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Computational pipelines

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries

Patricio Jeraldo, Krishna Kalari, Xianfeng Chen, Jaysheel Bhavsar, Ashutosh Mangalam, Bryan White, Heidi Nelson, Jean-Pierre Kocher, Nicholas Chia

published 15 Dec 2014

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FindFoci: A Focus Detection Algorithm with Automated Parameter Training That Closely Matches Human Assignments, Reduces Human Inconsistencies and Increases Speed of Analysis

Alex D. Herbert, Antony M. Carr, Eva Hoffmann

published 05 Dec 2014

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Extraction of Temporal Networks from Term Co-Occurrences in Online Textual Sources

Marko Popović, Hrvoje Štefančić, Borut Sluban, Petra Kralj Novak, Miha Grčar, Igor Mozetič, Michelangelo Puliga, Vinko Zlatić

published 03 Dec 2014

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Consensus between Pipelines in Structural Brain Networks

Christopher S. Parker, Fani Deligianni, M. Jorge Cardoso, Pankaj Daga, Marc Modat, Michael Dayan, Chris A. Clark, Sebastien Ourselin, Jonathan D. Clayden

published 30 Oct 2014

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RNA-Seq Gene Profiling - A Systematic Empirical Comparison

Nuno A. Fonseca, John Marioni, Alvis Brazma

published 30 Sep 2014

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Biological Time Series Analysis Using a Context Free Language: Applicability to Pulsatile Hormone Data

Dennis A. Dean II, Gail K. Adler, David P. Nguyen, Elizabeth B. Klerman

published 03 Sep 2014

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optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks

Panuwat Trairatphisan, Andrzej Mizera, Jun Pang, Alexandru Adrian Tantar, Thomas Sauter

published 01 Jul 2014

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Effect of Intrinsic and Extrinsic Factors on Global and Regional Cortical Thickness

Koushik A. Govindarajan, Leorah Freeman, Chunyan Cai, Mohammad H. Rahbar, Ponnada A. Narayana

published 02 May 2014

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Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

Jason Li, Maria A. Doyle, Isaam Saeed, Stephen Q. Wong, Victoria Mar, David L. Goode, Franco Caramia, Ken Doig, Georgina L. Ryland, Ella R. Thompson, Sally M. Hunter, Saman K. Halgamuge, Jason Ellul, Alexander Dobrovic, Ian G. Campbell, Anthony T. Papenfuss, Grant A. McArthur, Richard W. Tothill

published 21 Apr 2014

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Automated Quantification Reveals Hyperglycemia Inhibits Endothelial Angiogenic Function

Anthony R. Prisco, John D. Bukowy, Brian R. Hoffmann, Jamie R. Karcher, Eric C. Exner, Andrew S. Greene

published 09 Apr 2014

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TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

Jeffrey C. Glaubitz, Terry M. Casstevens, Fei Lu, James Harriman, Robert J. Elshire, Qi Sun, Edward S. Buckler

published 28 Feb 2014

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Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks

Johannes Stegmaier, Jens C. Otte, Andrei Kobitski, Andreas Bartschat, Ariel Garcia, G. Ulrich Nienhaus, Uwe Strähle, Ralf Mikut

published 27 Feb 2014

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RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

Guorong Xu, Michael J. Strong, Michelle R. Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor

published 25 Feb 2014

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