Core promoter T-blocks correlate with gene expression levels in C. elegans.

abstract：:The sequence of the first plant genome was completed and published at the end of 2000. This spawned a series of large-scale projects aimed at discovering the functions of the 25,000+ genes identified in Arabidopsis thaliana (Arabidopsis). This review summarizes progress made in the past five years and speculates about...

journal_title：Genome research

authors： Bevan M,Walsh S

更新日期：2005-12-01 00:00:00

abstract：:Although much is known about genetic variation in human and African great ape (chimpanzee, bonobo, and gorilla) genomes, substantially less is known about variation in gene-expression profiles within and among these species. This information is necessary for defining transcriptional regulatory networks that contribute...

journal_title：Genome research

authors： Karaman MW,Houck ML,Chemnick LG,Nagpal S,Chawannakul D,Sudano D,Pike BL,Ho VV,Ryder OA,Hacia JG

更新日期：2003-07-01 00:00:00

abstract：:One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproduct...

journal_title：Genome research

authors： Mack KL,Campbell P,Nachman MW

更新日期：2016-04-01 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：:In mammals, genetic recombination during meiosis is limited to a set of 1- to 2-kb regions termed hotspots. Their locations are predominantly determined by the zinc finger protein PRDM9, which binds to DNA in hotspots and subsequently uses its SET domain to locally trimethylate histone H3 at lysine 4 (H3K4me3). This s...

journal_title：Genome research

authors： Baker CL,Walker M,Kajita S,Petkov PM,Paigen K

更新日期：2014-05-01 00:00:00

abstract：:The vomeronasal system of mice is thought to be specialized in the detection of pheromones. Two multigene families have been identified that encode proteins with seven putative transmembrane domains and that are expressed selectively in subsets of neurons of the vomeronasal organ. The products of these vomeronasal rec...

journal_title：Genome research

authors： Del Punta K,Rothman A,Rodriguez I,Mombaerts P

更新日期：2000-12-01 00:00:00

abstract：:Annotation transfer is a principal process in genome annotation. It involves "transferring" structural and functional annotation to uncharacterized open reading frames (ORFs) in a newly completed genome from experimentally characterized proteins similar in sequence. To prevent errors in genome annotation, it is import...

journal_title：Genome research

authors： Hegyi H,Gerstein M

更新日期：2001-10-01 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 lack of long-term evolutionary conservation of microRNA (miRNA) target sites appears to contradict many analyses of their functions. Several hypotheses have been offered, but an attractive one-that the conservation may be a function of taxonomic hierarchy (vertebrates, mammals, primates, etc.)-has rarely been disc...

journal_title：Genome research

authors： Xu J,Zhang R,Shen Y,Liu G,Lu X,Wu CI

更新日期：2013-11-01 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：:We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spannin...

journal_title：Genome research

authors： Sharim H,Grunwald A,Gabrieli T,Michaeli Y,Margalit S,Torchinsky D,Arielly R,Nifker G,Juhasz M,Gularek F,Almalvez M,Dufault B,Chandra SS,Liu A,Bhattacharya S,Chen YW,Vilain E,Wagner KR,Pevsner J,Reifenberger J,Lam

更新日期：2019-04-01 00:00:00

abstract：:We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...

journal_title：Genome research

authors： Edwards YH,Putt W,Lekoape KM,Stott D,Fox M,Hopkinson DA,Sowden J

更新日期：1996-03-01 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：:Comparative gene mapping in mammals typically involves identification of segments of conserved synteny in diverse genomes. The development of maps that permit comparison of gene order within conserved synteny has not advanced beyond the mouse map that takes advantage of linkage analysis in interspecific backcrosses. R...

journal_title：Genome research

authors： Yang YP,Womack JE

更新日期：1998-07-01 00:00:00

abstract：:A rigorous analysis of the Merck-sponsored EST data with respect to known gene sequences increases the utility of the data set and helps refine methods for building a gene index. A highly curated human transcript data base was used as a reference data set of known genes. A detailed analysis of EST sequences derived fr...

journal_title：Genome research

authors： Aaronson JS,Eckman B,Blevins RA,Borkowski JA,Myerson J,Imran S,Elliston KO

更新日期：1996-09-01 00:00:00

abstract：:The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is ...

journal_title：Genome research

authors： Yáñez-Cuna JO,Dinh HQ,Kvon EZ,Shlyueva D,Stark A

更新日期：2012-10-01 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：:Translocations are known to affect the expression of genes at the breakpoints and, in the case of unbalanced translocations, alter the gene copy number. However, a comprehensive understanding of the functional impact of this class of variation is lacking. Here, we have studied the effect of balanced chromosomal rearra...

journal_title：Genome research

authors： Harewood L,Schütz F,Boyle S,Perry P,Delorenzi M,Bickmore WA,Reymond A

更新日期：2010-05-01 00:00:00

abstract：:Many missense substitutions are identified in single nucleotide polymorphism (SNP) data and large-scale random mutagenesis projects. Each amino acid substitution potentially affects protein function. We have constructed a tool that uses sequence homology to predict whether a substitution affects protein function. SIFT...

journal_title：Genome research

authors： Ng PC,Henikoff S

更新日期：2001-05-01 00:00:00

abstract：:We have developed a computer program that aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing error...

journal_title：Genome research

authors： Wheelan SJ,Church DM,Ostell JM

更新日期：2001-11-01 00:00:00

abstract：:Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously in...

journal_title：Genome research

authors： Hormozdiari F,Penn O,Borenstein E,Eichler EE

更新日期：2015-01-01 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：:Using both env and long terminal repeat (LTR) sequences, with maximal representation of genetic diversity within primate strains, we revise and expand the unique evolutionary history of human and simian T-cell leukemia/lymphotropic viruses (HTLV/STLV). Based on the robust application of three different phylogenetic al...

journal_title：Genome research

authors： Slattery JP,Franchini G,Gessain A

更新日期：1999-06-01 00:00:00

abstract：:Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships po...

journal_title：Genome research

authors： Horvath JE,Weisrock DW,Embry SL,Fiorentino I,Balhoff JP,Kappeler P,Wray GA,Willard HF,Yoder AD

更新日期：2008-03-01 00:00:00

abstract：:Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies of 82 synthetic single-stranded oligonucleotides comprising all tetra- and trinucleotide repeats revealed an inverse co...

journal_title：Genome research

authors： Bacolla A,Larson JE,Collins JR,Li J,Milosavljevic A,Stenson PD,Cooper DN,Wells RD

更新日期：2008-10-01 00:00:00

abstract：:Diversity in the antigen-binding receptors of the immune system has long been a primary interest of biologists. Recently it has been suggested that polymorphism in regulatory (noncoding) gene segments is of substantial importance as well. Here, we survey the level of variation in MHC class II gene promoters in man and...

journal_title：Genome research

authors： Cowell LG,Kepler TB,Janitz M,Lauster R,Mitchison NA

更新日期：1998-02-01 00:00:00

abstract：:Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchr...

journal_title：Genome research

authors： Kirsch S,Münch C,Jiang Z,Cheng Z,Chen L,Batz C,Eichler EE,Schempp W

更新日期：2008-07-01 00:00:00

abstract：:The human genome is estimated to contain 23,000 to 33,000 retropseudogenes. To study the properties of genes giving rise to these retroelements, we compared the structure and expression of genes with or without known retropseudogenes. Four main features have emerged from the analysis of 181 genes associated to retrops...

journal_title：Genome research

authors： Gonçalves I,Duret L,Mouchiroud D

更新日期：2000-05-01 00:00:00

abstract：:CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in hu...

journal_title：Genome research

authors： Smallwood A,Hon GC,Jin F,Henry RE,Espinosa JM,Ren B

更新日期：2012-08-01 00:00:00

abstract：:We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biologic...

journal_title：Genome research

authors： Castillo-Davis CI,Kondrashov FA,Hartl DL,Kulathinal RJ

更新日期：2004-05-01 00:00:00