Objective study validity diagnostics: a framework requiring pre-specified, empirical verification to increase trust in the reliability of real-world evidence. - Conover, Mitchell; Ryan, Patrick B.; Chen, Yong; Suchard, Marc A.; Hripcsak, George; Schuemie, Martijn J. (J. Am. Medical Informatics Assoc., 2025)

Standardized patient profile review using large language models for case adjudication in observational research. - Schuemie, Martijn J.; Ostropolets, Anna; Zhuk, Aleh; Korsik, Uladzislau; Seo, Seung In; Suchard, Marc A.; Hripcsak, George; Ryan, Patrick B. (npj Digit. Medicine, 2025)

OHDSI Standardized Vocabularies - a large-scale centralized reference ontology for international data harmonization. - Reich, Christian G.; Ostropolets, Anna; Ryan, Patrick B.; Rijnbeek, Peter R.; Schuemie, Martijn J.; Davydov, Alexander; Dymshyts, Dmitry; Hripcsak, George (J. Am. Medical Informatics Assoc., 2024)

Massive Parallelization of Massive Sample-Size Survival Analysis. - Yang, Jianxiao; Schuemie, Martijn J.; Ji, Xiang; Suchard, Marc A. (J. Comput. Graph. Stat., 2024)

European Health Data & Evidence Network - learnings from building out a standardized international health data network. - Voss, Erica A.; Blacketer, Clair; Sandijk, Sebastiaan van; Moinat, Maxim; Kallfelz, Michael; Speybroeck, Michel Van; Prieto-Alhambra, Daniel; Schuemie, Martijn J.; Rijnbeek, Peter R. (J. Am. Medical Informatics Assoc., 2023)

Padé approximant meets federated learning: A nearly lossless, one-shot algorithm for evidence synthesis in distributed research networks with rare outcomes. - Wu, Qiong; Schuemie, Martijn J.; Suchard, Marc A.; Ryan, Patrick B.; Hripcsak, George; Rohde, Charles A.; Chen, Yong (J. Biomed. Informatics, 2023)

Health-Analytics Data to Evidence Suite (HADES): Open-Source Software for Observational Research. - Schuemie, Martijn J.; Reps, Jenna; Black, Adam; DeFalco, Frank J.; Evans, Lee; Fridgeirsson, Egill A.; Gilbert, James P.; Knoll, Chris; Lavallee, Martin; Rao, Gowtham A.; Rijnbeek, Peter R.; Sadowski, Katy; et al. (2023)

dPQL: a lossless distributed algorithm for generalized linear mixed model with application to privacy-preserving hospital profiling. - Luo, Chongliang; Islam, Md. Nazmul; Sheils, Natalie E.; Buresh, John; Schuemie, Martijn J.; Doshi, Jalpa A.; Werner, Rachel M.; Asch, David A.; Chen, Yong (J. Am. Medical Informatics Assoc., 2022)

Adjusting for indirectly measured confounding using large-scale propensity score. - Zhang, Linying; Wang, Yixin; Schuemie, Martijn J.; Blei, David M.; Hripcsak, George (J. Biomed. Informatics, 2022)

PheValuator 2.0: Methodological improvements for the PheValuator approach to semi-automated phenotype algorithm evaluation. - Swerdel, Joel N.; Schuemie, Martijn J.; Murray, Gayle; Ryan, Patrick B. (J. Biomed. Informatics, 2022)

Learning patient-level prediction models across multiple healthcare databases: evaluation of ensembles for increasing model transportability. - Reps, Jenna Marie; Williams, Ross D.; Schuemie, Martijn J.; Ryan, Patrick B.; Rijnbeek, Peter R. (BMC Medical Informatics Decis. Mak., 2022)

A standardized analytics pipeline for reliable and rapid development and validation of prediction models using observational health data. - Khalid, Sara; Yang, Cynthia; Blacketer, Clair; Duarte-Salles, Talita; Fernández-Bertolín, Sergio; Kim, Chungsoo; Park, Rae Woong; Park, Jimyung; Schuemie, Martijn J.; Sena, Anthony G.; Suchard, Marc A.; You, Seng Chan; et al. (Comput. Methods Programs Biomed., 2021)

Erratum to: Large-Scale Evidence Generation and Evaluation across a Network of Databases (LEGEND): Assessing Validity Using Hypertension as a Case Study. - Schuemie, Martijn J.; Ryan, Patrick B.; Pratt, Nicole; Chen, Ruijun; You, Seng Chan; Krumholz, Harlan M.; Madigan, David; Hripcsak, George; Suchard, Marc A. (J. Am. Medical Informatics Assoc., 2021)

Design matters in patient-level prediction: evaluation of a cohort vs. case-control design when developing predictive models in observational healthcare datasets. - Reps, Jenna Marie; Ryan, Patrick B.; Rijnbeek, Peter R.; Schuemie, Martijn J. (J. Big Data, 2021)

An empirical analysis of dealing with patients who are lost to follow-up when developing prognostic models using a cohort design. - Reps, Jenna Marie; Rijnbeek, Peter R.; Cuthbert, Alana; Ryan, Patrick B.; Pratt, Nicole; Schuemie, Martijn J. (BMC Medical Informatics Decis. Mak., 2021)

Learning from electronic health records across multiple sites: A communication-efficient and privacy-preserving distributed algorithm. - Duan, Rui; Boland, Mary Regina; Liu, Zixuan; Liu, Yue; Chang, Howard H.; Xu, Hua; Chu, Haitao; Schmid, Christopher H.; Forrest, Christopher B.; Holmes, John H.; Schuemie, Martijn J.; Berlin, Jesse A.; et al. (J. Am. Medical Informatics Assoc., 2020)

Learning from local to global: An efficient distributed algorithm for modeling time-to-event data. - Duan, Rui; Luo, Chongliang; Schuemie, Martijn J.; Tong, Jiayi; Liang, C. Jason; Chang, Howard H.; Boland, Mary Regina; Bian, Jiang; Xu, Hua; Holmes, John H.; Forrest, Christopher B.; Morton, Sally C.; et al. (J. Am. Medical Informatics Assoc., 2020)

Large-scale evidence generation and evaluation across a network of databases (LEGEND): assessing validity using hypertension as a case study. - Schuemie, Martijn J.; Ryan, Patrick B.; Pratt, Nicole; Chen, Ruijun; You, Seng Chan; Krumholz, Harlan M.; Madigan, David; Hripcsak, George; Suchard, Marc A. (J. Am. Medical Informatics Assoc., 2020)

Principles of Large-scale Evidence Generation and Evaluation across a Network of Databases (LEGEND). - Schuemie, Martijn J.; Ryan, Patrick B.; Pratt, Nicole; Chen, Ruijun; You, Seng Chan; Krumholz, Harlan M.; Madigan, David; Hripcsak, George; Suchard, Marc A. (J. Am. Medical Informatics Assoc., 2020)

Evaluation of Large-scale Propensity Score Modeling and Covariate Balance on Potential Unmeasured Confounding in Observational Research. - Chen, Ruijun; Schuemie, Martijn J.; Suchard, Marc A.; Ostropolets, Anna; Zhang, Linying; Ryan, Patrick B.; Hripcsak, George (2020)

Causal Inference from Observational Healthcare Data: Implications, Impacts and Innovations. - Hripcsak, George; Blei, David M.; Bareinboim, Elias; Schuemie, Martijn J.; Zhang, Linying (2020)

Uncovering exposures responsible for birth season - disease effects: a global study. - Boland, Mary Regina; Parhi, Pradipta; Li, Li; Miotto, Riccardo; Carroll, Robert J.; Iqbal, Usman; Nguyen, Phung-Anh (Alex); Schuemie, Martijn J.; You, Seng Chan; Smith, Donahue; Mooney, Sean D.; Ryan, Patrick B.; et al. (J. Am. Medical Informatics Assoc., 2018)

Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data. - Reps, Jenna Marie; Schuemie, Martijn J.; Suchard, Marc A.; Ryan, Patrick B.; Rijnbeek, Peter R. (J. Am. Medical Informatics Assoc., 2018)

Accuracy of an automated knowledge base for identifying drug adverse reactions. - Voss, Erica A.; Boyce, Richard D.; Ryan, Patrick B.; Lei, Johan van der; Rijnbeek, Peter R.; Schuemie, Martijn J. (J. Biomed. Informatics, 2017)

Toward multimodal signal detection of adverse drug reactions. - Harpaz, Rave; DuMouchel, William; Schuemie, Martijn J.; Bodenreider, Olivier; Friedman, Carol; Horvitz, Eric; Ripple, Anna; Sorbello, Alfred; White, Ryen W.; Winnenburg, Rainer; Shah, Nigam H. (J. Biomed. Informatics, 2017)

Hierarchical models for multiple, rare outcomes using massive observational healthcare databases. - Shaddox, Trevor R.; Ryan, Patrick B.; Schuemie, Martijn J.; Madigan, David; Suchard, Marc A. (Stat. Anal. Data Min., 2016)

Feasibility and utility of applications of the common data model to multiple, disparate observational health databases. - Voss, Erica A.; Makadia, Rupa; Matcho, Amy; Ma, Qianli; Knoll, Chris; Schuemie, Martijn J.; DeFalco, Frank J.; Londhe, Ajit; Zhu, Vivienne J.; Ryan, Patrick B. (J. Am. Medical Informatics Assoc., 2015)

Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. - Hripcsak, George; Duke, Jon D.; Shah, Nigam H.; Reich, Christian G.; Huser, Vojtech; Schuemie, Martijn J.; Suchard, Marc A.; Park, Rae Woong; Wong, Ian Chi Kei; Rijnbeek, Peter R.; Lei, Johan van der; Pratt, Nicole; et al. (2015)

ContextD: an algorithm to identify contextual properties of medical terms in a Dutch clinical corpus. - Afzal, Zubair; Pons, Ewoud; Kang, Ning; Sturkenboom, Miriam C. J. M.; Schuemie, Martijn J.; Kors, Jan A. (BMC Bioinform., 2014)

Transforming NHANES Database to the OMOP Common Data Model. - Zhu, Vivienne J.; Makadia, Rupa; Matcho, Amy; Schuemie, Martijn J.; Ryan, Patrick B. (2014)

Harmonization process for the identification of medical events in eight European healthcare databases: the experience from the EU-ADR project. - Avillach, Paul; Coloma, Preciosa M.; Gini, Rosa; Schuemie, Martijn J.; Mougin, Fleur; Dufour, Jean-Charles; Mazzaglia, Giampiero; Giaquinto, Carlo; Fornari, Carla; Herings, Ron; Molokhia, Mariam; Pedersen, Lars; et al. (J. Am. Medical Informatics Assoc., 2013)

Improving sensitivity of machine learning methods for automated case identification from free-text electronic medical records. - Afzal, Zubair; Schuemie, Martijn J.; Blijderveen, Jan C. van; Sen, Elif F.; Sturkenboom, Miriam C. J. M.; Kors, Jan A. (BMC Medical Informatics Decis. Mak., 2013)

Literature-aided interpretation of gene expression data with the weighted global test. - Jelier, Rob; Goeman, Jelle J.; Hettne, Kristina M.; Schuemie, Martijn J.; Dunnen, Johan T. den; Hoen, Peter A. C. 't (Briefings Bioinform., 2011)

DutchHatTrick: Semantic Query Modeling, ConText, Section Detection, and Match Score Maximization. - Schuemie, Martijn J.; Trieschnigg, Dolf; Meij, Edgar (2011)

GeneE: Gene and protein query expansion with disambiguation. - Schuemie, Martijn J.; Kang, Ning; Hekkelman, Maarten L.; Kors, Jan A. (Bioinform., 2010)

Rewriting and suppressing UMLS terms for improved biomedical term identification. - Hettne, Kristina M.; Mulligen, Erik M. van; Schuemie, Martijn J.; Schijvenaars, Bob J. A.; Kors, Jan A. (J. Biomed. Semant., 2010)

A Concept Annotation System for Clinical Records. - Kang, Ning; Barendse, Rogier; Afzal, Zubair; Singh, Bharat; Schuemie, Martijn J.; Mulligen, Erik M. van; Kors, Jan A. (2010)

A Concept Annotation System for Clinical Records - Kang, Ning; Barendse, Rogier; Afzal, Zubair; Singh, Bharat; Schuemie, Martijn J.; Mulligen, Erik M. van; Kors, Jan A. (CoRR, 2010)

Literature-based priors for gene regulatory networks. - Steele, Emma; Tucker, Allan; Hoen, Peter A. C. 't; Schuemie, Martijn J. (Bioinform., 2009)

A dictionary to identify small molecules and drugs in free text. - Hettne, Kristina M.; Stierum, Rob H.; Schuemie, Martijn J.; Hendriksen, Peter J. M.; Schijvenaars, Bob J. A.; Mulligen, Erik M. van; Kleinjans, Jos; Kors, Jan A. (Bioinform., 2009)

Structuring and extracting knowledge for the support of hypothesis generation in molecular biology. - Roos, Marco; Marshall, M. Scott; Gibson, Andrew P.; Schuemie, Martijn J.; Meij, Edgar; Katrenko, Sophia; Hage, Willem Robert van; Krommydas, Konstantinos; Adriaans, Pieter W. (BMC Bioinform., 2009)

Jane: suggesting journals, finding experts. - Schuemie, Martijn J.; Kors, Jan A. (Bioinform., 2008)

Literature-based concept profiles for gene annotation: The issue of weighting. - Jelier, Rob; Schuemie, Martijn J.; Roes, Peter-Jan; Mulligen, Erik M. van; Kors, Jan A. (Int. J. Medical Informatics, 2008)

Do Self-Statements Enhance the Effectiveness of Virtual Reality Exposure Therapy? A Comparative Evaluation in Acrophobia. - Krijn, Merel; Emmelkamp, Paul M. G.; Olafsson, Ragnar; Schuemie, Martijn J.; Mast, Charles van der (Cyberpsychology Behav. Soc. Netw., 2007)

Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification. - Schuemie, Martijn J.; Mons, Barend; Weeber, Marc; Kors, Jan A. (J. Biomed. Informatics, 2007)

Cross Language Information Retrieval for Biomedical Literature. - Schuemie, Martijn J.; Trieschnigg, Dolf; Kraaij, Wessel (2007)

Concept Based Document Retrieval for Genomics Literature. - Trieschnigg, Dolf; Kraaij, Wessel; Schuemie, Martijn J. (2006)

Thesaurus-based disambiguation of gene symbols. - Schijvenaars, Bob J. A.; Mons, Barend; Weeber, Marc; Schuemie, Martijn J.; Mulligen, Erik M. van; Wain, Hester M.; Kors, Jan A. (BMC Bioinform., 2005)

Word Sense Disambiguation in the Biomedical Domain: An Overview. - Schuemie, Martijn J.; Kors, Jan A.; Mons, Barend (J. Comput. Biol., 2005)

TREC 2005 Genomics Track A Concept-Based Approach to Text Categorization. - Schijvenaars, Bob J. A.; Schuemie, Martijn J.; Mulligen, Erik M. van; Weeber, Marc; Jelier, Rob; Mons, Barend; Kors, Jan A.; Kraaij, Wessel (2005)

Distribution of information in biomedical abstracts and full-text publications. - Schuemie, Martijn J.; Weeber, Marc; Schijvenaars, Bob J. A.; Mulligen, Erik M. van; Eijk, C. Christiaan van der; Jelier, Rob; Mons, Barend; Kors, Jan A. (Bioinform., 2004)

Contextual Annotation of Web Pages for Interactive Browsing. - Mulligen, Erik M. van; Diwersy, Mario; Schijvenaars, Bob J. A.; Weeber, Marc; Eijk, C. Christiaan van der; Jelier, Rob; Schuemie, Martijn J.; Kors, Jan A.; Mons, Barend (2004)

Searching for geneRIFs: Concept-Based Query Expansion and Bayes Classification. - Jelier, Rob; Schuemie, Martijn J.; Eijk, C. Christiaan van der; Weeber, Marc; Mulligen, Erik M. van; Schijvenaars, Bob J. A.; Mons, Barend; Kors, Jan A. (2003)

Effect of an external viewpoint on therapist performance in virtual reality exposure therapy. - Schuemie, Martijn J. (2002)

Research on Presence in Virtual Reality: A Survey. - Schuemie, Martijn J.; Straaten, Peter van der; Krijn, Merel; Mast, Charles van der (Cyberpsychology Behav. Soc. Netw., 2001)

Design of virtual reality exposure therapy systems: task analysis. - Schuemie, Martijn J. (2000)

Information retrieval systems using an associative conceptual space. - Berg, Jan van den; Schuemie, Martijn J. (1999)