SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. - Paul Bertone; Yuval Kluger; Ning Lan; Deyou Zheng; Dinesh Christendat; Adelinda Yee; Aled M. Edwards; Cheryl H. Arrowsmith; Gaetano T. Montelione; Mark Gerstein (Nucleic Acids Res., 2001)

PseudoPipe: an automated pseudogene identification pipeline. - Zhaolei Zhang; Nicholas Carriero; Deyou Zheng; John E. Karro; Paul M. Harrison; Mark Gerstein (Bioinform., 2006)

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. - John E. Karro; Yangpan Yan; Deyou Zheng; Zhaolei Zhang; Nicholas Carriero; Philip Cayting; Paul M. Harrison; Mark Gerstein (Nucleic Acids Res., 2007)

Small RNAs Originated from Pseudogenes: cis- or trans-Acting? - Xingyi Guo; Zhaolei Zhang; Mark B. Gerstein; Deyou Zheng (PLoS Comput. Biol., 2009)

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions. - Shira Rockowitz; Wen-Hui Lien; Erika Pedrosa; Gang Wei; Mingyan Lin; Keji Zhao; Herbert M. Lachman; Elaine Fuchs; Deyou Zheng (PLoS Comput. Biol., 2014)

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. - Mingyan Lin; Erika Pedrosa; Anastasia Hrabovsky; Jian Chen; Benjamin R. Puliafito; Stephanie R. Gilbert; Deyou Zheng; Herbert M. Lachman (BMC Syst. Biol., 2016)

SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis. - Dejian Zhao; Deyou Zheng (BMC Bioinform., 2018)

Stereo3D: using stereo images to enrich 3D visualization. - Yang Liu 186; Vinod Kumar Singh; Deyou Zheng (Bioinform., 2020)

HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements. - Vinod Kumar Singh; Rohan Misra; Steven C. Almo; Ulrich G. Steidl; Hannes E. Bülow; Deyou Zheng (Bioinform., 2022)