Predicting deleterious amino acid substitutions.

abstract：:Next-generation sequencing technologies have made it possible to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for ...

journal_title：Genome research

authors： Bansal V,Harismendy O,Tewhey R,Murray SS,Schork NJ,Topol EJ,Frazer KA

更新日期：2010-04-01 00:00:00

abstract：:Human genomic data of many types are readily available, but the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it from a systems level, and apply it to the study of specific pathways or genetic disorders. An investigator could best explore a particular prot...

journal_title：Genome research

authors： Huttenhower C,Haley EM,Hibbs MA,Dumeaux V,Barrett DR,Coller HA,Troyanskaya OG

更新日期：2009-06-01 00:00:00

abstract：:Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities...

journal_title：Genome research

authors： Robinson MD,Strbenac D,Stirzaker C,Statham AL,Song J,Speed TP,Clark SJ

更新日期：2012-12-01 00:00:00

abstract：:Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form...

journal_title：Genome research

authors： Navin N,Krasnitz A,Rodgers L,Cook K,Meth J,Kendall J,Riggs M,Eberling Y,Troge J,Grubor V,Levy D,Lundin P,Månér S,Zetterberg A,Hicks J,Wigler M

更新日期：2010-01-01 00:00:00

abstract：:To gauge the complexity of gene regulation in yeast, it is essential to know how much promoter sequence is functional. Conservation across species can be a sensitive means of detecting functional sequences, provided that the significance of conservation can be accurately calibrated with the local neutral mutation rate...

journal_title：Genome research

authors： Chin CS,Chuang JH,Li H

更新日期：2005-02-01 00:00:00

abstract：:The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution--such as changes in gene expression regulation-remains unknown. A transition...

journal_title：Genome research

authors： Fraser HB,Levy S,Chavan A,Shah HB,Perez JC,Zhou Y,Siegal ML,Sinha H

更新日期：2012-10-01 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：:Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing-based methods for cell lineage analysis depend on low-resolution bulk analysis or rely on extensive single-cell sequencing, which is not scalable and could be biased ...

journal_title：Genome research

authors： Biezuner T,Spiro A,Raz O,Amir S,Milo L,Adar R,Chapal-Ilani N,Berman V,Fried Y,Ainbinder E,Cohen G,Barr HM,Halaban R,Shapiro E

更新日期：2016-11-01 00:00:00

abstract：:We developed a microarray platform for PCR amplification-independent expression profiling of minute samples. A novel scanning system combined with specialized biochips enables detection down to individual fluorescent oligonucleotide molecules specifically hybridized to their complementary sequence over the entire bioc...

journal_title：Genome research

authors： Hesse J,Jacak J,Kasper M,Regl G,Eichberger T,Winklmayr M,Aberger F,Sonnleitner M,Schlapak R,Howorka S,Muresan L,Frischauf AM,Schütz GJ

更新日期：2006-08-01 00:00:00

abstract：:The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we developed a method, termed "GeSNP," to mine the detailed hybridization patterns in oligonucleotide array expression data fo...

journal_title：Genome research

authors： Greenhall JA,Zapala MA,Cáceres M,Libiger O,Barlow C,Schork NJ,Lockhart DJ

更新日期：2007-08-01 00:00:00

abstract：:We have developed a simplified method for multiplex PCR based on the use of chimeric primers. Each primer contains a 3' region complementary to sequence-specific recognition sites and a 5' region made up of an unrelated 20-nucleotide sequence. Identical reaction conditions, cycling times, and annealing temperatures ha...

journal_title：Genome research

authors： Shuber AP,Grondin VJ,Klinger KW

更新日期：1995-12-01 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：:Remnants of more than 3 million transposable elements, primarily retroelements, comprise nearly half of the human genome and have generated much speculation concerning their evolutionary significance. We have exploited the draft human genome sequence to examine the distributions of retroelements on a genome-wide scale...

journal_title：Genome research

authors： Medstrand P,van de Lagemaat LN,Mager DL

更新日期：2002-10-01 00:00:00

abstract：:Eukaryotic translation initiation involves preinitiation ribosomal complex 5'-to-3' directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak ...

journal_title：Genome research

authors： Benitez-Cantos MS,Yordanova MM,O'Connor PBF,Zhdanov AV,Kovalchuk SI,Papkovsky DB,Andreev DE,Baranov PV

更新日期：2020-07-01 00:00:00

abstract：:One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of ...

journal_title：Genome research

authors： Guigó R,Agarwal P,Abril JF,Burset M,Fickett JW

更新日期：2000-10-01 00:00:00

abstract：:Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distan...

journal_title：Genome research

authors： Mortlock DP,Guenther C,Kingsley DM

更新日期：2003-09-01 00:00:00

abstract：:Telomeres shorten with each cell division and can ultimately become substrates for nonhomologous end-joining repair, leading to large-scale genomic rearrangements of the kind frequently observed in human cancers. We have characterized more than 1400 telomere fusion events at the single-molecule level, using a combinat...

journal_title：Genome research

authors： Liddiard K,Ruis B,Takasugi T,Harvey A,Ashelford KE,Hendrickson EA,Baird DM

更新日期：2016-05-01 00:00:00

abstract：:A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic l...

journal_title：Genome research

authors： Doerks T,Copley RR,Schultz J,Ponting CP,Bork P

更新日期：2002-01-01 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：: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：: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：:Recent computational and experimental work suggests that functional modules underlie much of cellular physiology and are a useful unit of cellular organization from the perspective of systems biology. Because interactions among modules can give rise to higher-level properties that are essential to cellular function, a...

journal_title：Genome research

authors： Petti AA,Church GM

更新日期：2005-09-01 00:00:00

abstract：:Here, we report that CRISPR guide RNAs (gRNAs) with a 5'-triphosphate group (5'-ppp gRNAs) produced via in vitro transcription trigger RNA-sensing innate immune responses in human and murine cells, leading to cytotoxicity. 5'-ppp gRNAs in the cytosol are recognized by DDX58, which in turn activates type I interferon r...

journal_title：Genome research

authors： Kim S,Koo T,Jee HG,Cho HY,Lee G,Lim DG,Shin HS,Kim JS

更新日期：2018-02-22 00:00:00

abstract：:The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we...

journal_title：Genome research

authors： Lee IY,Westaway D,Smit AF,Wang K,Seto J,Chen L,Acharya C,Ankener M,Baskin D,Cooper C,Yao H,Prusiner SB,Hood LE

更新日期：1998-10-01 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：: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：:Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized th...

journal_title：Genome research

authors： Nolte V,Pandey RV,Kofler R,Schlötterer C

更新日期：2013-01-01 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：:Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using...

journal_title：Genome research

authors： Fungtammasan A,Ananda G,Hile SE,Su MS,Sun C,Harris R,Medvedev P,Eckert K,Makova KD

更新日期：2015-05-01 00:00:00

abstract：:Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. Gr...

journal_title：Genome research

authors： Zhou Z,Alikhan NF,Sergeant MJ,Luhmann N,Vaz C,Francisco AP,Carriço JA,Achtman M

更新日期：2018-09-01 00:00:00