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Journal Articles
- 2021
[j32]Ramya Dhatri Vunikili, Benjamin S. Glicksberg, Kipp W. Johnson, Joel T. Dudley, Lakshminarayanan Subramanian, Khader Shameer:
Predictive Modelling of Susceptibility to Substance Abuse, Mortality and Drug-Drug Interactions in Opioid Patients. Frontiers Artif. Intell. 4: 742723 (2021)- [j31]Jessica K. De Freitas, Kipp W. Johnson, Eddye Golden, Girish N. Nadkarni, Joel T. Dudley, Erwin P. Bottinger, Benjamin S. Glicksberg, Riccardo Miotto:
Phe2vec: Automated disease phenotyping based on unsupervised embeddings from electronic health records. Patterns 2(9): 100337 (2021) - 2020
- [j30]Andrew C. Liu
, Krishna Patel, Ramya Dhatri Vunikili, Kipp W. Johnson, Fahad Abdu, Shivani Kamath Belman, Benjamin S. Glicksberg, Pratyush Tandale, Roberto Fontanez, Oommen K. Mathew, Andrew Kasarskis, Priyabrata Mukherjee, Lakshminarayanan Subramanian, Joel T. Dudley, Khader Shameer:
Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses. Briefings Bioinform. 21(4): 1182-1195 (2020) - [j29]Hao-Chih Lee, Osamu Ichikawa, Benjamin S. Glicksberg, Aparna A. Divaraniya, Christine E. Becker, Pankaj Agarwal, Joel T. Dudley:
Identification of therapeutic targets from genetic association studies using hierarchical component analysis. BioData Min. 13(1): 6 (2020) - [j28]Isotta Landi, Benjamin S. Glicksberg, Hao-Chih Lee, Sarah T. Cherng, Giulia Landi, Matteo Danieletto, Joel T. Dudley, Cesare Furlanello, Riccardo Miotto:
Deep representation learning of electronic health records to unlock patient stratification at scale. npj Digit. Medicine 3 (2020) - [j27]Fayzan F. Chaudhry, Matteo Danieletto, Eddye Golden, Jerome R. Scelza, Greg Botwin, Mark M. Shervey, Jessica K. De Freitas, Ishan Paranjpe, Girish N. Nadkarni, Riccardo Miotto, Patricia Glowe, Greg Stock, Bethany Percha, Noah Zimmerman, Joel T. Dudley, Benjamin S. Glicksberg:
Sleep in the Natural Environment: A Pilot Study. Sensors 20(5): 1378 (2020) - 2019
- [j26]Marcus A. Badgeley, Manway Liu, Benjamin S. Glicksberg, Mark M. Shervey, John R. Zech, Khader Shameer, Joseph Lehar, Eric K. Oermann, Michael V. McConnell, Thomas M. Snyder, Joel T. Dudley:
CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis. Bioinform. 35(9): 1610-1612 (2019) - [j25]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:
PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Bioinform. 35(21): 4515-4518 (2019) - [j24]Marcus A. Badgeley, John R. Zech, Luke Oakden-Rayner, Benjamin S. Glicksberg, Manway Liu, William Gale, Michael V. McConnell, Bethany Percha, Thomas M. Snyder, Joel T. Dudley:
Deep learning predicts hip fracture using confounding patient and healthcare variables. npj Digit. Medicine 2 (2019) - 2018
- [j23]Khader Shameer, Benjamin S. Glicksberg, Rachel Hodos, Kipp W. Johnson, Marcus A. Badgeley, Ben Readhead, Max S. Tomlinson, Timothy O'Connor, Riccardo Miotto, Brian A. Kidd, Rong Chen, Avi Ma'ayan, Joel T. Dudley:
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings Bioinform. 19(4): 656-678 (2018) - [j22]Riccardo Miotto, Fei Wang, Shuang Wang, Xiaoqian Jiang, Joel T. Dudley:
Deep learning for healthcare: review, opportunities and challenges. Briefings Bioinform. 19(6): 1236-1246 (2018) - [j21]Mary Regina Boland, Pradipta Parhi, Li Li, Riccardo Miotto, Robert J. Carroll, Usman Iqbal, Phung-Anh (Alex) Nguyen, Martijn J. Schuemie, Seng Chan You, Donahue Smith, Sean D. Mooney, Patrick B. Ryan, Yu-Chuan (Jack) Li, Rae Woong Park, Joshua C. Denny, Joel T. Dudley, George Hripcsak, Pierre Gentine, Nicholas P. Tatonetti:
Uncovering exposures responsible for birth season - disease effects: a global study. J. Am. Medical Informatics Assoc. 25(3): 275-288 (2018) - [j20]Khader Shameer, M. Mercedes Perez-Rodriguez, Roy Bachar, Li Li, Amy Johnson, Kipp W. Johnson, Benjamin S. Glicksberg, Milo R. Smith, Ben Readhead, Joseph Scarpa, Jebakumar Jebakaran, Patricia H. Kovatch, Sabina Lim, Wayne K. Goodman, David L. Reich, Andrew Kasarskis, Nicholas P. Tatonetti, Joel T. Dudley:
Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining. BMC Medical Informatics Decis. Mak. 18(S-3): 79:1-79:11 (2018) - [j19]Riccardo Miotto, Matteo Danieletto, Jerome R. Scelza, Brian A. Kidd, Joel T. Dudley:
Reflecting health: smart mirrors for personalized medicine. npj Digit. Medicine 1 (2018) - 2017
- [j18]Khader Shameer, Marcus A. Badgeley, Riccardo Miotto, Benjamin S. Glicksberg, Joseph W. Morgan, Joel T. Dudley:
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. Briefings Bioinform. 18(1): 105-124 (2017) - [j17]Hao-Chih Lee, Roman Kosoy, Christine E. Becker, Joel T. Dudley, Brian A. Kidd:
Automated cell type discovery and classification through knowledge transfer. Bioinform. 33(11): 1689-1695 (2017) - [j16]Zichen Wang, Li Li, Benjamin S. Glicksberg, Ariel Israel, Joel T. Dudley, Avi Ma'ayan:
Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. J. Biomed. Informatics 76: 59-68 (2017) - 2016
- [j15]Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini:
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. Briefings Bioinform. 17(5): 841-862 (2016) - [j14]Benjamin S. Glicksberg, Li Li, Marcus A. Badgeley, Khader Shameer, Roman Kosoy, Noam D. Beckmann, Nam Pho, Jörg Hakenberg, Meng Ma, Kristin L. Ayers, Gabriel E. Hoffman, Shuyu Dan Li, Eric E. Schadt, Chirag J. Patel, Rong Chen, Joel T. Dudley:
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinform. 32(12): 101-110 (2016) - 2012
- [j13]David Ruau, Joel Dudley, Rong Chen, Nicholas G. Phillips, Gary E. Swan, Laura Lazzeroni, J. David Clark, Atul J. Butte, Martin S. Angst:
Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases. PLoS Comput. Biol. 8(6) (2012) - 2011
- [j12]Joel Dudley, Tarangini Deshpande, Atul J. Butte:
Exploiting drug-disease relationships for computational drug repositioning. Briefings Bioinform. 12(4): 303-311 (2011) - [j11]Jesse M. Engreitz, Rong Chen, Alexander A. Morgan, Joel Dudley, Rohan Mallelwar, Atul J. Butte:
ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinform. 27(23): 3317-3318 (2011) - [j10]David Ruau, Michael Mbagwu, Joel T. Dudley, Vijay Krishnan, Atul J. Butte:
Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. J. Biomed. Informatics 44(Supplement-1): S39-S43 (2011) - 2010
- [j9]Jesse M. Engreitz, Alexander A. Morgan, Joel Dudley, Rong Chen, Rahul Thathoo, Russ B. Altman, Atul J. Butte:
Content-based microarray search using differential expression profiles. BMC Bioinform. 11: 603 (2010) - [j8]David P. Chen, Joel Dudley, Atul J. Butte:
Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. BMC Bioinform. 11(S-9): S4 (2010) - [j7]Nicholas P. Tatonetti, Joel Dudley, Hersh Sagreiya, Atul J. Butte, Russ B. Altman:
An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinform. 11(S-9): S9 (2010) - [j6]Silpa Suthram, Joel Dudley, Annie P. Chiang, Rong Chen, Trevor Hastie, Atul J. Butte:
Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets. PLoS Comput. Biol. 6(2) (2010) - [j5]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:
Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions. PLoS Comput. Biol. 6(9) (2010) - 2009
- [j4]Joel Dudley, Atul J. Butte:
A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Comput. Biol. 5(12) (2009) - 2008
- [j3]Sudhir Kumar, Masatoshi Nei, Joel Dudley, Koichiro Tamura:
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings Bioinform. 9(4): 299-306 (2008) - 2007
- [j2]Sudhir Kumar, Joel Dudley:
Bioinformatics software for biologists in the genomics era. Bioinform. 23(14): 1713-1717 (2007) - 2006
- [j1]S. Blair Hedges, Joel Dudley, Sudhir Kumar:
TimeTree: a public knowledge-base of divergence times among organisms. Bioinform. 22(23): 2971-2972 (2006)
Conference and Workshop Papers
- 2020
- [c21]Maxence Vandromme, Tomi Jun, Ponni Perumalswami, Joel T. Dudley, Andrea Branch, Li Li:
Automated Phenotyping of Patients with Non-Alcoholic Fatty Liver Disease Reveals Clinically RelevantDisease Subtypes. PSB 2020: 91-102 - [c20]Hao-Chih Lee, Matteo Danieletto, Riccardo Miotto, Sarah T. Cherng, Joel T. Dudley:
Scaling Structural Learning with NO-BEARS to Infer Causal Transcriptome Networks. PSB 2020: 391-402 - 2019
- [c19]Hao-Chih Lee, Sarah T. Cherng, Riccardo Miotto, Joel T. Dudley:
Enhancing high-content imaging for studying microtubule networks at large-scale. MLHC 2019: 592-613 - [c18]Kipp W. Johnson, Jessica K. De Freitas, Benjamin S. Glicksberg, Jason R. Bobe, Joel T. Dudley:
Evaluation of patient re-identification using laboratory test orders and mitigation via latent space variables. PSB 2019: 415-426 - 2018
- [c17]Venet Osmani, Li Li, Matteo Danieletto, Benjamin S. Glicksberg, Joel Dudley, Oscar Mayora:
Automatic processing of Electronic Medical Records using Deep Learning. PervasiveHealth 2018: 251-257 - [c16]Rachel Hodos, Ping Zhang, Hao-Chih Lee, Qiaonan Duan, Zichen Wang, Neil R. Clark, Avi Ma'ayan, Fei Wang, Brian A. Kidd, Jianying Hu, David A. Sontag, Joel Dudley:
Cell-specific prediction and application of drug-induced gene expression . PSB 2018: 32-43 - [c15]Milo R. Smith, Benjamin S. Glicksberg, Li Li, Rong Chen, Hirofumi Morishita, Joel T. Dudley:
Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disorders. PSB 2018: 68-79 - [c14]Benjamin S. Glicksberg, Riccardo Miotto, Kipp W. Johnson, Khader Shameer, Li Li, Rong Chen, Joel T. Dudley:
Automated disease cohort selection using word embeddings from Electronic Health Records. PSB 2018: 145-156 - [c13]Kipp W. Johnson, Benjamin S. Glicksberg, Rachel Hodos, Khader Shameer, Joel T. Dudley:
Causal inference on electronic health records to assess blood pressure treatment targets: An application of the parametric g formula. PSB 2018: 180-191 - 2017
- [c12]Matteo Danieletto, Li Li, Joel T. Dudley:
Application of I-COMO device towards geographic disease enrichment pattern revealed from electronic medical record at a large Urban academic medical center. PervasiveHealth 2017: 282-287 - [c11]Ariella Cohain, Aparna A. Divaraniya, Kuixi Zhu, Joseph R. Scarpa, Andrew Kasarskis, Jun Zhu, Rui Chang, Joel T. Dudley, Eric E. Schadt:
Exploring the Reproducibility of Probabilistic Causal Molecular Network Models>. PSB 2017: 120-131 - [c10]Khader Shameer, Kipp W. Johnson, Alexandre Yahi, Riccardo Miotto, Li Li, Doran Ricks, Jebakumar Jebakaran, Patricia H. Kovatch, Partho P. Sengupta, Annetine Gelijns, Alan Moskovitz, Bruce Darrow, David L. Reich, Andrew Kasarskis, Nicholas P. Tatonetti, Deborah F. Pinney, Joel T. Dudley:
Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort. PSB 2017: 276-287 - 2016
- [c9]Riccardo Miotto, Li Li, Joel T. Dudley:
Deep Learning to Predict Patient Future Diseases from the Electronic Health Records. ECIR 2016: 768-774 - [c8]Fei Wang, Ping Zhang, Joel Dudley:
Healthcare Data Mining with Matrix Models. KDD 2016: 2137-2138 - 2015
- [c7]Joel T. Dudley, Jennifer Listgarten, Oliver Stegle, Steven E. Brenner, Leopold Parts:
Session introduction. Pacific Symposium on Biocomputing 2015: 342-346 - [c6]Benjamin S. Glicksberg, Li Li, Wei-Yi Cheng, Khader Shameer, Jörg Hakenberg, Rafael Castellanos, Meng Ma, Lisong Shi, Hardik Shah, Joel T. Dudley, Rong Chen:
An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships. Pacific Symposium on Biocomputing 2015: 407-418 - 2012
- [c5]Konrad J. Karczewski, Robert P. Tirrell, Pablo Cordero, Nicholas P. Tatonetti, Joel T. Dudley, Keyan Salari, Michael Snyder, Russ B. Altman, Stuart K. Kim:
Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine. Pacific Symposium on Biocomputing 2012: 339-350 - 2011
- [c4]Joel Dudley, Rong Chen, Atul J. Butte:
Matching Cancer Genomes to Established Cell Lines for Personalized Oncology. Pacific Symposium on Biocomputing 2011: 243-252 - 2009
- [c3]Joel Dudley, Atul J. Butte:
Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology. Pacific Symposium on Biocomputing 2009: 27-38 - 2008
- [c2]Joel Dudley, David P. Chen, Atul J. Butte:
Using SNOMED CT For Translational Genomics Data Integration. KR-MED 2008 - [c1]Joel Dudley, Atul J. Butte:
Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining. Pacific Symposium on Biocomputing 2008: 580-591
Informal and Other Publications
- 2020
- [i6]Isotta Landi, Benjamin S. Glicksberg, Hao-Chih Lee, Sarah T. Cherng, Giulia Landi, Matteo Danieletto, Joel T. Dudley, Cesare Furlanello, Riccardo Miotto:
Deep Representation Learning of Electronic Health Records to Unlock Patient Stratification at Scale. CoRR abs/2003.06516 (2020) - 2019
- [i5]Seyedmostafa Sheikhalishahi, Riccardo Miotto, Joel T. Dudley, Alberto Lavelli, Fabio Rinaldi, Venet Osmani:
Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review. CoRR abs/1908.05780 (2019) - [i4]Hao-Chih Lee, Sarah T. Cherng, Riccardo Miotto, Joel T. Dudley:
Enhancing high-content imaging for studying microtubule networks at large-scale. CoRR abs/1910.00662 (2019) - [i3]Hao-Chih Lee, Matteo Danieletto, Riccardo Miotto, Sarah T. Cherng, Joel T. Dudley:
Scaling structural learning with NO-BEARS to infer causal transcriptome networks. CoRR abs/1911.00081 (2019) - 2018
- [i2]Venet Osmani, Li Li, Matteo Danieletto, Benjamin S. Glicksberg, Joel Dudley, Oscar Mayora:
Processing of Electronic Health Records using Deep Learning: A review. CoRR abs/1804.01758 (2018) - [i1]Marcus A. Badgeley, John R. Zech, Luke Oakden-Rayner, Benjamin S. Glicksberg, Manway Liu, William Gale, Michael V. McConnell, Beth Percha, Thomas M. Snyder, Joel T. Dudley:
Deep Learning Predicts Hip Fracture using Confounding Patient and Healthcare Variables. CoRR abs/1811.03695 (2018)
Coauthor Index
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