Nigam H. Shah

According to our database, Nigam H. Shah authored at least 201 papers between 1996 and 2024.

Collaborative distances:

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

2024

Characterizing the limitations of using diagnosis codes in the context of machine learning for healthcare.

Lin Lawrence Guo, Keith E. Morse, Catherine Aftandilian, Ethan Steinberg, Jason Alan Fries, José D. Posada, Scott Lanyon Fleming, Joshua Lemmon, Karim Jessa, Nigam Shah, Lillian Sung

BMC Medical Informatics Decis. Mak., December, 2024

Automating the Enterprise with Foundation Models.

Michael Wornow, Avanika Narayan, Krista Opsahl-Ong, Quinn McIntyre, Nigam Shah, Christopher Ré

Proc. VLDB Endow., July, 2024

A multi-center study on the adaptability of a shared foundation model for electronic health records.

Lin Lawrence Guo, Jason Alan Fries, Ethan Steinberg, Scott Lanyon Fleming, Keith E. Morse, Catherine Aftandilian, José D. Posada, Nigam Shah, Lillian Sung

npj Digit. Medicine, 2024

Ensuring useful adoption of generative artificial intelligence in healthcare.

Jenelle A. Jindal, Matthew P. Lungren, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2024

meds_reader: A fast and efficient EHR processing library.

Ethan Steinberg, Michael Wornow, Suhana Bedi, Jason Alan Fries, Matthew B. A. McDermott, Nigam H. Shah

CoRR, 2024

A Proposed S.C.O.R.E. Evaluation Framework for Large Language Models : Safety, Consensus, Objectivity, Reproducibility and Explainability.

Ting Fang Tan, Kabilan Elangovan, Jasmine Chiat Ling Ong, Nigam Shah, Joseph Jao-Yiu Sung, Tien Yin Wong, Lan Xue, Nan Liu, Haibo Wang, Chang Fu Kuo, Simon Chesterman, Zee Kin Yeong, Daniel S. W. Ting

CoRR, 2024

Answering real-world clinical questions using large language model based systems.

Yen Sia Low, Michael L. Jackson, Rebecca J. Hyde, Robert E. Brown, Neil M. Sanghavi, Julian D. Baldwin, C. William Pike, Jananee Muralidharan, Gavin Hui, Natasha Alexander, Hadeel Hassan, Rahul V. Nene, Morgan Pike, Courtney J. Pokrzywa, Shivam Vedak, Adam Paul Yan, Dong-han Yao, Amy R. Zipursky, Christina Dinh, Philip Ballentine, Dan C. Derieg, Vladimir Polony, Rehan N. Chawdry, Jordan Davies, Brigham B. Hyde, Nigam H. Shah, Saurabh Gombar

CoRR, 2024

Do Multimodal Foundation Models Understand Enterprise Workflows? A Benchmark for Business Process Management Tasks.

Michael Wornow, Avanika Narayan, Ben Viggiano, Ishan S. Khare, Tathagat Verma, Tibor Thompson, Miguel Angel Fuentes Hernandez, Sudharsan Sundar, Chloe Trujillo, Krrish Chawla, Rongfei Lu, Justin Shen, Divya Nagaraj, Joshua Martinez, Vardhan Agrawal, Althea Hudson, Nigam H. Shah, Christopher Ré

CoRR, 2024

Merlin: A Vision Language Foundation Model for 3D Computed Tomography.

Louis Blankemeier, Joseph Paul Cohen, Ashwin Kumar, Dave Van Veen, Syed Jamal Safdar Gardezi, Magdalini Paschali, Zhihong Chen, Jean-Benoit Delbrouck, Eduardo Pontes Reis, Cesar Truyts, Christian Bluethgen, Malte Engmann Kjeldskov Jensen, Sophie Ostmeier, Maya Varma, Jeya Maria Jose Valanarasu, Zhongnan Fang, Zepeng Huo, Zaid Nabulsi, Diego Ardila, Wei-Hung Weng, Edson Amaro Júnior, Neera Ahuja, Jason Alan Fries, Nigam H. Shah, Andrew Johnston, Robert D. Boutin, Andrew Wentland, Curtis P. Langlotz, Jason Hom, Sergios Gatidis, Akshay S. Chaudhari

CoRR, 2024

Standing on FURM ground - A framework for evaluating Fair, Useful, and Reliable AI Models in healthcare systems.

Alison Callahan, Duncan C. McElfresh, Juan M. Banda, Gabrielle Bunney, Danton Char, Jonathan H. Chen, Conor K. Corbin, Debadutta Dash, Norman L. Downing, Sneha S. Jain, Nikesh Kotecha, Jonathan Masterson, Michelle M. Mello, Keith E. Morse, Srikar Nallan, Abby Pandya, Anurang Revri, Aditya Sharma, Christopher D. Sharp, Rahul Thapa, Michael Wornow, Alaa Youssef, Michael A. Pfeffer, Nigam H. Shah

CoRR, 2024

Zero-Shot Clinical Trial Patient Matching with LLMs.

Michael Wornow, Alejandro Lozano, Dev Dash, Jenelle A. Jindal, Kenneth W. Mahaffey, Nigam H. Shah

CoRR, 2024

MOTOR: A Time-to-Event Foundation Model For Structured Medical Records.

Ethan Steinberg, Jason Alan Fries, Yizhe Xu, Nigam Shah

Proceedings of the Twelfth International Conference on Learning Representations, 2024

MedAlign: A Clinician-Generated Dataset for Instruction Following with Electronic Medical Records.

Scott L. Fleming, Alejandro Lozano, William J. Haberkorn, Jenelle A. Jindal, Eduardo Pontes Reis, Rahul Thapa, Louis Blankemeier, Julian Z. Genkins, Ethan Steinberg, Ashwin Nayak, Birju S. Patel, Chia-Chun Chiang, Alison Callahan, Zepeng Huo, Sergios Gatidis, Scott J. Adams, Oluseyi Fayanju, Shreya J. Shah, Thomas Savage, Ethan Goh, Akshay S. Chaudhari, Nima Aghaeepour, Christopher D. Sharp, Michael A. Pfeffer, Percy Liang, Jonathan H. Chen, Keith E. Morse, Emma P. Brunskill, Jason A. Fries, Nigam H. Shah

Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024

2023

Self-supervised machine learning using adult inpatient data produces effective models for pediatric clinical prediction tasks.

Joshua Lemmon, Lin Lawrence Guo, Ethan Steinberg, Keith E. Morse, Scott Lanyon Fleming, Catherine Aftandilian, Stephen R. Pfohl, José D. Posada, Nigam Shah, Jason Alan Fries, Lillian Sung

J. Am. Medical Informatics Assoc., November, 2023

DEPLOYR: a technical framework for deploying custom real-time machine learning models into the electronic medical record.

Conor K. Corbin, Rob Maclay, Aakash Acharya, Sreedevi Mony, Soumya Punnathanam, Rahul Thapa, Nikesh Kotecha, Nigam H. Shah, Jonathan H. Chen

J. Am. Medical Informatics Assoc., August, 2023

Clinical utility gains from incorporating comorbidity and geographic location information into risk estimation equations for atherosclerotic cardiovascular disease.

Yizhe Xu, Agata Foryciarz, Ethan Steinberg, Nigam H. Shah

J. Am. Medical Informatics Assoc., April, 2023

A framework to identify ethical concerns with ML-guided care workflows: a case study of mortality prediction to guide advance care planning.

Diana Cagliero, Natalie Deuitch, Nigam Shah, Chris Feudtner, Danton Char

J. Am. Medical Informatics Assoc., April, 2023

APLUS: A Python library for usefulness simulations of machine learning models in healthcare.

Michael Wornow, Elsie Gyang Ross, Alison Callahan, Nigam H. Shah

J. Biomed. Informatics, March, 2023

Assessing the net benefit of machine learning models in the presence of resource constraints.

Karandeep Singh, Nigam H. Shah, Andrew J. Vickers

J. Am. Medical Informatics Assoc., March, 2023

The shaky foundations of large language models and foundation models for electronic health records.

Michael Wornow, Yizhe Xu, Rahul Thapa, Birju S. Patel, Ethan Steinberg, Scott L. Fleming, Michael A. Pfeffer, Jason Alan Fries, Nigam H. Shah

npj Digit. Medicine, 2023

Principled estimation and evaluation of treatment effect heterogeneity: A case study application to dabigatran for patients with atrial fibrillation.

Yizhe Xu, Katelyn K. Bechler, Alison Callahan, Nigam Shah

J. Biomed. Informatics, 2023

INSPECT: A Multimodal Dataset for Pulmonary Embolism Diagnosis and Prognosis.

Shih-Cheng Huang, Zepeng Huo, Ethan Steinberg, Chia-Chun Chiang, Matthew P. Lungren, Curtis P. Langlotz, Serena Yeung, Nigam H. Shah, Jason A. Fries

CoRR, 2023

Clinfo.ai: An Open-Source Retrieval-Augmented Large Language Model System for Answering Medical Questions using Scientific Literature.

Alejandro Lozano, Scott L. Fleming, Chia-Chun Chiang, Nigam Shah

CoRR, 2023

All models are local: time to replace external validation with recurrent local validation.

Alexey Youssef, Michael Pencina, Anshul Thakur, Tingting Zhu, David A. Clifton, Nigam H. Shah

CoRR, 2023

Evaluation of GPT-3.5 and GPT-4 for supporting real-world information needs in healthcare delivery.

Debadutta Dash, Rahul Thapa, Juan M. Banda, Akshay Swaminathan, Morgan Cheatham, Mehr Kashyap, Nikesh Kotecha, Jonathan H. Chen, Saurabh Gombar, Lance Downing, Rachel Pedreira, Ethan Goh, Angel Arnaout, Garret Kenn Morris, Honor Magon, Matthew P. Lungren, Eric Horvitz, Nigam H. Shah

CoRR, 2023

The Shaky Foundations of Clinical Foundation Models: A Survey of Large Language Models and Foundation Models for EMRs.

Michael Wornow, Yizhe Xu, Rahul Thapa, Birju S. Patel, Ethan Steinberg, Scott L. Fleming, Michael A. Pfeffer, Jason A. Fries, Nigam H. Shah

CoRR, 2023

Self-Supervised Time-to-Event Modeling with Structured Medical Records.

Ethan Steinberg, Yizhe Xu, Jason A. Fries, Nigam Shah

CoRR, 2023

EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models.

Michael Wornow, Rahul Thapa, Ethan Steinberg, Jason A. Fries, Nigam Shah

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

INSPECT: A Multimodal Dataset for Patient Outcome Prediction of Pulmonary Embolisms.

Shih-Cheng Huang, Zepeng Huo, Ethan Steinberg, Chia-Chun Chiang, Curtis P. Langlotz, Matthew P. Lungren, Serena Yeung, Nigam Shah, Jason Alan Fries

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

Efficient Diagnosis Assignment Using Unstructured Clinical Notes.

Louis Blankemeier, Jason A. Fries, Robert Tinn, Joseph Preston, Nigam Shah, Akshay Chaudhari

Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers), 2023

2022

Considerations in the reliability and fairness audits of predictive models for advance care planning.

Jonathan Lu, Amelia Sattler, Samantha Wang, Ali Raza Khaki, Alison Callahan, Scott L. Fleming, Rebecca Fong, Benjamin Ehlert, Ron C. Li, Lisa Shieh, Kavitha Ramchandran, Michael Gensheimer, Sarah Chobot, Stephen Pfohl, Siyun Li, Kenny Shum, Nitin Parikh, Priya Desai, Briththa Seevaratnam, Melanie Hanson, Margaret Smith, Yizhe Xu, Arjun Gokhale, Steven Lin, Michael A. Pfeffer, Winifred Teuteberg, Nigam H. Shah

Frontiers Digit. Health, 2022

Instability in clinical risk stratification models using deep learning.

Daniel Lopez Martinez, Alex Yakubovich, Martin Seneviratne, Ádám D. Lelkes, Akshit Tyagi, Jonas Kemp, Ethan Steinberg, N. Lance Downing, Ron C. Li, Keith E. Morse, Nigam H. Shah, Ming-Jun Chen

Proceedings of the Machine Learning for Health, 2022

Net benefit, calibration, threshold selection, and training objectives for algorithmic fairness in healthcare.

Stephen Pfohl, Yizhe Xu, Agata Foryciarz, Nikolaos Ignatiadis, Julian Genkins, Nigam Shah

Proceedings of the FAccT '22: 2022 ACM Conference on Fairness, Accountability, and Transparency, Seoul, Republic of Korea, June 21, 2022

Predicting patients who are likely to develop Lupus Nephritis of those newly diagnosed with Systemic Lupus Erythematosus.

Katelyn K. Bechler, Nigam Shah

Proceedings of the AMIA 2022, 2022

2021

Summarizing Patients Like Mine via an On-demand Consultation Service.

Nigam Shah

Proc. VLDB Endow., 2021

An informatics consult approach for generating clinical evidence for treatment decisions.

Alvina Grace Lai, Wai Hoong Chang, Constantinos A. Parisinos, Michail Katsoulis, Ruth M. Blackburn, Anoop D. Shah, Vincent Nguyen, Spiros C. Denaxas, George Davey Smith, Tom R. Gaunt, Krishnarajah Nirantharakumar, Murray P. Cox, Donall Forde, Folkert W. Asselbergs, Steve K. Harris, Sylvia Richardson, Reecha Sofat, Richard J. B. Dobson, Aroon D. Hingorani, Riyaz Patel, Jonathan Sterne, Amitava Banerjee, Alastair K. Denniston, Simon Ball, Neil J. Sebire, Nigam H. Shah, Graham R. Foster, Bryan Williams, Harry Hemingway

BMC Medical Informatics Decis. Mak., 2021

Language models are an effective representation learning technique for electronic health record data.

Ethan Steinberg, Kenneth Jung, Jason A. Fries, Conor K. Corbin, Stephen R. Pfohl, Nigam H. Shah

J. Biomed. Informatics, 2021

An empirical characterization of fair machine learning for clinical risk prediction.

Stephen R. Pfohl, Agata Foryciarz, Nigam H. Shah

J. Biomed. Informatics, 2021

Improving hospital readmission prediction using individualized utility analysis.

Michael Ko, Emma Chen, Ashwin Agrawal, Pranav Rajpurkar, Anand Avati, Andrew Yan-Tak Ng, Sanjay Basu, Nigam H. Shah

J. Biomed. Informatics, 2021

Learning decision thresholds for risk stratification models from aggregate clinician behavior.

Birju S. Patel, Ethan Steinberg, Stephen R. Pfohl, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2021

A survey of extant organizational and computational setups for deploying predictive models in health systems.

Sehj Kashyap, Keith E. Morse, Birju S. Patel, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2021

A framework for making predictive models useful in practice.

Kenneth Jung, Sehj Kashyap, Anand Avati, Stephanie Harman, Heather Shaw, Ron C. Li, Margaret Smith, Kenny Shum, Jacob Javitz, Yohan Vetteth, Tina Seto, Steven C. Bagley, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2021

Corrigendum: Conflicting information from the Food and Drug Administration: Missed opportunity to lead standards for safe and effective medical artificial intelligence solutions.

Tina Hernandez-Boussard, Matthew P. Lungren, Nigam Shah

J. Am. Medical Informatics Assoc., 2021

Conflicting information from the Food and Drug Administration: Missed opportunity to lead standards for safe and effective medical artificial intelligence solutions.

Tina Hernandez-Boussard, Matthew P. Lungren, Nigam Shah

J. Am. Medical Informatics Assoc., 2021

Automated model versus treating physician for predicting survival time of patients with metastatic cancer.

Michael Francis Gensheimer, Sonya Aggarwal, Kathryn R. K. Benson, Justin N. Carter, Solomon Henry, Douglas J. Wood, Scott G. Soltys, Steven Hancock, Erqi Pollom, Nigam H. Shah, Daniel T. Chang

J. Am. Medical Informatics Assoc., 2021

ACE: the Advanced Cohort Engine for searching longitudinal patient records.

Alison Callahan, Vladimir Polony, José D. Posada, Juan M. Banda, Saurabh Gombar, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2021

Computational drug repositioning of atorvastatin for ulcerative colitis.

Lawrence Bai, Madeleine K. D. Scott, Ethan Steinberg, Laurynas Kalesinskas, Aida Habtezion, Nigam H. Shah, Purvesh Khatri

J. Am. Medical Informatics Assoc., 2021

RadFusion: Benchmarking Performance and Fairness for Multimodal Pulmonary Embolism Detection from CT and EHR.

Yuyin Zhou, Shih-Cheng Huang, Jason Alan Fries, Alaa Youssef, Timothy J. Amrhein, Marcello Chang, Imon Banerjee, Daniel L. Rubin, Lei Xing, Nigam Shah, Matthew P. Lungren

CoRR, 2021

A comparison of approaches to improve worst-case predictive model performance over patient subpopulations.

Stephen R. Pfohl, Haoran Zhang, Yizhe Xu, Agata Foryciarz, Marzyeh Ghassemi, Nigam H. Shah

CoRR, 2021

Systematic Review of Approaches to Preserve Machine Learning Performance in the Presence of Temporal Dataset Shift in Clinical Medicine.

Lin Lawrence Guo, Stephen R. Pfohl, Jason Alan Fries, José D. Posada, Scott L. Fleming, Catherine Aftandilian, Nigam Shah, Lillian Sung

Appl. Clin. Inform., 2021

Multi-Modal Data Science for Healthcare: State of the Art, Challenges, and Opportunities.

Yuan Luo, Fei Wang, Benjamin S. Glicksberg, Jessilyn Dunn, Nigam Shah

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020

Assessing the accuracy of automatic speech recognition for psychotherapy.

Adam S. Miner, Albert Haque, Jason A. Fries, Scott L. Fleming, Denise E. Wilfley, G. Terence Wilson, Arnold Milstein, Dan Jurafsky, Bruce A. Arnow, W. Stewart Agras, Li Fei-Fei, Nigam H. Shah

npj Digit. Medicine, 2020

Developing a delivery science for artificial intelligence in healthcare.

Ron C. Li, Steven M. Asch, Nigam H. Shah

npj Digit. Medicine, 2020

Estimating the efficacy of symptom-based screening for COVID-19.

Alison Callahan, Ethan Steinberg, Jason A. Fries, Saurabh Gombar, Birju S. Patel, Conor K. Corbin, Nigam H. Shah

npj Digit. Medicine, 2020

Deep phenotyping: Embracing complexity and temporality - Towards scalability, portability, and interoperability.

Chunhua Weng, Nigam H. Shah, George Hripcsak

J. Biomed. Informatics, 2020

Development and validation of phenotype classifiers across multiple sites in the observational health data sciences and informatics network.

Mehr Kashyap, Martin G. Seneviratne, Juan M. Banda, Thomas Falconer, Borim Ryu, Sooyoung Yoo, George Hripcsak, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2020

Measure what matters: Counts of hospitalized patients are a better metric for health system capacity planning for a reopening.

Sehj Kashyap, Saurabh Gombar, Steve Yadlowsky, Alison Callahan, Jason A. Fries, Benjamin A. Pinsky, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2020

MINIMAR (MINimum Information for Medical AI Reporting): Developing reporting standards for artificial intelligence in health care.

Tina Hernandez-Boussard, Selen Bozkurt, John P. A. Ioannidis, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2020

Trove: Ontology-driven weak supervision for medical entity classification.

Jason A. Fries, Ethan Steinberg, Saelig Khattar, Scott L. Fleming, José D. Posada, Alison Callahan, Nigam H. Shah

CoRR, 2020

A new paradigm for accelerating clinical data science at Stanford Medicine.

Somalee Datta, José D. Posada, Garrick Olson, Wencheng Li, Ciaran O'Reilly, Deepa Balraj, Joseph Mesterhazy, Joseph Pallas, Priyamvada Desai, Nigam Shah

CoRR, 2020

Language Models Are An Effective Patient Representation Learning Technique For Electronic Health Record Data.

Ethan Steinberg, Kenneth Jung, Jason A. Fries, Conor K. Corbin, Stephen R. Pfohl, Nigam H. Shah

CoRR, 2020

Normalizing Clinical Document Titles to LOINC Document Ontology: an Initial Study.

Xu Zuo, Jianfu Li, Bo Zhao, Yujia Zhou, Xiao Dong, Jon D. Duke, Karthik Natarajan, George Hripcsak, Nigam Shah, Juan M. Banda, Ruth M. Reeves, Hua Xu

Proceedings of the AMIA 2020, 2020

Data Quality Assessment of Laboratory Data.

Vojtech Huser, Clair Blacketer, Karthik Natarajan, Robert T. Miller, Andrew Williams, Selva Muthu Kumaran Sathappan, José D. Posada, Nigam Shah

Proceedings of the AMIA 2020, 2020

2019

It is time to learn from patients like mine.

Saurabh Gombar, Alison Callahan, Robert M. Califf, Robert A. Harrington, Nigam H. Shah

npj Digit. Medicine, 2019

Medical device surveillance with electronic health records.

Alison Callahan, Jason A. Fries, Christopher Ré, James I Huddleston III, Nicholas J. Giori, Scott L. Delp, Nigam H. Shah

npj Digit. Medicine, 2019

Finding missed cases of familial hypercholesterolemia in health systems using machine learning.

Juan M. Banda, Ashish Sarraju, Fahim Abbasi, Justin Parizo, Mitchel Pariani, Hannah Ison, Elinor Briskin, Hannah Wand, Sébastien Dubois, Kenneth Jung, Seth A. Myers, Daniel J. Rader, Joseph B. Leader, Michael F. Murray, Kelly D. Myers, Katherine Wilemon, Nigam H. Shah, Joshua W. Knowles

npj Digit. Medicine, 2019

Predicting need for advanced illness or palliative care in a primary care population using electronic health record data.

Kenneth Jung, Sylvia E. K. Sudat, Nicole Kwon, Walter F. Stewart, Nigam H. Shah

J. Biomed. Informatics, 2019

The number needed to benefit: estimating the value of predictive analytics in healthcare.

Vincent X. Liu, David W. Bates, Jenna Wiens, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2019

The accuracy vs. coverage trade-off in patient-facing diagnosis models.

Anitha Kannan, Jason Alan Fries, Eric Kramer, Jen Jen Chen, Nigam Shah, Xavier Amatriain

CoRR, 2019

Missingness as Stability: Understanding the Structure of Missingness in Longitudinal EHR data and its Impact on Reinforcement Learning in Healthcare.

Scott L. Fleming, Kuhan Jeyapragasan, Tony Duan, Daisy Yi Ding, Saurabh Gombar, Nigam Shah, Emma Brunskill

CoRR, 2019

A Semi-Supervised Machine Learning Approach to Detecting Recurrent Metastatic Breast Cancer Cases Using Linked Cancer Registry and Electronic Medical Record Data.

Albee Y. Ling, Allison W. Kurian, Jennifer L. Caswell-Jin, George W. Sledge Jr., Nigam H. Shah, Suzanne R. Tamang

CoRR, 2019

Countdown Regression: Sharp and Calibrated Survival Predictions.

Anand Avati, Tony Duan, Sharon Zhou, Kenneth Jung, Nigam H. Shah, Andrew Y. Ng

Proceedings of the Thirty-Fifth Conference on Uncertainty in Artificial Intelligence, 2019

The Effectiveness of Multitask Learning for Phenotyping with Electronic Health Records Data.

Daisy Yi Ding, Chloé Simpson, Stephen Pfohl, Dave C. Kale, Kenneth Jung, Nigam H. Shah

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

Counterfactual Reasoning for Fair Clinical Risk Prediction.

Stephen R. Pfohl, Tony Duan, Daisy Yi Ding, Nigam H. Shah

Proceedings of the Machine Learning for Healthcare Conference, 2019

Creating Fair Models of Atherosclerotic Cardiovascular Disease Risk.

Stephen Pfohl, Ben J. Marafino, Adrien Coulet, Fátima Rodriguez, Latha Palaniappan, Nigam H. Shah

Proceedings of the 2019 AAAI/ACM Conference on AI, Ethics, and Society, 2019

2018

Biomedical Data/Content Acquisition, Curation.

Nigam Shah

Proceedings of the Encyclopedia of Database Systems, Second Edition, 2018

Scalable and accurate deep learning with electronic health records.

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

npj Digit. Medicine, 2018

Improving palliative care with deep learning.

Anand Avati, Kenneth Jung, Stephanie Harman, Lance Downing, Andrew Y. Ng, Nigam H. Shah

BMC Medical Informatics Decis. Mak., 2018

Call for papers: Deep phenotyping for Precision Medicine.

Chunhua Weng, Nigam Shah, George Hripcsak

J. Biomed. Informatics, 2018

An evaluation of clinical order patterns machine-learned from clinician cohorts stratified by patient mortality outcomes.

Jason K. Wang, Jason Hom, Santhosh Balasubramanian, Alejandro Schuler, Nigam H. Shah, Mary K. Goldstein, Michael T. M. Baiocchi, Jonathan H. Chen

J. Biomed. Informatics, 2018

Predicting Inpatient Discharge Prioritization With Electronic Health Records.

Anand Avati, Stephen Pfohl, Chris Lin, Thao Nguyen, Meng Zhang, Philip Hwang, Jessica Wetstone, Kenneth Jung, Andrew Y. Ng, Nigam H. Shah

CoRR, 2018

Countdown Regression: Sharp and Calibrated Survival Predictions.

Anand Avati, Tony Duan, Kenneth Jung, Nigam H. Shah, Andrew Y. Ng

CoRR, 2018

General-purpose validation and model selection when estimating individual treatment effects.

Alejandro Schuler, Nigam Shah

CoRR, 2018

Scalable and accurate deep learning for electronic health records.

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

CoRR, 2018

Addressing vital sign alarm fatigue using personalized alarm thresholds.

Sarah Poole, Nigam Shah

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

Session introduction.

Philip R. O. Payne, Nigam H. Shah, Jessica D. Tenenbaum, Lara M. Mangravite

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

Identifying cases of metastatic prostate cancer using machine learning on electronic health records.

Martin G. Seneviratne, Juan M. Banda, James D. Brooks, Nigam Shah, Tina Hernandez-Boussard

Proceedings of the AMIA 2018, 2018

Transfer learning to adapt predictive models for pediatric patients in the EHR.

Stephen R. Pfohl, Nigam Shah

Proceedings of the AMIA 2018, 2018

Treatment Pathways in Patients with Cancer Using a Large-scale Observational Data Network.

Ruijun Chen, Patrick B. Ryan, Karthik Natarajan, Thomas Falconer, Christian G. Reich, Rohit Vashisht, Nigam Shah, George Hripcsak

Proceedings of the AMIA 2018, 2018

2017

Toward multimodal signal detection of adverse drug reactions.

Rave Harpaz, William DuMouchel, Martijn J. Schuemie, Olivier Bodenreider, Carol Friedman, Eric Horvitz, Anna Ripple, Alfred Sorbello, Ryen W. White, Rainer Winnenburg, Nigam H. Shah

J. Biomed. Informatics, 2017

Synergistic drug combinations from electronic health records and gene expression.

Yen S. Low, Aaron C. Daugherty, Elizabeth A. Schroeder, William Chen, Tina Seto, Susan C. Weber, Michael Lim, Trevor Hastie, Maya Mathur, Manisha Desai, Carl Farrington, Andrew A. Radin, Marina Sirota, Pragati Kenkare, Caroline A. Thompson, Peter P. Yu, Scarlett L. Gomez, George W. Sledge, Allison W. Kurian, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2017

Learning Effective Representations from Clinical Notes.

Sébastien Dubois, Nathanael Romano, Nigam Shah, Kenneth Jung

CoRR, 2017

Open Data for Discovery Science.

Philip R. O. Payne, Kun Huang, Nigam H. Shah, Jessica D. Tenenbaum

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

Learning Attributes of Disease Progression from Trajectories of Sparse Lab Values.

Vibhu Agarwal, Nigam H. Shah

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

The Effectiveness of Transfer Learning in Electronic Health Records Data.

Sébastien Dubois, Nathanael Romano, Kenneth Jung, Nigam Shah, David C. Kale

Proceedings of the 5th International Conference on Learning Representations, 2017

A novel propensity modeling approach to estimate the causal impact of acute organ dysfunction on long-term survival in sepsis.

Alejandro Schuler, David A. Wulf, Yun Lu, Jennifer M. Baker, Gabriel J. Escobar, Nigam Shah, Vincent X. Liu

Proceedings of the Summit on Clinical Research Informatics, 2017

Electronic phenotyping with APHRODITE and the Observational Health Sciences and Informatics (OHDSI) data network.

Juan M. Banda, Yoni Halpern, David A. Sontag, Nigam Shah

Proceedings of the Summit on Clinical Research Informatics, 2017

Quantifying the relative change in physical activity after Total Knee Arthroplasty using accelerometer based measurements.

Vibhu Agarwal, Mathew Smuck, Nigam Shah

Proceedings of the Summit on Clinical Research Informatics, 2017

Impact of Clinician Experience on Machine Learned Clinical Order Patterns.

Jason K. Wang, Alejandro Schuler, Nigam Shah, Jonathan H. Chen

Proceedings of the AMIA 2017, 2017

From Large-Scale Network Analytics to Clinical Solutions in OHDSI.

Jon D. Duke, George Hripcsak, Patrick B. Ryan, Nigam Shah

Proceedings of the AMIA 2017, 2017

2016

An unsupervised learning method to identify reference intervals from a clinical database.

Sarah Poole, Lee Frederick Schroeder, Nigam Shah

J. Biomed. Informatics, 2016

Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting.

Laura K. Wiley, Peter Tarczy-Hornoch, Joshua C. Denny, Robert R. Freimuth, Casey L. Overby, Nigam Shah, Ross D. Martin, Indra Neil Sarkar

J. Am. Medical Informatics Assoc., 2016

Learning statistical models of phenotypes using noisy labeled training data.

Vibhu Agarwal, Tanya Podchiyska, Juan M. Banda, Veena Goel, Tiffany I. Leung, Evan P. Minty, Timothy E. Sweeney, Elsie Gyang, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2016

Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature.

Rainer Winnenburg, Nigam H. Shah

BMC Bioinform., 2016

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.

Karin Verspoor, Anika Oellrich, Nigel Collier, Tudor Groza, Philippe Rocca-Serra, Larisa N. Soldatova, Michel Dumontier, Nigam Shah

J. Biomed. Semant., 2016

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Alison Callahan, Saminda Abeyruwan, Hassan Al-Ali, Kunie Sakurai, Adam R. Ferguson, Phillip G. Popovich, Nigam H. Shah, Ubbo Visser, John L. Bixby, Vance P. Lemmon

Database J. Biol. Databases Curation, 2016

The digital revolution in phenotyping.

Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo I. Georgiev, Hongfang Liu, Kevin M. Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier

Briefings Bioinform., 2016

Discovering Patient Phenotypes Using Generalized Low Rank Models.

Alejandro Schuler, Vincent X. Liu, Joe Wan, Alison Callahan, Madeleine Udell, David E. Stark, Nigam H. Shah

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Session Introduction.

Kelly Regan, Zachary B. Abrams, Michael F. Sharpnack, Arunima Srivastava, Kun Huang, Nigam Shah, Philip R. O. Payne

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Predicting Emergency Department Visits.

Sarah F. Poole, Shaun J. Grannis, Nigam Shah

Proceedings of the Summit on Clinical Research Informatics, 2016

A Pilot Study of the Integration of a Quantified-self Wearable Device with EMR data in the Acute Postoperative Setting.

Justin Norden, Timothy E. Sweeney, Aleksandra Pavlovic, Euan A. Ashley, Nigam Shah, Cindy Kin, Alexander Morgan

Proceedings of the Summit on Clinical Research Informatics, 2016

Observational Health Data Sciences and Informatics (OHDSI): A Rapidly Growing International Network for Open Science and Data Analytics in Healthcare.

Jon D. Duke, George Hripcsak, Nigam Shah, Patrick B. Ryan, Vojtech Huser

Proceedings of the Summit on Clinical Research Informatics, 2016

Predicting hospital visits from geo-tagged Internet search logs.

Vibhu Agarwal, Lichy Han, Isaac Madan, Shaurya Saluja, Aaditya Shidham, Nigam Shah

Proceedings of the Summit on Clinical Research Informatics, 2016

Learning Effective Treatment Pathways for Type-2 Diabetes from a clinical data warehouse.

Rohit Vashisht, Kenneth Jung, Nigam Shah

Proceedings of the AMIA 2016, 2016

Big Data for Healthcare and Life Sciences: Learning Useful Insights from Imperfect Data.

Jianying Hu, Nigam H. Shah, Bradley A. Malin, Patrick B. Ryan, Anil Jain

Proceedings of the AMIA 2016, 2016

Ensuring Reproducibility in Observational Research: Building and Sharing Knowledge Resources in the OHDSI Network.

Jon D. Duke, Nigam H. Shah, George Hripcsak, Patrick B. Ryan

Proceedings of the AMIA 2016, 2016

2015

A formal concept analysis and semantic query expansion cooperation to refine health outcomes of interest.

Olivier C. Curé, Henri Maurer, Nigam H. Shah, Paea LePendu

BMC Medical Informatics Decis. Mak., 2015

Implications of non-stationarity on predictive modeling using EHRs.

Kenneth Jung, Nigam H. Shah

J. Biomed. Informatics, 2015

A method for systematic discovery of adverse drug events from clinical notes.

Guan Wang, Kenneth Jung, Rainer Winnenburg, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2015

Functional evaluation of out-of-the-box text-mining tools for data-mining tasks.

Kenneth Jung, Paea LePendu, Srinivasan Iyer, Anna Bauer-Mehren, Bethany Percha, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2015

Special issue on bio-ontologies and phenotypes.

Larisa N. Soldatova, Nigel Collier, Anika Oellrich, Tudor Groza, Karin Verspoor, Philippe Rocca-Serra, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2015

Provenance-Centered Dataset of Drug-Drug Interactions.

Juan M. Banda, Tobias Kuhn, Nigam H. Shah, Michel Dumontier

Proceedings of the Semantic Web - ISWC 2015, 2015

Analyzing Search Behavior of Healthcare Professionals for Drug Safety Surveillance.

David J. Odgers, Rave Harpaz, Alison Callahan, Gregor Stiglic, Nigam H. Shah

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

Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers.

George Hripcsak, Jon D. Duke, Nigam H. Shah, Christian G. Reich, Vojtech Huser, Martijn J. Schuemie, Marc A. Suchard, Rae Woong Park, Ian Chi Kei Wong, Peter R. Rijnbeek, Johan van der Lei, Nicole Pratt, G. Niklas Norén, Yu-Chuan Li, Paul E. Stang, David Madigan, Patrick B. Ryan

Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

The Value of an Open-Source Observational Research Collaboratory: Results from the OHDSI Initiative.

Jon D. Duke, George Hripcsak, Nigam Shah, Patrick B. Ryan

Proceedings of the AMIA 2015, 2015

Recent Advances in Computational Drug Repositioning.

Atul J. Butte, Nigam Shah, Nicholas P. Tatonetti, Hua Xu, Ping Zhang

Proceedings of the AMIA 2015, 2015

2014

Mining clinical text for signals of adverse drug-drug interactions.

Srinivasan V Iyer, Rave Harpaz, Paea LePendu, Anna Bauer-Mehren, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2014

Toward personalizing treatment for depression: predicting diagnosis and severity.

Sandy Huang, Paea LePendu, Srinivasan V Iyer, Ming Tai-Seale, David Carrell, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2014

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting.

Larisa N. Soldatova, Philippe Rocca-Serra, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2014

Finding progression stages in time-evolving event sequences.

Jaewon Yang, Julian J. McAuley, Jure Leskovec, Paea LePendu, Nigam Shah

Proceedings of the 23rd International World Wide Web Conference, 2014

Session introduction.

Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye

Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

Medicine in the age of electronic health records.

Nigam Shah

Proceedings of the 20th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2014

2013

Web-scale pharmacovigilance: listening to signals from the crowd.

Ryen W. White, Nicholas P. Tatonetti, Nigam H. Shah, Russ B. Altman, Eric Horvitz

J. Am. Medical Informatics Assoc., 2013

Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions.

Rave Harpaz, Santiago Vilar, William DuMouchel, Hojjat Salmasian, Krystl Haerian, Nigam H. Shah, Herbert S. Chase, Carol Friedman

J. Am. Medical Informatics Assoc., 2013

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation.

Tobias Wittkop, Emily TerAvest, Uday S. Evani, K. Mathew Fleisch, Ari E. Berman, Corey Powell, Nigam H. Shah, Sean D. Mooney

BMC Bioinform., 2013

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.

Larisa N. Soldatova, Susanna-Assunta Sansone, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2013

Session introduction.

Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Empirical bayes model to combine signals of adverse drug reactions.

Rave Harpaz, William DuMouchel, Paea LePendu, Nigam H. Shah

Proceedings of the 19th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2013

Mining Biomedical Ontologies and Data Using RDF Hypergraphs.

Haishan Liu, Dejing Dou, Ruoming Jin, Paea LePendu, Nigam Shah

Proceedings of the 12th International Conference on Machine Learning and Applications, 2013

Refining health outcomes of interest using formal concept analysis and semantic query expansion.

Olivier Curé, Henri Maurer, Nigam Shah, Paea LePendu

Proceedings of the Proceeding of the 7rd International Workshop on Data and Text Mining in Bioinformatics, 2013

Learning Practice-based Evidence from Unstructured Clinical Notes.

Nigam Shah, Paea LePendu, Anna Bauer-Mehren, Srinivasan V Iyer, Kenneth Jung, Tyler Cole, Rave Harpaz

Proceedings of the AMIA 2013, 2013

Predictive Models in Mental Health: From Diagnosis to Treatment.

Sandy Huang, Paea LePendu, Srinivasan V Iyer, Ming Tai-Seale, David Carrell, Nigam Shah

Proceedings of the AMIA 2013, 2013

2012

Changing computational research. The challenges ahead.

Cameron Neylon, Jan Aerts, C. Titus Brown, Simon J. Coles, Les Hatton, Daniel Lemire, K. Jarrod Millman, Peter Murray-Rust, Fernando Pérez, Neil F. W. Saunders, Nigam Shah, Arfon M. Smith, Gaël Varoquaux, Egon L. Willighagen

Source Code Biol. Medicine, 2012

Chapter 9: Analyses Using Disease Ontologies.

Nigam H. Shah, Tyler Cole, Mark A. Musen

PLoS Comput. Biol., 2012

Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.

Stephen T. Wu, Hongfang Liu, Dingcheng Li, Cui Tao, Mark A. Musen, Christopher G. Chute, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2012

The coming age of data-driven medicine: translational bioinformatics' next frontier.

Nigam H. Shah, Jessica D. Tenenbaum

J. Am. Medical Informatics Assoc., 2012

The National Center for Biomedical Ontology.

Mark A. Musen, Natalya Fridman Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne D. Storey, Barry Smith

J. Am. Medical Informatics Assoc., 2012

Using ontology-based annotation to profile disease research.

Yi Liu, Adrien Coulet, Paea LePendu, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2012

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.

Larisa N. Soldatova, Susanna-Assunta Sansone, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2012

Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes.

Paea LePendu, Srinivasan V Iyer, Cédrick Fairon, Nigam H. Shah

J. Biomed. Semant., 2012

Mining the pharmacogenomics literature - a survey of the state of the art.

Udo Hahn, Kevin Bretonnel Cohen, Yael Garten, Nigam H. Shah

Briefings Bioinform., 2012

Session introduction.

Kevin Bretonnel Cohen, Yael Garten, Nigam Shah, Udo Hahn

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

Performance of Left Outer Join on Hadoop with Right Side within Single Node Memory Size.

Byambajargal Byambajav, Tomasz Wiktor Wlodarczyk, Chunming Rong, Paea LePendu, Nigam Shah

Proceedings of the 26th International Conference on Advanced Information Networking and Applications Workshops, 2012

2011

NCBO Resource Index: Ontology-based search and mining of biomedical resources.

Clément Jonquet, Paea LePendu, Sean M. Falconer, Adrien Coulet, Natalya Fridman Noy, Mark A. Musen, Nigam H. Shah

J. Web Semant., 2011

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Patricia L. Whetzel, Natalya Fridman Noy, Nigam H. Shah, Paul R. Alexander, Csongor Nyulas, Tania Tudorache, Mark A. Musen

Nucleic Acids Res., 2011

Enabling enrichment analysis with the Human Disease Ontology.

Paea LePendu, Mark A. Musen, Nigam H. Shah

J. Biomed. Informatics, 2011

Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in <i>JAMIA</i>.

Atul J. Butte, Nigam H. Shah

J. Am. Medical Informatics Assoc., 2011

Mapping between the OBO and OWL ontology languages.

Syed Hamid Tirmizi, Stuart Aitken, Dilvan A. Moreira, Chris Mungall, Juan F. Sequeda, Nigam H. Shah, Daniel P. Miranker

J. Biomed. Semant., 2011

Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting.

Larisa N. Soldatova, Susanna-Assunta Sansone, Susie Stephens, Nigam H. Shah

J. Biomed. Semant., 2011

Integration and publication of heterogeneous text-mined relationships on the Semantic Web.

Adrien Coulet, Yael Garten, Michel Dumontier, Russ B. Altman, Mark A. Musen, Nigam H. Shah

J. Biomed. Semant., 2011

HyQue: evaluating hypotheses using Semantic Web technologies.

Alison Callahan, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2011

Workshop Introduction.

Kevin Bretonnel Cohen, Yael Garten, Udo Hahn, Nigam H. Shah

Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse.

Patricia L. Whetzel, Natasha F. Noy, Nigam Shah, Paul R. Alexander, Michael Dorf, Ray W. Fergerson, Margaret-Anne D. Storey, Barry Smith, Christopher G. Chute, Mark A. Musen

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

The NCBO Annotator: Ontology-Based Annotation as a Web Service.

Patricia L. Whetzel, Clément Jonquet, Cherie Youn, Michael Dorf, Ray W. Fergerson, Mark A. Musen, Nigam Shah

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

The Age of Data-Driven Medicine: Mining the Electronic Health Record.

Paea LePendu, Mark A. Musen, Nigam H. Shah

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Proposed SKOS Extensions for BioPortal Terminology Services.

Cui Tao, Natalya Fridman Noy, Harold R. Solbrig, Nigam H. Shah, Mark A. Musen, Christopher G. Chute

Proceedings of the Semantic Web - Joint International Semantic Technology Conference, 2011

2010

Using text to build semantic networks for pharmacogenomics.

Adrien Coulet, Nigam H. Shah, Yael Garten, Mark A. Musen, Russ B. Altman

J. Biomed. Informatics, 2010

Selected papers from the 12^th annual Bio-Ontologies meeting.

Larisa N. Soldatova, Phillip W. Lord, Susanna-Assunta Sansone, Susie Stephens, Nigam H. Shah

J. Biomed. Semant., 2010

Building a biomedical ontology recommender web service.

Clément Jonquet, Mark A. Musen, Nigam H. Shah

J. Biomed. Semant., 2010

A UIMA wrapper for the NCBO annotator.

Christophe Roeder, Clément Jonquet, Nigam H. Shah, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter

Bioinform., 2010

Optimize First, Buy Later: Analyzing Metrics to Ramp-Up Very Large Knowledge Bases.

Paea LePendu, Natalya Fridman Noy, Clément Jonquet, Paul R. Alexander, Nigam H. Shah, Mark A. Musen

Proceedings of the Semantic Web - ISWC 2010 - 9th International Semantic Web Conference, 2010

Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics Application.

Adrien Coulet, Nigam H. Shah, Lawrence Hunter, Chitta Baral, Russ B. Altman

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Indexation et intégration de ressources textuelles à l'aide d'ontologies : application au domaine biomédical.

Clément Jonquet, Adrien Coulet, Nigam H. Shah, Mark A. Musen

Proceedings of the IC 2010 : 21es Journées Ingénierie des Connaissances 2010 (Proceedings of the 21st French Knowledge Engineering Conference), 2010

2009

Ontologies for Formal Representation of Biological Systems.

Nigam H. Shah, Mark A. Musen

Proceedings of the Handbook on Ontologies, 2009

Biomedical Data/Content Acquisition, Curation.

Nigam Shah

Proceedings of the Encyclopedia of Database Systems, 2009

BioPortal: ontologies and integrated data resources at the click of a mouse.

Natalya Fridman Noy, Nigam H. Shah, Patricia L. Whetzel, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clément Jonquet, Daniel L. Rubin, Margaret-Anne D. Storey, Christopher G. Chute, Mark A. Musen

Nucleic Acids Res., 2009

Ontology-driven indexing of public datasets for translational bioinformatics.

Nigam H. Shah, Clément Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen

BMC Bioinform., 2009

Comparison of concept recognizers for building the Open Biomedical Annotator.

Nigam H. Shah, Nipun Bhatia, Clément Jonquet, Daniel L. Rubin, Annie P. Chiang, Mark A. Musen

BMC Bioinform., 2009

OBO & OWL: Roundtrip Ontology Transformations.

Syed Hamid Tirmizi, Stuart Aitken, Dilvan A. Moreira, Chris Mungall, Juan F. Sequeda, Nigam H. Shah, Daniel P. Miranker

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, 2009

What Four Million Mappings Can Tell You about Two Hundred Ontologies.

Amir Ghazvinian, Natalya Fridman Noy, Clément Jonquet, Nigam H. Shah, Mark A. Musen

Proceedings of the Semantic Web - ISWC 2009, 8th International Semantic Web Conference, 2009

2008

The Stanford Tissue Microarray Database.

Robert J. Marinelli, Kelli Montgomery, Chih Long Liu, Nigam H. Shah, Wijan Prapong, Michael Nitzberg, Zachariah K. Zachariah, Gavin Sherlock, Yasodha Natkunam, Robert B. West, Matt van de Rijn, Patrick O. Brown, Catherine A. Ball

Nucleic Acids Res., 2008

Biomedical ontologies: a functional perspective.

Daniel L. Rubin, Nigam Shah, Natalya Fridman Noy

Briefings Bioinform., 2008

Pathway knowledge base: An integrated pathway resource using BioPAX.

Nikesh Kotecha, Kyle Bruck, William Lu, Nigam Shah

Appl. Ontology, 2008

BioPortal: A Web Repository for Biomedical Ontologies and Data Resources.

Natalya Fridman Noy, Nigam Shah, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clément Jonquet, Michael Montegut, Daniel L. Rubin, Cherie Youn, Mark A. Musen

Proceedings of the Poster and Demonstration Session at the 7th International Semantic Web Conference (ISWC2008), 2008

A System for Ontology-Based Annotation of Biomedical Data.

Clément Jonquet, Mark A. Musen, Nigam Shah

Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

UMLS-Query: A Perl Module for Querying the UMLS.

Nigam H. Shah, Mark A. Musen

Proceedings of the AMIA 2008, 2008

Comparison of Ontology-based Semantic-Similarity Measures.

Wei-Nchih Lee, Nigam Shah, Karanjot Sundlass, Mark A. Musen

Proceedings of the AMIA 2008, 2008

2007

Annotation and query of tissue microarray data using the NCI Thesaurus.

Nigam H. Shah, Daniel L. Rubin, Inigo Espinosa, Kelli Montgomery, Mark A. Musen

BMC Bioinform., 2007

Current progress in network research: toward reference networks for key model organisms.

Balaji S. Srinivasan, Nigam H. Shah, Jason Flannick, Eduardo Abeliuk, Antal F. Novak, Serafim Batzoglou

Briefings Bioinform., 2007

Searching ontologies based on content: experiments in the biomedical domain.

Harith Alani, Natasha Fridman Noy, Nigam Shah, Nigel Shadbolt, Mark A. Musen

Proceedings of the 4th International Conference on Knowledge Capture (K-CAP 2007), 2007

Using Annotations from Controlled Vocabularies to Find Meaningful Associations.

Woei-Jyh Lee, Louiqa Raschid, Padmini Srinivasan, Nigam Shah, Daniel L. Rubin, Natasha Fridman Noy

Proceedings of the Data Integration in the Life Sciences, 4th International Workshop, 2007

Interpretation Errors related to the GO Annotation File Format.

Dilvan A. Moreira, Nigam H. Shah, Mark A. Musen

Proceedings of the AMIA 2007, 2007

2006

A case study in pathway knowledgebase verification.

Stephen A. Racunas, Nigam Shah, Nina V. Fedoroff

BMC Bioinform., 2006

Ontology-based Annotation and Query of Tissue Microarray Data.

Nigam H. Shah, Daniel L. Rubin, Kaustubh S. Supekar, Mark A. Musen

Proceedings of the AMIA 2006, 2006

2004

CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.

N. H. Shah, Nina V. Fedoroff

Bioinform., 2004

HyBrow: a prototype system for computer-aided hypothesis evaluation.

Stephen A. Racunas, N. H. Shah, István Albert, Nina V. Fedoroff

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

A Finite Model Theory for Biological Hypotheses.

Stephen A. Racunas, Christopher Griffin, Nigam Shah

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003

A tool-kit for cDNA microarray and promoter analysis.

N. H. Shah, D. C. King, P. N. Shah, Nina V. Fedoroff

Bioinform., 2003

Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data?

Nigam Shah, Jorge Lepre, Yuhai Tu, Gustavo Stolovitzky

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

A Contradiction-Based Framework for Testing Gene Regulation Hypotheses.

Steve Racunas, Nigam Shah, Nina V. Fedoroff

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

1996

PGEN: A Novel Approach to Sequential Circuit Test Generation.

Wen-Ben Jone, Nigam Shah, Anita Gleason, Sunil R. Das

VLSI Design, 1996