Searching for SNPs with cloud computing.

abstract：BACKGROUND:Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. RESULT:To develop a...

journal_title：Genome biology

authors： Gentles AJ,Hui AB,Feng W,Azizi A,Nair RV,Bouchard G,Knowles DA,Yu A,Jeong Y,Bejnood A,Forgó E,Varma S,Xu Y,Kuong A,Nair VS,West R,van de Rijn M,Hoang CD,Diehn M,Plevritis SK

更新日期：2020-05-07 00:00:00

abstract：:Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-...

journal_title：Genome biology

authors： Hashimshony T,Senderovich N,Avital G,Klochendler A,de Leeuw Y,Anavy L,Gennert D,Li S,Livak KJ,Rozenblatt-Rosen O,Dor Y,Regev A,Yanai I

更新日期：2016-04-28 00:00:00

abstract：BACKGROUND:Using oligonucleotide microarrays, we compared transcriptional profiles corresponding to the initial cell cycle stages of mouse fibroblasts lacking the small GTPases H-Ras and/or N-Ras with those of matching, wild-type controls. RESULTS:Serum-starved wild-type and knockout ras fibroblasts had very similar t...

journal_title：Genome biology

authors： Castellano E,Guerrero C,Núñez A,De Las Rivas J,Santos E

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Many different methods exist to adjust for variability in cell-type mixture proportions when analyzing DNA methylation studies. Here we present the result of an extensive simulation study, built on cell-separated DNA methylation profiles from Illumina Infinium 450K methylation data, to compare the performanc...

journal_title：Genome biology

authors： McGregor K,Bernatsky S,Colmegna I,Hudson M,Pastinen T,Labbe A,Greenwood CM

更新日期：2016-05-03 00:00:00

abstract：BACKGROUND:Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. RESULTS:To investigate the genetic architecture of therm...

journal_title：Genome biology

authors： Mallard F,Nolte V,Tobler R,Kapun M,Schlötterer C

更新日期：2018-08-20 00:00:00

abstract：BACKGROUND:Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations. RESULTS:We propose a new strategy to identify synergistic TFs by fu...

journal_title：Genome biology

authors： Hu Z,Hu B,Collins JF

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Four hypervariable minisatellite loci were scored on a panel of 116 individuals of various geographical origins representing a large part of the diversity present in house mouse subspecies. Internal structures of alleles were determined by minisatellite variant repeat mapping PCR to produce maps of interming...

journal_title：Genome biology

authors： Bonhomme F,Rivals E,Orth A,Grant GR,Jeffreys AJ,Bois PR

更新日期：2007-01-01 00:00:00

abstract：:Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to ...

journal_title：Genome biology

authors： Sánchez-Martín J,Steuernagel B,Ghosh S,Herren G,Hurni S,Adamski N,Vrána J,Kubaláková M,Krattinger SG,Wicker T,Doležel J,Keller B,Wulff BB

更新日期：2016-10-31 00:00:00

abstract：BACKGROUND:The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. RESULTS:The relative content o...

journal_title：Genome biology

authors： Pushker R,Mira A,Rodríguez-Valera F

更新日期：2004-01-01 00:00:00

abstract：:MAP1-family proteins are classical microtubule-associated proteins (MAPs) that bind along the microtubule lattice. The founding members, MAP1A and MAP1B, are predominantly expressed in neurons, where they are thought to be important in the formation and development of axons and dendrites. Mammalian genomes usually con...

journal_title：Genome biology

authors： Halpain S,Dehmelt L

更新日期：2006-01-01 00:00:00

abstract：:Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released ...

journal_title：Genome biology

authors： Eöry L,Gilbert MT,Li C,Li B,Archibald A,Aken BL,Zhang G,Jarvis E,Flicek P,Burt DW

更新日期：2015-01-29 00:00:00

abstract：BACKGROUND:Differences in 5-hydroxymethylcytosine, 5hmC, distributions may complicate previous observations of abnormal cytosine methylation statuses that are used for the identification of new tumor suppressor gene candidates that are relevant to human hepatocarcinogenesis. The simultaneous detection of 5-methylcytosi...

journal_title：Genome biology

authors： Gao F,Xia Y,Wang J,Lin Z,Ou Y,Liu X,Liu W,Zhou B,Luo H,Zhou B,Wen B,Zhang X,Huang J

更新日期：2014-12-03 00:00:00

abstract：BACKGROUND:We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and m...

journal_title：Genome biology

authors： Clark TG,Andrew T,Cooper GM,Margulies EH,Mullikin JC,Balding DJ

更新日期：2007-01-01 00:00:00

abstract：:Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...

journal_title：Genome biology

authors： Plenge R

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Synthetic genetic interactions have recently been mapped on a genome scale in the budding yeast Saccharomyces cerevisiae, providing a functional view of the central processes of eukaryotic life. Currently, comprehensive genetic interaction networks have not been determined for other species, and we therefore...

journal_title：Genome biology

authors： Koch EN,Costanzo M,Bellay J,Deshpande R,Chatfield-Reed K,Chua G,D'Urso G,Andrews BJ,Boone C,Myers CL

更新日期：2012-07-02 00:00:00

abstract：BACKGROUND:The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have ...

journal_title：Genome biology

authors： Cheung WA,Shao X,Morin A,Siroux V,Kwan T,Ge B,Aïssi D,Chen L,Vasquez L,Allum F,Guénard F,Bouzigon E,Simon MM,Boulier E,Redensek A,Watt S,Datta A,Clarke L,Flicek P,Mead D,Paul DS,Beck S,Bourque G,Lathrop M,

更新日期：2017-03-10 00:00:00

abstract：:Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-p...

journal_title：Genome biology

authors： Hosur R,Peng J,Vinayagam A,Stelzl U,Xu J,Perrimon N,Bienkowska J,Berger B

更新日期：2012-08-31 00:00:00

abstract：BACKGROUND:DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence b...

journal_title：Genome biology

authors： Karabacak Calviello A,Hirsekorn A,Wurmus R,Yusuf D,Ohler U

更新日期：2019-02-21 00:00:00

abstract：BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...

journal_title：Genome biology

authors： Mitchell K,Brito JJ,Mandric I,Wu Q,Knyazev S,Chang S,Martin LS,Karlsberg A,Gerasimov E,Littman R,Hill BL,Wu NC,Yang HT,Hsieh K,Chen L,Littman E,Shabani T,Enik G,Yao D,Sun R,Schroeder J,Eskin E,Zelikovsky A,S

更新日期：2020-03-17 00:00:00

abstract：BACKGROUND:During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole...

journal_title：Genome biology

authors： Siddiqui NU,Li X,Luo H,Karaiskakis A,Hou H,Kislinger T,Westwood JT,Morris Q,Lipshitz HD

更新日期：2012-02-20 00:00:00

abstract：:Big projects in biology - such as the human genome project and a number of related and ensuing enterprises - require big funding. A new tradition is growing in which some types of basic research take place within commercial organizations. This article reviews some of the reasons for this and some of the key players, i...

journal_title：Genome biology

authors： Swindells M

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the deca...

journal_title：Genome biology

authors： Chen H,Li J,Wang Y,Ng PK,Tsang YH,Shaw KR,Mills GB,Liang H

更新日期：2020-02-20 00:00:00

abstract：:Early gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative breast cancers, few are informative for ER negative/HER2 negative an...

journal_title：Genome biology

authors： Haibe-Kains B,Desmedt C,Rothé F,Piccart M,Sotiriou C,Bontempi G

更新日期：2010-01-01 00:00:00

abstract：:The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of...

journal_title：Genome biology

authors： Carter MG,Sharov AA,VanBuren V,Dudekula DB,Carmack CE,Nelson C,Ko MS

更新日期：2005-01-01 00:00:00

abstract：:PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...

journal_title：Genome biology

authors： Wang C,Lin H

更新日期：2021-01-08 00:00:00

abstract：:A report on the 18th Congress of the European Society for Evolutionary Biology (ESEB), Aarhus, Denmark, 20-25 August, 2001. ...

journal_title：Genome biology

authors： Liberles DA

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bay...

journal_title：Genome biology

authors： Castillo-Ramírez S,Corander J,Marttinen P,Aldeljawi M,Hanage WP,Westh H,Boye K,Gulay Z,Bentley SD,Parkhill J,Holden MT,Feil EJ

更新日期：2012-12-27 00:00:00

abstract：:The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....

journal_title：Genome biology

authors： Krakau S,Richard H,Marsico A

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental stud...

journal_title：Genome biology

authors： Coyne RS,Hannick L,Shanmugam D,Hostetler JB,Brami D,Joardar VS,Johnson J,Radune D,Singh I,Badger JH,Kumar U,Saier M,Wang Y,Cai H,Gu J,Mather MW,Vaidya AB,Wilkes DE,Rajagopalan V,Asai DJ,Pearson CG,Findly RC,Di

更新日期：2011-10-17 00:00:00

abstract：BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...

journal_title：Genome biology

authors： Park G,Park JK,Shin SH,Jeon HJ,Kim NKD,Kim YJ,Shin HT,Lee E,Lee KH,Son DS,Park WY,Park D

更新日期：2017-07-21 00:00:00