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Computational pipelines

ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification

Riyue Bao, Kyle Hernandez, Lei Huang, Wenjun Kang, Elizabeth Bartom, Kenan Onel, Samuel Volchenboum, Jorge Andrade

published 13 Aug 2015

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Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects

Shantanu Singh, Xiaoyun Wu, Vebjorn Ljosa, Mark-Anthony Bray, Federica Piccioni, David E. Root, John G. Doench, Jesse S. Boehm, Anne E. Carpenter

published 21 Jul 2015

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A Benchmark Data Set to Evaluate the Illumination Robustness of Image Processing Algorithms for Object Segmentation and Classification

Arif ul Maula Khan, Ralf Mikut, Markus Reischl

published 20 Jul 2015

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elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

Charlotte Herzeel, Pascal Costanza, Dries Decap, Jan Fostier, Joke Reumers

published 16 Jul 2015

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An Automated, Adaptive Framework for Optimizing Preprocessing Pipelines in Task-Based Functional MRI

Nathan W. Churchill, Robyn Spring, Babak Afshin-Pour, Fan Dong, Stephen C. Strother

published 10 Jul 2015

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Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes

Suyash S. Shringarpure, Andrew Carroll, Francisco M. De La Vega, Carlos D. Bustamante

published 25 Jun 2015

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Comparison of the Association of Sac Growth and Coil Compaction with Recurrence in Coil Embolized Cerebral Aneurysms

Anna L. Hoppe, Madhavan L. Raghavan, David M. Hasan

published 20 Apr 2015

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Novel R Pipeline for Analyzing Biolog Phenotypic Microarray Data

Minna Vehkala, Mikhail Shubin, Thomas R Connor, Nicholas R Thomson, Jukka Corander

published 18 Mar 2015

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Head-to-Head Comparison of Two Popular Cortical Thickness Extraction Algorithms: A Cross-Sectional and Longitudinal Study

Alberto Redolfi, David Manset, Frederik Barkhof, Lars-Olof Wahlund, Tristan Glatard, Jean-François Mangin, Giovanni B. Frisoni, neuGRID Consortium, for the Alzheimer’s Disease Neuroimaging Initiative

published 17 Mar 2015

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A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies

Steven D. Essinger, Erin Reichenberger, Calvin Morrison, Christopher B. Blackwood, Gail L. Rosen

published 21 Jan 2015

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Elastography Using Multi-Stream GPU: An Application to Online Tracked Ultrasound Elastography, In-Vivo and the da Vinci Surgical System

Nishikant P. Deshmukh, Hyun Jae Kang, Seth D. Billings, Russell H. Taylor, Gregory D. Hager, Emad M. Boctor

published 26 Dec 2014

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Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression

Carol A. Soderlund, William M. Nelson, Stephen A. Goff

published 26 Dec 2014

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Optimized Brain Extraction for Pathological Brains (optiBET)

Evan S. Lutkenhoff, Matthew Rosenberg, Jeffrey Chiang, Kunyu Zhang, John D. Pickard, Adrian M. Owen, Martin M. Monti

published 16 Dec 2014

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