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Abstract
MOTIVATION: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions, however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users. RESULTS: We present the Experimental Factor Ontology (EFO), designed to meet cross-domain, application focused use cases for gene expression data. We describe our methodology and open source tools ...
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Scientific American, Vol. 303, No. 6. (December 2010), pp. 80-85
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Abstract
For some, a lack of tenure creates a dynamic lab environment. For others, it's a gamble not worth taking. ...
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Nature, Vol. 479, No. 7373. (17 November 2011), pp. 433-435
posted to buggotea janelia-farm
by dullhunk
on 2011-11-23 20:09:28
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European journal of biochemistry / FEBS, Vol. 137, No. 3. (15 December 1983), pp. 501-507
posted to buggotea steve-oliver
by dullhunk
on 2011-05-30 15:16:55
Abstract
A double-stranded ribonuclease has been purified more than 90-fold to near homogeneity from the yeast, Saccharomyces cerevisiae. The enzyme shows a high specificity for double-stranded RNA as its substrate. It has a molecular weight of 27000 as determined by sodium dodecyl sulphate/polyacrylamide gel electrophoresis. The enzyme degrades dsRNA optimally at 30 degrees C; it is stimulated by KCl and by the -SH reagent, dithiothreitol. In contrast to RNase III from Escherichia coli, the yeast enzyme is inhibited by divalent cations. Physiological ...
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posted to buggotea steve-oliver
by dullhunk
on 2011-05-30 15:16:14
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Journal of theoretical biology, Vol. 67, No. 2. (21 July 1977), pp. 195-201
posted to buggotea steve-oliver
by dullhunk
on 2011-05-30 15:12:13
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posted to buggotea steve-oliver
by dullhunk
on 2011-05-30 15:11:53
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Molecular & general genetics : MGG, Vol. 146, No. 3. (2 August 1976), pp. 253-259
posted to buggotea steve-oliver
by dullhunk
on 2011-05-30 11:21:39
Abstract
The fluorinated pyrimidines 5-fluorouracil (5FU) and 5-fluorocytosine (5FC) induce the cytoplasmic petite mutation in the yeast Saccharomyces cerevisiae with high efficiency. It was found that in order to induce the mutation, 5FC must first be deaminated to 5FU. However, mutagenesis does not depend on the further conversion of 5FU to its deoxyriboside (5FUDR) and subsequent blockade of intracellular thymidine synthesis, since 5FUDR itself was found not to be mutagenic, and 5FU-induced mutagenesis was not antagonised by supplying thymidine monophosphate (dTMP) to ...
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posted to buggotea steve-oliver
by dullhunk
on 2011-05-30 11:21:27
Abstract
The fluorinated pyrimidines 5-fluorouracil (5FU) and 5-fluorocytosine (5FC) induce the cytoplasmic petite mutation in the yeastSaccharomyces cerevisiae with high efficiency. It was found that in order to induce the mutation, 5FC must first be deaminated to 5FU. However, mutagenesis does not depend on the further conversion of 5FU to its deoxyriboside (5FUDR) and subsequent blockade of intracellular thymidine synthesis, since 5FUDR itself was found not to be mutagenic, and 5FU-induced mutagenesis was not antagonised by supplying thymidine monophosphate (dTMP) to a ...
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Abstract
Computational efficiency of stochastic kinetic algorithms depend on factors such as the overall species population, the total number of reactions, and the average number of nodal interactions or connectivity in a network. These size measures of the network model can have a significant impact on computational efficiency. In this study, two scalable biological networks are used to compare the size scaling efficiencies of two popular and conceptually distinct stochastic kinetic simulation algorithms—the random substrate method of Firth and Bray (FB), and ...
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The Journal of chemical physics, Vol. 123, No. 11. (15 September 2005)
Abstract
Computational efficiency of stochastic kinetic algorithms depend on factors such as the overall species population, the total number of reactions, and the average number of nodal interactions or connectivity in a network. These size measures of the network model can have a significant impact on computational efficiency. In this study, two scalable biological networks are used to compare the size scaling efficiencies of two popular and conceptually distinct stochastic kinetic simulation algorithms--the random substrate method of Firth and Bray (FB), and ...
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by Emek Demir, Michael P. Cary, Suzanne Paley, et al.Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D'Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C. Lopez-Fuentes, Huaiyu Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Ozgün Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Reubenacker, Matthias Samwald, Martijn van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kei-Hoi H. Cheung, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H. Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S. Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le L. Novère, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D. Karp, Chris Sander, Gary D. Bader
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Abstract
MOTIVATION: Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible ...
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by R. Leinonen, R. Akhtar, E. Birney, et al.L. Bower, A. Cerdeno-Tarraga, Y. Cheng, I. Cleland, N. Faruque, N. Goodgame, R. Gibson, G. Hoad, M. Jang, N. Pakseresht, S. Plaister, R. Radhakrishnan, K. Reddy, S. Sobhany, P. Ten Hoopen, R. Vaughan, V. Zalunin, G. Cochrane
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The objective of ENA is to support and promote the use of nucleotide sequencing as an experimental research platform by providing data submission, archive, search and download services. In this article, we outline these services and describe major changes and improvements introduced during 2010. These include extended EMBL-Bank and SRA-data submission services, extended ...
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Abstract
http://bioonto.de/pmwiki.php/Main/PheneOntology. ...
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by Rasko Leinonen, Ruth Akhtar, Ewan Birney, et al.Lawrence Bower, Ana Cerdeno-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Mikyung Jang, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Siamak Sobhany, Petra Ten Hoopen, Robert Vaughan, Vadim Zalunin, Guy Cochrane
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The objective of ENA is to support and promote the use of nucleotide sequencing as an experimental research platform by providing data submission, archive, search and download services. In this article, we outline these services and describe ...
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Abstract
Motivation: In silico experiments necessitate the virtual organization of people, data, tools and machines. The scientific process also necessitates an awareness of the experience base, both of personal data as well as the wider context of work. The management of all these data and the co-ordination of resources to manage such virtual organizations and the data surrounding them needs significant computational infra-structure support.Results: In this paper, we show that myGrid, middleware for the Semantic Grid, enables biologists to perform and manage ...
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posted to buggotea science-is-vital
by dullhunk
on 2010-10-07 20:25:55
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Abstract
One in seven couples worldwide are infertile, and male factor infertility accounts for approximately 30%–50% of these cases. Although many genes are known to be essential for gametogenesis, there are surprisingly few monogenic mutations that have been conclusively demonstrated to cause human spermatogenic failure. A nuclear receptor, NR5A1 (also called steroidogenic factor 1), is a key transcriptional regulator of genes involved in the hypothalamic-pituitary-steroidogenic axis, and it is expressed in the steroidogenic tissue of the developing and adult human gonad. ...
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Am J Hum Genet (30 September 2010)
by Anu Bashamboo, Bruno Ferraz-de-Souza, Diana Lourenço, et al.Lin Lin, Neil J. Sebire, Debbie Montjean, Joelle Bignon-Topalovic, Jacqueline Mandelbaum, Jean-Pierre Siffroi, Sophie Christin-Maitre, Uppala Radhakrishna, Hassan Rouba, Celia Ravel, Jacob Seeler, John C. Achermann, Ken McElreavey
posted to buggotea human human-genetics
by dullhunk
on 2010-10-05 06:32:19
Abstract
One in seven couples worldwide are infertile, and male factor infertility accounts for approximately 30%50% of these cases. Although many genes are known to be essential for gametogenesis, there are surprisingly few monogenic mutations that have been conclusively demonstrated to cause human spermatogenic failure. A nuclear receptor, NR5A1 (also called steroidogenic factor 1), is a key transcriptional regulator of genes involved in the hypothalamic-pituitary-steroidogenic axis, and it is expressed in the steroidogenic tissue of the developing and adult human gonad. Mutations ...
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by Emek Demir, Michael P. Cary, Suzanne Paley, et al.Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D'Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C. Lopez-Fuentes, Huaiyu Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Ozgun Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Ruebenacker, Matthias Samwald, Martijn van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kei-Hoi Cheung, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H. Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S. Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le Novere, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D. Karp, Chris Sander, Gary D. Bader
Abstract
Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway ...
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Abstract
Bioinformaticians routinely analyse vast amounts of information held both in large remote databases and in flat data files hosted on local machines. The contemporary toolkit available for this purpose consists of an ad hoc collection of data manipulation tools, scripting languages and visualization systems; these must often be combined in complex and bespoke ways, the result frequently being an unwieldy artefact capable of one specific task, which cannot easily be exploited or extended by other practitioners. Owing to the sizes of ...
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Nature, Vol. 465, No. 7301. (24 June 2010), pp. 1104-1107
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Abstract
Highly active (i.e., "hot") long interspersed element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of hot L1s in the human population remains largely unexplored. Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s that are differentially present among individuals but are absent from the human genome reference sequence. The majority ...
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Vol. 141, No. 7. (25 June 2010), pp. 1159-1170
Abstract
Highly active (i.e., hot) long interspersed element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of hot L1s in the human population remains largely unexplored. Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s that are differentially present among individuals but are absent from the human genome reference sequence. The majority of these L1s were highly active in a cultured cell retrotransposition assay. Genotyping 26 elements revealed ...
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Science (New York, N.Y.), Vol. 211, No. 4487. (13 March 1981), pp. 1137-1139
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Nature, Vol. 227, No. 5258. (8 August 1970), pp. 561-563
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Abstract
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. ...
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by Gil Atzmon, Li Hao, Itsik Pe'er, et al.Christopher Velez, Alexander Pearlman, Pier Francesco F. Palamara, Bernice Morrow, Eitan Friedman, Carole Oddoux, Edward Burns, Harry Ostrer
Abstract
For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, ...
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Abstract
SUMMARY: A tool to predict the effect newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants. In Ensembl a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species. AVAILABILITY: The Ensembl SNP Effect Predictor can be accessed via the Ensembl website at http://www.ensembl.org/. The Ensembl API (see Ensembl A for installation instructions) is open source software. CONTACT: wm2@ebi.ac.uk, fiona@ebi.ac.uk. ...
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Abstract
SUMMARY: A tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants. In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species. AVAILABILITY: The Ensembl SNP Effect Predictor can be accessed via the Ensembl website at http://www.ensembl.org/. The ...
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posted to buggotea taverna
by dullhunk
on 2010-06-21 15:22:32
Abstract
When the emergence of ‘service-oriented science,’ the need arises to orchestrate multiple services to facilitate scientific investigation—that is, to create ‘science workflows.’ We present here our findings in providing a workflow solution for the caGrid service-based grid infrastructure. We choose BPEL and Taverna as candidates, and compare their usability in the lifecycle of a scientific workflow, including workflow composition, execution, and result analysis. Our experience shows that BPEL as an imperative language offers a comprehensive set of modeling primitives for workflows ...
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Concurrency and computation : practice & experience, Vol. 22, No. 9. (25 June 2010), pp. 1098-1117, doi:10.1002/cpe.1547
Abstract
With the emergence of "service oriented science," the need arises to orchestrate multiple services to facilitate scientific investigation-that is, to create "science workflows." We present here our findings in providing a workflow solution for the caGrid service-based grid infrastructure. We choose BPEL and Taverna as candidates, and compare their usability in the lifecycle of a scientific workflow, including workflow composition, execution, and result analysis. Our experience shows that BPEL as an imperative language offers a comprehensive set of modeling primitives for ...
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Psychological review, Vol. 63, No. 2. (March 1956), pp. 81-97
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Abstract
Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly ...
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Vol. 86, No. 6. (11 June 2010), pp. 850-859
by Gil Atzmon, Li Hao, Itsik Pe'er, et al.Christopher Velez, Alexander Pearlman, Pier F. Palamara, Bernice Morrow, Eitan Friedman, Carole Oddoux, Edward Burns, Harry Ostrer
Abstract
For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, ...
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by Gil Atzmon, Li Hao, Itsik Pe'er, et al.Christopher Velez, Alexander Pearlman, Pier F. Palamara, Bernice Morrow, Eitan Friedman, Carole Oddoux, Edward Burns, Harry Ostrer
Abstract
For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, ...
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Nature, Vol. 463, No. 7277. (7 January 2010)
posted to buggotea geek peter-fiske
by dullhunk
on 2010-06-07 16:05:16
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by Daan Peric-Hupkes, Wouter Meuleman, Ludo Pagie, et al.Sophia W. Bruggeman, Irina Solovei, Wim Brugman, Stefan Gräf, Paul Flicek, Ron M. Kerkhoven, Maarten van Lohuizen, Marcel Reinders, Lodewyk Wessels, Bas van Steensel
Abstract
The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, we generated high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells via lineage-committed neural precursor cells into terminally differentiated astrocytes. This reveals that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units ...
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by D. Peric-Hupkes, W. Meuleman, L. Pagie, et al.S. W. M. Bruggeman, I. Solovei, W. Brugman, S. Graf, P. Flicek, R. M. Kerkhoven, M. van Lohuizen, M. Reinders, L. Wessels, B. van Steensel
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Abstract
SUMMARY: Genome-wide association studies (GWAS), which produce huge volumes of data, are now being carried out by many groups around the world, creating a need for user-friendly tools for data quality control (QC) and analysis. One critical aspect of GWAS QC is evaluating genotype cluster plots to verify sensible genotype calling in putatively associated single nucleotide polymorphisms (SNPs). Evoker is a tool for visualizing genotype ...
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Abstract
SUMMARY: Genome-wide association studies, which produce huge volumes of data, are now being carried out by many groups around the world, creating a need for user friendly tools for data quality control and analysis. One critical aspect of GWAS quality control is evaluating genotype cluster plots to verify sensible genotype calling in putatively associated SNPs. Evoker is a tool for visualizing genotype cluster plots, and provides a solution to the computational and storage problems related to working with such large datasets. ...
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Abstract
MOTIVATION: Existing sequence assembly editors struggle with the volumes of data now readily available from the latest generation of DNA sequencing instruments. RESULTS: We describe the Gap5 software along with the data structures and algorithms used that allow it to be scalable. We demonstrate this with an assembly of 1.1 billion sequence fragments and compare the performance with several other programs. We analyse the memory, ...
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