Unsupervised knowledge discovery in medical databases using relevance networks. - Atul J. Butte; Isaac S. Kohane (AMIA, 1999)

Enrolling patients into clinical trials faster using RealTime Recuiting. - Atul J. Butte; David A. Weinstein; Isaac S. Kohane (AMIA, 2000)

Determining Significant Fold Differences in Gene Expression Analysis. - Atul J. Butte; J. Ye; G. Niederfellner; K. Rett; H. U. Häring; M. F. White; Isaac S. Kohane (Pacific Symposium on Biocomputing, 2001)

The Personal Internetworked Notary and Guardian. - Alberto Riva; Kenneth D. Mandl; Do Hoon Oh; Daniel J. Nigrin; Atul J. Butte; Peter Szolovits; Isaac S. Kohane (Int. J. Medical Informatics, 2001)

Comparing the Similarity of Time-Series Gene Expression Using Signal Processing Metrics. - Atul J. Butte; Ling Bao; Ben Y. Reis; Timothy W. Watkins; Isaac S. Kohane (J. Biomed. Informatics, 2001)

Extracting Knowledge from Dynamics in Gene Expression. - Ben Y. Reis; Atul J. Butte; Isaac S. Kohane (J. Biomed. Informatics, 2001)

Reply. - Ben Y. Reis; Atul J. Butte; Isaac S. Kohane (J. Biomed. Informatics, 2001)

Analysis of matched mRNA measurements from two different microarray technologies. - Winston Patrick Kuo; Tor-Kristian Jenssen; Atul J. Butte; Lucila Ohno-Machado; Isaac S. Kohane (Bioinform., 2002)

Comparing expression profiles of genes with similar promoter regions. - Peter J. Park; Atul J. Butte; Isaac S. Kohane (Bioinform., 2002)

PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications. - Kyungjoon Lee; Isaac S. Kohane; Atul J. Butte (Bioinform., 2003)

Reproducibility of gene expression across generations of Affymetrix microarrays. - Ashish Nimgaonkar; Despina Sanoudou; Atul J. Butte; Judith N. Haslett; Louis M. Kunkel; Alan H. Beggs; Isaac S. Kohane (BMC Bioinform., 2003)

Quantifying the relationship between co-expression, co-regulation and gene function. - Dominic J. Allocco; Isaac S. Kohane; Atul J. Butte (BMC Bioinform., 2004)

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. - Cecily J. Wolfe; Isaac S. Kohane; Atul J. Butte (BMC Bioinform., 2005)

Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics. - Atul J. Butte; Rong Chen 006 (AMIA, 2006)

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 (AMIA, 2007)

Methodologies for Extracting Functional Pharmacogenomic Experiments from International Repository. - Yi-An Lin; Annie P. Chiang; Ray Lin; Peggy Yao; Rong Chen 006; Atul J. Butte (AMIA, 2007)

Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. - Sangeeta B. English; Atul J. Butte (Bioinform., 2007)

Using SNOMED CT For Translational Genomics Data Integration. - Joel Dudley; David P. Chen; Atul J. Butte (KR-MED, 2008)

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 (Pacific Symposium on Biocomputing, 2008)

Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining. - Joel Dudley; Atul J. Butte (Pacific Symposium on Biocomputing, 2008)

Session Introduction. - Yves A. Lussier; Younghee Lee; Predrag Radivojac; Yanay Ofran; Marco Punta; Atul J. Butte; Maricel G. Kann (Pacific Symposium on Biocomputing, 2008)

GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed. - Rong Chen 006; Rohan Mallelwar; Ajit Thosar; Shivkumar Venkatasubrahmanyam; Atul J. Butte (BMC Bioinform., 2008)

Viewpoint Paper: Translational Bioinformatics: Coming of Age. - Atul J. Butte (J. Am. Medical Informatics Assoc., 2008)

Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology. - Joel Dudley; Atul J. Butte (Pacific Symposium on Biocomputing, 2009)

Session Introduction. - Yves A. Lussier; Younghee Lee; Predrag Radivojac; Yanay Ofran; Atul J. Butte; Maricel G. Kann (Pacific Symposium on Biocomputing, 2009)

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 (Pacific Symposium on Biocomputing, 2009)

A Classifier-based approach to identify genetic similarities between diseases. - Marc A. Schaub; Irene M. Kaplow; Marina Sirota; Chuong B. Do; Atul J. Butte; Serafim Batzoglou (Bioinform., 2009)

Selected proceedings of the First Summit on Translational Bioinformatics 2008. - Atul J. Butte; Indra Neil Sarkar; Marco Ramoni; Yves A. Lussier; Olga G. Troyanskaya (BMC Bioinform., 2009)

Infection in the intensive care unit alters physiological networks. - Adam D. Grossman; Mitchell J. Cohen; Geoffrey T. Manley; Atul J. Butte (BMC Bioinform., 2009)

The "etiome": identification and clustering of human disease etiological factors. - Yueyi I. Liu; Paul H. Wise; Atul J. Butte (BMC Bioinform., 2009)

Ontology-driven indexing of public datasets for translational bioinformatics. - Nigam H. Shah; Clément Jonquet; Annie P. Chiang; Atul J. Butte; Rong Chen 006; Mark A. Musen (BMC Bioinform., 2009)

Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR. - Sangeeta B. English; Shou-Ching Shih; Marco Ramoni; Lois E. Smith; Atul J. Butte (J. Biomed. Informatics, 2009)

A Quick Guide for Developing Effective Bioinformatics Programming Skills. - Joel Dudley; Atul J. Butte (PLoS Comput. Biol., 2009)

Immunological response in normal healthy twins across age. - Sanchita Bhattacharya; Shai Shen-Orr; Holden T. Maecker; Laura Lazzeroni; Gary E. Swan; J. David Clark; Martin S. Angst; Atul J. Butte; Mark M. Davis (BCB, 2010)

Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. - David P. Chen; Joel Dudley; Atul J. Butte (BMC Bioinform., 2010)

Content-based microarray search using differential expression profiles. - Jesse M. Engreitz; Alexander A. Morgan; Joel Dudley; Rong Chen 006; Rahul Thathoo; Russ B. Altman; Atul J. Butte (BMC Bioinform., 2010)

Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. - Alexander A. Morgan; Purvesh Khatri; Richard Hayden Jones; Minnie M. Sarwal; Atul J. Butte (BMC Bioinform., 2010)

An integrative method for scoring candidate genes from association studies: application to warfarin dosing. - Nicholas P. Tatonetti; Joel Dudley; Hersh Sagreiya; Atul J. Butte; Russ B. Altman (BMC Bioinform., 2010)

Validating pathophysiological models of aging using clinical electronic medical records. - David P. Chen; Alexander A. Morgan; Atul J. Butte (J. Biomed. Informatics, 2010)

Current methodologies for translational bioinformatics. - Yves A. Lussier; Atul J. Butte; Lawrence Hunter (J. Biomed. Informatics, 2010)

Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions. - Rong Chen 006; Tara K. Sigdel; Li Li 062; Neeraja Kambham; Joel Dudley; Szu-chuan Hsieh; R. Bryan Klassen; Amery Chen; Tuyen Caohuu; Alexander A. Morgan; Hannah A. Valantine; Kiran K. Khush; et al. (PLoS Comput. Biol., 2010)

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets. - Silpa Suthram; Joel Dudley; Annie P. Chiang; Rong Chen 006; Trevor Hastie; Atul J. Butte (PLoS Comput. Biol., 2010)

The Reference Human Genome Demonstrates High Risk of Type 1 Diabetes and Other Disorders. - Rong Chen 006; Atul J. Butte (Pacific Symposium on Biocomputing, 2011)

Matching Cancer Genomes to Established Cell Lines for Personalized Oncology. - Joel Dudley; Rong Chen 006; Atul J. Butte (Pacific Symposium on Biocomputing, 2011)

Exploiting drug-disease relationships for computational drug repositioning. - Joel Dudley; Tarangini Deshpande; Atul J. Butte (Briefings Bioinform., 2011)

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. - Jesse M. Engreitz; Rong Chen 006; Alexander A. Morgan; Joel Dudley; Rohan Mallelwar; Atul J. Butte (Bioinform., 2011)

Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. - Atul J. Butte; Nigam H. Shah (J. Am. Medical Informatics Assoc., 2011)

Translational bioinformatics: linking knowledge across biological and clinical realms. - Indra Neil Sarkar; Atul J. Butte; Yves A. Lussier; Peter Tarczy-Hornoch; Lucila Ohno-Machado (J. Am. Medical Informatics Assoc., 2011)

Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. - David Ruau; Michael Mbagwu; Joel T. Dudley; Vijay Krishnan; Atul J. Butte (J. Biomed. Informatics, 2011)

Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. - Chirag J. Patel; Rong Chen 006; Atul J. Butte (Bioinform., 2012)

Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. - Alexander A. Morgan; Rong Chen 006; Atul J. Butte (J. Am. Medical Informatics Assoc., 2012)

Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. - Alexander A. Morgan; Vasilios J. Pyrgos; Kari C. Nadeau; Peter R. Williamson; Atul J. Butte (J. Am. Medical Informatics Assoc., 2012)

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. - Purvesh Khatri; Marina Sirota; Atul J. Butte (PLoS Comput. Biol., 2012)

Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases. - David Ruau; Joel Dudley; Rong Chen 006; Nicholas G. Phillips; Gary E. Swan; Laura Lazzeroni; J. David Clark; Atul J. Butte; Martin S. Angst (PLoS Comput. Biol., 2012)

Translating a trillion points of data into therapies, diagnostics, and new insights into disease. - Atul J. Butte (DTMBIO, 2013)

DTMBIO 2013: international workshop on data and text mining in biomedical informatics. - Atul J. Butte; Doheon Lee; Hua Xu 001; Min Song 001 (CIKM, 2013)

Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical Records. - Li Li 062; David Ruau; Rong Chen 006; Susan C. Weber; Atul J. Butte (Pacific Symposium on Biocomputing, 2013)

Session Introduction. - Zhiyong Lu; Pankaj Agarwal; Atul J. Butte (Pacific Symposium on Biocomputing, 2013)

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. - Raymond K. Auerbach; Bin Chen; Atul J. Butte (Bioinform., 2013)

Making it personal: translational bioinformatics. - Atul J. Butte; Lucila Ohno-Machado (J. Am. Medical Informatics Assoc., 2013)

Investigating the Genetic Architecture of Pulmonary Arterial Hypertension Shared with Other Diseases. - Luke Yancy Jr.; Atul J. Butte (AMIA, 2014)

Towards the characterization of normal peripheral immune cells with data from ImmPort. - Sandra Andorf; Jennifer B. Bollyky; Patrick J. Dunn; Jeffrey A. Wiser; Sanchita Bhattacharya; Atul J. Butte (BCB, 2014)

RImmPort: enabling ready-for-analysis immunology research data. - Ravi D. Shankar; Sandra Andorf; Sanchita Bhattacharya; Jeffrey A. Wiser; Atul J. Butte (BCB, 2014)

Session Introduction. - S. Joshua Swamidass; Zhiyong Lu; Pankaj Agarwal; Atul J. Butte (Pacific Symposium on Biocomputing, 2014)

Recent Advances in Computational Drug Repositioning. - Atul J. Butte; Nigam Shah; Nicholas P. Tatonetti; Hua Xu 001; Ping Zhang (AMIA, 2015)

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; et al. (AMIA, 2015)

ImmPort: Shared research data for bioinformatics and immunology. - Patrick J. Dunn; Elizabeth Thomson; John Campbell 004; Thomas Smith; Vincent Desborough; Jeffrey A. Wiser; Henry Schaefer; Sanchita Bhattacharya; Atul J. Butte; Sandra Andorf; Mazen Nasrallah (BIBM, 2015)

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 (Pacific Symposium on Biocomputing, 2015)

Characteristics of Drug Combination Therapy in Oncology by Analyzing Clinical Trial Data on Clinicaltrials.Gov. - Menghua Wu; Marina Sirota; Atul J. Butte; Bin Chen (Pacific Symposium on Biocomputing, 2015)

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 (PSB, 2016)

A survey of current trends in computational drug repositioning. - Jiao Li 001; Si Zheng 001; Bin Chen; Atul J. Butte; S. Joshua Swamidass; Zhiyong Lu (Briefings Bioinform., 2016)

Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression. - Nophar Geifman; Sanchita Bhattacharya; Atul J. Butte (J. Am. Medical Informatics Assoc., 2016)

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. - Steven C. Bagley; Marina Sirota; Richard O. Chen; Atul J. Butte; Russ B. Altman (PLoS Comput. Biol., 2016)

Ethnic and gender disparity in organ transplant clinical trials and electronic health records. - Jieming Chen; Sanchita Bhattacharya; Marina Sirota; Minnie M. Sarwal; Atul J. Butte (CRI, 2017)

Scalable and accurate deep learning for electronic health records. - Alvin Rajkomar; Eyal Oren; Kai Chen 010; Andrew M. Dai; Nissan Hajaj; Peter J. Liu; Xiaobing Liu; Mimi Sun; Patrik Sundberg; Hector Yee; Kun Zhang 043; Gavin E. Duggan; et al. (CoRR, 2018)

Time Aggregation and Model Interpretation for Deep Multivariate Longitudinal Patient Outcome Forecasting Systems in Chronic Ambulatory Care. - Beau Norgeot; Dmytro Lituiev; Benjamin S. Glicksberg; Atul J. Butte (CoRR, 2018)

Scalable and accurate deep learning with electronic health records. - Alvin Rajkomar; Eyal Oren; Kai Chen 010; Andrew M. Dai; Nissan Hajaj; Michaela Hardt; Peter J. Liu; Xiaobing Liu; Jake Marcus; Mimi Sun; Patrik Sundberg; Hector Yee; et al. (npj Digit. Medicine, 2018)

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 (PSB, 2019)

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. - Benjamin S. Glicksberg; Boris Oskotsky; Phyllis M. Thangaraj; Nicholas Giangreco; Marcus A. Badgeley; Kipp W. Johnson; Debajyoti Datta; Vivek A. Rudrapatna; Nadav Rappoport; Mark M. Shervey; Riccardo Miotto; Theodore C. Goldstein; et al. (Bioinform., 2019)

Robust prediction of clinical outcomes using cytometry data. - Zicheng Hu; Benjamin S. Glicksberg; Atul J. Butte (Bioinform., 2019)

Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes. - Beau Norgeot; Kathleen Muenzen; Thomas A. Peterson; Xuancheng Fan; Benjamin S. Glicksberg; Gundolf Schenk; Eugenia Rutenberg; Boris Oskotsky; Marina Sirota; Jinoos Yazdany; Gabriela Schmajuk; Dana Ludwig; et al. (npj Digit. Medicine, 2020)

Characteristics and challenges of the clinical pipeline of digital therapeutics. - Nisarg A. Patel; Atul J. Butte (npj Digit. Medicine, 2020)

A Generalizable Framework for Cost-Effectiveness Analysis of Antihypertensive Drugs Leveraging Real-World Evidence. - Douglas Arneson; Rohit Vashisht; Vivek A. Rudrapatna; Atul J. Butte (AMIA, 2021)

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 (AMIA, 2021)

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 (AMIA, 2021)

Rethinking PICO in the Machine Learning Era: ML-PICO. - Xinran Liu; James Anstey; Ron C. Li; Chethan Sarabu; Reiri Sono; Atul J. Butte (Appl. Clin. Inform., 2021)

Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers. - Subha Madhavan; Lisa Bastarache; Jeffrey S. Brown; Atul J. Butte; David A. Dorr; Peter J. Embí; Charles P. Friedman; Kevin B. Johnson; Jason H. Moore; Isaac S. Kohane; Philip R. O. Payne; Jessica D. Tenenbaum; et al. (J. Am. Medical Informatics Assoc., 2021)

Understanding the Impact of Demographics and Socioeconomic Parameters on Treatment Selection and Utilization in Type 2 Diabetes. - Jaysón M. Davidson; Rohit Davidson; Ayan Patel; Atul J. Butte (AMIA, 2022)

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 (AMIA, 2022)

Training a Transferrable Clinical Language Model from 75 million Notes. - Madhumita Sushil; Dana Ludwig; Atul J. Butte; Vivek A. Rudrapatna (AMIA, 2022)

Developing a general-purpose clinical language inference model from a large corpus of clinical notes. - Madhumita Sushil; Dana Ludwig; Atul J. Butte; Vivek A. Rudrapatna (CoRR, 2022)

Topic Modeling on Clinical Social Work Notes for Exploring Social Determinants of Health Factors. - Shenghuan Sun; Travis Zack; Madhumita Sushil; Atul J. Butte (CoRR, 2022)

Toward a causal model of chronic back pain: Challenges and opportunities. - J. Russell Huie; Rohit Vashisht; Anoop Galivanche; Constance Hadjadj; Saam Morshed; Atul J. Butte; Adam R. Ferguson; Conor O'Neill (Frontiers Comput. Neurosci., 2022)

Embedding electronic health records onto a knowledge network recognizes prodromal features of multiple sclerosis and predicts diagnosis. - Charlotte A. Nelson; Riley Bove; Atul J. Butte; Sergio E. Baranzini (J. Am. Medical Informatics Assoc., 2022)

Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics. - Daniel R. Wong; Jay Conrad; Noah R. Johnson; Jacob Ayers; Annelies Laeremans; Joanne C. Lee; Jisoo Lee; Stanley B. Prusiner; Sourav Bandyopadhyay; Atul J. Butte; Nick A. Paras; Michael J. Keiser (Nat. Mach. Intell., 2022)

Aligning Synthetic Medical Images with Clinical Knowledge using Human Feedback. - Shenghuan Sun; Gregory M. Goldgof; Atul J. Butte; Ahmed M. Alaa (NeurIPS, 2023)

Cross-institution text mining to uncover clinical associations: a case study relating social factors and code status in intensive care medicine. - Madhumita Sushil; Atul J. Butte; Ewoud Schuit; Maarten van Smeden; Artuur M. Leeuwenberg (CoRR, 2023)

Revealing the impact of social circumstances on the selection of cancer therapy through natural language processing of social work notes. - Shenghuan Sun; Travis Zack; Christopher Y. K. Williams; Atul J. Butte; Madhumita Sushil (CoRR, 2023)

Extracting detailed oncologic history and treatment plan from medical oncology notes with large language models. - Madhumita Sushil; Vanessa E. Kennedy; Brenda Y. Miao; Divneet Mandair; Travis Zack; Atul J. Butte (CoRR, 2023)

Large Language Models as Agents in the Clinic. - Nikita Mehandru; Brenda Y. Miao; Eduardo Rodriguez Almaraz; Madhumita Sushil; Atul J. Butte; Ahmed M. Alaa (CoRR, 2023)

Bottom-up and top-down paradigms of artificial intelligence research approaches to healthcare data science using growing real-world big data. - Michelle Wang; Madhumita Sushil; Brenda Y. Miao; Atul J. Butte (J. Am. Medical Informatics Assoc., 2023)

Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies. - Yu-Ning Huang; Michael I. Love; Cynthia Flaire Ronkowski; Dhrithi Deshpande; Lynn M. Schriml; Annie Wong-Beringer; Barend Mons; Russell Corbett-Detig; Christopher I Hunter; Jason H. Moore; Lana X. Garmire; T. B. K. Reddy; et al. (CoRR, 2024)

A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification. - Madhumita Sushil; Travis Zack; Divneet Mandair; Zhiwei Zheng; Ahmed Wali; Yan-Ning Yu; Yuwei Quan; Atul J. Butte (CoRR, 2024)

Identifying Reasons for Contraceptive Switching from Real-World Data Using Large Language Models. - Brenda Y. Miao; Christopher Y. K. Williams; Ebenezer Chinedu-Eneh; Travis Zack; Emily Alsentzer; Atul J. Butte; Irene Y. Chen (CoRR, 2024)

Updating the Minimum Information about CLinical Artificial Intelligence (MI-CLAIM) checklist for generative modeling research. - Brenda Y. Miao; Irene Y. Chen; Christopher Y. K. Williams; Jaysón M. Davidson; Augusto Garcia-Agundez; Harry Sun; Travis Zack; Atul J. Butte; Madhumita Sushil (CoRR, 2024)

Dr-LLaVA: Visual Instruction Tuning with Symbolic Clinical Grounding. - Shenghuan Sun; Gregory M. Goldgof; Alexander Schubert; Zhiqing Sun; Thomas Hartvigsen; Atul J. Butte; Ahmed M. Alaa (CoRR, 2024)

A comparative study of large language model-based zero-shot inference and task-specific supervised classification of breast cancer pathology reports. - Madhumita Sushil; Travis Zack; Divneet Mandair; Zhiwei Zheng; Ahmed Wali; Yan-Ning Yu; Yuwei Quan; Dmytro Lituiev; Atul J. Butte (J. Am. Medical Informatics Assoc., 2024)

Evaluating large language models as agents in the clinic. - Nikita Mehandru; Brenda Y. Miao; Eduardo Rodriguez Almaraz; Madhumita Sushil; Atul J. Butte; Ahmed M. Alaa (npj Digit. Medicine, 2024)

Understanding contraceptive switching rationales from real world clinical notes using large language models. - Brenda Y. Miao; Christopher Y. K. Williams; Ebenezer Chinedu-Eneh; Travis Zack; Emily Alsentzer; Atul J. Butte; Irene Y. Chen (npj Digit. Medicine, 2025)

From trial data to personalized medicine: a validated framework with an application to Crohn's disease. - Vivek A. Rudrapatna; Vignesh G. Ravindranath; Douglas Arneson; Arman Mosenia; Atul J. Butte; Shan Wang (npj Digit. Medicine, 2025)