Identifying transcription factor binding sites through Markov chain optimization. - Kyle Ellrott; Chuhu Yang; Frances M. Sladek; Tao Jiang 001 (ECCB, 2002)

A computational pipeline for protein structure prediction and analysis at genome scale. - Manesh J. Shah; Sergei Passovets; Dongsup Kim; Kyle Ellrott; Li Wang 008; Inna Vokler; Philip F. LoCascio; Dong Xu 002; Ying Xu 001 (Bioinform., 2003)

PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. - Jun-tao Guo; Kyle Ellrott; Won Jae Chung; Dong Xu 002; Sergei Passovets; Ying Xu 001 (Nucleic Acids Res., 2004)

Improving the Performance of protein Threading Using Insertion/Deletion Frequency Arrays. - Kyle Ellrott; Jun-tao Guo; Victor Olman; Ying Xu 001 (J. Bioinform. Comput. Biol., 2008)

Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families. - Kyle Ellrott; Lukasz Jaroszewski; Weizhong Li 002; John C. Wooley; Adam Godzik (PLoS Comput. Biol., 2010)

TOPSAN: a dynamic web database for structural genomics. - Kyle Ellrott; Christian M. Zmasek; Dana Weekes; S. Sri Krishna; Constantina Bakolitsa; Adam Godzik; John C. Wooley (Nucleic Acids Res., 2011)

The UCSC Cancer Genomics Browser: update 2013. - Mary Goldman; Brian Craft; Teresa Swatloski; Kyle Ellrott; Melissa S. Cline; Mark Diekhans; Singer Ma; Chris Wilks; Joshua M. Stuart; David Haussler; Jingchun Zhu (Nucleic Acids Res., 2013)

Valection: design optimization for validation and verification studies. - Christopher I Cooper; Delia Yao; Dorota H. Sendorek; Takafumi N. Yamaguchi; Christine P'ng; Kathleen E. Houlahan; Cristian Caloian; Michael Fraser; Kyle Ellrott; Adam A. Margolin; Robert G. Bristow; Joshua M. Stuart; et al. (BMC Bioinform., 2018)

Germline contamination and leakage in whole genome somatic single nucleotide variant detection. - Dorota H. Sendorek; Cristian Caloian; Kyle Ellrott; J. Christopher Bare; Takafumi N. Yamaguchi; Adam D. Ewing; Kathleen E. Houlahan; Thea C. Norman; Adam A. Margolin; Joshua M. Stuart; Paul C. Boutros (BMC Bioinform., 2018)

neoepiscope improves neoepitope prediction with multivariant phasing. - Mary A Wood; Austin Nguyen; Adam J. Struck; Kyle Ellrott; Abhinav Nellore; Reid F. Thompson (Bioinform., 2020)

TCGA Kidney Cancers. - John N. Weinstein; Eric A. Collisson; Gordon B. Mills; Kenna R. Mills Shaw; Brad A. Ozenberger; Kyle Ellrott; Ilya Shmulevich; Chris Sander; Joshua M. Stuart (UCI Machine Learning Repository, 2023)

The GA4GH Task Execution API: Enabling Easy Multi Cloud Task Execution. - Alexander Kanitz; Matthew H. McLoughlin; Liam Beckman; Venkat S. Malladi; Kyle Ellrott (CoRR, 2024)

The GA4GH Task Execution Application Programming Interface: Enabling Easy Multicloud Task Execution. - Alexander Kanitz; Matthew H. McLoughlin; Liam Beckman; Venkat S. Malladi; Kyle Ellrott (Comput. Sci. Eng., 2024)