Correcting Reference Bias in High-throughput Sequencing Analysis

Victor Missirian, Isabelle Henry, Luca Comai, Vladimir Filkov, POPE: pipeline of parentally-biased expression international symposium on bioinformatics research and applications. pp. 177- 188 ,(2012) , 10.1007/978-3-642-30191-9_17

, A User's Guide to the Encyclopedia of DNA Elements (ENCODE) PLOS Biology. ,vol. 9, ,(2011) , 10.1371/JOURNAL.PBIO.1001046

Lee M. Silver, Mouse Genetics: Concepts and Applications ,(1995)

C. Gregg, J. Zhang, B. Weissbourd, S. Luo, G. P. Schroth, D. Haig, C. Dulac, High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain Science. ,vol. 329, pp. 643- 648 ,(2010) , 10.1126/SCIENCE.1190830

Dan Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology ,(1997)

Brian DeVeale, Derek van der Kooy, Tomas Babak, Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective PLoS Genetics. ,vol. 8, pp. e1002600- ,(2012) , 10.1371/JOURNAL.PGEN.1002600

Thomas M. Keane, Leo Goodstadt, Petr Danecek, Michael A. White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avigail Agam, Guy Slater, Martin Goodson, Nicholas A. Furlotte, Eleazar Eskin, Christoffer Nellåker, Helen Whitley, James Cleak, Deborah Janowitz, Polinka Hernandez-Pliego, Andrew Edwards, T. Grant Belgard, Peter L. Oliver, Rebecca E. McIntyre, Amarjit Bhomra, Jérôme Nicod, Xiangchao Gan, Wei Yuan, Louise van der Weyden, Charles A. Steward, Sendu Bala, Jim Stalker, Richard Mott, Richard Durbin, Ian J. Jackson, Anne Czechanski, José Afonso Guerra-Assunção, Leah Rae Donahue, Laura G. Reinholdt, Bret A. Payseur, Chris P. Ponting, Ewan Birney, Jonathan Flint, David J. Adams, Mouse genomic variation and its effect on phenotypes and gene regulation Nature. ,vol. 477, pp. 289- 294 ,(2011) , 10.1038/NATURE10413

James Holt, Shunping Huang, Leonard McMillan, Wei Wang, None, Read Annotation Pipeline for High-Throughput Sequencing Data international conference on bioinformatics. pp. 605- 612 ,(2013) , 10.1145/2506583.2506645

Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher M. Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang, GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences PLoS ONE. ,vol. 6, pp. e25279- ,(2011) , 10.1371/JOURNAL.PONE.0025279

Chen-Ping Fu, Catherine E. Welsh, Fernando Pardo-Manuel de Villena, Leonard McMillan, Inferring ancestry in admixed populations using microarray probe intensities Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '12. pp. 105- 112 ,(2012) , 10.1145/2382936.2382950