| 2022 | AMIA | Understanding the Impact of Demographics and Socioeconomic Parameters on Treatment Selection and Utilization in Type 2 Diabetes. | Jaysn M. Davidson, Rohit Davidson, Ayan Patel, Atul J. Butte |
| 2022 | AMIA | Deidentifying a Corpus of 100 Million Clinical Text Documents for Information Extraction: Lessons Learned. | Lakshmi Radhakrishnan, Gundolf Schenk, Kathlene Muenzen, Boris Oskotsky, Sharat Israni, Atul J. Butte |
| 2022 | AMIA | Training a Transferrable Clinical Language Model from 75 million Notes. | Madhumita Sushil, Dana Ludwig, Atul J. Butte, Vivek A. Rudrapatna |
| 2021 | AMIA | A Generalizable Framework for Cost-Effectiveness Analysis of Antihypertensive Drugs Leveraging Real-World Evidence. | Douglas Arneson, Rohit Vashisht, Vivek A. Rudrapatna, Atul J. Butte |
| 2021 | AMIA | Use of Healthcare Information Technology and Data Platforms to Inform Pandemic Response: Perspectives at the Intersection of Academic Healthcare Provider Organizations and Industry Partners. | Atul J. Butte, Christopher A. Longhurst, Amy Abernethy, Gretchen P. Jackson, Philip R. O. Payne |
| 2021 | AMIA | Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients. | Navchetan Kaur, Boris Oskotsky, Atul J. Butte, Zicheng Hu |
| 2019 | PSB | Translational informatics of population Health: How large biomolecular and clinical datasets unite. | Yves A. Lussier, Atul J. Butte, Haiquan Li, Rong Chen, Jason H. Moore |
| 2016 | PSB | Do Cancer Clinical Trial Populations Truly Represent Cancer Patients? A Comparison of Open Clinical Trials to the Cancer Genome Atlas. | Nophar Geifman, Atul J. Butte |
| 2015 | AMIA | Recent Advances in Computational Drug Repositioning. | Atul J. Butte, Nigam Shah, Nicholas P. Tatonetti, Hua Xu, Ping Zhang |
| 2015 | AMIA | Human Computation of Big Data in Biomedicine: Making STAR annotations for large scale functional characterization of disease. | Dexter Hadley, James Pan, Osama M. El-Sayed, Jihad Al-Jabban, Imad Al-Jabban, Tej Azad, Shuaib Raza, Mohamed Hadied, Bin Chen, Hyojung Paik, Sanchita Bhattacharya, Marina Sirota, Atul J. Butte |
| 2015 | PSB | A Systematic Assessment of Linking Gene Expression with Genetic Variants for Prioritizing Candidate Targets. | Hua Fan-Minogue, Bin Chen, Weronika Sikora-Wohlfeld, Marina Sirota, Atul J. Butte |
| 2015 | PSB | Characteristics of Drug Combination Therapy in Oncology by Analyzing Clinical Trial Data on Clinicaltrials.Gov. | Menghua Wu, Marina Sirota, Atul J. Butte, Bin Chen |
| 2014 | AMIA | Investigating the Genetic Architecture of Pulmonary Arterial Hypertension Shared with Other Diseases. | Luke Yancy Jr., Atul J. Butte |
| 2014 | PSB | Session Introduction. | S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte |
| 2013 | CIKM | Translating a trillion points of data into therapies, diagnostics, and new insights into disease. | Atul J. Butte |
| 2013 | CIKM | DTMBIO 2013: international workshop on data and text mining in biomedical informatics. | Atul J. Butte, Doheon Lee, Hua Xu, Min Song |
| 2013 | PSB | Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical Records. | Li Li, David Ruau, Rong Chen, Susan C. Weber, Atul J. Butte |
| 2013 | PSB | Session Introduction. | Zhiyong Lu, Pankaj Agarwal, Atul J. Butte |
| 2011 | PSB | The Reference Human Genome Demonstrates High Risk of Type 1 Diabetes and Other Disorders. | Rong Chen, Atul J. Butte |
| 2011 | PSB | Matching Cancer Genomes to Established Cell Lines for Personalized Oncology. | Joel Dudley, Rong Chen, Atul J. Butte |
| 2009 | PSB | Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology. | Joel Dudley, Atul J. Butte |
| 2009 | PSB | Session Introduction. | Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann |
| 2009 | PSB | Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune System. | Shai Shen-Orr, Ofir Goldberger, Yael Garten, Yael Rosenberg-Hasson, Patricia A. Lovelace, David L. Hirschberg, Russ B. Altman, Mark M. Davis, Atul J. Butte |
| 2008 | PSB | Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation. | David P. Chen, Susan C. Weber, Philip S. Constantinou, Todd A. Ferris, Henry J. Lowe, Atul J. Butte |
| 2008 | PSB | Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining. | Joel Dudley, Atul J. Butte |
| 2008 | PSB | Session Introduction. | Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann |
| 2007 | AMIA | Clinical Arrays of Laboratory Measures, or "Clinarrays", Built from an Electronic Health Record Enable Disease Subtyping by Severity. | David P. Chen, Susan C. Weber, Philip S. Constantinou, Todd A. Ferris, Henry J. Lowe, Atul J. Butte |
| 2007 | AMIA | Methodologies for Extracting Functional Pharmacogenomic Experiments from International Repository. | Yi-An Lin, Annie P. Chiang, Ray Lin, Peggy Yao, Rong Chen, Atul J. Butte |
| 2006 | AMIA | Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics. | Atul J. Butte, Rong Chen |
| 2001 | PSB | Determining Significant Fold Differences in Gene Expression Analysis. | Atul J. Butte, J. Ye, G. Niederfellner, K. Rett, H. U. Hring, M. F. White, Isaac S. Kohane |
| 2000 | AMIA | Enrolling patients into clinical trials faster using RealTime Recuiting. | Atul J. Butte, David A. Weinstein, Isaac S. Kohane |
| 1999 | AMIA | Unsupervised knowledge discovery in medical databases using relevance networks. | Atul J. Butte, Isaac S. Kohane |