Finding Protein Domain Boundaries: An Automated, Non-Homology-Based Method. - Brian M. Gurbaxani; Parag Mallick (IEEE Intell. Syst., 2005)

The PeptideAtlas project. - Frank Desiere; Eric W. Deutsch; Nichole L. King; Alexey I. Nesvizhskii; Parag Mallick; Jimmy K. Eng; Sharon Chen; James Eddes; Sandra N. Loevenich; Ruedi Aebersold (Nucleic Acids Res., 2006)

ProteoWizard: open source software for rapid proteomics tools development. - Darren Kessner; Matt Chambers; Robert Burke; David B. Agus; Parag Mallick (Bioinform., 2008)

Interactively Mapping Data Sources into the Semantic Web. - Craig A. Knoblock; Pedro A. Szekely; José Luis Ambite; Shubham Gupta; Aman Goel; Maria Muslea; Kristina Lerman; Parag Mallick (LISC, 2011)

Semi-automatically Mapping Structured Sources into the Semantic Web. - Craig A. Knoblock; Pedro A. Szekely; José Luis Ambite; Aman Goel; Shubham Gupta; Kristina Lerman; Maria Muslea; Mohsen Taheriyan; Parag Mallick (ESWC, 2012)

Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments. - Kyle D. Bemis; April Harry; Livia S. Eberlin; Christina Ferreira; Stephanie M. van de Ven; Parag Mallick; Mark L. Stolowitz; Olga Vitek (Bioinform., 2015)

Towards Continuous Scientific Data Analysis and Hypothesis Evolution. - Yolanda Gil; Daniel Garijo; Varun Ratnakar; Rajiv Mayani; Ravali Adusumilli; Hunter Boyce; Arunima Srivastava; Parag Mallick (AAAI, 2017)

Improving Publication and Reproducibility of Computational Experiments through Workflow Abstractions. - Yolanda Gil; Daniel Garijo; Margaret Knoblock; Alyssa Deng; Ravali Adusumilli; Varun Ratnakar; Parag Mallick (K-CAP Workshops, 2017)

Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles. - Arunima Srivastava; Chaitanya Kulkarni; Parag Mallick; Kun Huang 001; Raghu Machiraju (PSB, 2018)

A Bayesian Active Learning Experimental Design for Inferring Signaling Networks. - Robert Osazuwa Ness; Karen Sachs; Parag Mallick; Olga Vitek (J. Comput. Biol., 2018)

Geostatistical visualization of ecological interactions in tumors. - Hunter Boyce; Parag Mallick (BIBM, 2019)

Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibility. - Arunima Srivastava; Ravali Adusumilli; Hunter Boyce; Daniel Garijo; Varun Ratnakar; Rajiv Mayani; Thomas Yu; Raghu Machiraju; Yolanda Gil; Parag Mallick (PSB, 2019)

PTR Explorer: An approach to identify and explore Post Transcriptional Regulatory mechanisms usingproteogenomics. - Arunima Srivastava; Michael F. Sharpnack; Kun Huang 001; Parag Mallick; Raghu Machiraju (PSB, 2020)

ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network. - Michelle B. Atallah; Varun Tandon; Kamir J. Hiam; Hunter Boyce; Michelle Hori; Waleed Atallah; Matthew H. Spitzer; Edgar Engleman; Parag Mallick (BMC Bioinform., 2020)

A Dataset Generation Framework for Evaluating Megapixel Image Classifiers and Their Explanations. - Gautam Machiraju; Sylvia K. Plevritis; Parag Mallick (ECCV (12), 2022)

Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images. - Grigorios M. Karageorgos; Sanghee Cho; Elizabeth McDonough; Chrystal Chadwick; Soumya Ghose; Jonathan Owens; Kyeong Joo Jung; Raghu Machiraju; Robert West; James D. Brooks; Parag Mallick; Fiona Ginty (Frontiers Bioinform., 2023)

Prospector Heads: Generalized Feature Attribution for Large Models & Data. - Gautam Machiraju; Alexander Derry; Arjun D. Desai; Neel Guha; Amir-Hossein Karimi; James Zou 001; Russ B. Altman; Christopher Ré; Parag Mallick (ICML, 2024)