Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing.

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：:Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We presen...

journal_title：Genome research

authors： Florea L,Di Francesco V,Miller J,Turner R,Yao A,Harris M,Walenz B,Mobarry C,Merkulov GV,Charlab R,Dew I,Deng Z,Istrail S,Li P,Sutton G

更新日期：2005-01-01 00:00:00

abstract：:Large scale gene perturbation experiments generate information about the number of genes whose activity is directly or indirectly affected by a gene perturbation. From this information, one can numerically estimate coarse structural network features such as the total number of direct regulatory interactions and the nu...

journal_title：Genome research

authors： Wagner A

更新日期：2002-02-01 00:00:00

abstract：:Spatial organization of different epigenomic marks was used to infer functions of the epigenome. It remains unclear what can be learned from the temporal changes of the epigenome. Here, we developed a probabilistic model to cluster genomic sequences based on the similarity of temporal changes of multiple epigenomic ma...

journal_title：Genome research

authors： Yu P,Xiao S,Xin X,Song CX,Huang W,McDee D,Tanaka T,Wang T,He C,Zhong S

更新日期：2013-02-01 00:00:00

abstract：:Previously, we have described novel families of genes, warthog (wrt) and groundhog (grd), in Caenorhabditis elegans. They are related to Hedgehog (Hh) through the carboxy-terminal autoprocessing domain (called Hog or Hint). A comprehensive survey revealed 10 genes with Hog/Hint modules in C. elegans. Five of these are...

journal_title：Genome research

authors： Aspöck G,Kagoshima H,Niklaus G,Bürglin TR

更新日期：1999-10-01 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：:Early embryogenesis is characterized by the maternal to zygotic transition (MZT), in which maternally deposited messenger RNAs are degraded while zygotic transcription begins. Before the MZT, post-transcriptional gene regulation by RNA-binding proteins (RBPs) is the dominant force in embryo patterning. We used two mRN...

journal_title：Genome research

authors： Wessels HH,Imami K,Baltz AG,Kolinski M,Beldovskaya A,Selbach M,Small S,Ohler U,Landthaler M

更新日期：2016-07-01 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：:Advances in high-throughput technologies, such as ChIP-chip, and the completion of human and mouse genomic sequences now allow analysis of the mechanisms of gene regulation on a systems level. In this study, we have developed a computational genomics approach (termed ChIPModules), which begins with experimentally dete...

journal_title：Genome research

authors： Jin VX,Rabinovich A,Squazzo SL,Green R,Farnham PJ

更新日期：2006-12-01 00:00:00

abstract：:Facio-scapulo-humeral dystrophy (FSHD), a muscular hereditary disease with a prevalence of 1 in 20,000, is caused by a partial deletion of a subtelomeric repeat array on chromosome 4q. Earlier, we demonstrated the existence in the vicinity of the D4Z4 repeat of a nuclear matrix attachment site, FR-MAR, efficient in no...

journal_title：Genome research

authors： Petrov A,Allinne J,Pirozhkova I,Laoudj D,Lipinski M,Vassetzky YS

更新日期：2008-01-01 00:00:00

abstract：:CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occ...

journal_title：Genome research

authors： Beagan JA,Duong MT,Titus KR,Zhou L,Cao Z,Ma J,Lachanski CV,Gillis DR,Phillips-Cremins JE

更新日期：2017-07-01 00:00:00

abstract：:CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environ...

journal_title：Genome research

authors： Wang H,Maurano MT,Qu H,Varley KE,Gertz J,Pauli F,Lee K,Canfield T,Weaver M,Sandstrom R,Thurman RE,Kaul R,Myers RM,Stamatoyannopoulos JA

更新日期：2012-09-01 00:00:00

abstract：:An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under wha...

journal_title：Genome research

authors： Dupuy D,Li QR,Deplancke B,Boxem M,Hao T,Lamesch P,Sequerra R,Bosak S,Doucette-Stamm L,Hope IA,Hill DE,Walhout AJ,Vidal M

更新日期：2004-10-01 00:00:00

abstract：:Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized...

journal_title：Genome research

authors： Shao W,Wang T

更新日期：2021-01-01 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：:Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed ampli...

journal_title：Genome research

authors： Nabilsi NH,Deleyrolle LP,Darst RP,Riva A,Reynolds BA,Kladde MP

更新日期：2014-02-01 00:00:00

abstract：:The alignment of full-length human cDNA sequences to the finished sequence of the human genome provides a unique opportunity to study the distribution of genes throughout the genome. By analyzing the distances between 23,752 genes, we identified a class of divergently transcribed gene pairs, representing more than 10%...

journal_title：Genome research

authors： Trinklein ND,Aldred SF,Hartman SJ,Schroeder DI,Otillar RP,Myers RM

更新日期：2004-01-01 00:00:00

abstract：:Gene amplification occurs in most solid tumors and is associated with poor prognosis. Amplification of 20q13.2 is common to several tumor types including breast cancer. The 1 Mb of sequence spanning the 20q13.2 breast cancer amplicon is one of the most exhaustively studied segments of the human genome. These studies h...

journal_title：Genome research

authors： Collins C,Volik S,Kowbel D,Ginzinger D,Ylstra B,Cloutier T,Hawkins T,Predki P,Martin C,Wernick M,Kuo WL,Alberts A,Gray JW

更新日期：2001-06-01 00:00:00

abstract：:Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering ...

journal_title：Genome research

authors： Ayele M,Haas BJ,Kumar N,Wu H,Xiao Y,Van Aken S,Utterback TR,Wortman JR,White OR,Town CD

更新日期：2005-04-01 00:00:00

abstract：:We have used the FANTOM2 mouse cDNA set (60,770 clones), public mRNA data, and mouse genome sequence data to identify 2481 pairs of sense-antisense transcripts and 899 further pairs of nonantisense bidirectional transcription based upon genomic mapping. The analysis greatly expands the number of known examples of sens...

journal_title：Genome research

authors： Kiyosawa H,Yamanaka I,Osato N,Kondo S,Hayashizaki Y,RIKEN GER Group.,GSL Members.

更新日期：2003-06-01 00:00:00

abstract：:The epistatically interacting modifier loci (Apmt1 and Apmt2) accelerate the polyoma Middle-T (PyVT)-induced mammary tumor. To identify potential candidate genes loci, a combined bioinformatics and genomics strategy was used. On the basis of the assumption that the loci were functioning in the same or intersecting pat...

journal_title：Genome research

authors： Cozma D,Lukes L,Rouse J,Qiu TH,Liu ET,Hunter KW

更新日期：2002-06-01 00:00:00

abstract：:Mirtrons are intronic hairpin substrates of the dicing machinery that generate functional microRNAs. In this study, we describe experimental assays that defined the essential requirements for entry of introns into the mirtron pathway. These data informed a bioinformatic screen that effectively identified functional mi...

journal_title：Genome research

authors： Chung WJ,Agius P,Westholm JO,Chen M,Okamura K,Robine N,Leslie CS,Lai EC

更新日期：2011-02-01 00:00:00

abstract：:Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted...

journal_title：Genome research

authors： Court F,Tayama C,Romanelli V,Martin-Trujillo A,Iglesias-Platas I,Okamura K,Sugahara N,Simón C,Moore H,Harness JV,Keirstead H,Sanchez-Mut JV,Kaneki E,Lapunzina P,Soejima H,Wake N,Esteller M,Ogata T,Hata K,Nakabayashi

更新日期：2014-04-01 00:00:00

abstract：:Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumula...

journal_title：Genome research

authors： Keith N,Tucker AE,Jackson CE,Sung W,Lucas Lledó JI,Schrider DR,Schaack S,Dudycha JL,Ackerman M,Younge AJ,Shaw JR,Lynch M

更新日期：2016-01-01 00:00:00

abstract：:We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which a...

journal_title：Genome research

authors： Skinner BM,Sargent CA,Churcher C,Hunt T,Herrero J,Loveland JE,Dunn M,Louzada S,Fu B,Chow W,Gilbert J,Austin-Guest S,Beal K,Carvalho-Silva D,Cheng W,Gordon D,Grafham D,Hardy M,Harley J,Hauser H,Howden P,Howe K,

更新日期：2016-01-01 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：:By surveying a filtered, high-quality set of SNPs in the human genome, we have found that SNPs positioned 1, 2, 4, 6, or 8 bp apart are more frequent than SNPs positioned 3, 5, 7, or 9 bp apart. The observed pattern is not restricted to genomic regions that are known to cause sequencing or alignment errors, for exampl...

journal_title：Genome research

authors： Madsen BE,Villesen P,Wiuf C

更新日期：2007-10-01 00:00:00

abstract：:It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood ...

journal_title：Genome research

authors： Liu X,Fu YX,Maxwell TJ,Boerwinkle E

更新日期：2010-01-01 00:00:00

abstract：:The recently identified mouse obese (ob) gene apparently encodes a secreted protein that may function in the signaling pathway of adipose tissue. Mutations in the mouse ob gene are associated with the early development of gross obesity. A detailed knowledge concerning the RNA expression pattern and precise genomic loc...

journal_title：Genome research

authors： Green ED,Maffei M,Braden VV,Proenca R,DeSilva U,Zhang Y,Chua SC Jr,Leibel RL,Weissenbach J,Friedman JM

更新日期：1995-08-01 00:00:00

abstract：:Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g., granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs)...

journal_title：Genome research

authors： Fehniger TA,Wylie T,Germino E,Leong JW,Magrini VJ,Koul S,Keppel CR,Schneider SE,Koboldt DC,Sullivan RP,Heinz ME,Crosby SD,Nagarajan R,Ramsingh G,Link DC,Ley TJ,Mardis ER

更新日期：2010-11-01 00:00:00