DNA Analysis

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Noninvasive Prenatal Testing Using Cell‐Free Fetal DNA in Maternal Plasma
Nilesh Dharajiya, Tricia Zwiefelhofer, Xiaojun Guan, Vach Angkachatchai, Juan‐Sebastian Saldivar
Published online: January 2015
ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide
Jason D. Buenrostro, Beijing Wu, Howard Y. Chang, William J. Greenleaf
Published online: January 2015
Genome Annotation and Curation Using MAKER and MAKER‐P
Michael S. Campbell, Carson Holt, Barry Moore, Mark Yandell
Published online: December 2014
Next‐Gen Sequencing‐Based Mapping and Identification of Ethyl Methanesulfonate‐Induced Mutations in Arabidopsis thaliana
Xue‐Cheng Zhang, Yves Millet, Frederick M. Ausubel, Mark Borowsky
Published online: October 2014
BEDTools: The Swiss‐Army Tool for Genome Feature Analysis
Aaron R. Quinlan
Published online: September 2014
Best Practices for Mapping Replication Origins in Eukaryotic Chromosomes
Emilie Besnard, Romain Desprat, Michael Ryan, Malik Kahli, Mirit I. Aladjem, Jean‐Marc Lemaitre
Published online: September 2014
Molecular Typing of Borrelia burgdorferi
Guiqing Wang, Dionysios Liveris, Priyanka Mukherjee, Sabrina Jungnick, Gabriele Margos, Ira Schwartz
Published online: August 2014
Getting Started with Microbiome Analysis: Sample Acquisition to Bioinformatics
Ranjit Kumar, Peter Eipers, Rebecca B. Little, Michael Crowley, David K. Crossman, Elliot J. Lefkowitz, Casey D. Morrow
Published online: July 2014
Next‐Generation Sequencing Fragment Library Construction
Jessica Podnar, Heather Deiderick, Scott Hunicke‐Smith
Published online: July 2014
The UCSC Genome Browser: What Every Molecular Biologist Should Know
Mary E. Mangan, Jennifer M. Williams, Robert M. Kuhn, Warren C. Lathe
Published online: July 2014
Using VAAST to Identify Disease‐Associated Variants in Next‐Generation Sequencing Data
Brett Kennedy, Zev Kronenberg, Hao Hu, Barry Moore, Steven Flygare, Martin G. Reese, Lynn B. Jorde, Mark Yandell, Chad Huff
Published online: April 2014
Using XHMM Software to Detect Copy Number Variation in Whole‐Exome Sequencing Data
Menachem Fromer, Shaun M. Purcell
Published online: April 2014
Using SomaticSniper to Detect Somatic Single Nucleotide Variants
David E. Larson, Travis E. Abbott, Richard K. Wilson
Published online: March 2014
BreakDancer: Identification of Genomic Structural Variation from Paired‐End Read Mapping
Xian Fan, Travis E. Abbott, David Larson, Ken Chen
Published online: March 2014
mtDNA Variation and Analysis Using Mitomap and Mitomaster
Marie T. Lott, Jeremy N. Leipzig, Olga Derbeneva, H. Michael Xie, Dimitra Chalkia, Mahdi Sarmady, Vincent Procaccio, Douglas C. Wallace
Published online: December 2013
Using SOAPaligner for Short Reads Alignment
Shengchang Gu, Lin Fang, Xun Xu
Published online: December 2013
Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection
Daniel C. Koboldt, David E. Larson, Richard K. Wilson
Published online: December 2013
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
Geraldine A. Van der Auwera, Mauricio O. Carneiro, Christopher Hartl, Ryan Poplin, Guillermo del Angel, Ami Levy‐Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault, Eric Banks, Kiran V. Garimella, David Altshuler, Stacey Gabriel, Mark A. DePristo
Published online: October 2013
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