ENCODE whole-genome data in the UCSC genome browser (2011 update). - Brian J. Raney; Melissa S. Cline; Kate R. Rosenbloom; Timothy R. Dreszer; Katrina Learned; Galt P. Barber; Laurence R. Meyer; Cricket A. Sloan; Venkat S. Malladi; Krishna M. Roskin; Bernard B. Suh; Angie S. Hinrichs; et al. (Nucleic Acids Res., 2011)

The UCSC Genome Browser database: extensions and updates 2011. - Timothy R. Dreszer; Donna Karolchik; Ann S. Zweig; Angie S. Hinrichs; Brian J. Raney; Robert M. Kuhn; Laurence R. Meyer; Matthew C. Wong; Cricket A. Sloan; Kate R. Rosenbloom; Greg Roe; Brooke L. Rhead; et al. (Nucleic Acids Res., 2012)

ENCODE whole-genome data in the UCSC Genome Browser: update 2012. - Kate R. Rosenbloom; Timothy R. Dreszer; Jeffrey C. Long; Venkat S. Malladi; Cricket A. Sloan; Brian J. Raney; Melissa S. Cline; Donna Karolchik; Galt P. Barber; Hiram Clawson; Mark Diekhans; Pauline A. Fujita; et al. (Nucleic Acids Res., 2012)

The UCSC Genome Browser database: extensions and updates 2013. - Laurence R. Meyer; Ann S. Zweig; Angie S. Hinrichs; Donna Karolchik; Robert M. Kuhn; Matthew C. Wong; Cricket A. Sloan; Kate R. Rosenbloom; Greg Roe; Brooke L. Rhead; Brian J. Raney; Andy Pohl; et al. (Nucleic Acids Res., 2013)

ENCODE Data in the UCSC Genome Browser: year 5 update. - Kate R. Rosenbloom; Cricket A. Sloan; Venkat S. Malladi; Timothy R. Dreszer; Katrina Learned; Vanessa Kirkup; Matthew C. Wong; Morgan Maddren; Ruihua Fang; Steven G. Heitner; Brian T. Lee; Galt P. Barber; et al. (Nucleic Acids Res., 2013)

Ontology application and use at the ENCODE DCC. - Venkat S. Malladi; Drew T. Erickson; Nikhil R. Podduturi; Laurence D. Rowe; Esther T. Chan; Jean M. Davidson; Benjamin C. Hitz; Marcus Ho; Brian T. Lee; Stuart R. Miyasato; Greg R. Roe; Matt Simison; et al. (Database J. Biol. Databases Curation, 2015)

Principles of metadata organization at the ENCODE data coordination center. - Eurie L. Hong; Cricket A. Sloan; Esther T. Chan; Jean M. Davidson; Venkat S. Malladi; J. Seth Strattan; Benjamin C. Hitz; Idan Gabdank; Aditi K. Narayanan; Marcus Ho; Brian T. Lee; Laurence D. Rowe; et al. (Database J. Biol. Databases Curation, 2016)

ENCODE data at the ENCODE portal. - Cricket A. Sloan; Esther T. Chan; Jean M. Davidson; Venkat S. Malladi; J. Seth Strattan; Benjamin C. Hitz; Idan Gabdank; Aditi K. Narayanan; Marcus Ho; Brian T. Lee; Laurence D. Rowe; Timothy R. Dreszer; et al. (Nucleic Acids Res., 2016)

Open collaborative writing with Manubot. - Daniel S. Himmelstein; Vincent Rubinetti; David R. Slochower; Dongbo Hu; Venkat S. Malladi; Casey S. Greene; Anthony Gitter (PLoS Comput. Biol., 2019)

SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers. - Christopher G. Bennett; Micah Thornton; Chanhee Park; Gervaise Henry; Yun Zhang; Venkat S. Malladi; Daehwan Kim (Bioinform., 2022)

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)

Continuous Analysis: Evolution of Software Engineering and Reproducibility for Science. - Venkat S. Malladi; Maria Yazykova; Olesya Melnichenko; Yulia Dubinina (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)

BioAgents: Democratizing Bioinformatics Analysis with Multi-Agent Systems. - Nikita Mehandru; Amanda K. Hall; Olesya Melnichenko; Yulia Dubinina; Daniel Tsirulnikov; David Bamman; Ahmed M. Alaa; T. Scott Saponas; Venkat S. Malladi (CoRR, 2025)