Joel Dudley

According to our database, Joel Dudley authored at least 55 papers between 2006 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2021

Phe2vec: Automated disease phenotyping based on unsupervised embeddings from electronic health records.

Jessica K. De Freitas, Kipp W. Johnson, Eddye Golden, Girish N. Nadkarni, Joel T. Dudley, Erwin P. Bottinger, Benjamin S. Glicksberg, Riccardo Miotto

Patterns, 2021

Predictive Modelling of Susceptibility to Substance Abuse, Mortality and Drug-Drug Interactions in Opioid Patients.

Ramya Dhatri Vunikili, Benjamin S. Glicksberg, Kipp W. Johnson, Joel T. Dudley, Lakshminarayanan Subramanian, Khader Shameer

Frontiers Artif. Intell., 2021

2020

Sleep in the Natural Environment: A Pilot Study.

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

Sensors, 2020

Deep representation learning of electronic health records to unlock patient stratification at scale.

Isotta Landi, Benjamin S. Glicksberg, Hao-Chih Lee, Sarah T. Cherng, Giulia Landi, Matteo Danieletto, Joel T. Dudley, Cesare Furlanello, Riccardo Miotto

npj Digit. Medicine, 2020

Identification of therapeutic targets from genetic association studies using hierarchical component analysis.

Hao-Chih Lee, Osamu Ichikawa, Benjamin S. Glicksberg, Aparna A. Divaraniya, Christine E. Becker, Pankaj Agarwal, Joel T. Dudley

BioData Min., 2020

Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses.

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

Briefings Bioinform., 2020

Automated Phenotyping of Patients with Non-Alcoholic Fatty Liver Disease Reveals Clinically RelevantDisease Subtypes.

Maxence Vandromme, Tomi Jun, Ponni Perumalswami, Joel T. Dudley, Andrea Branch, Li Li

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

Scaling Structural Learning with NO-BEARS to Infer Causal Transcriptome Networks.

Hao-Chih Lee, Matteo Danieletto, Riccardo Miotto, Sarah T. Cherng, Joel T. Dudley

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2019

Deep learning predicts hip fracture using confounding patient and healthcare variables.

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

npj Digit. Medicine, 2019

Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review.

Seyedmostafa Sheikhalishahi, Riccardo Miotto, Joel T. Dudley, Alberto Lavelli, Fabio Rinaldi, Venet Osmani

CoRR, 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, Eugenia Rutenberg, Remi Frazier, Nelson Lee, Sharat Israni, Rick Larsen, Bethany Percha, Li Li, Joel T. Dudley, Nicholas P. Tatonetti, Atul J. Butte

Bioinform., 2019

CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis.

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

Bioinform., 2019

Evaluation of patient re-identification using laboratory test orders and mitigation via latent space variables.

Kipp W. Johnson, Jessica K. De Freitas, Benjamin S. Glicksberg, Jason R. Bobe, Joel T. Dudley

Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

Enhancing high-content imaging for studying microtubule networks at large-scale.

Hao-Chih Lee, Sarah T. Cherng, Riccardo Miotto, Joel T. Dudley

Proceedings of the Machine Learning for Healthcare Conference, 2019

2018

Reflecting health: smart mirrors for personalized medicine.

Riccardo Miotto, Matteo Danieletto, Jerome R. Scelza, Brian A. Kidd, Joel T. Dudley

npj Digit. Medicine, 2018

Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining.

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

BMC Medical Informatics Decis. Mak., 2018

Uncovering exposures responsible for birth season - disease effects: a global study.

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

J. Am. Medical Informatics Assoc., 2018

Processing of Electronic Health Records using Deep Learning: A review.

Venet Osmani, Li Li, Matteo Danieletto, Benjamin S. Glicksberg, Joel Dudley, Oscar Mayora

CoRR, 2018

Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.

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

Briefings Bioinform., 2018

Deep learning for healthcare: review, opportunities and challenges.

Riccardo Miotto, Fei Wang, Shuang Wang, Xiaoqian Jiang, Joel T. Dudley

Briefings Bioinform., 2018

Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disorders.

Milo R. Smith, Benjamin S. Glicksberg, Li Li, Rong Chen, Hirofumi Morishita, Joel T. Dudley

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Causal inference on electronic health records to assess blood pressure treatment targets: An application of the parametric g formula.

Kipp W. Johnson, Benjamin S. Glicksberg, Rachel Hodos, Khader Shameer, Joel T. Dudley

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Cell-specific prediction and application of drug-induced gene expression .

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

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Automated disease cohort selection using word embeddings from Electronic Health Records.

Benjamin S. Glicksberg, Riccardo Miotto, Kipp W. Johnson, Khader Shameer, Li Li, Rong Chen, Joel T. Dudley

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Automatic processing of Electronic Medical Records using Deep Learning.

Venet Osmani, Li Li, Matteo Danieletto, Benjamin S. Glicksberg, Joel Dudley, Oscar Mayora

Proceedings of the 12th EAI International Conference on Pervasive Computing Technologies for Healthcare, 2018

2017

Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age.

Zichen Wang, Li Li, Benjamin S. Glicksberg, Ariel Israel, Joel T. Dudley, Avi Ma'ayan

J. Biomed. Informatics, 2017

Automated cell type discovery and classification through knowledge transfer.

Hao-Chih Lee, Roman Kosoy, Christine E. Becker, Joel T. Dudley, Brian A. Kidd

Bioinform., 2017

Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams.

Khader Shameer, Marcus A. Badgeley, Riccardo Miotto, Benjamin S. Glicksberg, Joseph W. Morgan, Joel T. Dudley

Briefings Bioinform., 2017

Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort.

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

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Exploring the Reproducibility of Probabilistic Causal Molecular Network Models>.

Ariella Cohain, Aparna A. Divaraniya, Kuixi Zhu, Joseph R. Scarpa, Andrew Kasarskis, Jun Zhu, Rui Chang, Joel T. Dudley, Eric E. Schadt

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Application of I-COMO device towards geographic disease enrichment pattern revealed from electronic medical record at a large Urban academic medical center.

Matteo Danieletto, Li Li, Joel T. Dudley

Proceedings of the 11th EAI International Conference on Pervasive Computing Technologies for Healthcare, 2017

2016

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.

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

Bioinform., 2016

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini

Briefings Bioinform., 2016

Healthcare Data Mining with Matrix Models.

Fei Wang, Ping Zhang, Joel Dudley

Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016

Deep Learning to Predict Patient Future Diseases from the Electronic Health Records.

Riccardo Miotto, Li Li, Joel T. Dudley

Proceedings of the Advances in Information Retrieval, 2016

2015

An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships.

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

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

Session introduction.

Joel T. Dudley, Jennifer Listgarten, Oliver Stegle, Steven E. Brenner, Leopold Parts

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2012

Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases.

David Ruau, Joel Dudley, Rong Chen, Nicholas G. Phillips, Gary E. Swan, Laura Lazzeroni, J. David Clark, Atul J. Butte, Martin S. Angst

PLoS Comput. Biol., 2012

Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine.

Konrad J. Karczewski, Robert P. Tirrell, Pablo Cordero, Nicholas P. Tatonetti, Joel T. Dudley, Keyan Salari, Michael Snyder, Russ B. Altman, Stuart K. Kim

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

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

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.

Jesse M. Engreitz, Rong Chen, Alexander A. Morgan, Joel Dudley, Rohan Mallelwar, Atul J. Butte

Bioinform., 2011

Exploiting drug-disease relationships for computational drug repositioning.

Joel Dudley, Tarangini Deshpande, Atul J. Butte

Briefings Bioinform., 2011

Matching Cancer Genomes to Established Cell Lines for Personalized Oncology.

Joel Dudley, Rong Chen, Atul J. Butte

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.

Silpa Suthram, Joel Dudley, Annie P. Chiang, Rong Chen, Trevor Hastie, Atul J. Butte

PLoS Comput. Biol., 2010

Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions.

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

PLoS Comput. Biol., 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

Content-based microarray search using differential expression profiles.

Jesse M. Engreitz, Alexander A. Morgan, Joel Dudley, Rong Chen, Rahul Thathoo, Russ B. Altman, Atul J. Butte

BMC Bioinform., 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

2009

A Quick Guide for Developing Effective Bioinformatics Programming Skills.

Joel Dudley, Atul J. Butte

PLoS Comput. Biol., 2009

Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology.

Joel Dudley, Atul J. Butte

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences.

Sudhir Kumar, Masatoshi Nei, Joel Dudley, Koichiro Tamura

Briefings Bioinform., 2008

Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining.

Joel Dudley, Atul J. Butte

Proceedings of the Biocomputing 2008, 2008

Using SNOMED CT For Translational Genomics Data Integration.

Joel Dudley, David P. Chen, Atul J. Butte

Proceedings of the Third International Conference on Knowledge Representation in Medicine, Phoenix, Arizona, USA, May 31st, 2008

2007

Bioinformatics software for biologists in the genomics era.

Sudhir Kumar, Joel Dudley

Bioinform., 2007

2006

TimeTree: a public knowledge-base of divergence times among organisms.

S. Blair Hedges, Joel Dudley, Sudhir Kumar

Bioinform., 2006