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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

A Concept Annotation System for Clinical Records. - Ning Kang 002; Rogier Barendse; Zubair Afzal; Bharat Singh; Martijn J. Schuemie; Erik M. van Mulligen; Jan A. Kors (SWAT4LS, 2010)

GeneE: Gene and protein query expansion with disambiguation. - Martijn J. Schuemie; Ning Kang 002; Maarten L. Hekkelman; Jan A. Kors (Bioinform., 2010)

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

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

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

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

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

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

ContextD: an algorithm to identify contextual properties of medical terms in a Dutch clinical corpus. - Zubair Afzal; Ewoud Pons; Ning Kang 002; Miriam C. J. M. Sturkenboom; Martijn J. Schuemie; Jan A. Kors (BMC Bioinform., 2014)

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; et al. (MedInfo, 2015)

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

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

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)

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

Uncovering exposures responsible for birth season - disease effects: a global study. - Mary Regina Boland; Pradipta Parhi; Li Li 062; 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; 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. - Jenna Marie Reps; Martijn J. Schuemie; Marc A. Suchard; Patrick B. Ryan; Peter R. Rijnbeek (J. Am. Medical Informatics Assoc., 2018)

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

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

Learning from electronic health records across multiple sites: A communication-efficient and privacy-preserving distributed algorithm. - Rui Duan 004; Mary Regina Boland; Zixuan Liu; Yue Liu; Howard H. Chang; Hua Xu 001; Haitao Chu; Christopher H. Schmid; Christopher B. Forrest; John H. Holmes; Martijn J. Schuemie; Jesse A. Berlin; et al. (J. Am. Medical Informatics Assoc., 2020)

Learning from local to global: An efficient distributed algorithm for modeling time-to-event data. - Rui Duan 004; Chongliang Luo; Martijn J. Schuemie; Jiayi Tong; C. Jason Liang; Howard H. Chang; Mary Regina Boland; Jiang Bian 001; Hua Xu 001; John H. Holmes; Christopher B. Forrest; Sally C. Morton; 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. - Martijn J. Schuemie; Patrick B. Ryan; Nicole Pratt; Ruijun Chen; Seng Chan You; Harlan M. Krumholz; David Madigan; George Hripcsak; Marc A. Suchard (J. Am. Medical Informatics Assoc., 2020)

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

A standardized analytics pipeline for reliable and rapid development and validation of prediction models using observational health data. - Sara Khalid; Cynthia Yang; Clair Blacketer; Talita Duarte-Salles; Sergio Fernández-Bertolín; Chungsoo Kim; Rae Woong Park; Jimyung Park; Martijn J. Schuemie; Anthony G. Sena; Marc A. Suchard; Seng Chan You; 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. - Martijn J. Schuemie; Patrick B. Ryan; Nicole Pratt; Ruijun Chen; Seng Chan You; Harlan M. Krumholz; David Madigan; George Hripcsak; Marc A. Suchard (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. - Jenna Marie Reps; Patrick B. Ryan; Peter R. Rijnbeek; Martijn J. Schuemie (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. - Jenna Marie Reps; Peter R. Rijnbeek; Alana Cuthbert; Patrick B. Ryan; Nicole Pratt; Martijn J. Schuemie (BMC Medical Informatics Decis. Mak., 2021)

dPQL: a lossless distributed algorithm for generalized linear mixed model with application to privacy-preserving hospital profiling. - Chongliang Luo; Md. Nazmul Islam; Natalie E. Sheils; John Buresh; Martijn J. Schuemie; Jalpa A. Doshi; Rachel M. Werner; David A. Asch; Yong Chen 016 (J. Am. Medical Informatics Assoc., 2022)

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

Adjusting for indirectly measured confounding using large-scale propensity score. - Linying Zhang; Yixin Wang 002; Martijn J. Schuemie; David M. Blei; George Hripcsak (J. Biomed. Informatics, 2022)

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

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

Padé approximant meets federated learning: A nearly lossless, one-shot algorithm for evidence synthesis in distributed research networks with rare outcomes. - Qiong Wu; Martijn J. Schuemie; Marc A. Suchard; Patrick B. Ryan; George Hripcsak; Charles A. Rohde; Yong Chen 016 (J. Biomed. Informatics, 2023)

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

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

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

Evaluation of the impact of defining observable time in real-world data on outcome incidence. - Clair Blacketer; Frank J. DeFalco; Mitchell M. Conover; Patrick B. Ryan; Martijn J. Schuemie; Peter R. Rijnbeek (J. Am. Medical Informatics Assoc., 2025)

Objective study validity diagnostics: a framework requiring pre-specified, empirical verification to increase trust in the reliability of real-world evidence. - Mitchell Conover; Patrick B. Ryan; Yong Chen 016; Marc A. Suchard; George Hripcsak; Martijn J. Schuemie (J. Am. Medical Informatics Assoc., 2025)

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

COLA-GLM: collaborative one-shot and lossless algorithms of generalized linear models for decentralized observational healthcare data. - Qiong Wu; Jenna Marie Reps; Lu Li; Bingyu Zhang; Yiwen Lu; Jiayi Tong; Dazheng Zhang; Thomas Lumley; Milou T. Brand; Mui Van Zandt; Thomas Falconer; Xing He 003; et al. (npj Digit. Medicine, 2025)