Perelman School of Medicine at the University of Pennsylvania

Boland Lab

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Publications

For a complete listing of all of my publications along with citation information, please see my Google Scholar Profile. In Addition, my NCBI pubmed profile contains a list of publications and my ORCID.


Journal Publications

  1. MR Boland, A Kashyap, J Xiong, JH Holmes, S Lorch. Development and Validation of the PEPPER Framework (Prenatal Exposure PubMed ParsER) with Applications to Food Additives. J Am Med Inform Assoc. 2018; In press.
  2. MR Boland,  MS Kraus, E Dziuk, AR Gelzer. Cardiovascular Disease Risk Varies by Birth Month in Canines. Scientific Reports; 2018; 8:7130. 
  3. MR Boland, F Polubriaginof, NP Tatonetti. Development of A Machine Learning Algorithm to Classify Drugs Of Unknown Fetal Effect. Scientific Reports. 2017; 7: 12839.
  4. MR Boland, P Parhi, L Li, R Miotto, R Carroll, U Iqbal, P-A Nguyen, M Schuemie, SC You, D Smith, S Mooney, P Ryan, Y-C Li, RW Park, J Denny, JT Dudley, G Hripcsak, P Gentine, NP Tatonetti. Uncovering exposures responsible for birth season – disease effects: a global study..J Am Med Inform Assoc. 2018; 25(3): 275-288. 
  5. MR Boland, P Parhi, P Gentine, NP Tatonetti. Climate Classification is an Important Factor in Assessing Quality-of-Care Across Hospitals. Scientific Reports. 2017; 7: 4948.
  6. MR Boland, K Karczewski, NP Tatonetti. Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing. PLOS Computational Biology. 2017; 13 (1), e1005278.
  7. MR Boland, NP Tatonetti. Investigation of 7-DeHydroCholesterol Reductase Pathway to Elucidate Off-Target Prenatal Effects of Pharamceuticals: A Systematic Review. The Pharmacogenomics Journal. 2016; 16(5): 411–429.
  8. L Li*, MR Boland*, R Miotto*, NP Tatonetti, J Dudley. Replicating Cardiovascular Condition-Birth Month Associations. Scientific Reports.  2016; 6: 33166. *Joint Contribution First-Author.
  9. K Roberts, MR Boland, L Pruinelli, JD Cruz, A Berry, M Georgsson, R Hazen, RF Sarmiento, U Backonja, K-H Yu, Y Jiang, PF Brennan. Biomedical informatics advancing the national health agenda: The AMIA 2015 Year-in-Review in clinical & consumer informatics. J Am Med Inform Assoc. 2016; 24 (e1), e185-e190.
  10. K Gayvert, E Dardenne, C Cheung, MR Boland, T Lorberbaum, J Wanjala, Y Chen, M Rubin, NP Tatonetti, D Rickman, O Elemento. A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors. Cell Reports. 2016; 15 (11), 2348-2356.  
  11. N Nissim, MR Boland, NP Tatonetti, Y Elovici, G Hripcsak, Y Shahar, R Moskovitch. Improving Condition Severity Classification with an Efficient Active Learning Based Framework. Journal of biomedical informatics. 2016; 61, 44-54.
  12. MR Boland*, A Jacunski*, T Lorberbaum*, JD Romano, R Moskovitch, NP Tatonetti. Systems Biology Approaches for Identifying Adverse Drug Reactions and Elucidating Their Underlying Biological Mechanisms. WIREs Systems Biology and Medicine, 2016; 8 (2), 104-122. * Equal contribution first-author.
  13. A Oellrich*, N Collier*, T Groza*, D Rebholz-Schuhmann*, N Shah*, O Bodenreider, MR Boland, I Georgiev, H Liu, K Livingston, A Luna, A-M Mallon, P Manda, PN Robinson, G Rustici, M Simon, L Wang, R Winnenburg, M Dumontier. The digital revolution in phenotyping. Briefings in Bioinformatics, 2015; 17 (5), 819-830. * Equal contribution first-author. 
  14. MR Boland,  Z Shahn, D Madigan, G Hripcsak, NP Tatonetti. Birth Month Affects Lifetime Disease Risk: A Phenome-Wide Method.  Journal of the American Medical Informatics Association, 2015; 22(5):1042-1053. 
  15. BA Kidd, A Wroblewska, MR Boland, J Agudo, M Merad, NP Tatonetti, BD Brown, JT Dudley. Mapping the effects of drugs on the immune system. Nature Biotechnology. 2016; 34:47-54.
  16. MR Boland, NP Tatonetti, G Hripcsak. Development and Validation of a Classification Approach for Extracting Severity Automatically from Electronic Health Records. Journal of Biomedical Semantics, 2015; 6(14). Highly Accessed. 
  17. T Hao, A Rusanov, MR Boland, C Weng. Clustering clinical trials with similar eligibility features.  Journal of Biomedical Informatics, 2014;  52 : 112-120. 
  18. MR Boland, A Rusanov, Y So, Y Li, C Lopez-Jimenez, L Busacca, RC Steinman, S Bakken, JT Bigger, C Weng. 
From Expert-Derived User Needs to User-Perceived Usability and Usefulness: A Two-Phase Mixed-Methods Evaluation Framework, Journal of Biomedical Informatics, 2014; 52 : 141-150.
  19. MR Boland, G Hripcsak, Y Shen, WK Chung, C Weng. Defining a Comprehensive Verotype Using Electronic Health Records for Personalized Medicine. Journal of the American Medical Informatics Association, 2013; 20(e2)e232-8.
  20. C Weng, Y Li, S Berhe, MR Boland, J Gao, GW Hruby, RC Steinman, C Lopez Jimenez, L Busacca, G Hripcsak, S Bakken, JT Bigger. An Integrated Model for Patient Care and Clinical Trials (IMPACT) to Support Clinical Research Visit Scheduling Workflow for Future Learning Health Systems. Journal of Biomedical Informatics, 2013; 46 (4): 642-652. 
  21. MR Boland, R Miotto, J Gao, C Weng. Feasibility of feature-based indexing, clustering, and search of clinical trials: A case study of breast cancer trials from ClinicalTrials.gov. Methods of Information in Medicine, 2013; 52(5): 382-394. Bioportal Ontology
  22. MR Boland, G Hripcsak, DJ Albers, Y Wei, AB Wilcox, J Wei, J Li, S Lin, M Breene, R Myers, J Zimmerman, PN Papapanou, C Weng, Discovering Medical Conditions Associated with Periodontitis Using Linked Electronic Health Records. Journal of Clinical Periodontology, 2013; 40(5): 474-82. Top Paper in the "Practice of Informatics", 2013 AMIA Annual Year in Review
  23. MR Boland, S Trembowlski, S Bakken, C Weng, An Initial Log Analysis of Usage Patterns on a Research Networking System. Clinical and Translational Science, 2012; 5(4): 340-347. 
  24. C Weng, X Wu, Z Luo, MR Boland, D Theodoratos, SB Johnson, EliXR: An Approach to Eligibility Criteria Extraction and Representation. Journal of the American Medical Informatics Association. 2011; 18 Suppl 1:i116-i124. (Distinguished Paper of the 2011 AMIA Translational Summit Meeting).

Conference/Workshop Proceedings

  1. R Duan*, MR Boland*, JH Moore, Y Chen. ODAL: A one-shot distributed algorithm to perform logistic regressions on electronic health records data from multiple clinical sites. In Press at 2019 Pacific Symposium on Biocomputing. *Equal-contribution first-author
  2. MR Boland, NP Tatonetti. In Search of ‘Birth Month Genes’: Using Existing Data Repositories to Locate Genes Underlying Birth Month-Disease Relationships. AMIA Summits on Translational Science Proceedings; 2016: 189–198. Finalist for Distinguished Student Paper Award 
  3. MR Boland, NP Tatonetti. Are All Vaccines Created Equal? Using Electronic Health Records to Discover Vaccines Associated With Clinician-Coded Adverse Events. AMIA Summits on Translational Science Proceedings 2015, San Francisco, CA, USA. 2015; 196-200. 1st Place Winner Student Paper Competition
  4. N Nissim, MR Boland, R Moskovitch, NP Tatonetti, Y Elovici, Y Shahar, G Hripcsak. Active Learning Framework for EfficientCondition Severity Classification. Artificial Intelligence in Medicine. 2015; 13-24. Mario Stefanelli Best Student Paper Award
  5. V Agarwal, P LePendu, T Podchiyska, R Barber, MR Boland, G Hripcsak, N Shah. Using narratives as a source to automatically learn phenotype models. Data Mining for Medicine and Healthcare (DMMI) Proc. 2014; Washington DC, USA 2014.
  6. N Nissim, MR Boland, R Moskovitch, N Tatonetti, Y Elovici, Y Shahar, G Hripcsak. CAESAR-ALE: An Active Learning Enhancement for Conditions Severity Classification. ACM KDD on Workshop on Connected Health at Big Data Era; NYC, USA, 2014. 
  7. MR Boland, NP Tatonetti, G Hripcsak. CAESAR: a Classification Approach for Extracting Severity Automatically from Electronic Health Records. Intelligent Systems for Molecular Biology Phenotype Day. 2014; Boston, MA. 
  8. C Weng, MR Boland,  Y So, A Rusanov, C Lopez-Jiminez, R Steinman, L Busacca, S Bakken, JT Bigger. Using Software to Elicit User Needs for Clinical Research Visit Scheduling. AMIA Summits on Translational Science Proceedings. 2014: 109–115.
  9. CL Gordon, S Pouch, LG Cowell, MR Boland, HL Platt, A Goldfain, C Weng. Design and Evaluation of a Bacterial Clinical Infectious Diseases Ontology. Proceedings of the AMIA Annual Symposium 2013; 502-511. Finalist Student Paper Competition
  10. MR Boland*, R Miotto*, C Weng. A Method for Probing Disease Relatedness Using Common Clinical Eligibility Criteria. MEDINFO 2013, Copenhagen, Denmark. Stud Health Technol Inform. 2013; 192:481-5. * Equal contribution first-author. 
  11. G Hruby, MR Boland, JJ Cimino, J Gao, AB Wilcox, J Hirschberg, C Weng, Characterization of the Biomedical Query Mediation Process. AMIA Summits on Translational Science Proceedings, San Francisco, CA, 2013; 89-93. Finalist Distinguished Paper 
  12. MR Boland, SW Tu, S Carini, I Sim, C Weng, EliXR-TIME: A Temporal Knowledge Representation for Clinical Research Eligibility Criteria. AMIA Summits on Translational Science Proceedings, San Francisco, CA, 2012; 71-80.

Scientific Technical Reports

  1. YJ Lee, MR Boland, S Bakken, C Weng. Ontology Alignment for Linking a Homegrown Research Networking System to VIVO: Findings and Implications for Standards Development. 2013.
  2. MR Boland, S Trembowelski, DC Dine, RC Steinman, S Bakken, C Weng. How Are Research Networking Systems Used and by Whom? A Case Study Using Google Analytics. 2013.

Peer-Reviewed Conference/Workshop/Symposium Abstracts

  1. MR Boland, C DeVoto. Mapping Regional Effects of Exposure to Hydraulic Fracturing Fluid and Linking with Information on Toxicity. Presented at 2018 Fall Meeting, AGU, Washington DC, 10-14 December. (poster presentation)
  2. *MR Boland, LH John, PR Rijnbeek. Condition Coding Practice Differences Between USA, Asia and Europe. Presented at Observational Health Data Sciences and Informatics Symposium 2018, October 12, Bethesda MD, USA (podium presentation).
  3. *MR Boland, A Kashyap, J Xiong, JH Holmes, S Lorch. Construction of PEPPER: Prenatal Exposure Pubmed ParsER. AMIA Annu Symp Proc. 2018, San Francisco, CA, USA. In Press. (podium presentation)
  4. F Martin-Sanchez, R Bellazzi, *MR Boland, G Lopez-Campos. Contributions from Informatics and Data science to Environmental Health and Exposome Research. Medical Informatics in Europe (MIE) 2018; Gottenburg, Sweden, 24-27 April. (panel presentation)
  5. *MR Boland, F Polubriginof, NP Tatonetti. Development of A Machine Learning Algorithm to Classify Drugs of Unknown Fetal Effect. American Society of Clinical Pharmacology & Therapeutics. 2018; Orlando, FL, 21-24 March. Top Scoring Poster Award. (poster and flash talk presentation)
  6. *MR Boland, P Parhi, P Gentine, NP Tatonetti. Climate Classification is an Important Factor in Assessing Quality-of-Care Across Hospitals. Presented at 2017 Fall Meeting, AGU, New Orleans, LA, 11-15 December.
  7. *MR Boland, NP Tatonetti. Assessing the Mutational Spectrum of 7-DeHydroCholesterol Reductase and the Toxicological Effects of Pharmacological Inhibition During the Prenatal Period; (Abstract / Prenatal, Perinatal and Reproductive Genetics #3260T). Presented at the 66th Annual Meeting of The American Society of Human Genetics, October 20, 2016, Vancouver, Canada.
  8. *MR Boland, P Parhi, U Iqbal, A Nguyen, M Schuemie, SC You, P Ryan, J Li, RW Park, G Hripcsak, NP Tatonetti. A Climate-Wide Journey to Explore Mechanisms Underlying Birth Month-Disease Risk Associations: Preliminary Results. Observational Health Data Sciences and Informatics Symposium 2016, Washington DC, USA (poster).
  9. *MR Boland, L Li, R Miotto, J Dudley, NP Tatonetti. Cardiovascular Disease Risk And Birth Month? Discovering and Replicating Novel Birth Month Associations. Data Science Day at Columbia University, New York, NY, USA (poster), April 3, 2016
  10. *MR Boland, NP Tatonetti. In Search of ‘Birth Month Genes’: Using Existing Data Repositories to Locate Genes Underlying Birth Month-Disease Relationships. AMIA Summits on Translational Science Proceedings 2016, San Francisco, CA, USA.
  11. F Polubriaginof, A Perotte, MR Boland, D Vawdrey. Quality of Race and Ethnicity Data in Electronic Health Records. AMIA Summits on Translational Science Proceedings 2016 , San Francisco, CA, USA (podium).
  12. *MR Boland, G Hripcsak, P Ryan, NP Tatonetti. A Climate-Wide Journey to Explore Mechanisms Underlying Birth Month-Disease Risk Associations: A Call for Collaboration. Observational Heatlh Data Sciences and Informatics Symposium 2015, Washington DC, USA (poster).
  13. *MR Boland, Z Shahn, D Madigan, G Hripcsak, NP Tatonetti. Using Electronic Health Records to Uncover Disease-Birth Month Dependencies. National Library of Medicine Informatics Trainee Conference 2015, National Library of Medicine, Bethesda, MD, USA (focus session).
  14. *MR Boland, Z Shahn, D Madigan, G Hripcsak, NP Tatonetti. Using Electronic Health Records to Uncover Disease-Birth Month Dependencies. 2015 Symposium on Advances in Genomics, Epidemiology and Statistics (SAGES), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA (poster). Received Travel Award
  15.  N Nissim, MR Boland, R Moskovitch, NP Tatonetti, Y Elovici, Y Shahar, G Hripcsak. Active Learning Framework for Efficient Condition Severity Classification. Conference on Artificial Intelligence in Medicine (AIME). 2015; Pavia, Italy.
  16. *MR Boland, NP Tatonetti. Are All Vaccines Created Equal? Using Electronic Health Records to Discover Vaccines Associated With Clinician-Coded Adverse Events. AMIA Summits on Translational Science Proceedings 2015, San Francisco, CA, USA. (oral presentation).
  17. *MR Boland, Z Shahn, D Madigan, G Hripcsak, NP Tatonetti. Using Electronic Health Records to Uncover Disease-Birth Month Dependencies. AMIA Summits on Translational Science Proceedings 2015, San Francisco, CA, USA (poster). 
  18. B Kidd, A Wroblewska, MR Boland, J Agudo, M Merad, NP Tatonetti, B Brown, J Dudley. Systematic integrative analysis of immune pharmacology. AMIA Summits on Translational Science Proceedings 2015, San Francisco, CA, USA (poster).
  19. V Agarwal, P LePendu, T Podchiyska, R Barber, MR Boland, G Hripcsak, N Shah. Using narratives as a source to automatically learn phenotype models. Data Mining for Medicine and Healthcare (DMMI) Proc. 2014, Washington DC, USA.
  20. N Nissim, MR Boland, R Moskovitch, NP Tatonetti, Y Elovici, YShahar, G Hripcsak. CAESAR-ALE: An Active Learning Enhancement for Conditions Severity Classification. SIGKDD 2014, New York, NY, USA.
  21. *MR Boland, NP Tatonetti, G Hripcsak. CAESAR: a Classification Approach for Extracting Severity Automatically from Electronic Health Records. Intelligent Systems for Molecular Biology Phenotype Day. 2014; Boston, MA. [Link]
  22. MR Boland, R Miotto, C Weng. A method for probing disease relatedness using common clinical eligibility criteria. MEDINFO 2013, Copenhagen, Denmark.
  23. YJ Lee, MR Boland, S Bakken, C Weng. Ontology Alignment for Linking a Homegrown Research Networking System to VIVO: Findings and Implications for Standards Development. AMIA Summits on Translational Science Proceedings 2013 p.99 (poster)
  24. *MR Boland, S Trembowelski, D Dine, RC Steinman, S Bakken, C Weng. Using Google Analytics to Elucidate Research Networking System Usage. Clinical and Translational Science Award Annual Meeting 2012 (poster). 
  25. YJ Lee, MR Boland, S Bakken, C Weng. Aligning One CTSA’s Research Networking System to VIVO. Clinical and Translational Science Award Annual Meeting 2012 (podium).
  26. *MR Boland, G Hripcsak, DJ Albers, Y Wei, A Wilcox, J Wei, M Breene, J Zimmerman, C Weng. Linked Records Reveal Associations between Oral and Overall Health. Clinical and Translational Science Award Annual Meeting 2012 (poster). 
  27. *MR Boland, SB Johnson, S Trembowelski, DC Dine, RC Steinman, S Bakken, C Weng. An Initial Log-based Usage Analysis of Research Networking Systems. AMIA Summits on Translational Science Proceedings, San Francisco, CA, 2012; 148. (Podium) 
  28. *MR Boland, S Tu, S Carini, I Sim, C Weng. EliXR-TIME: A Temporal Knowledge Representation for Clinical Research Eligibility Criteria. AMIA Summits on Translational Science Proceedings 2012: 71-80 (oral presentation). 
  29. *MR Boland, ML Sierk. Annotation of Putatively Conserved Non-Coding Regions in Branchiostoma Floridae. National Conference for Undergraduate Research 2010, Missoula MT (poster). 
  30. *MR Boland, R Parker. Optimizing Cancer Chemotherapy Administration: Effect of Model Structure on Treatment Cost and Effect. Undergraduate Research in Tissue Engineering (Pittsburgh-Based Affiliate Research Institutes) 2009, Pittsburgh PA (poster No 3).
  31. *MR Boland, M Raab, M Sangimino. Data Design & Flow for RAE: An interactive web- based biomedical informatics system for pediatric orthopedic patients. Duquesne University Summer Research Symposium 2008, Pittsburgh PA (poster No 84). [Link] [File]

*Mary Regina Boland Gave Oral Presentation of Research