Assessment of genome-wide protein function classification for Drosophila melanogaster.

abstract：:Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of the relative importance of these two forces is the observation that both diversity within species and interspecies diver...

journal_title：Genome research

authors： Hellmann I,Prüfer K,Ji H,Zody MC,Pääbo S,Ptak SE

更新日期：2005-09-01 00:00:00

abstract：:We have identified three new families of insulin homologs in Caenorhabditis elegans. In two of these families, concerted mutations suggest that an additional disulfide bond links B and A domains, and that the A-domain internal disulfide bond is substituted by a hydrophobic interaction. Homology modeling remarkably con...

journal_title：Genome research

authors： Duret L,Guex N,Peitsch MC,Bairoch A

更新日期：1998-04-01 00:00:00

abstract：:Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for speci...

journal_title：Genome research

authors： Cui L,Wall PK,Leebens-Mack JH,Lindsay BG,Soltis DE,Doyle JJ,Soltis PS,Carlson JE,Arumuganathan K,Barakat A,Albert VA,Ma H,dePamphilis CW

更新日期：2006-06-01 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：:The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical m...

journal_title：Genome research

authors： Bankier AT,Spriggs HF,Fartmann B,Konfortov BA,Madera M,Vogel C,Teichmann SA,Ivens A,Dear PH

更新日期：2003-08-01 00:00:00

abstract：:Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to the GART gene. This cluster includes both components of the interferon alpha/beta-receptor (IFNAR1 and IFNAR2) and the second components o...

journal_title：Genome research

authors： Reboul J,Gardiner K,Monneron D,Uzé G,Lutfalla G

更新日期：1999-03-01 00:00:00

abstract：:The detailed genomic organization of a gene-dense region at human chromosome 12p13, spanning 223 kb of contiguous sequence, was determined. This region is composed of 20 genes and several other expressed sequences. Experimental tools including RT-PCR and cDNA sequencing, combined with gene prediction programs, were ut...

journal_title：Genome research

authors： Ansari-Lari MA,Shen Y,Muzny DM,Lee W,Gibbs RA

更新日期：1997-03-01 00:00:00

abstract：:Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host plasma membrane and is involved in protein transport and trafficking. We have identified a novel subtelomeric gene famil...

journal_title：Genome research

authors： Sam-Yellowe TY,Florens L,Johnson JR,Wang T,Drazba JA,Le Roch KG,Zhou Y,Batalov S,Carucci DJ,Winzeler EA,Yates JR 3rd

更新日期：2004-06-01 00:00:00

abstract：:Mutations in the human AIRE gene (hAIRE) result in the development of an autoimmune disease named APECED (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy; OMIM 240300). Previously, we have cloned hAIRE and shown that it codes for a putative transcription-associated factor. Here we report the cloning and...

journal_title：Genome research

authors： Blechschmidt K,Schweiger M,Wertz K,Poulson R,Christensen HM,Rosenthal A,Lehrach H,Yaspo ML

更新日期：1999-02-01 00:00:00

abstract：:Analysis procedures are needed to extract useful information from the large amount of gene expression data that is becoming available. This work describes a set of analytical tools and their application to yeast cell cycle data. The components of our approach are (1) a similarity measure that reduces the number of fal...

journal_title：Genome research

authors： Heyer LJ,Kruglyak S,Yooseph S

更新日期：1999-11-01 00:00:00

abstract：:We have identified previously a putative tumor suppressor gene (TSG) locus at human chromosome (hchr) 7q31 showing that it is altered in a variety of human epithelial tumors. To determine whether this TSG is conserved in mice, we studied loss of heterozygosity (LOH) in chemically induced mouse liver adenomas. The LOH ...

journal_title：Genome research

authors： Zenklusen JC,Rodriguez LV,LaCava M,Wang Z,Goldstein LS,Conti CJ

更新日期：1996-11-01 00:00:00

abstract：:The in vitro cloning of DNA molecules traditionally uses PCR amplification or site-specific restriction endonucleases to generate linear DNA inserts with defined termini and requires DNA ligase to covalently join those inserts to vectors with the corresponding ends. We have used the properties of Vaccinia DNA topoisom...

journal_title：Genome research

authors： Heyman JA,Cornthwaite J,Foncerrada L,Gilmore JR,Gontang E,Hartman KJ,Hernandez CL,Hood R,Hull HM,Lee WY,Marcil R,Marsh EJ,Mudd KM,Patino MJ,Purcell TJ,Rowland JJ,Sindici ML,Hoeffler JP

更新日期：1999-04-01 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：:Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions and confirmed their robust functional signatures. Of the ASC base pairs, 99.7% were noncoding, suggesting tha...

journal_title：Genome research

authors： del Rosario RC,Rayan NA,Prabhakar S

更新日期：2014-09-01 00:00:00

abstract：:High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs with various lengths, and GC content covering a 2(20) concentration ra...

journal_title：Genome research

authors： Jiang L,Schlesinger F,Davis CA,Zhang Y,Li R,Salit M,Gingeras TR,Oliver B

更新日期：2011-09-01 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：:Mosaic mutations present in the germline have important implications for reproductive risk and disease transmission. We previously demonstrated a phenomenon occurring in the male germline, whereby specific mutations arising spontaneously in stem cells (spermatogonia) lead to clonal expansion, resulting in elevated mut...

journal_title：Genome research

authors： Maher GJ,Ralph HK,Ding Z,Koelling N,Mlcochova H,Giannoulatou E,Dhami P,Paul DS,Stricker SH,Beck S,McVean G,Wilkie AOM,Goriely A

更新日期：2018-12-01 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：: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：:Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...

journal_title：Genome research

authors： Feber A,Wilson GA,Zhang L,Presneau N,Idowu B,Down TA,Rakyan VK,Noon LA,Lloyd AC,Stupka E,Schiza V,Teschendorff AE,Schroth GP,Flanagan A,Beck S

更新日期：2011-04-01 00:00:00

abstract：:RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolki...

journal_title：Genome research

authors： Derr A,Yang C,Zilionis R,Sergushichev A,Blodgett DM,Redick S,Bortell R,Luban J,Harlan DM,Kadener S,Greiner DL,Klein A,Artyomov MN,Garber M

更新日期：2016-10-01 00:00:00

abstract：:Identifying genes in the genomic context is central to a cell's ability to interpret the genome. Yet, in general, the signals used to define eukaryotic genes are poorly described. Here, we derived simple classifiers that identify where transcription will initiate and terminate using nucleic acid sequence features dete...

journal_title：Genome research

authors： de Boer CG,van Bakel H,Tsui K,Li J,Morris QD,Nislow C,Greenblatt JF,Hughes TR

更新日期：2014-01-01 00:00:00

abstract：:Metagenomic projects generate short, overlapping fragments of DNA sequence, each deriving from a different individual. We report a new method for inferring the scaled mutation rate, theta = 2Neu, and the scaled exponential growth rate, R = Ner, from the site-frequency spectrum of these data while accounting for sequen...

journal_title：Genome research

authors： Johnson PL,Slatkin M

更新日期：2006-10-01 00:00:00

abstract：:Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have charac...

journal_title：Genome research

authors： Enuameh MS,Asriyan Y,Richards A,Christensen RG,Hall VL,Kazemian M,Zhu C,Pham H,Cheng Q,Blatti C,Brasefield JA,Basciotta MD,Ou J,McNulty JC,Zhu LJ,Celniker SE,Sinha S,Stormo GD,Brodsky MH,Wolfe SA

更新日期：2013-06-01 00:00:00

abstract：:Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-...

journal_title：Genome research

authors： Martinez JM,Breidenbach HH,Cawthon R

更新日期：1996-01-01 00:00:00

abstract：:In this study we quantify the features of meiotic recombination on the long arm of human chromosome 21. We constructed a 67. 3-centimorgan (cM) high-resolution, comprehensive, and accurate genetic linkage map of chromosome 21q using 187 highly polymorphic markers covering almost the entire long arm; 46 loci, consistin...

journal_title：Genome research

authors： Lynn A,Kashuk C,Petersen MB,Bailey JA,Cox DR,Antonarakis SE,Chakravarti A

更新日期：2000-09-01 00:00:00

abstract：:We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and othe...

journal_title：Genome research

authors： MackiewiczP,Gierlik A,Kowalczuk M,Dudek MR,Cebrat S

更新日期：1999-05-01 00:00:00

abstract：:A contiguous high-resolution map of 44 loci from a 35-Mb portion of the distal region of the long arm of human chromosome 5, q21-q35, was produced using radiation hybrid (RH) mapping in conjunction with a natural deletion mapping panel. The map includes 30 genes, four sequence-tagged site (STS) loci, and 10 DNA marker...

journal_title：Genome research

authors： Warrington JA,Wasmuth JJ

更新日期：1996-07-01 00:00:00

abstract：:Despite much research, our understanding of the architecture and cis-regulatory elements of human promoters is still lacking. Here, we devised a high-throughput assay to quantify the activity of approximately 15,000 fully designed sequences that we integrated and expressed from a fixed location within the human genome...

journal_title：Genome research

authors： Weingarten-Gabbay S,Nir R,Lubliner S,Sharon E,Kalma Y,Weinberger A,Segal E

更新日期：2019-02-01 00:00:00

abstract：:Organisms with large genomes contain vast amounts of repetitive DNA sequences, much of which is composed of retrotransposons. Amplification of retrotransposons has been postulated to be a major mechanism increasing genome size and leading to "genomic obesity." To gain insights into the relation between retrotransposon...

journal_title：Genome research

authors： Shirasu K,Schulman AH,Lahaye T,Schulze-Lefert P

更新日期：2000-07-01 00:00:00