccharomyces cerevisiae regulatory elements and disc...

journal_title：Genome research

authors： Liu Y,Liu XS,Wei L,Altman RB,Batzoglou S

更新日期：2004-03-01 00:00:00

abstract：:Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover rates and how these rates are integrated into cellular decisions. We decided to measure mRNA decay rates in two human ce...

journal_title：Genome research

authors： Yang E,van Nimwegen E,Zavolan M,Rajewsky N,Schroeder M,Magnasco M,Darnell JE Jr

更新日期：2003-08-01 00:00:00

abstract：:A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We desc...

journal_title：Genome research

authors： van Opijnen T,Camilli A

更新日期：2012-12-01 00:00:00

abstract：:Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these hu...

journal_title：Genome research

authors： Peyrégne S,Boyle MJ,Dannemann M,Prüfer K

更新日期：2017-09-01 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：:Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...

journal_title：Genome research

authors： Grishkevich V,Hashimshony T,Yanai I

更新日期：2011-05-01 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：:Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcri...

journal_title：Genome research

authors： Liang H,Landweber LF

更新日期：2006-02-01 00:00:00