Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing by Chen Zuozhou, Miller Christopher A, Yu Fuli, Coarfa Cristian, Harris R Alan, Milosavljevic Aleksandar

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An integrative variant analysis suite for whole exome next-generation sequencing data by Challis Danny, Yu Jin, Evani Uday S, Jackson Andrew R, Paithankar Sameer, Coarfa Cristian, Milosavljevic Aleksandar, Gibbs Richard A, Yu Fuli

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Atlas2 Cloud: a framework for personal genome analysis in the cloud by Evani Uday S, Challis Danny, Yu Jin, Jackson Andrew R, Paithankar Sameer, Bainbridge Matthew N, Jakkamsetti Adinarayana, Pham Peter, Coarfa Cristian, Milosavljevic Aleksandar, Yu Fuli

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci by Altshuler, Robert Charles, Onuchic, Vitor, Lurie, Eugene, Carrero, Ivenise, Pawliczek, Piotr, Patel, Ronak Y., Rozowsky, Joel, Galeev, Timur, Huang, Zhuoyi, Harris, R. Alan, Coarfa, Cristian, Ashmore, Lillian, Bertol, Jessica W., Fakhouri, Walid D., Yu, Fuli, Kellis, Manolis, Gerstein, Mark, Milosavljevic, Aleksandar

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Intermediate DNA methylation is a conserved signature of genome regulation by Elliott, GiNell, Hong, Chibo, Xing, Xiaoyun, Zhou, Xin, Li, Daofeng, Coarfa, Cristian, Bell, Robert J.A., Maire, Cecile L., Ligon, Keith L., Sigaroudinia, Mahvash, Gascard, Philippe, Tlsty, Thea D., Harris, R. Alan, Schalkwyk, Leonard C., Bilenky, Misha, Mill, Jonathan, Farnham, Peggy J., Kellis, Manolis, Marra, Marco A., Milosavljevic, Aleksandar, Hirst, Martin, Stormo, Gary D., Wang, Ting, Costello, Joseph F.

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