TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. - Yan W. Asmann; Sumit Middha; Asif Hossain; Saurabh Baheti; Ying Li; High-Seng Chai; Zhifu Sun; Patrick H. Duffy; Ahmed A. Hadad; Asha A. Nair; Xiaoyu Liu; Yuji Zhang 001; et al. (Bioinform., 2012)

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. - Zhifu Sun; Saurabh Baheti; Sumit Middha; Rahul Kanwar; Yuji Zhang 001; Xing Li; Andreas S. Beutler; Eric W. Klee; Yan W. Asmann; E. Aubrey Thompson; Jean-Pierre A. Kocher (Bioinform., 2012)

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. - Krishna R. Kalari; Asha A. Nair; Jaysheel D. Bhavsar; Daniel R. O'Brien; Jaime I. Dávila; Matthew A. Bockol; Jinfu J. Nie; Xiaojia Tang; Saurabh Baheti; Jay B. Doughty; Sumit Middha; Hugues Sicotte; et al. (BMC Bioinform., 2014)

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. - Huihuang Yan; Jared Evans; Mike Kalmbach; Raymond M. Moore; Sumit Middha; Stanislav Luban; Liguo Wang 002; Aditya Bhagwate; Ying Li; Zhifu Sun; Xianfeng Chen; Jean-Pierre A. Kocher (BMC Bioinform., 2014)

MPath - Results Manager, a comprehensive solution to store, review and manage genomic variants from NGS-based clinical tests. - Aijazuddin Syed; Anoop Balakrishnan; Aaron Dack; John Ziegler; Shruti H. Madur; Jack Birnbaum; Jason Hwee; Meera Prasad; Mustafa Syed; Mohammad Haque; Zhen Y. Liu; Sumit Middha; et al. (AMIA, 2018)