Atul J. Butte - RankMe

112 papers A* 1A 1Misc 30Journal 72Unranked 7

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	From trial data to personalized medicine: a validated framework with an application to Crohn's disease. npj Digit. Medicine Vivek A. Rudrapatna, Vignesh G. Ravindranath, Douglas Arneson, Arman Mosenia, Atul J. Butte, Shan Wang
2025	J	`jnl`	Understanding contraceptive switching rationales from real world clinical notes using large language models. npj Digit. Medicine Brenda Y. Miao, Christopher Y. K. Williams, Ebenezer Chinedu-Eneh, Travis Zack, Emily Alsentzer, Atul J. Butte, Irene Y. Chen
2024	J	`jnl`	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. Madhumita Sushil, Travis Zack, Divneet Mandair, Zhiwei Zheng, Ahmed Wali, Yan-Ning Yu, Yuwei Quan, Dmytro Lituiev, Atul J. Butte
2024	J	`jnl`	A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification. CoRR Madhumita Sushil, Travis Zack, Divneet Mandair, Zhiwei Zheng, Ahmed Wali, Yan-Ning Yu, Yuwei Quan, Atul J. Butte
2024	J	`jnl`	Dr-LLaVA: Visual Instruction Tuning with Symbolic Clinical Grounding. CoRR Shenghuan Sun, Gregory M. Goldgof, Alexander Schubert, Zhiqing Sun, Thomas Hartvigsen, Atul J. Butte, Ahmed M. Alaa
2024	J	`jnl`	Evaluating large language models as agents in the clinic. npj Digit. Medicine Nikita Mehandru, Brenda Y. Miao, Eduardo Rodriguez Almaraz, Madhumita Sushil, Atul J. Butte, Ahmed M. Alaa
2024	J	`jnl`	Identifying Reasons for Contraceptive Switching from Real-World Data Using Large Language Models. CoRR Brenda Y. Miao, Christopher Y. K. Williams, Ebenezer Chinedu-Eneh, Travis Zack, Emily Alsentzer, Atul J. Butte, Irene Y. Chen
2024	J	`jnl`	Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies. CoRR 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, Winston A. Hide, Atul J. Butte, Mark D. Robinson, Serghei Mangul
2024	J	`jnl`	Updating the Minimum Information about CLinical Artificial Intelligence (MI-CLAIM) checklist for generative modeling research. CoRR 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
2023	A*	`conf`	Aligning Synthetic Medical Images with Clinical Knowledge using Human Feedback. NeurIPS Shenghuan Sun, Gregory M. Goldgof, Atul J. Butte, Ahmed M. Alaa
2023	J	`jnl`	Aligning Synthetic Medical Images with Clinical Knowledge using Human Feedback. CoRR Shenghuan Sun, Gregory M. Goldgof, Atul J. Butte, Ahmed M. Alaa
2023	J	`jnl`	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. Michelle Wang, Madhumita Sushil, Brenda Y. Miao, Atul J. Butte
2023	J	`jnl`	Cross-institution text mining to uncover clinical associations: a case study relating social factors and code status in intensive care medicine. CoRR Madhumita Sushil, Atul J. Butte, Ewoud Schuit, Maarten van Smeden, Artuur M. Leeuwenberg
2023	J	`jnl`	Extracting detailed oncologic history and treatment plan from medical oncology notes with large language models. CoRR Madhumita Sushil, Vanessa E. Kennedy, Brenda Y. Miao, Divneet Mandair, Travis Zack, Atul J. Butte
2023	J	`jnl`	Large Language Models as Agents in the Clinic. CoRR Nikita Mehandru, Brenda Y. Miao, Eduardo Rodriguez Almaraz, Madhumita Sushil, Atul J. Butte, Ahmed M. Alaa
2023	J	`jnl`	Revealing the impact of social circumstances on the selection of cancer therapy through natural language processing of social work notes. CoRR Shenghuan Sun, Travis Zack, Christopher Y. K. Williams, Atul J. Butte, Madhumita Sushil
2022	Misc	`conf`	Deidentifying a Corpus of 100 Million Clinical Text Documents for Information Extraction: Lessons Learned. AMIA Lakshmi Radhakrishnan, Gundolf Schenk, Kathlene Muenzen, Boris Oskotsky, Sharat Israni, Atul J. Butte
2022	J	`jnl`	Developing a general-purpose clinical language inference model from a large corpus of clinical notes. CoRR Madhumita Sushil, Dana Ludwig, Atul J. Butte, Vivek A. Rudrapatna
2022	J	`jnl`	Embedding electronic health records onto a knowledge network recognizes prodromal features of multiple sclerosis and predicts diagnosis. J. Am. Medical Informatics Assoc. Charlotte A. Nelson, Riley Bove, Atul J. Butte, Sergio E. Baranzini
2022	J	`jnl`	Topic Modeling on Clinical Social Work Notes for Exploring Social Determinants of Health Factors. CoRR Shenghuan Sun, Travis Zack, Madhumita Sushil, Atul J. Butte
2022	J	`jnl`	Toward a causal model of chronic back pain: Challenges and opportunities. Frontiers Comput. Neurosci. J. Russell Huie, Rohit Vashisht, Anoop Galivanche, Constance Hadjadj, Saam Morshed, Atul J. Butte, Adam R. Ferguson, Conor O'neill
2022	Misc	`conf`	Training a Transferrable Clinical Language Model from 75 million Notes. AMIA Madhumita Sushil, Dana Ludwig, Atul J. Butte, Vivek A. Rudrapatna
2022	J	`jnl`	Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics. Nat. Mach. Intell. 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
2022	Misc	`conf`	Understanding the Impact of Demographics and Socioeconomic Parameters on Treatment Selection and Utilization in Type 2 Diabetes. AMIA Jaysón M. Davidson, Rohit Davidson, Ayan Patel, Atul J. Butte
2021	Misc	`conf`	A Generalizable Framework for Cost-Effectiveness Analysis of Antihypertensive Drugs Leveraging Real-World Evidence. AMIA Douglas Arneson, Rohit Vashisht, Vivek A. Rudrapatna, Atul J. Butte
2021	J	`jnl`	Rethinking PICO in the Machine Learning Era: ML-PICO. Appl. Clin. Inform. Xinran Liu, James Anstey, Ron C. Li, Chethan Sarabu, Reiri Sono, Atul J. Butte
2021	Misc	`conf`	Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients. AMIA Navchetan Kaur, Boris Oskotsky, Atul J. Butte, Zicheng Hu
2021	Misc	`conf`	Use of Healthcare Information Technology and Data Platforms to Inform Pandemic Response: Perspectives at the Intersection of Academic Healthcare Provider Organizations and Industry Partners. AMIA Atul J. Butte, Christopher A. Longhurst, Amy Abernethy, Gretchen P. Jackson, Philip R. O. Payne
2021	J	`jnl`	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. 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, Mark G. Weiner, Adam B. Wilcox, Lucila Ohno-Machado
2020	J	`jnl`	Characteristics and challenges of the clinical pipeline of digital therapeutics. npj Digit. Medicine Nisarg A. Patel, Atul J. Butte
2020	J	`jnl`	Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes. npj Digit. Medicine 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, Theodore C. Goldstein, Atul J. Butte
2019	J	`jnl`	PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Bioinform. 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, Eugenia Rutenberg, Remi Frazier, Nelson Lee, Sharat Israni, Rick Larsen, Bethany Percha, Li Li, Joel T. Dudley, Nicholas P. Tatonetti, Atul J. Butte
2019	J	`jnl`	Robust prediction of clinical outcomes using cytometry data. Bioinform. Zicheng Hu, Benjamin S. Glicksberg, Atul J. Butte
2019	Misc	`conf`	Translational informatics of population Health: How large biomolecular and clinical datasets unite. PSB Yves A. Lussier, Atul J. Butte, Haiquan Li, Rong Chen, Jason H. Moore
2018	J	`jnl`	Scalable and accurate deep learning for electronic health records. CoRR Alvin Rajkomar, Eyal Oren, Kai Chen, Andrew M. Dai, Nissan Hajaj, Peter J. Liu, Xiaobing Liu, Mimi Sun, Patrik Sundberg, Hector Yee, Kun Zhang, Gavin E. Duggan, Gerardo Flores, Michaela Hardt, Jamie Irvine, Quoc V. Le, Kurt Litsch, Jake Marcus, Alexander Mossin, Justin Tansuwan, De Wang, James Wexler, Jimbo Wilson, Dana Ludwig, Samuel L. Volchenboum, Katherine Chou, Michael Pearson, Srinivasan Madabushi, Nigam H. Shah, Atul J. Butte, Michael D. Howell, Claire Cui, Greg Corrado, Jeff Dean
2018	J	`jnl`	Scalable and accurate deep learning with electronic health records. npj Digit. Medicine Alvin Rajkomar, Eyal Oren, Kai Chen, Andrew M. Dai, Nissan Hajaj, Michaela Hardt, Peter J. Liu, Xiaobing Liu, Jake Marcus, Mimi Sun, Patrik Sundberg, Hector Yee, Kun Zhang, Yi Zhang, Gerardo Flores, Gavin E. Duggan, Jamie Irvine, Quoc Le, Kurt Litsch, Alexander Mossin, Justin Tansuwan, De Wang, James Wexler, Jimbo Wilson, Dana Ludwig, Samuel L. Volchenboum, Katherine Chou, Michael Pearson, Srinivasan Madabushi, Nigam H. Shah, Atul J. Butte, Michael D. Howell, Claire Cui, Gregory S. Corrado, Jeffrey Dean
2018	J	`jnl`	Time Aggregation and Model Interpretation for Deep Multivariate Longitudinal Patient Outcome Forecasting Systems in Chronic Ambulatory Care. CoRR Beau Norgeot, Dmytro Lituiev, Benjamin S. Glicksberg, Atul J. Butte
2017	—	`conf`	Ethnic and gender disparity in organ transplant clinical trials and electronic health records. CRI Jieming Chen, Sanchita Bhattacharya, Marina Sirota, Minnie M. Sarwal, Atul J. Butte
2016	J	`jnl`	A survey of current trends in computational drug repositioning. Briefings Bioinform. Jiao Li, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu
2016	J	`jnl`	Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput. Biol. Steven C. Bagley, Marina Sirota, Richard O. Chen, Atul J. Butte, Russ B. Altman
2016	Misc	`conf`	Do Cancer Clinical Trial Populations Truly Represent Cancer Patients? A Comparison of Open Clinical Trials to the Cancer Genome Atlas. PSB Nophar Geifman, Atul J. Butte
2016	J	`jnl`	Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression. J. Am. Medical Informatics Assoc. Nophar Geifman, Sanchita Bhattacharya, Atul J. Butte
2015	Misc	`conf`	A Systematic Assessment of Linking Gene Expression with Genetic Variants for Prioritizing Candidate Targets. Pacific Symposium on Biocomputing Hua Fan-Minogue, Bin Chen, Weronika Sikora-Wohlfeld, Marina Sirota, Atul J. Butte
2015	Misc	`conf`	Characteristics of Drug Combination Therapy in Oncology by Analyzing Clinical Trial Data on Clinicaltrials.Gov. Pacific Symposium on Biocomputing Menghua Wu, Marina Sirota, Atul J. Butte, Bin Chen
2015	Misc	`conf`	Human Computation of Big Data in Biomedicine: Making STAR annotations for large scale functional characterization of disease. AMIA 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	—	`conf`	ImmPort: Shared research data for bioinformatics and immunology. BIBM Patrick J. Dunn, Elizabeth Thomson, John Campbell, Thomas Smith, Vincent Desborough, Jeffrey A. Wiser, Henry Schaefer, Sanchita Bhattacharya, Atul J. Butte, Sandra Andorf, Mazen Nasrallah
2015	Misc	`conf`	Recent Advances in Computational Drug Repositioning. AMIA Atul J. Butte, Nigam Shah, Nicholas P. Tatonetti, Hua Xu, Ping Zhang
2014	Misc	`conf`	Investigating the Genetic Architecture of Pulmonary Arterial Hypertension Shared with Other Diseases. AMIA Luke Yancy Jr., Atul J. Butte
2014	—	`conf`	RImmPort: enabling ready-for-analysis immunology research data. BCB Ravi D. Shankar, Sandra Andorf, Sanchita Bhattacharya, Jeffrey A. Wiser, Atul J. Butte
2014	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte
2014	—	`conf`	Towards the characterization of normal peripheral immune cells with data from ImmPort. BCB Sandra Andorf, Jennifer B. Bollyky, Patrick J. Dunn, Jeffrey A. Wiser, Sanchita Bhattacharya, Atul J. Butte
2013	A	`conf`	DTMBIO 2013: international workshop on data and text mining in biomedical informatics. CIKM Atul J. Butte, Doheon Lee, Hua Xu, Min Song
2013	J	`jnl`	Making it personal: translational bioinformatics. J. Am. Medical Informatics Assoc. Atul J. Butte, Lucila Ohno-Machado
2013	—	`ed.`	Proceeding of the 7rd International Workshop on Data and Text Mining in Bioinformatics, DTMBIO 2013, San Francisco, CA, USA, November 1, 2013 DTMBIO Atul J. Butte, Doheon Kim, Min Song, Hua Xu
2013	J	`jnl`	Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinform. Raymond K. Auerbach, Bin Chen, Atul J. Butte
2013	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Zhiyong Lu, Pankaj Agarwal, Atul J. Butte
2013	Misc	`conf`	Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical Records. Pacific Symposium on Biocomputing Li Li, David Ruau, Rong Chen, Susan C. Weber, Atul J. Butte
2013	—	`conf`	Translating a trillion points of data into therapies, diagnostics, and new insights into disease. DTMBIO Atul J. Butte
2012	J	`jnl`	Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. J. Am. Medical Informatics Assoc. Alexander A. Morgan, Rong Chen, Atul J. Butte
2012	J	`jnl`	Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Bioinform. Chirag J. Patel, Rong Chen, Atul J. Butte
2012	J	`jnl`	Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases. PLoS Comput. Biol. David Ruau, Joel Dudley, Rong Chen, Nicholas G. Phillips, Gary E. Swan, Laura Lazzeroni, J. David Clark, Atul J. Butte, Martin S. Angst
2012	J	`jnl`	Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. J. Am. Medical Informatics Assoc. Alexander A. Morgan, Vasilios J. Pyrgos, Kari C. Nadeau, Peter R. Williamson, Atul J. Butte
2012	J	`jnl`	Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. PLoS Comput. Biol. Purvesh Khatri, Marina Sirota, Atul J. Butte
2011	J	`jnl`	Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. J. Biomed. Informatics David Ruau, Michael Mbagwu, Joel T. Dudley, Vijay Krishnan, Atul J. Butte
2011	J	`jnl`	Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in J. Am. Medical Informatics Assoc. Atul J. Butte, Nigam H. Shah
2011	J	`jnl`	Exploiting drug-disease relationships for computational drug repositioning. Briefings Bioinform. Joel Dudley, Tarangini Deshpande, Atul J. Butte
2011	Misc	`conf`	Matching Cancer Genomes to Established Cell Lines for Personalized Oncology. Pacific Symposium on Biocomputing Joel Dudley, Rong Chen, Atul J. Butte
2011	J	`jnl`	ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinform. Jesse M. Engreitz, Rong Chen, Alexander A. Morgan, Joel Dudley, Rohan Mallelwar, Atul J. Butte
2011	Misc	`conf`	The Reference Human Genome Demonstrates High Risk of Type 1 Diabetes and Other Disorders. Pacific Symposium on Biocomputing Rong Chen, Atul J. Butte
2011	J	`jnl`	Translational bioinformatics: linking knowledge across biological and clinical realms. J. Am. Medical Informatics Assoc. Indra Neil Sarkar, Atul J. Butte, Yves A. Lussier, Peter Tarczy-Hornoch, Lucila Ohno-Machado
2010	J	`jnl`	An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinform. Nicholas P. Tatonetti, Joel Dudley, Hersh Sagreiya, Atul J. Butte, Russ B. Altman
2010	J	`jnl`	Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. BMC Bioinform. Alexander A. Morgan, Purvesh Khatri, Richard Hayden Jones, Minnie M. Sarwal, Atul J. Butte
2010	J	`jnl`	Content-based microarray search using differential expression profiles. BMC Bioinform. Jesse M. Engreitz, Alexander A. Morgan, Joel Dudley, Rong Chen, Rahul Thathoo, Russ B. Altman, Atul J. Butte
2010	J	`jnl`	Current methodologies for translational bioinformatics. J. Biomed. Informatics Yves A. Lussier, Atul J. Butte, Lawrence Hunter
2010	J	`jnl`	Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions. PLoS Comput. Biol. Rong Chen, Tara K. Sigdel, Li Li, Neeraja Kambham, Joel Dudley, Szu-chuan Hsieh, R. Bryan Klassen, Amery Chen, Tuyen Caohuu, Alexander A. Morgan, Hannah A. Valantine, Kiran K. Khush, Minnie M. Sarwal, Atul J. Butte
2010	—	`conf`	Immunological response in normal healthy twins across age. BCB 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
2010	J	`jnl`	Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. BMC Bioinform. David P. Chen, Joel Dudley, Atul J. Butte
2010	J	`jnl`	Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets. PLoS Comput. Biol. Silpa Suthram, Joel Dudley, Annie P. Chiang, Rong Chen, Trevor Hastie, Atul J. Butte
2010	J	`jnl`	Validating pathophysiological models of aging using clinical electronic medical records. J. Biomed. Informatics David P. Chen, Alexander A. Morgan, Atul J. Butte
2009	J	`jnl`	A Classifier-based approach to identify genetic similarities between diseases. Bioinform. Marc A. Schaub, Irene M. Kaplow, Marina Sirota, Chuong B. Do, Atul J. Butte, Serafim Batzoglou
2009	J	`jnl`	A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Comput. Biol. Joel Dudley, Atul J. Butte
2009	Misc	`conf`	Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology. Pacific Symposium on Biocomputing Joel Dudley, Atul J. Butte
2009	J	`jnl`	Infection in the intensive care unit alters physiological networks. BMC Bioinform. Adam D. Grossman, Mitchell J. Cohen, Geoffrey T. Manley, Atul J. Butte
2009	J	`jnl`	Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinform. Nigam H. Shah, Clément Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen
2009	J	`jnl`	Selected proceedings of the First Summit on Translational Bioinformatics 2008. BMC Bioinform. Atul J. Butte, Indra Neil Sarkar, Marco Ramoni, Yves A. Lussier, Olga G. Troyanskaya
2009	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann
2009	J	`jnl`	The "etiome": identification and clustering of human disease etiological factors. BMC Bioinform. Yueyi I. Liu, Paul H. Wise, Atul J. Butte
2009	Misc	`conf`	Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune System. Pacific Symposium on Biocomputing 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
2009	J	`jnl`	Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR. J. Biomed. Informatics Sangeeta B. English, Shou-Ching Shih, Marco Ramoni, Lois E. Smith, Atul J. Butte
2008	Misc	`conf`	Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining. Pacific Symposium on Biocomputing Joel Dudley, Atul J. Butte
2008	J	`jnl`	GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinform. Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J. Butte
2008	Misc	`conf`	Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation. Pacific Symposium on Biocomputing David P. Chen, Susan C. Weber, Philip S. Constantinou, Todd A. Ferris, Henry J. Lowe, Atul J. Butte
2008	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann
2008	—	`conf`	Using SNOMED CT For Translational Genomics Data Integration. KR-MED Joel Dudley, David P. Chen, Atul J. Butte
2008	J	`jnl`	Viewpoint Paper: Translational Bioinformatics: Coming of Age. J. Am. Medical Informatics Assoc. Atul J. Butte
2007	Misc	`conf`	Clinical Arrays of Laboratory Measures, or "Clinarrays", Built from an Electronic Health Record Enable Disease Subtyping by Severity. AMIA David P. Chen, Susan C. Weber, Philip S. Constantinou, Todd A. Ferris, Henry J. Lowe, Atul J. Butte
2007	J	`jnl`	Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. Bioinform. Sangeeta B. English, Atul J. Butte
2007	Misc	`conf`	Methodologies for Extracting Functional Pharmacogenomic Experiments from International Repository. AMIA Yi-An Lin, Annie P. Chiang, Ray Lin, Peggy Yao, Rong Chen, Atul J. Butte
2006	Misc	`conf`	Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics. AMIA Atul J. Butte, Rong Chen
2005	J	`jnl`	Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinform. Cecily J. Wolfe, Isaac S. Kohane, Atul J. Butte
2004	J	`jnl`	Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinform. Dominic J. Allocco, Isaac S. Kohane, Atul J. Butte
2003	J	`jnl`	PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications. Bioinform. Kyungjoon Lee, Isaac S. Kohane, Atul J. Butte
2003	J	`jnl`	Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinform. Ashish Nimgaonkar, Despina Sanoudou, Atul J. Butte, Judith N. Haslett, Louis M. Kunkel, Alan H. Beggs, Isaac S. Kohane
2002	J	`jnl`	Analysis of matched mRNA measurements from two different microarray technologies. Bioinform. Winston Patrick Kuo, Tor-Kristian Jenssen, Atul J. Butte, Lucila Ohno-Machado, Isaac S. Kohane
2002	J	`jnl`	Comparing expression profiles of genes with similar promoter regions. Bioinform. Peter J. Park, Atul J. Butte, Isaac S. Kohane
2001	J	`jnl`	Comparing the Similarity of Time-Series Gene Expression Using Signal Processing Metrics. J. Biomed. Informatics Atul J. Butte, Ling Bao, Ben Y. Reis, Timothy W. Watkins, Isaac S. Kohane
2001	Misc	`conf`	Determining Significant Fold Differences in Gene Expression Analysis. Pacific Symposium on Biocomputing Atul J. Butte, J. Ye, G. Niederfellner, K. Rett, H. U. Häring, M. F. White, Isaac S. Kohane
2001	J	`jnl`	Extracting Knowledge from Dynamics in Gene Expression. J. Biomed. Informatics Ben Y. Reis, Atul J. Butte, Isaac S. Kohane
2001	J	`jnl`	Reply. J. Biomed. Informatics Ben Y. Reis, Atul J. Butte, Isaac S. Kohane
2001	J	`jnl`	The Personal Internetworked Notary and Guardian. Int. J. Medical Informatics Alberto Riva, Kenneth D. Mandl, Do Hoon Oh, Daniel J. Nigrin, Atul J. Butte, Peter Szolovits, Isaac S. Kohane
2000	Misc	`conf`	Enrolling patients into clinical trials faster using RealTime Recuiting. AMIA Atul J. Butte, David A. Weinstein, Isaac S. Kohane
1999	Misc	`conf`	Unsupervised knowledge discovery in medical databases using relevance networks. AMIA Atul J. Butte, Isaac S. Kohane