GEMINI: integrative exploration of genetic variation and genome annotations
Paila, Umadevi, Chapman, Brad A, Kirchner, Rory, Quinlan, Aaron R
Published in PLoS computational biology (01.07.2013)
Published in PLoS computational biology (01.07.2013)
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Journal Article
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Cock, Peter J. A., Antao, Tiago, Chang, Jeffrey T., Chapman, Brad A., Cox, Cymon J., Dalke, Andrew, Friedberg, Iddo, Hamelryck, Thomas, Kauff, Frank, Wilczynski, Bartek, de Hoon, Michiel J. L.
Published in Bioinformatics (01.06.2009)
Published in Bioinformatics (01.06.2009)
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Journal Article
genomic binding sites of a noncoding RNA
Simon, Matthew D, Wang, Charlotte I, Kharchenko, Peter V, West, Jason A, Chapman, Brad A, Alekseyenko, Artyom A, Borowsky, Mark L, Kuroda, Mitzi I, Kingston, Robert E
Published in Proceedings of the National Academy of Sciences - PNAS (20.12.2011)
Published in Proceedings of the National Academy of Sciences - PNAS (20.12.2011)
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Journal Article
Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
Talevich, Eric, Invergo, Brandon M, Cock, Peter J A, Chapman, Brad A
Published in BMC bioinformatics (21.08.2012)
Published in BMC bioinformatics (21.08.2012)
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Journal Article
Histone H3R2 Symmetric Dimethylation and Histone H3K4 Trimethylation Are Tightly Correlated in Eukaryotic Genomes
Yuan, Chih-Chi, Matthews, Adam G.W., Jin, Yi, Chen, Chang Feng, Chapman, Brad A., Ohsumi, Toshiro K., Glass, Karen C., Kutateladze, Tatiana G., Borowsky, Mark L., Struhl, Kevin, Oettinger, Marjorie A.
Published in Cell reports (Cambridge) (23.02.2012)
Published in Cell reports (Cambridge) (23.02.2012)
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Journal Article
Buffering of Crucial Functions by Paleologous Duplicated Genes May Contribute Cyclicality to Angiosperm Genome Duplication
Chapman, Brad A., Bowers, John E., Feltus, Frank A., Paterson, Andrew H.
Published in Proceedings of the National Academy of Sciences - PNAS (21.02.2006)
Published in Proceedings of the National Academy of Sciences - PNAS (21.02.2006)
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Journal Article
Prioritisation of structural variant calls in cancer genomes
Ahdesmäki, Miika J, Chapman, Brad A, Cingolani, Pablo, Hofmann, Oliver, Sidoruk, Aleksandr, Lai, Zhongwu, Zakharov, Gennadii, Rodichenko, Mikhail, Alperovich, Mikhail, Jenkins, David, Carr, T Hedley, Stetson, Daniel, Dougherty, Brian, Barrett, J Carl, Johnson, Justin H
Published in PeerJ (San Francisco, CA) (04.04.2017)
Published in PeerJ (San Francisco, CA) (04.04.2017)
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Journal Article
Best practices for benchmarking germline small-variant calls in human genomes
Krusche, Peter, Trigg, Len, Boutros, Paul C, Mason, Christopher E, De La Vega, Francisco M, Moore, Benjamin L, Gonzalez-Porta, Mar, Eberle, Michael A, Tezak, Zivana, Lababidi, Samir, Truty, Rebecca, Asimenos, George, Funke, Birgit, Fleharty, Mark, Chapman, Brad A, Salit, Marc, Zook, Justin M
Published in Nature biotechnology (01.05.2019)
Published in Nature biotechnology (01.05.2019)
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Journal Article
Identification of Novel Alzheimer's Disease Loci Using Sex-Specific Family-Based Association Analysis of Whole-Genome Sequence Data
Prokopenko, Dmitry, Hecker, Julian, Kirchner, Rory, Chapman, Brad A, Hoffman, Oliver, Mullin, Kristina, Hide, Winston, Bertram, Lars, Laird, Nan, DeMeo, Dawn L, Lange, Christoph, Tanzi, Rudolph E
Published in Scientific reports (19.03.2020)
Published in Scientific reports (19.03.2020)
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Journal Article
Aβ-accelerated neurodegeneration caused by Alzheimer's-associated ACE variant R1279Q is rescued by angiotensin system inhibition in mice
Cuddy, Leah K, Prokopenko, Dmitry, Cunningham, Eric P, Brimberry, Ross, Song, Peter, Kirchner, Rory, Chapman, Brad A, Hofmann, Oliver, Hide, Winston, Procissi, Daniele, Hanania, Taleen, Leiser, Steven C, Tanzi, Rudolph E, Vassar, Robert
Published in Science translational medicine (30.09.2020)
Published in Science translational medicine (30.09.2020)
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Journal Article
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
Paterson, Andrew H, Bowers, John E, Chapman, Brad A, Rong, Junkang
Published in Nature (London) (27.03.2003)
Published in Nature (London) (27.03.2003)
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Journal Article
Targeted exome sequencing of suspected mitochondrial disorders
Lieber, Daniel S, Calvo, Sarah E, Shanahan, Kristy, Slate, Nancy G, Liu, Shangtao, Hershman, Steven G, Gold, Nina B, Chapman, Brad A, Thorburn, David R, Berry, Gerard T, Schmahmann, Jeremy D, Borowsky, Mark L, Mueller, David M, Sims, Katherine B, Mootha, Vamsi K
Published in Neurology (07.05.2013)
Published in Neurology (07.05.2013)
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Journal Article
Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon
Paterson, Andrew H., Chapman, Brad A., Kissinger, Jessica C., Bowers, John E., Feltus, Frank A., Estill, James C.
Published in Trends in genetics (01.11.2006)
Published in Trends in genetics (01.11.2006)
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Journal Article
Author Correction: Best practices for benchmarking germline small-variant calls in human genomes
Krusche, Peter, Trigg, Len, Boutros, Paul C, Mason, Christopher E, De La Vega, Francisco M, Moore, Benjamin L, Gonzalez-Porta, Mar, Eberle, Michael A, Tezak, Zivana, Lababidi, Samir, Truty, Rebecca, Asimenos, George, Funke, Birgit, Fleharty, Mark, Chapman, Brad A, Salit, Marc, Zook, Justin M
Published in Nature biotechnology (01.05.2019)
Published in Nature biotechnology (01.05.2019)
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Journal Article
Community-driven development for computational biology at Sprints, Hackathons and Codefests
Möller, Steffen, Afgan, Enis, Banck, Michael, Bonnal, Raoul J P, Booth, Timothy, Chilton, John, Cock, Peter J A, 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, Katayama, Toshiaki, Chapman, Brad A
Published in BMC bioinformatics (27.11.2014)
Published in BMC bioinformatics (27.11.2014)
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Journal Article
Pairwise selection assembly for sequence-independent construction of long-length DNA
Blake, William J, Chapman, Brad A, Zindal, Anuradha, Lee, Michael E, Lippow, Shaun M, Baynes, Brian M
Published in Nucleic acids research (01.05.2010)
Published in Nucleic acids research (01.05.2010)
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Journal Article
The Bioinformatics Open Source Conference (BOSC) 2013
Harris, Nomi L, Cock, Peter J A, Chapman, Brad A, Goecks, Jeremy, Hotz, Hans-Rudolf, Lapp, Hilmar
Published in Bioinformatics (Oxford, England) (15.01.2015)
Published in Bioinformatics (Oxford, England) (15.01.2015)
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Journal Article
bcbioRNASeq: R package for bcbio RNA-seq analysis [version 2; peer review: 1 approved, 1 approved with reservations]
Steinbaugh, Michael J, Pantano, Lorena, Kirchner, Rory D, Barrera, Victor, Chapman, Brad A, Piper, Mary E, Mistry, Meeta, Khetani, Radhika S, Rutherford, Kayleigh D, Hofmann, Oliver, Hutchinson, John N, Ho Sui, Shannan
Published in F1000 research (2018)
Published in F1000 research (2018)
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Journal Article
Structure and evolution of cereal genomes
Paterson, Andrew H, Bowers, John E, Peterson, Daniel G, Estill, James C, Chapman, Brad A
Published in Current opinion in genetics & development (01.12.2003)
Published in Current opinion in genetics & development (01.12.2003)
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