Now showing items 1-9 of 9

    • The 2015 Bioinformatics Open Source Conference (BOSC 2015) 

      Harris, Nomi L.; Cock, Peter J. A.; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica (Public Library of Science, 2016)
      The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open ...
    • Bio.Phylo: A Unified Toolkit for Processing, Analyzing and Visualizing Phylogenetic Trees in Biopython 

      Talevich, Eric; Invergo, Brandon M; Cock, Peter JA; Chapman, Brad Alan (BioMed Central, 2012)
      Background: Ongoing innovation in phylogenetics and evolutionary biology has been accompanied by a proliferation of software tools, data formats, analytical techniques and web servers. This brings with it the challenge of ...
    • Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community 

      Krampis, Konstantinos; Booth, Tim; Chapman, Brad Alan; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E (BioMed Central, 2012)
      Background: A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck ...
    • Community-driven development for computational biology at Sprints, Hackathons and Codefests 

      Möller, Steffen; Afgan, Enis; Banck, Michael; Bonnal, Raoul JP; Booth, Timothy; Chilton, John; Cock, Peter JA; Gumbel, Markus; Harris, Nomi; Holland, Richard; Kalaš, Matúš; Kaján, László; Kibukawa, Eri; Powel, David R; Prins, Pjotr; Quinn, Jacqueline; Sallou, Olivier; Strozzi, Francesco; Seemann, Torsten; Sloggett, Clare; Soiland-Reyes, Stian; Spooner, William; Steinbiss, Sascha; Tille, Andreas; Travis, Anthony J; Guimera, Roman Valls; Katayama, Toshiaki; Chapman, Brad A (BioMed Central, 2014)
      Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools ...
    • Comparison of Illumina and 454 Deep Sequencing in Participants Failing Raltegravir-Based Antiretroviral Therapy 

      Li, Jonathan Z.; Chapman, Brad; Charlebois, Patrick; Hofmann, Oliver; Weiner, Brian; Porter, Alyssa J.; Samuel, Reshmi; Vardhanabhuti, Saran; Zheng, Lu; Eron, Joseph; Taiwo, Babafemi; Zody, Michael C.; Henn, Matthew R.; Kuritzkes, Daniel R.; Hide, Winston; Wilson, Cara C.; Berzins, Baiba I.; Acosta, Edward P.; Bastow, Barbara; Kim, Peter S.; Read, Sarah W.; Janik, Jennifer; Meres, Debra S.; Lederman, Michael M.; Mong-Kryspin, Lori; Shaw, Karl E.; Zimmerman, Louis G.; Leavitt, Randi; De La Rosa, Guy; Jennings, Amy (Public Library of Science, 2014)
      Background: The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral ...
    • Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities 

      Lindström, Sara; Ablorh, Akweley; Chapman, Brad; Gusev, Alexander; Chen, Gary; Turman, Constance; Eliassen, A. Heather; Price, Alkes L.; Henderson, Brian E.; Le Marchand, Loic; Hofmann, Oliver; Haiman, Christopher A.; Kraft, Peter (BioMed Central, 2016)
      Background: Although genome-wide association studies (GWASs) have identified thousands of disease susceptibility regions, the underlying causal mechanism in these regions is not fully known. It is likely that the GWAS ...
    • GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations 

      Paila, Umadevi; Chapman, Brad A.; Kirchner, Rory; Quinlan, Aaron R. (Public Library of Science, 2013)
      Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable ...
    • Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls 

      Zook, Justin M; Chapman, Brad Alan; Wang, Jason; Mittelman, David; Hofmann, Oliver Marc; Hide, Winston; Salit, Marc (Nature Publishing Group, 2014)
      Clinical adoption of human genome sequencing requires methods that output genotypes with known accuracy at millions or billions of positions across a genome. Because of substantial discordance among calls made by existing ...
    • The Stem Cell Discovery Engine: An Integrated Repository and Analysis System for Cancer Stem Cell Comparisons 

      Begley, Kimberly; Reilly, Dorothy; McGovern, Ray; Rocca-Sera, Philippe; Maguire, Eamonn; Altschuler, Gabriel M.; Culhane, Aedín C.; Correll, Mick; Sansone, Susanna-Assunta; Ho Sui, Shannan; Chapman, Brad Alan; Hansen, Terah; Sompallae, Ramakrishna Rao; Krivtsov, Andrei V.; Shivdasani, Ramesh Arjun; Armstrong, Scott A.; Hofmann, Oliver Marc; Hide, Winston (Oxford University Press, 2011)
      Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However, descriptions of stem-like gene ...