RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. - Lukas Habegger; Andrea Sboner; Tara A. Gianoulis; Joel S. Rozowsky; Ashish Agarwal; Michael Snyder 001; Mark Gerstein (Bioinform., 2011)

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. - Lukas Habegger; Suganthi Balasubramanian; David Z. Chen; Ekta Khurana; Andrea Sboner; Arif Ozgun Harmanci; Joel S. Rozowsky; Declan Clarke; Michael Snyder 001; Mark Gerstein (Bioinform., 2012)

CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data. - Jonathan S. Packer; Evan K. Maxwell; Colm O'Dushlaine; Alexander E. Lopez; Frederick E. Dewey; Rostislav Chernomorsky; Aris Baras; John D. Overton; Lukas Habegger; Jeffrey G. Reid (Bioinform., 2016)