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Validation of Illumina's Isaac variant calling workflow [article]

Liudmila Sergeevna Mainzer, Brad A. Chapman, Oliver Hofmann, Gloria Rendon, Zachary D. Stephens, Victor Jongeneel
2015 bioRxiv   pre-print
We note that iSAAC is indeed quite fast, and provide some benchmarks on a few hardware architectures.  ...  The call accuracy is especially high on NA12878, however exomes and genomic data outside the Platinum sets tend to have a high fraction of false positive calls.  ...  Blue Waters is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications.  ... 
doi:10.1101/031021 fatcat:varvyha5sjddzg2222hyexba7m

CloudMan as a platform for tool, data, and analysis distribution

Enis Afgan, Brad Chapman, James Taylor
2012 BMC Bioinformatics  
environment and associated data in a scalable and precisely reproducible way.  ...  Conclusions: With the enabled customization and sharing of instances, CloudMan can be used as a platform for collaboration.  ...  a web browser.  ... 
doi:10.1186/1471-2105-13-315 pmid:23181507 pmcid:PMC3556322 fatcat:lma3lbbwyfg4nbcvmr7pye6uke

Bioconda: A sustainable and comprehensive software distribution for the life sciences [article]

Björn Grüning, Ryan Dale, Andreas Sjödin, Jillian Rowe, Brad A. Chapman, Christopher H. Tomkins-Tinch, Renan Valieris, Johannes Köster
2017 bioRxiv   pre-print
Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors.  ...  We present Bioconda (, a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda.  ...  modified in a harmful way.  ... 
doi:10.1101/207092 fatcat:h34tbpyjrbfebprwa6rfyx33dq

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

Eric Talevich, Brandon M Invergo, Peter JA Cock, Brad A Chapman
2012 BMC Bioinformatics  
We also provide examples of the benefits of building a community around a shared open-source project.  ...  Results: We built a Python software library for working with phylogenetic data that is tightly integrated with Biopython, a broad-ranging toolkit for computational biology.  ...  Zmasek co-mentored the original Google Summer of Code project with Brad A. Chapman, guiding the implementation of phyloXML.  ... 
doi:10.1186/1471-2105-13-209 pmid:22909249 pmcid:PMC3468381 fatcat:252rrkv2tvbdrdmc5pidepesfq

Finding a Place for Agriculture in Intellectual Property Law

Susannah Chapman, Brad Sherman
2018 IIC - International Review of Intellectual Property and Competition Law  
Over the last decade, the situation has changed, primarily as a result of a growing awareness of the role that intellectual property law plays in relation to food security.  ...  Agricultural and intellectual property have a complex, but largely neglected history.  ... 
doi:10.1007/s40319-018-0753-8 fatcat:u6asod5x7jewvhuquthivsw3tu

Structure and evolution of cereal genomes

Andrew H Paterson, John E Bowers, Daniel G Peterson, James C Estill, Brad A Chapman
2003 Current Opinion in Genetics and Development  
The rice genome sequence provides a platform for organizing information about diverse cereals, and together with genetic maps and sequence samples from other cereals is yielding new insights into both  ...  and genomic survey sequence data deposited in GenBank for maize, sorghum, the Triticeae, and rice for the past 5 years in reference to the left axis, and the relative growth of cereal sequence data as a  ...  Current Opinion in Genetics & Development 2003, 13:644-650 Structure and evolution of cereal genomes Paterson, Bowers, Peterson, Estill and Chapman 645  ... 
doi:10.1016/j.gde.2003.10.002 pmid:14638328 fatcat:3kup2mj4analnjdijhsog7qaae

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

Nomi L. Harris, Peter J. A. Cock, Hilmar Lapp, Brad Chapman, Rob Davey, Christopher Fields, Karsten Hokamp, Monica Munoz-Torres
2016 PLoS Computational Biology  
BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference.  ...  Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community.  ...  Acknowledgments BOSC is a community effort.  ... 
doi:10.1371/journal.pcbi.1004691 pmid:26914653 pmcid:PMC4767331 fatcat:tveqo2l6krbxtfxhdu4k6t7o6e

Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library

Shaun M. Lippow, Tae Seok Moon, Subhayu Basu, Sang-Hwal Yoon, Xiazhen Li, Brad A. Chapman, Keith Robison, Daša Lipovšek, Kristala L.J. Prather
2010 Chemistry and Biology  
We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid.  ...  Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which interresidue correlations favored by the design are encoded into a defined-sequence  ...  ; W = A,T; B = C,G,T; D = A,G,T; H = A,C,T; V = A,C,G; N = A,C,G,T.  ... 
doi:10.1016/j.chembiol.2010.10.012 pmid:21168766 fatcat:2mbqudqofzcvfhmjim52p7ngle

Pairwise selection assembly for sequence-independent construction of long-length DNA

William J. Blake, Brad A. Chapman, Anuradha Zindal, Michael E. Lee, Shaun M. Lippow, Brian M. Baynes
2010 Nucleic Acids Research  
Biological engineering at the level of pathways and genomes, however, requires a scalable and cost-effective assembly of DNA molecules that are longer than $10 kb, and this remains a challenge.  ...  Here we present the development of pairwise selection assembly (PSA), a process that involves hierarchical construction of long-length DNA through the use of a standard set of components and operations  ...  In both cassettes, a BsaI cut produces a 5 0 -TTCA overhang, while a BsmBI cut produces a 5 0 -CTCA overhang (Figure 2a) .  ... 
doi:10.1093/nar/gkq123 pmid:20194119 pmcid:PMC2860126 fatcat:ht6w3yx3urdabkbfqpeugqq3am

Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity

Andrew H Paterson, John E Bowers, Brad A Chapman, Daniel G Peterson, Junkang Rong, Thomas M Wicker
2004 Current Opinion in Biotechnology  
For the first time, we have access to large numbers (and in some cases all) of the genes in a genome, albeit for a small subset of angiosperms.  ...  A small subset of domesticates, plus a few botanical models such as Arabidopsis thaliana, account for most of our present knowledge of the repertoire, organization and function of plant genes.  ... 
doi:10.1016/j.copbio.2004.03.001 pmid:15081049 fatcat:he3erbhxi5gcrasdxvs7ovmkia

bcbioRNASeq: R package for bcbio RNA-seq analysis

Michael J. Steinbaugh, Lorena Pantano, Rory D. Kirchner, Victor Barrera, Brad A. Chapman, Mary E. Piper, Meeta Mistry, Radhika S. Khetani, Kayleigh D. Rutherford, Oliver Hofmann, John N. Hutchinson, Shannan Ho Sui
2017 F1000Research  
Robinson MD, Oshlack A: A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010; 11(3): R25. PubMed Abstract | Publisher Full Text | Free Full Text 21.  ...  Huber W, von Heydebreck A, Sültmann H, et al.: Variance stabilization applied to microarray data calibration and to the quantification of differential expression.  ...  The RNA-seq data is from a study of acute kidney injury in a mouse model (GSE65267) 18 .  ... 
doi:10.12688/f1000research.12093.1 fatcat:guo3a7ixqfcsritdqrpmy57sda

bcbioRNASeq: R package for bcbio RNA-seq analysis

Michael J. Steinbaugh, Lorena Pantano, Rory D. Kirchner, Victor Barrera, Brad A. Chapman, Mary E. Piper, Meeta Mistry, Radhika S. Khetani, Kayleigh D. Rutherford, Oliver Hofmann, John N. Hutchinson, Shannan Ho Sui
2018 F1000Research  
We have developed bcbioRNASeq, a Bioconductor package that provides ready-to-render templates, objects and wrapper functions to post-process bcbio RNA sequencing output data. bcbioRNASeq helps automate  ...  a "library(DOSE)".  ...  The RNA-seq data is from a study of acute kidney injury in a mouse model (GSE65267) 17 .  ... 
doi:10.12688/f1000research.12093.2 fatcat:wbfsdai44ja5tnstdwyd6n27de

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

Zhongwu Lai, Aleksandra Markovets, Miika Ahdesmaki, Brad Chapman, Oliver Hofmann, Robert McEwen, Justin Johnson, Brian Dougherty, J. Carl Barrett, Jonathan R. Dry
2016 Nucleic Acids Research  
Here we present VarDict, a novel and versatile variant caller for both DNA-and RNA-sequencing data.  ...  Harvard University Department of Biostatistics, for his contributions to the incorporation of VarDict into their BCBio framework that made VarDict more broadly available to the public; David Jenkins, a  ...  a patient therapy (2) .  ... 
doi:10.1093/nar/gkw227 pmid:27060149 pmcid:PMC4914105 fatcat:46uid6xw7zeinfmjavuahb55ta

Gain-of-function mutant p53 upregulates CXC chemokines and enhances cell migration

W.Andrew Yeudall, Catherine A. Vaughan, Hiroshi Miyazaki, Mahesh Ramamoorthy, Mi-Yon Choi, Christopher G. Chapman, Huixin Wang, Elena Black, Anna A. Bulysheva, Swati Palit Deb, Brad Windle, Sumitra Deb
2011 Carcinogenesis  
The data suggest a mechanistic link between GOF p53 proteins and chemokines in enhanced cell motility.  ...  In cells with engineered or endogenous p53 mutants, enhanced migration was reduced by downregulation of nuclear factor-kappaB2, a GOF p53 target.  ...  mutation, a known GOF mutant (4) .  ... 
doi:10.1093/carcin/bgr270 pmid:22114072 fatcat:kd5upk6xafcunlrpfd5zgzq7cy

Data processing pipeline for a time-sampled imaging Fourier transform spectrometer

David A. Naylor, Trevor R. Fulton, Peter W. Davis, Ian M. Chapman, Brad G. Gom, Locke D. Spencer, John V. Lindner, Nathan E. Nelson-Fitzpatrick, Margaret K. Tahic, Gary R. Davis, Sylvia S. Shen, Paul E. Lewis
2004 Imaging Spectrometry X  
spectrometers (IFTS) are becoming the preferred systems for remote sensing spectral imaging applications because of their ability to provide, simultaneously, both high spatial and spectral resolution images of a  ...  The step-and-integrate mode requires a translation stage with fast and precise point-to-point motion and additional external trigger circuitry for the detector focal plane array (FPA), and produces uniformly  ...  presented in this paper; Guillaume Patanchon from the University of British Columbia, Canada for providing sample data from the BLAST test flight; and Daniel Potts at Lübeck University, Germany for providing a  ... 
doi:10.1117/12.560096 fatcat:6v52d6t7lnbfjdwvs3aouxuvay
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