Atul J. Butte
Orcid: 0000-0002-7433-2740
According to our database1,
Atul J. Butte
authored at least 108 papers
between 1999 and 2024.
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Bibliography
2024
A comparative study of large language model-based zero-shot inference and task-specific supervised classification of breast cancer pathology reports.
J. Am. Medical Informatics Assoc., 2024
Updating the Minimum Information about CLinical Artificial Intelligence (MI-CLAIM) checklist for generative modeling research.
CoRR, 2024
Identifying Reasons for Contraceptive Switching from Real-World Data Using Large Language Models.
CoRR, 2024
A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification.
CoRR, 2024
Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.
CoRR, 2024
2023
Bottom-up and top-down paradigms of artificial intelligence research approaches to healthcare data science using growing real-world big data.
J. Am. Medical Informatics Assoc., June, 2023
Extracting detailed oncologic history and treatment plan from medical oncology notes with large language models.
CoRR, 2023
Revealing the impact of social circumstances on the selection of cancer therapy through natural language processing of social work notes.
CoRR, 2023
Cross-institution text mining to uncover clinical associations: a case study relating social factors and code status in intensive care medicine.
CoRR, 2023
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
2022
Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics.
Nat. Mach. Intell., 2022
Embedding electronic health records onto a knowledge network recognizes prodromal features of multiple sclerosis and predicts diagnosis.
J. Am. Medical Informatics Assoc., 2022
Frontiers Comput. Neurosci., 2022
Topic Modeling on Clinical Social Work Notes for Exploring Social Determinants of Health Factors.
CoRR, 2022
Developing a general-purpose clinical language inference model from a large corpus of clinical notes.
CoRR, 2022
Proceedings of the AMIA 2022, 2022
Deidentifying a Corpus of 100 Million Clinical Text Documents for Information Extraction: Lessons Learned.
Proceedings of the AMIA 2022, 2022
Understanding the Impact of Demographics and Socioeconomic Parameters on Treatment Selection and Utilization in Type 2 Diabetes.
Proceedings of the AMIA 2022, 2022
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.
J. Am. Medical Informatics Assoc., 2021
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 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.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
A Generalizable Framework for Cost-Effectiveness Analysis of Antihypertensive Drugs Leveraging Real-World Evidence.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
2020
npj Digit. Medicine, 2020
Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.
npj Digit. Medicine, 2020
2019
PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.
Bioinform., 2019
Translational informatics of population Health: How large biomolecular and clinical datasets unite.
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019
2018
npj Digit. Medicine, 2018
Time Aggregation and Model Interpretation for Deep Multivariate Longitudinal Patient Outcome Forecasting Systems in Chronic Ambulatory Care.
CoRR, 2018
2017
Ethnic and gender disparity in organ transplant clinical trials and electronic health records.
Proceedings of the Summit on Clinical Research Informatics, 2017
2016
Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.
PLoS Comput. Biol., 2016
Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression.
J. Am. Medical Informatics Assoc., 2016
Briefings Bioinform., 2016
Do Cancer Clinical Trial Populations Truly Represent Cancer Patients? A Comparison of Open Clinical Trials to the Cancer Genome Atlas.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
2015
Characteristics of Drug Combination Therapy in Oncology by Analyzing Clinical Trial Data on Clinicaltrials.Gov.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015
A Systematic Assessment of Linking Gene Expression with Genetic Variants for Prioritizing Candidate Targets.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
Human Computation of Big Data in Biomedicine: Making STAR annotations for large scale functional characterization of disease.
Proceedings of the AMIA 2015, 2015
Proceedings of the AMIA 2015, 2015
2014
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014
Proceedings of the 5th ACM Conference on Bioinformatics, 2014
Towards the characterization of normal peripheral immune cells with data from ImmPort.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014
Investigating the Genetic Architecture of Pulmonary Arterial Hypertension Shared with Other Diseases.
Proceedings of the AMIA 2014, 2014
2013
J. Am. Medical Informatics Assoc., 2013
Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.
Bioinform., 2013
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013
Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical Records.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013
DTMBIO 2013: international workshop on data and text mining in biomedical informatics.
Proceedings of the 22nd ACM International Conference on Information and Knowledge Management, 2013
Translating a trillion points of data into therapies, diagnostics, and new insights into disease.
Proceedings of the Proceeding of the 7rd International Workshop on Data and Text Mining in Bioinformatics, 2013
2012
Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases.
PLoS Comput. Biol., 2012
PLoS Comput. Biol., 2012
Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction.
J. Am. Medical Informatics Assoc., 2012
Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays.
J. Am. Medical Informatics Assoc., 2012
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease.
Bioinform., 2012
2011
Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets.
J. Biomed. Informatics, 2011
Translational bioinformatics: linking knowledge across biological and clinical realms.
J. Am. Medical Informatics Assoc., 2011
Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in <i>JAMIA</i>.
J. Am. Medical Informatics Assoc., 2011
ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.
Bioinform., 2011
Briefings Bioinform., 2011
Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011
The Reference Human Genome Demonstrates High Risk of Type 1 Diabetes and Other Disorders.
Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011
2010
Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets.
PLoS Comput. Biol., 2010
Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions.
PLoS Comput. Biol., 2010
Validating pathophysiological models of aging using clinical electronic medical records.
J. Biomed. Informatics, 2010
An integrative method for scoring candidate genes from association studies: application to warfarin dosing.
BMC Bioinform., 2010
Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants.
BMC Bioinform., 2010
BMC Bioinform., 2010
Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays.
BMC Bioinform., 2010
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010
2009
PLoS Comput. Biol., 2009
Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR.
J. Biomed. Informatics, 2009
BMC Bioinform., 2009
BMC Bioinform., 2009
BMC Bioinform., 2009
BMC Bioinform., 2009
Bioinform., 2009
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
2008
J. Am. Medical Informatics Assoc., 2008
GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed.
BMC Bioinform., 2008
Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining.
Proceedings of the Biocomputing 2008, 2008
Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation.
Proceedings of the Biocomputing 2008, 2008
Proceedings of the Third International Conference on Knowledge Representation in Medicine, Phoenix, Arizona, USA, May 31st, 2008
2007
Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes.
Bioinform., 2007
Methodologies for Extracting Functional Pharmacogenomic Experiments from International Repository.
Proceedings of the AMIA 2007, 2007
Clinical Arrays of Laboratory Measures, or "Clinarrays", Built from an Electronic Health Record Enable Disease Subtyping by Severity.
Proceedings of the AMIA 2007, 2007
2006
Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics.
Proceedings of the AMIA 2006, 2006
2005
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks.
BMC Bioinform., 2005
2004
BMC Bioinform., 2004
2003
BMC Bioinform., 2003
PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications.
Bioinform., 2003
2002
Bioinform., 2002
Bioinform., 2002
2001
Comparing the Similarity of Time-Series Gene Expression Using Signal Processing Metrics.
J. Biomed. Informatics, 2001
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001
2000
Proceedings of the AMIA 2000, 2000
1999
Proceedings of the AMIA 1999, 1999