Faculty

Xinghua Lu, MD, PhD, MS

Directory Listing Information
Lu, Xinghua
Computational methods for identifying signaling pathways underlying biological processes and diseases, statistical methods for acquiring knowledge from biomedical literature, translational bioinformatics and systems/computational biology, natural language processing and text mining.
Dr. Lu’s research focuses on the computational methods for identifying signaling pathways underlying biological processes and diseases as well as Statistical methods for acquiring knowledge from biomedical literature.
Room 525
5607 Baum Boulevard
Pittsburgh, PA 15206
412-624-3303
412-624-5310
Professor of Biomedical Informatics
Biomedical Informatics Training Program Core Faculty
University of Pittsburgh School of Medicine
Publications: 

Lu S, Fan X, Chen L, Lu X. A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways. Plos One. September 2018; 13(9). https://doi.org/10.1371/journal.pone.0203871. 

Pangeni RP, Zhang Z, Alvarez AA, Wan X, Sastry N, Lu S, Shi T, Huang T, Lei CX, James CD, Kessler JA, Brennan CW, Nakano I, Lu X, Hu B, Zhang W, Cheng SY. Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma. Epigenetics. 2018;13(4):432-448. doi: 10.1080/15592294.2018.1469892. Epub 2018 Aug 6. PMID: 29927689.

Sadahiro H, Kang K, Gibson J, Minata M, Yu H, Shi J, Chhipa R, Chen Z, Lu S, Simoni Y, Furuta T, Sabit H, Zhang S, Bastola S, Yamaguchi S, Alsheikh H, Komarova S, Wang J, Kim S, Hambardzumyan D, Lu X, Newell E, Dasgupta B, Nakada M, Lee L, Nabors B, Norian L, Nakano I. Activation of the receptor tyrosine kinase AXL mediates the immune microenvironment in glioblastoma.  2018 Jun 1;78(11):3002-3013. doi: 10.1158/0008-5472.CAN-17-2433. Epub 2018 Mar 12. PMID: 29531161.

Yan G, Chen V, Lu X, Lu S. A signal-based method for finding driver modules of breast cancer metastasis to the lung. Sci Rep. 2017 Aug 30; 7(1):10023. doi: 10.1038/s41598-09951-2. PMID: 28855549. PMC ID: PMC5577160.

Chen V, Paisley J, Lu X. Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling. BMC Genomics. 2017 Mar 14;18 (Suppl 2):105. doi: 10.1186/s12864-017-3494-z. PMID: 28361690. PMC ID: PMC5374647.

Watters RJ, Hartmaier RJ, Osmanbeyoglu HU, Gillihan RM, Rae JM, Liao L, Chen K, Li W, Lu X, Oesterreich S. Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen. Mol Cell Endocrinol. 2017 Jun 15; 448:21-27. doi: 10.1016/j.mce.2017.03.005. Epub 2017 Mar 7. PMID: 28286232

Huang T, Kim CK, Alvarez AA, Pangeni RP, Wan X, Song X, Shi T, Yang Y, Sastry N, Horbinski CM, Lu S, Stupp R, Kessler JA, Nishikawa R, Nakano I, Sulman EP, Lu X, James CD, Yin XM, Hu B, Cheng SY. MST4 Phosphorylation of ATG4B Regulates Autophagic Activity, Tumorigenicity, and Radioresistance in Glioblastoma. Cancer Cell. 2017 Dec 11; 32(6):840-855.e8. doi: 10.1016/j.ccell.2017.11.005. PMID: 29232556

Ding MQ, Chen L, Cooper GF, Young JD, Lu X. Precision Oncology Beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics. Mol Cancer Res. 2017 Nov 13. pii: molcanres.0378.2017. doi: 10.1158/1541-7786.MCR-17-0378. [Epub ahead of print] PMID: 29133589

Young JD, Cai C, Lu X. Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma. BMC Bioinformatics. 2017 Oct 3;18(Suppl 11): 381. doi: 10.1186/s12859-017-1798-2. PMID: 28984190. PMCID: PMC5629551

Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer Res. 206 Dec 1:76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. Epub 2016 Oct 10. PMID: 27758891. PMCID: PMC5165695.

Lu S, Mandava G, Yan G, and Lu X. An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem. Algorithms Mol Biol. 2016 May 4;11:11. doi: 10.1186/s13015-016-0073-9. PMID: 27148394. PMCID: PMC4855522.

Huang T, Alvarez AA, Pangeni RP, Horbinski CM, Lu S, Kim SH, James CD, J Raizer J, A Kessler J, Brenann CW, Sulman EP, Finocchiaro G, Tan M, Nishikawa R, Lu X, Nakano I, Hu B, Cheng SY. A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways. Nat Commun. 2016 Oct 4;7:12885. doi: 10.1038/ncomms12885. PMID: 27698350. PMCID: PMC5059456.

Lu S, Lu KN, Cheng SY, Hu B, Ma X, Nystrom N, Lu X. Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets. PLoS Comput Biol. 2015 Aug 28; 11(8):e1004257. doi: 10.1371/journal.pcbi.1004257. eCollection 2015 Aug. PMID:26317392. PMCID: PMC4552843.

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team. The Center for causal discovery of biomedical knowledge from Big Data. J Am Med Inform Assoc. 2015 Nov;22(6): 1132-6. doi: 10.1093/jamia/ocv059. Epub 2015 Jul 2.  PMID: 26138794. PMCID: PMC5009908.

Ogoe, HA, Visweswaran, S, Lu, X, Gopalakrishnan, V.  (2015) Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data.  BMC Bioinformatics 16:226 (designated as a Highly Accessed paper) PMID: 26202217 PMCID: PMC4512094

Jiang X, Cai B, Xue D, Lu X, Cooper GF, Neapolitan RE. A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets. Journal of the American Medical Informatics Association (2014). Oct;21(e2):e312-9. doi: 10.1136/amiajnl-2013-002358. Epub 2014 Apr 15. PMID: 24737607. PMC4173174.

Cai C, Chen L, Jiang X, Lu X. Integrating protein phosphorylation and gene expression data to infer signaling pathways. Cancer Informatics Supplement on Cancer Clinical Information Systems. 2014; 13(s1): 59-67. doi: 10.4137/CIN.S13883

Lu S, Jin B, Cowart LA. Lu X. From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data. PLoS One. 2013 Apr 23;8(4):e61134. doi: 10.1371/journal.pone.0061134. Print 2013. PMID: 23637789. PMCID: PMC3634064.

Lu S, Lu X. Using graph models to find transcription factor modules: the hitting set problem and an exact algorithm. Algorithms Mol Biol. 2013 Jan 16;8(1):2. doi: 10.1186/1748-7188-8-2. PMID: 23324335. PMCID: PMC3622577.

Montefusco DJ, Chen L, Matmati N, Lu S, Newcomb B, Cooper GF, Hannun YA, Lu X. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses. Sci Signal. 2013 Oct 29;6(299): rs14. doi: 10.1126/scisignal.2004515. PMID: 24170935. PMC3974757.

Zhao, Z., Shen, B., Lu, X., and Vongsangnak, W (2013) Translational Biomedical Informatics and Computational Systems Medicine. BioMed Research International, vol. 2013, Article ID 237465, 2013. doi:10.1155/2013/237465

Chen, V and Lu, X (2013) Conceptualization of molecular findings by mining gene annotations. BMC Proceedings 7(Suppl 7):S2

Mowrey, D., Cheng, M., Liu, L., Willenbring, D., Lu, X., Wymore, T., Xu, Y., and Tang, P.. (2013) Asymmetric ligand binding facilitates conformational transitions in pentameric ligand-gated ion channels. J Am Chem Soc. 135(6):2172-80. PMCID: PMC3582375

Lu SLu X. A graph model and an exact algorithm for finding cooperative transcription factor modules. Proc. 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2012 Jul 31-Aug 3; 355-359.

Lu SLu, X. Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers. 2012 AMIA Jt Summits Transl Sci Proc. 2012;2012:72-8. Epub 2012 Mar 19. PMID: 22779056. PMCID: PMC3392049.

Qin, T., Tsoi, LC., Sims KJ, Lu, X and Zheng, WJ (2012) Signaling network prediction using the ontology fingerprint enhanced Bayesian networks. BMC Systems Biology 6 (Suppl 3) : S3 (co-corresponding author)

Richards, A., Schwacke, J., Rohrer, B., Cowart, LA. and Lu, X (2012) Revealing functionally coherent gene subset using spectral clustering and information integration approaches. BMC Systems Biology 6 (Suppl 3) : S7

Osmanbeyoglu, H, Hartmaier, R., Oesterreich, S., and Lu, X. (2012) Improving ChIP-seq peak-calling for functional indirect co-regulator binding by integrating multiple sources of biological information. BMC Genomics 13(Suppl 1):S1

Feng, H, Hu, B, Liu, KW, Lu, X, Yiin, JJ, Lu, S, Keezer, S, Fenton, T, Furnari, FB, Hamilton, RL, Vuori, K, Nagane, M, Nishikawa, R, Cavenee, WK and Cheng, SY (2012) Aberrant Activation of Rac1 by Src-dependent Phosphorylation of Dock180Y1811 Mediates PDGFRα-stimulated Glioma Growth and Invasion. Journal of Clinical Investigation 121(12):4670–4684

Feng H, Hu B, Liu KW, Li Y, Lu X, Cheng T, Yiin JJ, Lu S, Keezer S, Fenton T, Furnari FB, Hamilton RL, Vuori K, Sarkaria JN, Nagane M, Nishikawa R, Cavenee WK, Cheng SY. Activation of Rac1 by Src-dependent phosphorylation of Dock180(Y1811) mediates PDGFRα-stimulated glioma tumorigenesis in mice and humans. J Clin Invest. 2011 Dec;121(12):4670-84. doi: 10.1172/JCI58559. Epub 2011 Nov 14. PMID: 22080864. PMCID: PMC3223070.

Jin, B., Chen, V., Chen, L., and Lu, X. (2011) Mapping annotations with textual evidence using an scLDA model. Proceedings of AMIA Annual Symposium, Washington DC

Jin, B. and Lu, X (2010). Identifying informative subsets of the Gene Ontology with information bottleneck methods. Bioinformatics 26 (19): 2445-2451

Cowart, LA., Shotwell, M., Worley, ML.,  Richards, AJ, Montefusco, DJ, Hannun YA, and Lu, X. (2010) Revealing a signaling role of PHS1P in yeast using integrative systems approaches.  Molecular Systems Biology 6:349 PMID: 20160710(Selected for presentation at the Highlight Track of ISMB 2010 as a major advance in the field)

Richards*, AJ, Muller, B., Shotwell, M, Cowart, LA, Rohrer, B, and Lu, X (2010) Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.  Bioinformatics, supplement issue for the Proceedings for the Intelligent Systems in Molecular Biology (ISMB) 2010 (19% acceptance) PMID: 20529941

Zheng*, B. and Lu, X (2009) Application of semantic modeling in bioinformatics domain.  In: Data Management in Semantic Web, Ed. Jin, H. and Lv, Z,.  Nova Science Publishers, Inc.

Muller*, B., Richards, AJ., Jin, B., Lu, X. (2009) GOGrapher; A Python library for GO graph representation and analysis.  BMC Research Notes 2:122 PMID:19583843

Xia Jiang, PhD

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Jiang, Xia
Dr. Jiang has over 13 years of teaching and research experience in Bayesian Network modeling, machine learning, and algorithm design. She is the coauthor of the book “Probabilistic Methods for Financial and Marketing Informatics” published by Morgan Kaufmann in 2007 (http://www.amazon.com). She is currently focusing on developing novel algorithms/systems that improve the computational efficiency of high-dimensional data analysis, and network modeling of cancer genome data.
Dr. Jiang's research focuses on developing novel algorithms/systems that improve the computational efficiency of high-dimensional data analysis, and network modeling of cancer genome data.
Associate Professor, Department of Biomedical Informatics
Biomedical Informatics Training Program Core Faculty
University of Pittsburgh School of Medicine
Publications: 

Zeng Z, Jiang X, Li X, Wells A, Luo Y, Neapolitan RE. Conjugated equine estrogen and medroxyprogesterone acetate are associated with decreased risk of breast cancer relative to bioidentical hormone therapy and controls. PLoS One. 2018 May 16;13(5):e0197064. doi: 10.1371/journal.pone.0197064. eCollection 2018. PMID: 29768475.

Lee S, Jiang X. Modeling miRNA-mRNA interactions that cause phenotypic abnormality in breast cancer patients. PLOS One. Online 9 August 2017.

Rathnam C, Lee S, Jiang X. An algorithm for direct causal learning of influences on patient outcomes. Artif Intell Med. 2017 Jan; 75: 1-15. doi: 10.1016/j.artmed.2016.10.003. Epub 2016 Nov 5. PMID: 28363452. PMC ID: PMC5415921

Neapolitan RE, Jiang X. A Note of Caution on Maximizing Entropy. Entropy. 2014; 16 (7):4004-14. doi: 10.3390/e16074004.

Neapolitan RE, Xue D, Jiang X. Modeling the Altered Expression Levels of Genes on Signaling Pathways in Tumors as Causal Bayesian Networks. Cancer Informatics. 2014; 13:77-84. PMCID: PMC4051800. doi: 10.4137/CIN.S13578.

Jiang X, Cai B, Xue D, Lu X, Cooper GF, Neapolitan RE. A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets. Journal of the American Medical Informatics Association (2014). Oct;21(e2):e312-9. doi: 10.1136/amiajnl-2013-002358. Epub 2014 Apr 15. PMID: 24737607. PMC4173174.

Cai B, Jiang X. Novel Artificial Neural Network Method for Biomedical Prediction based on Matrix Pseudo-Inversion. Journal of Biomedical Informatics. 2014 Apr; 48:114-21. doi: 10.1016/j.jbi.2013.12.009.

Jiang X, Xue D, Brufsky AM, Khan SA, Neapolitan RE. A new method for predicting patient survivorship using efficient Bayesian network learning. Cancer Informatics. 2014; 13 (2):47-57. PMCID: PMC3928477. PMID: 24558297. doi: 10.4137/CIN.S13053.

Neapolitan RE, Jiang X. Inferring Aberrant Signal Transduction Pathways in Ovarian Cancer from TCGA Data. Cancer Informatics Supplement on Cancer Clinical Information Systems. 2014; 13(s1): 29-36. doi: 10.4137/CIN.S13881

Cai C, Chen L, Jiang X, Lu X. Integrating protein phosphorylation and gene expression data to infer signaling pathways. Cancer Informatics Supplement on Cancer Clinical Information Systems. 2014; 13(s1): 59-67. doi: 10.4137/CIN.S13883

Neapolitan RE, Jiang X. Contemporary Artificial Intelligence. 1st ed. Boca Raton, FL: Chapman and Hall/CRC, 2012.

Jiang X, Neapolitan RE. Mining Strict Epistatic Interactions From High-Dimensional Datasets: Ameliorating the Curse of Dimensionality. PLoS ONE. 2012; 7 (10):e46771. PMCID: PMC3470561. PMID: 23071633

Jiang X, Neapolitan RE, Barmada M, Visweswaran S, Cooper GF. A fast algorithm for learning epistatic genomic relationships. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2010) 341-345. PMID: 21346997. PMC3041370.

Chakrabarti S, Jiang X, et al. Data Mining: Know It All, Morgan Kaufmann, Burlington, MA, 2009.

Jiang X, Cooper GF. Modeling the Temporal Trend of the Daily Severity of an Outbreak using Bayesian Networks. In: Holmes DE, Jain LC, editors. Innovations in Bayesian Networks of Studies in Computational Intelligence. NY: Springer-Verlag, 2008.

Neapolitan RE, Jiang X. Probabilistic Methods for Financial and Marketing Informatics. San Mateo, CA: Morgan Kaufmann, 2007.

Neapolitan RE, Jiang X. A Tutorial on Learning Casual Influences. In: Holmes DE, Jain LC, editors. Innovations in Machine Learning. NY: Springer-Verlag, 2006.

Richard Boyce, PhD

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Boyce, Richard
Informatics interventions to improve medication safety, especially for older adults Structured publishing of biomedical knowledge and data to improve information retrieval and knowledge synthesis Computational methods for simplifying biomedical knowledge-base development, curation, and use
Dr. Boyce is interested in the intersection of informatics, comparative effectiveness research, and medication safety (including pharmacoepidemiology).
Associate Professor, Department of Biomedical Informatics
Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research and Training Program
Faculty, Center for Pharmaceutical Policy and Prescribing
University of Pittsburgh School of Medicine
Publications: 

Judkins J, Tay-Sontheimer J, Boyce RD, Brochhausen M. Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse. J Biomed Semantics. 2018 May 9;9(1):15. doi: 10.1186/s13326-018-0183-z. PMID: 29743102. PMCID: PMC59444177.

Boyce RD, Jao J, Miller T, Kane-Gill SL. Automated Screening of Emergency Department Notes for Drug-Associated Bleeding Adverse Events Occurring in Older Adults. Appl Clin Inform. 2017 Oct; 8(4):1022-1030. doi: 10.4338/ACI-2017-02-RA-0036. Epub 2017 Dec 14. PMID: 29241242.

Freimuth RR, Formea CM, Hoffman JM, Matey E, Peterson JF, Boyce RD. Implementing Genomic Clinical Decision Support for Drug-Based Precision Medicine. CPT Pharmacometrics Syst Pharmacol. 2017 Mar;6(3):153-155. Doi: 10.1002/psp4.12173. Review. PubMed PMID: 28109071. PubMed Central PMCID: PMC5351408.

Boyce RD, Voss E, Huser V, Evans L, Reich C, Duke JD, Tatonetti NP, Lorberbaum T., Dumontier M, Hauben M, Wallberg M, Peng L, Dempster S, He O, Sena A, Koutkias V, Natsiavas P, Ryan P. (Knowledge Base Workgroup of the Observational Health Data Sciences and Informatics [OHDSI] collaborative). Large-scale Adverse Effects Related to Treatment Evidence Standardization (LAERTES): an Open Scalable System for Linking Pharmacovigilance Evidence Sources with Clinical Data. J Biomed Semantics. 2017 Mar 7;8(1):11. doi: 10.1186/s13326-017-0115-3. PubMed PMID: 28270198. PubMed Central PMCID: PMC5341176.

Kane-Gill SL, Niznik JD, Kellum JA, Culley CM, Boyce RD, Marcum ZA, He H, Perera S, Handler, SM. Use of Telemedicine to Enhance Pharmacist Services in the Nursing Facility. Consult Pharm. 2017 Feb 1;32(2):93-98. doi: 10.4140/TCP.n.2017.93. Pub Med PMID: 28569660. PubMed Central PMCID: PMC5454780.

Voss EA, Boyce RD, Ryan PB, van der Lei J, Rijnbeek PR, Schuemie MJ. Accuracy of an Automated Knowledge Base for Identifying Drug Adverse Reactions. J Biomed Inform. 2017 Feb;66:72-81. doi: 10.1016/j.jbi.2016.12.005. PubMed PMID: 27993747. PubMed Central PMCID: PMC5316295

Hochheiser H, Ning Y, Hernandez A, Horn, JR, Jacobson R, Boyce RD. Using Nonexperts for Annotating Pharmacokinetic Drug-Drug Interaction Mentions in Product Labeling: A Feasibility Study. JMIR Res Protoc. 2016 Apr 11;5(2):e40. doi: 10.2196/resprot.5028. PMID: 27066806 PMCID: PMC4844909.

Romagnoli KM, Boyce RD, Empey PE, Adams S, Hochheiser H. Bringing clinical pharmacogenomics information to pharmacists: A qualitative study of information needs and resource requirements. Int J Med Inform. 2016 Feb;86:54-61. doi: 10.1016/j.ijmedinf.2015.11.015. Epub 2015 Nov 30. PMID: 26725696. PMCID: PMC4720137.

Huser V, DeFalco F, Schuemie M, Ryan P, Shang N, Velez M, Park RW, Boyce RD, Duke J, Khare R, Utidjian L, Bailey C. (2016) "Multisite Evaluation of a Data Quality Tool for Patient-Level Clinical Datasets," eGEMs (Generating Evidence & Methods to improve patient outcomes): Vol. 4: Iss. 1, Article 24. DOI: http://dx.doi.org/10.13063/2327-9214.1239

Samwald M, Xu H, Blagec K, Empey PE, Malone DC, Ahmed SM, Boyce RD, et al. (2016) Incidence of Exposure of Patients in the United States to Multiple Drugs for Which Pharmacogenomic Guidelines Are Available. PLoS ONE 11(10): e0164972. PMID: 27764192  DOI: 10.1371/journal.pone.0164972

Boyce RD, Handler SM, Karp JF, Perera S, Reynolds CF 3rd. Preparing Nursing. Home Data from Multiple Sites for Clinical Research - A Case Study Using Observational Health Data Sciences and Informatics. EGEMS (Wash DC). 2016 Oct 26;4(1):1252. PubMed PMID: 27891528. DOI: http://dx.doi.org/10.13063/2327-9214.1252

Ayvaz S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce RD, Toward a complete dataset of drug-drug interaction information from publicly available sources, Journal of Biomedical Informatics. 55 (2015), 206-217.  DOI:10.1016/j.jbi.2015.04.006. PMID 25917055

Pfundner A, Schönberg T, Horn J, Boyce RD, Samwald M. Utilizing the Wikidata system to improve the quality of medical content in Wikipedia in diverse languages: a pilot study. Journal of Medical Internet Research. 2015; 17(5). http://www.jmir.org/2015/5/e110/ .PMCID: PMC4468594

Samwald M, Miñarro Giménez JA, Boyce RD, Freimuth RR, Adlassnig K-P, Dumontier M. Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies. BMC MedRical Informatics and Decision Making. 2015;15:12. doi:10.1186/s12911-015-0130-1.  PubMed4340468

Scheife RT, Hines LE, Boyce RD, Chung SP, Momper JD, Sommer CD, Abernethy DR, Horn JR, Sklar SJ, Wong SK, Jones G, Brown ML, Grizzle AJ, Comes S, Wilkins TL, Borst C, Wittie MA, Malone DC. Consensus Recommendations for Systematic Evaluation of Drug-Drug Interaction Evidence for Clinical Decision Support. Drug Saf. 2015 Jan 3.  http://link.springer.com/article/10.1007%2Fs40264-014-0262-8  [Epub ahead of print] PubMed PMID: 25556085. [PMCID – in process]

Boyce RD, Ryan PB, Noren N. et al., Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest.  Drug Safety. 2014. DOI: 10.1007/s40264-014-0189-0

Ayvaz S, Zhu Q, Hochheiser H, Brochhausen M, Horn J, Dumontier M, … Boyce RD. (2014). Drug-Drug Interaction Data Source Survey and Linking. AMIA Summits on Translational Science Proceedings, 2014, 16. PMID: 25717393 PMCID: PMC4333686

Rasteger-Mojarad, M., Boyce RD., Prasad, R. UWM-TRIADS: Classifying Drug-Drug Interactions with Two-Stage SVM and Post-Processing. Proceedings of the 2013 International Workshop on Semantic Evaluation (SemEval), Task 9 - Extraction of Drug-drug Interactions from BioMedical Texts. Atlanta Georgia, June 2013.

Hassanzadeh O, Zhu Q, Freimuth RR, Boyce R. Extending the “Web of Drug Identity” with Knowledge Extracted from United States Product Labels. Proceedings of the 2013 AMIA Summit on Translational Bioinformatics. San Francisco, March 2013. 

Handler SM, Boyce RD, Ligons FM, Perera S, Nace DA, Hochheiser H. Use and Perceived Benefits of Mobile Devices by Physicians in Preventing Adverse Drug Events in the Nursing Home. Journal of The American Medical Directors Association. 2013 Oct 2. PMID: 24094901.

Boyce RD, Horn JR, Hassanzadeh O, de Waard A, Schneider J, Luciano JS, Rastegar-Mojarad M, Liakata M. Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness. J Biomed Semantics. 2013 Jan 26;4(1):5. [Epub ahead of print] DOI 10.1186/2041-1480-4-5 PMID:23351881. [PMCID – in process]

Rodríguez-González A, Pathak J, Wilkinson MD, Shah NH, Stevens R, Boyce RD, García-Crespo Á. “Proceedings of the Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine (SATBI+SWIM 2012),” Held at the 11th International Semantic Web Conference (ISWC 2012), November 12th, Boston, USA. http://ceur-ws.org/Vol-930/

Marshall MS, Boyce RD (Eds). Health Care and Life Science (HCLS) Linked Data Guide. World Wide Web Consortium (W3C). November 2012. http://www.w3.org/2001/sw/hcls/notes/hcls-rdf-guide/


Conference Papers and Presentations at National and Local Meetings:

 

Michael M. Wagner, MD, PhD

Directory Listing Information
Wagner, Michael M.
Dr. Wagner’s research focuses on real-time methods for detecting and characterizing disease outbreaks, including the development and testing of operational biosurveillance systems. In his role as director of the RODS Laboratory, Dr. Wagner led the development and implementation of two widely used biosurveillance systems: the RODS system and the National Retail Data Monitor (NRDM). Currently, Dr. Wagner is developing a third system called BioEcon. BioEcon is a decision analytic tool for use by analysts working in health departments. BioEcon is a logical extension of Dr. Wagner’s research in biosurveillance. BioEcon addresses the problem of what is the optimal action to take in response to incoming biosurveillance data.
Room 434
5607 Baum Boulevard
Pittsburgh, PA 15206
412-648-8640
412-648-9118
Vice Chairman, Population Informatics
Director, RODS Laboratory
Professor of Biomedical Informatics and Intelligent Systems
Biomedical Informatics Training Program Core Faculty
University of Pittsburgh School of Medicine
Publications: 

Tajgardoon M, Wagner MM, Visweswaran S, Zimmerman RK. A Novel Representation of Vaccine Efficacy Trial Datasets for Use in Computer Simulation of Vaccination Policy. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:389-398. eCollection 2018. PubMed PMID: 29888097. PMCID: PMC5961808.

Ferraro JP, Ye Y, Gesteland PH, Haug PJ, Tsui F-C, Cooper GF, Van Bree R, Ginter T, Nowalk AJ, Wagner MM. The effects of natural language processing on cross-institutional portability of influenza case detection for disease surveillance. Appl Clin Inform. 2017 May 31;8(2):560-580. doi:10.4338/ACI-2016-12-RA-0211. PubMed PMID: 28561130.

Ye Y, Wagner MM, Cooper GF, Ferraro JP, Su H, Gesteland PH, Haug PJ, Millett NE, Aronis JM, Nowalk AJ, Ruiz VM, López Pineda A, Shi L, Van Bree R, Ginter T, Tsui F. A study of the transferability of influenza case detection systems between two large healthcare systems. PLoS One. 2017 Apr 5;12(4):e0174970. doi: 10.1371/journal.pone.0174970. eCollection 2017. PMID: 28380048 PMCID: PMC5381795

Tsui F, Ye Y, Ruiz V, Cooper GF, Wagner MM. Automated influenza case detection for public health surveillance and clinical diagnosis using dynamic influenza prevalence method. J Public Health (Oxf). 2017 Oct 20:1-8. doi: 10.1093/pubmed/fdx141. [Epub ahead of print]. PMID: 29059331.

Hogan WR, Wagner MM, Brochhausen M, Levander J, Brown ST, Millett N, DePasse J, Hanna J. The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simluation. J Biomed Semantics. 2016 Aug 18;7:50. doi: 10.1186/s13326-016-0092-y. PMID: 27538448. PMCID: PMC4989460.

Cooper GF, Villamarin R, Rich Tsui FC, Millett N, Espino JU, Wagner MM. A method for detecting and characterizing outbreaks of infectious disease from clinical reports. J Biomed Inform. 2015 Feb; 53:15-26.  doi: 10.1016/j.jbi.2014.08.011. Epub 2014 Aug 30.  PMID: 25181466. PMCID: PMC4441330.

López Pineda A, Ye Y, Visweswaran S, Cooper GF, Wagner MM, Tsui FR. Comparison of Machine Learning Classifiers for Influenza Detection from Emergency Department Free-text Reports. J Biomed Inform. 2015 Dec;58:60-69. doi: 10.1016/j.jbi.2015.08.019. Epub 2015 Sep 16. PMID: 26385375. PMCID: PMC4684714.

Ye Y, Tsui FR, Wagner M, Espino JU, Li Q.  Influenza detection from emergency department reports using natural language processing and Bayesian network classifiers.  J Am Med Inform Assoc. 2014 Sep-Oct; 21(5):815-23. doi: 10.1136/amiajnl-2013-001934. Epub 2014 Jan 9. PMID: 24406261. PMCID: PMC4147621.

Wagner MM, Levander JD, Brown S, Hogan WR, Millett N, Hanna J. Apollo: Giving application developers a single point of access to public health models using structured vocabularies and Web services. AMIA Annu Symp Proc. 2013 Nov 16;2013: 1415-24. eCollection 2013. PubMed PMID: 24551417.  PMCID: PMC3900155.

Lee BY, Tai JH, McGlone SM, Bailey RR, Wateska AR, Zimmer SM, Zimmerman RK, Wagner MM. The potential economic value of a 'universal' (multi-year) influenza vaccine. Influenza and other respiratory viruses. 2012 May;6(3):167-75. doi: 10.1111/j.1750-2659.2011.00288.x. Epub 2011 Sep 21. PMID: 21933357. PMCID: PMC3253949.

M. Wagner et al., "A Decision-Theoretic Model of Disease Surveillance and Control and a Prototype Implementation for the Disease Influenza," Data Engineering Workshops (ICDEW), 2012 IEEE 28th International Conference on, Arlington, VA, 2012, pp. 49-54.
doi: 10.1109/ICDEW.2012.32

Lee BY, Stalter RM, Bacon KM, Tai JH, Bailey RR, Zimmer SM, Wagner MM. Cost-effectiveness of adjuvanted versus nonadjuvanted influenza vaccine in adult hemodialysis patients. Am J Kidney Dis. 2011 May;57(5):724-32. doi: 10.1053/j.ajkd.2010.12.016. Epub 2011 Mar 10. PMID: 21396760. PMCID: PMC3085888.

Stebbins S, Cummings DA,  Stark JH, Vukotich C, Mitruka K, Thompson W, Rinaldo C, Roth L, Wagner M, Wisniewski SR, Dato V, Eng H, Burke DS. Reduction in the incidence of Influenza A but not Influenza B associated with use of hand sanitizer and cough hygiene in schools: A randomized controlled trial. Pediatr Infect Dis J.  2011 Nov;30(11):921-6. doi: 10.1097/INF.0b013e3182218656. PubMed PMID: 21691245.  PMCID: PMC3470868.

Wu TS, Shih FY, Yen MY, Wu JS, Lu SW, Chang KC, Hsiung C, Chou JH, Chu YT, Chang H, Chiu CH, Tsui FC, Wagner MM, Su IJ, King CC. Establishing a nationwide emergency department-based syndromic surveillance system for better public health responses in Taiwan. BMC Public Health. 2008 Jan 18;8:18.  doi: 10.1186/1471-2458-8-18.  PMID: 18201388. PMCID:PMC2249581.

Tsai M-C, Tsui F-C, Wagner MM. An Evaluation of Biosurveillance Grid—Dynamic Algorithm Distribution Across Multiple Computer Nodes. AMIA Annu Symp Proc. 2007:746-750. PMID: 18693936.  PMCID:PMC2655926.

Shaffer L, Funk J, Rajala-Schultz P, Wallstrom G, Wagner MM, Saville W. Early Outbreak Detection using an Automated Data Feed of Test Orders from a Veterinary Diagnostic Laboratory.  Lecture Notes in Computer Science: Intelligence and Security Informatics: Biosurveillance, 2007; 4506: 1-10. ISSN 0302-9743 (Print); 1611-3349 (Online).

Wagner MM, Robinson JM, Tsui FC, Espino JU, Hogan WR. Design of a national retail data monitor for public health surveillance. J Am Med Inform Assoc. 2003 Sep-Oct; 10(5):409-18. Epub 2003 Jun 4. PMID: 12807802. PMCID: PMC212777.

Gesteland PH, Gardner RM, Tsui FC, Espino JU, Rolfs RT, James BC, Chapman WW, Moore AW, Wagner MM. Automated syndromic surveillance for the 2002 Winter Olympics. J Amer Med Inform Assoc. 2003, 10(6): 547-54. PMID: 12925547. PMCID: PMC264432.

 

Current Research Projects and Collaborations

University of Pittsburgh Center for Advanced Study of Informatics in Public Health (CASIPH)                                               09/01/09-08/31/14

Shyam Visweswaran, MD, PhD

Directory Listing Information
Visweswaran, Shyam
Application of artificial intelligence and machine learning to problems in the Learning Health System with a specific focus on learning electronic medical record (EMR) and computerized clinical decision support, precision medicine and personalized modeling, data mining and causal discovery from genomic and biomedical data, and enabling reuse of EMR data and research data warehousing.
Dr. Visweswaran's research interests lie in the application of artificial intelligence, machine learning, data mining and Bayesian methods to problems in clinical medicine and bioinformatics.

Associate Professor, Department of Biomedical Informatics

Associate Professor of Intelligent Systems, Clinical and Translational Science, and Computational Biology

Director of Clinical Informatics, Department of Biomedical Informatics

Director of the Data Enabled Clinical Informatics Center (DECIC)

Director of the Biomedical Informatics Core, Clinical and Translational Science Institute

Biomedical Informatics Program Director of the Medical Scientist Training Program

Biomedical Informatics Training Program Core Faculty

University of Pittsburgh School of Medicine

Publications: 

Tajgardoon M, Wagner MM, Visweswaran S, Zimmerman RK. A Novel Representation of Vaccine Efficacy Trial Datasets for Use in Computer Simulation of Vaccination Policy. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:389-398. eCollection 2018. PubMed PMID: 29888097. PMCID: PMC5961808.

King AJ, Hochheiser H, Visweswaran S, Clermont G, Cooper GF. Eye-tracking for Clinical Decision Support: A Method to Capture Automatically What Physicians Are Viewing in the EMR. AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:512-521. eCollection 2017. PMID: 28815151. PMCID: PMC5543363.

Castro SM, Tseytlin E, Medvedeva O, Mitchell K, Visweswaran S, Bekhuis T, Jacobson RS. Automated annotation and classification of BI-RADS assessment from radiology reports, J Biomed Inform. 2017 May;69:177-187. doi: 10.1016/j.jbi.2017.04.011. Epub 2017 Apr 18. PMID: 28428140. PMCID: PMC5706448.

Culbertson A, Goel S, Madden MB, Safaeinili N, Jackson KL, Carton T, Waitman R, Liu M, Krishnamurthy A, Hall L, Cappella N, Visweswaran S, Becich MJ, Applegate R, Bernstam E, Rothman R, Matheny M, Lipori G, Bian J, Hogan W, Bell D, Martin A, Grannis S, Klann J, Sutphen R, O’Hara AB, Kho A. The Building Blocks of Interoperability. A Multisite Analysis of Patient Demographic Attributes Available for Matching. Appl Clin Inform. 2017 Apr 5;8(2):322-336. doi: 10.4338/ACI-2016-11-RA-0196. PMID: 28378025.

Lustgarten JL, Balasubramanian JB, Visweswaran S, Gopalakrishnan V, Learning Parsimonious Classification Rules from Gene Expression Data Using Bayesian Networks with Local Structure. Data (Basel).  2017 Mar;2(1). pii: 5. Epub 2017 Jan 18. PMID: 28331847.  PMCID: PMC5358670.  DOI: 10.3390/data2010005.

Strobl EV, Visweswaran S. Approximate Kernel-based Conditional Independence Tests for Fast Non-Parametric Causal Discovery. 2017. arXiv:1702.03877.

Tenenbaum JD, Bhuvaneshwar K, Gagliardi JP, Fultz Hollis K, Jia P, Ma L, Nagarajan R, Rakesh G, Subbian V, Visweswaran S, Zhao Z, Rozenblit L. Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. Brief Bioinform. 2017 Nov 27. doi: 10.1093/bib/bbx157. [Epub ahead of print] PMID: 29186302

Pineda AL, Ogoe HA, Balasubramanian JB, Rangel Escareño C, Visweswaran S, Herman JG, Gopalakrishnan V. On Predicting lung cancer subtypes using 'omic' data from tumor and tumor-adjacent histologically-normal tissue. BMC Cancer. 2016 Mar 4;16:184. doi: 10.1186/s12885-016-2223-3. PMID:  26944944  PMCID:  PMC4778315  DOI: 10.1186/s12885-016-2223-3.

Hauskrecht M, Batal I, Hong C, Nguyen Q, Cooper GF, Visweswaran S, Clermont G. Outlier-based detection of unusual patient-management actions: An ICU study. Journal of Biomedical Informatics (2016) Oct 5  pii: S1532-0464(16)30135-6. doi: http://dx.doi.org/10.1016/j.jbi.2016.10.002. PMID: 27720983. PMCID: PMC5207478.

Ogoe, HA, Visweswaran, S, Lu, X, Gopalakrishnan, V.  (2015) Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data.  BMC Bioinformatics 16:226 (designated as a Highly Accessed paper) PMID: 26202217 PMCID: PMC4512094

Visweswaran S, Ferreira A, Cooper GF. Personalized modeling for prediction with decision-path models. PLoS One. 2015 Jun 22;10(6):e0131022 PMID: 26098570 PMCID: PMC4476684.

López Pineda A, Ye Y, Visweswaran S, Cooper GF, Wagner MM, Tsui FR. Comparison of Machine Learning Classifiers for Influenza Detection from Emergency Department Free-text Reports. J Biomed Inform. 2015 Dec;58:60-69. doi: 10.1016/j.jbi.2015.08.019. Epub 2015 Sep 16. PMID: 26385375. PMCID: PMC4684714.

Eric Strobl, Shyam Visweswaran. Markov boundary discovery with ridge regularized linear models. Journal of Causal Inference. ISSN (Online) 2193-3685, ISSN (Print) 2193-3677, DOI: 10.1515/jci-2015-0011, November 2015

King AJ, Cooper GF, Hochheiser H, Clermont G. Development and preliminary evaluation of a prototype of a learning electronic medical record system. AMIA Annu Symp Proc. 2015 Nov 5;2015:1967-75. eCollection 2015. PMID: 26958296 PMCID: PMC4765593.

Balasubramanian JB, Cooper GF, Visweswaran SGopalakrishnan V. Selective Model Averaging with Bayesian Rule Learning for Predictive Biomedicine. Proceedings of the AMIA 2014 Joint Summits in Translational Science (In Press); April 2014; San Francisco, CA, USA2014.

Stokes ME, Barmada MM, Kamboh MI, Visweswaran S. The application of network label propagation to rank biomarkers in genome-wide Alzheimer's data. BMC Genomics. 2014 Apr 14;15(1):282. PMID: 24731236

Bhavnani SK, Dang B, Caro M, Bellala G, Visweswaran S, Asuncion M, Divekar R. Heterogeneity within and across pediatric pulmonary infections: From bipartite networks to at-risk subphenotypes. In: Proceedings of the 2014 AMIA Summit on Translational Bioinformatics (Apr 2014).

Aflakparast M, Salimi H, Gerami A, Dubé M-P, Visweswaran S, Masoudi-Nejad A. Cuckoo search epistasis: A new method for exploring significant genetic interactions. Heredity, 2014 Feb 19; doi: 10.1038/hdy.2014.4. PMID: 24549111

Pineda AL, Tsui FC, Visweswaran S, Cooper GF. (2013). Detection of Patients with Influenza Syndrome Using Machine-Learning Models Learned from Emergency Department Reports. Online Journal of Public Health Informatics, 5(1), e41.

Kalamangalam GP, Pestana Knight EM, Visweswaran S, Gupta A. Noninvasive predictors of subdural grid seizure localization in children with nonlesional focal epilepsy. Journal of Clinical Neurophysiology. 2013 Feb;30(1):45-50. PMID: 23377441

Strobl EV, Visweswaran S. Deep multiple kernel learning. In: Proceedings of the 12th International Conference on Machine Learning and Applications (ICMLA'13), Miami, FL. (Dec 2013).

Sverchkov Y, Visweswaran S, Clermont G, Hauskrecht M, Cooper GF. A multivariate probabilistic method for comparing two clinical datasets. In: Proceedings of the ACM International Health Informatics Symposium (2012) 795-800.

Jiang X, Neapolitan RE, Barmada M, Visweswaran S, Cooper GF. A fast algorithm for learning epistatic genomic relationships. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2010) 341-345. PMID: 21346997. PMC3041370.

Harry Hochheiser, PhD

Directory Listing Information
Hochheiser, Harry
Dr. Hochheiser’s research focuses on the design of usable systems for use in clinical and research settings. He is particularly interested in using user-centered design techniques to inform the design of highly-interactive information visualization systems for the interpretation of complex data sets in domains such as bioinformatics and health care. Dr. Hochheiser is currently working on the development of user-centered tools for annotating, searching, and browsing of biomedical data in online repositories. As part of the FaceBase (www.facebase.org) project, he is working on the design, implementation, and evaluation of highly-interactive tools for exploring genomic, genetic, demographic, and phenotypic data sets from craniofacial research, with ultimate goal of developing tools and techniques that can be applied to a other domains.
Dr. Hochheiser’s research focuses on the design of usable systems for use in clinical and research settings. His other interests include universal usability, security, privacy, and public policy implications of computing systems.
Associate Professor, Department of Biomedical Informatics
Associate Professor in the Intelligent Systems Program
Director, Biomedical Informatics Training Program
University of Pittsburgh School of Medicine
Publications: 

Markham H, Hochheiser H, Kuntoro K, Notobroto HB. Exploring Midwives' Need and Intention to Adopt Electronic Integrated Antenatal Care. Perspect Health Inf Manag. 2018 Jan 1;15(Winter):1e. eCollection 2018 Winter. PMID: 29618961. PMCID: PMC5869442.

Trivedi G, Pham P, Chapman WW, Hwa R, Wiebe J, Hochheiser H. NLPReViz: an interactive tool for natural language processing on clinical text. J Am Med Inform Assoc. 2017 Jul 22. doi: 10.1093/jamia/ocx070. [Epub ahead of print] PMID: 29016825.

King AJ, Hochheiser H, Visweswaran S, Clermont G, Cooper GF. Eye-tracking for Clinical Decision Support: A Method to Capture Automatically What Physicians Are Viewing in the EMR. AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:512-521. eCollection 2017. PMID: 28815151. PMCID: PMC5543363.

Calvitti A, Hochheiser H, Ashfaq S, Bell K, Chen Y, El Kareh R, Gabuzda MT, Liu L, Mortensen S, Pandey B, Rick S, Street RL, Weibel N, Weir C, Agha Z. Physician activity during outpatient visits and subjective workload. J. Biomed. Inf. 2017 May;69:135-149. doi: 10.1016/j.jbi.2017.03.011. Epub 2017 Mar 18. PubMed PMID: 28323144.

Savova GK, Tseytlin E, Finan S, Castine M, Miller T, Medvedeva O, Harris D, Hochheiser H, Lin C, Chavan G, Jacobson RS. DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records. Cancer Res. 2017 Nov 1;77(21):e115-e118. doi: 10.1158/0008-5472.CAN-17-0615. PMID: 29092954. PMCID: PMC5690492 [Available on 2018-11-01].

Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobson JOB, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. The Monarch Initiative: An Integrative Data and Analytic Platform Connecting Phenotypes to Genotypes across Species. Nucleic Acids Res. 2017 Jan 4;45(D1):D712-D722. doi: 10.1093/nar/gkw1128. Epub 2016 Nov 29. PubMed PMID: 27899636. PubMed Central PMCID: PMC5210586.

Hochheiser H, Castine M, Harris D, Savova G, Jacobson RS.  An information model for computable cancer phenotypes. BMC Medical Informatics and Decision Making. Sept. 2016: 1-15. doi=10.1186/s12911-016-0358-4.

Fisher A. Ding M, Hochheiser H, Douglas G. (2016) Measuring time utilization of pharmacists in the Birmingham Free Clinic dispensary. BMC Health Services Research 16(1-7) DOI: 10.1186/s12913-016-17.

McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA. Navigating the Phenotype Frontier: The Monarch Initiative. Genetics. 2016 Aug;203(4):1491-5. PMID: 27516611 PMCID: PMC4981258.

Lazar J, Abascal J, Barbosa S, Barksdale J, Friedman B, Grossklags J, Gulliksen J, Johnson J, McEwan T, Martínez-Normand L, Michalk W, Tsai J, van der Veer G, von Axelson H, Walldius A, Whitney G, Winckler M, Wulf V, Churchill EF, Cranor L, Davis J, Hedge A, Hochheiser H, Hourcade JP, Lewis C, Nathan L, Paterno F, Reid B, Quesenbery W, Selker T, Wentz B. (2016), "Human–Computer Interaction and International Public Policymaking: A Framework for Understanding and Taking Future Actions", Foundations and Trends® Human–Computer Interaction: Vol. 9: No. 2, pp 69-149. http://dx.doi.org/10.1561/1100000062.

Hochheiser H, Ning Y, Hernandez A, Horn, JR, Jacobson R, Boyce RD. Using Nonexperts for Annotating Pharmacokinetic Drug-Drug Interaction Mentions in Product Labeling: A Feasibility Study. JMIR Res Protoc. 2016 Apr 11;5(2):e40. doi: 10.2196/resprot.5028. PMID: 27066806 PMCID: PMC4844909.

Romagnoli KM, Boyce RD, Empey PE, Adams S, Hochheiser H. Bringing clinical pharmacogenomics information to pharmacists: A qualitative study of information needs and resource requirements. Int J Med Inform. 2016 Feb;86:54-61. doi: 10.1016/j.ijmedinf.2015.11.015. Epub 2015 Nov 30. PMID: 26725696. PMCID: PMC4720137.

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team. The Center for causal discovery of biomedical knowledge from Big Data. J Am Med Inform Assoc. 2015 Nov;22(6): 1132-6. doi: 10.1093/jamia/ocv059. Epub 2015 Jul 2.  PMID: 26138794. PMCID: PMC5009908.

Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, … Smedley D. (2015). Disease insights through cross-species phenotype comparisons. Mammalian Genome, 26(9-10), 548–555. http://doi.org/10.1007/s00335-015-9577-8  PMID: 26092691  PMCID: PMC4602072

Landis-Lewis Z, Douglas GP, Hochheiser H, Kam M, Gadabu O, Bwanali M, Jacobson RS. (2015). Computer-Supported Feedback Message Tailoring for Healthcare Providers in Malawi: Proof-of-Concept. AMIA Annual Symposium Proceedings, 2015, 814–823.

King AJ, Cooper GF, Hochheiser H, Clermont G. Development and preliminary evaluation of a prototype of a learning electronic medical record system. AMIA Annu Symp Proc. 2015 Nov 5;2015:1967-75. eCollection 2015. PMID: 26958296 PMCID: PMC4765593.

Strange C, Senior RM, Sciurba F, O'Neal S, Morris A, Wisniewski SR, Bowler R, Hochheiser HSBecich MJ, Zhang Y, Leader JK, Methé BA, Kaminski N, Sandhaus RA; GRADS Alpha-1 Study Group. Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study. Alpha-1 Protocol.  Ann Am Thorac Soc. 2015 Oct; 12(10): 1551-60. doi: 10.1513/AnnalsATS.201503-143OC. PMID: 26153726. PMCID: PMC4627425.

Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K., Hochheiser H, Robinson PN, Lewis SE and Haendel MA. (2015), Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. Human Mutation, 36: 979–984. doi:10.1002/humu.22857  PMID:  26269093

Landis-Lewis Z, Brehaut JC, Hochheiser H, Douglas GP, Jacobson RS. (2015). Computer-supported feedback message tailoring: theory-informed adaptation of clinical audit and feedback for learning and behavior change. Implementation Science, 10(1), 1.

Borromeo CD, Schleyer TK, Becich MJ, Hochheiser H.  Finding Collaborators: Toward Interactive Discovery Tools for Research Network Systems. J Med Internet Res 2014;16(11):e244 DOI: 10.2196/jmir.3444 PMID: 25370463

Ayvaz S, Zhu Q, Hochheiser H, Brochhausen M, Horn J, Dumontier M, … Boyce RD. (2014). Drug-Drug Interaction Data Source Survey and Linking. AMIA Summits on Translational Science Proceedings, 2014, 16. PMID: 25717393 PMCID: PMC4333686

Ligons FM, Mello-Thoms C, Handler SM, Romagnoli KM, Hochheiser H. (2014). Assessing the impact of cognitive impairment on the usability of an electronic medication delivery unit in an assisted living population. International Journal of Medical Informatics, 83(11), 841–848. http://doi.org/10.1016/j.ijmedinf.2014.07.004 PMID: 25153770 PMCID: PMC4268135

Wentz B, Hochheiser H, Lazar J. 2013. A survey of blind users on the usability of email applications. Univers. Access Inf. Soc. 12, 3 (August 2013), 327-336. DOI=http://dx.doi.org/10.1007/s10209-012-0285-9

Romagnoli KM, Handler SM, Ligons FM, Hochheiser H. Home-care nurses’ perceptions of unmet information needs and communication difficulties of older patients in the immediate post-hospital discharge period. BMJ quality & safety. 2013 Apr; 22 (4):324-32. PMCID: PMC3694324. PMID: 23362507.

Lazar J, Hochheiser H. Legal Aspects of Interface Accessibility in the U.S. Communications of the ACM. 2013 Dec; 56 (12):74-80.

Brinkley, J. F., Borromeo, C., Clarkson, M., Cox, T. C., Cunningham, M. J., Detwiler, L. T., … Shapiro, L. G. (2013). The Ontology of Craniofacial Development and Malformation for translational craniofacial research. American Journal of Medical Genetics. Part C, Seminars in Medical Genetics, 0(4), 232–245. http://doi.org/10.1002/ajmg.c.31377 PMID: 24124010 PMCID: PMC4041627

Handler SM, Boyce RD, Ligons FM, Perera S, Nace DA, Hochheiser H. Use and Perceived Benefits of Mobile Devices by Physicians in Preventing Adverse Drug Events in the Nursing Home. Journal of The American Medical Directors Association. 2013 Oct 2. PMID: 24094901.

Hochheiser H, Shneiderman B. From Bowling Alone to Tweeting Together: Technology- Mediated Social Participation. interactions. 2010; 17(2):64-67. (Invited)

Lazar J, Feng J,Hochheiser H. Research Methods in Human-Computer Interaction. London: Wiley; 2010.

Primary Appointment: 
Assistant Professor, Department of Biomedical Informatics
Assistant Professor in the Intelligent Systems Program
Associate Director, Biomedical Informatics Training Program
University of Pittsburgh School of Medicine
Peer-reviewed Publications: 
43

Vanathi Gopalakrishnan, PhD

Directory Listing Information
Gopalakrishnan, Vanathi
Design and development of computational methods for solving clinically relevant biological problems, application of machine learning and data mining techniques to the analysis of proteomic data, prediction of protein sequence-structure-function relationships, and biomarker discovery from genotype-phenotype studies.
Dr. Gopalakrishnan is interested in the design and development of computational methods for solving clinically relevant biological problems.
Associate Professor of Biomedical Informatics
Associate Professor of Intelligent Systems
Associate Professor of Computational and Systems Biology
Director, PRoBE Laboratory for Pattern Recognition from Biomedical Evidence
Core Faculty Member, Biomedical Informatics Training Program
Faculty Member, Intelligent Systems Program
Faculty Member, Joint CMU-Pitt Program in Computational Biology
Faculty Member, Medical Scientist Training Program
Faculty Member, Cardiovascular Bioengineering Training Program
Co-Director of Bioengineering, Biotechnology and Innovation (BBI) Area of Concentration, School of Medicine (About)
 
Publications: 

Ceschin R, Zahner A, Reynolds W, Gaesser J, Zuccoli G, Lo CW, Gopalakrishnan V, Panigrahy A. A computational framework for the detection of subcortical brain dysmaturation in neonatal MRI using 3D Convolutional Neural Networks. Neuroimage. 2018 Sep;178:183-197. doi: 10.1016/j.neuroimage.2018.05.049. Epub 2018 May 21. PMID: 29793060.

Balasubramanian JB, Gopalakrishnan V. Tunable structure priors for Bayesian rule learning for knowledge integrated biomarker discovery. World J Clin Oncol. 2018 Sep 14;9(5): 89-109. doi: 10.5306/wjco.v9.i5.98.

Lustgarten JL, Balasubramanian JB, Visweswaran S, Gopalakrishnan V, Learning Parsimonious Classification Rules from Gene Expression Data Using Bayesian Networks with Local Structure. Data (Basel).  2017 Mar;2(1). pii: 5. Epub 2017 Jan 18. PMID: 28331847.  PMCID: PMC5358670.  DOI: 10.3390/data2010005.

Liu Y, Gopalakrishnan V. An Overview and Evaluation of Recent Machine Learning Imputation Methods Using Cardiac Imaging Data. Data 2017, 2(1), 8; doi: 10.3390/data2010008.

Pineda AL, Ogoe HA, Balasubramanian JB, Rangel Escareño C, Visweswaran S, Herman JG, Gopalakrishnan V. On Predicting lung cancer subtypes using 'omic' data from tumor and tumor-adjacent histologically-normal tissue. BMC Cancer. 2016 Mar 4;16:184. doi: 10.1186/s12885-016-2223-3. PMID:  26944944  PMCID:  PMC4778315  DOI: 10.1186/s12885-016-2223-3.

Torbati ME, Mitreva M, Gopalakrishnan V. Application of Taxonomic Modeling to Microbiota Data Mining for Detection of Helminth Infection in Global Populations.  2016 Dec;1(3). pii: 19. doi: 10.3390/data1030019. Epub 2016 Dec 13.    PMID: 28239609  PMCID: PMC5325162  DOI: 10.3390/data1030019
 
Gopalakrishnan V, Menon PG, Madan S., cMRI-BED: A novel informatics framework for cardiac MRI biomarker extraction and discovery applied to pediatric cardiomyopathy classification. Biomed Eng Online. 2015;14 Suppl 2:S7. doi: 10.1186/1475-925X-14-S2-S7. Epub 2015 Aug 13. PMID: 26329721 PMCID: PMC4547147 DOI: 10.1186/1475-925X-14-S2-S7
 

Ogoe, HA, Visweswaran, S, Lu, X, Gopalakrishnan, V.  (2015) Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data.  BMC Bioinformatics 16:226 (designated as a Highly Accessed paper) PMID: 26202217 PMCID: PMC4512094

Pineda, AL, Gopalakrishnan, V. Novel Application of Junction Trees to the Interpretation of Epigenetic Differences among Lung Cancer Subtypes. Proceedings of the AMIA Translational Bioinformatics Summit. March 21-23, 2015. PMID: 26306226   Winner of the Marco Ramoni Distinguished Paper Award.

R. Ceschin, A. Panigrahy, and V. Gopalakrishnan, “Sfdm: Open-source software for temporal analysis and visualization of brain tumor diffusion mr using serial functional diffusion mapping,” Cancer Inform., vol. 14, pp. 1–9, 2015. PMID: 25673970 PMCID: PMC4315050 DOI: 10.4137/CIN.S17293

Balasubramanian JB, Cooper GF, Visweswaran SGopalakrishnan V. Selective Model Averaging with Bayesian Rule Learning for Predictive Biomedicine. Proceedings of the AMIA 2014 Joint Summits in Translational Science (In Press); April 2014; San Francisco, CA, USA2014.

Menon PG, Morris L, Staines M, Lima J, Lee DC, Gopalakrishnan V. Novel MRI-derived quantitative biomarker for cardiac function applied to classifying ischemic cardiomyopathy within a Bayesian rule learning framework. Proceedings of the SPIE Medical Imaging 2014; February 15-20, 2014; San Diego, CA, USA. 2014.

Dutta-Moscato J, Gopalakrishnan V, Lotze MT, Becich MJ. Creating a Pipeline of Talent for Informatics: STEM Initiative for High School Students in Computer Science, Biology and Biomedical Informatics (CoSBBI). Journal of Pathology Informatics. 2014; In Press. PMC In Process.

McMillan A, Visweswaran S, Gopalakrishnan V. Machine Learning for Biomarker-based Classification of Alzheimer's Disease Progression Journal of Pathology Informatics. 2014; In Press.

Staines M, Morris L, Menon PG, Lima J, Lee DC, Gopalakrishnan V. Discovering Biomarkers for Cardiovascular Disease Using Rule Learning. Journal of Pathology Informatics. 2014; In Press.

Floudas, C. S., Balasubramanian, J, Romkes, M., Gopalakrishnan, V. An empirical workflow for genome-wide single nucleotide polymorphism-based predictive modeling. In the Proceedings of the AMIA Translational Bioinformatics Summit 2013, March 18-20, San Francisco, CA.

Grover H, Wallstrom G, Wu CC, Gopalakrishnan V. Context-Sensitive Markov Models for Peptide Scoring and Identification from Tandem Mass Spectrometry. Omics : a journal of integrative biology. 2013 Feb;17(2):94-105. doi: 10.1089/omi.2012.0073. Epub 2013 Jan 5 PMID: 23289783 PMCID: PMC3567622 [Available on 2014/2/1]

Bigbee, W. L*., Gopalakrishnan, V*, Weissfeld J, L., Wilson, D. O., Dacic, S. Lokshin, A. E., Siegfried, J. M.  A Multiplexed Serum Biomarker Immunoassay Panel Discriminates Clinical Lung Cancer Patients from High-Risk Individuals Found to be Cancer-Free by CT Screening. J Thorac Oncol. 2012 Apr;7(4):698-708. (*These authors contributed equally to the study). PMID: 22425918 PMCID: PMC3308353

Liu, G., Kong, L., Gopalakrishnan, V. A Partitioning Based Adaptive Method for Robust Removal of Irrelevant Features from High-dimensional Biomedical Datasets. In Proceedings of the 2012 AMIA Summit on Translational Bioinformatics. San Francisco, March 19-23, 2012. Pages 52-61. PMCID: PMC3392052

Grover, H., Gopalakrishnan, V. Efficient Processing of Models for Large-scale Shotgun Proteomics Data. In Proceedings of the International Workshop on Collaborative Big Data (C-Big 2012), Pittsburgh, PA, October 14, 2012.

Zeng X, Hood BL, Zhao T, Conrads TP, Sun M, Gopalakrishnan V, Grover H, Day RS, Weissfeld JL, Siegfried JM, Bigbee WL. Lung Cancer Serum Biomarker Discovery Using Label Free Liquid Chromatography-Tandem Mass Spectrometry. J Thorac Oncol. 2011 Apr;6(4):725-34. PMCID:PMC3104087.

Ganchev, P., Malehorn, D., Bigbee, W. L., Gopalakrishnan, V. Transfer Learning of Classification Rules for Biomarker Discovery and Verification from Molecular Profiling Studies. J Biomed Inform. 2011 Dec;44 Suppl 1:S17-23. Epub 2011 May 6. (Won a Distinguished Paper Award at AMIA 2011 - Translational Bioinformatics) PMID: 21571094

Li, X., LeBlanc, J., Truong, A., Vuthoori, R., Chen, S. S., Lustgarten, J. L., Roth, B., Allard, J., Andrew Ippoliti, A., Presley, L.L., Borneman, J., Bigbee, W.L., Gopalakrishnan, V., Graeber, T.G., Elashoff, D., Braun, J., Goodglick, L. A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface. 2011. PLoS ONE 6(11): e26542. PMCID:PMC3221670

Ryberg, H., An, J., Darko, S, Lustgarten, J.L., Jaffa, M.,  Gopalakrishnan, V.,  Lacomis, D, Cudkowicz, M, E., Bowser, R. Discovery and Verification of Amyotrophic Lateral Sclerosis Biomarkers by Proteomics. Muscle & nerve. 2010;42(1):104-11. PMID: 20583124

Madhavi Ganapathiraju, PhD

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Ganapathiraju, Madhavi
Translational Systems Biology, protein-protein Interaction Prediction, machine learning, and Genome Sequence Analysis.
Assistant Professor whose current research focus is in the area of computational molecular and systems biology, translational bioinformatics and biomedical text mining, using signal processing and machine learning.
Associate Professor, Department of Biomedical Informatics
Associate Professor, Intelligent Systems, Intelligent Systems Program
Associate Professor, Computational Biology, Department of Computational Biology
University of Pittsburgh School of Medicine
Publications: 

Chattopadhyay A, Ganapathiraju MK. Demonstration Study: A Protocol to Combine Online Tools and Databases for Identifying Potentially Repurposable Drugs. Data 2017, 2, 15.

Liu X, Yagi H, Saeed S, Bais AS, Gabriel GC, Chen Z, Peterson KA, Li Y, Schwartz MC, Reynolds WT, Saydmohammed M, Gibbs B, Wu Y, Devine W, Chatterjee B, Klena NT, Kostka D, de Mesy Bentley KL, Ganapathiraju MK, Dexheimer P, Leatherbury L, Khalifa O, Bhagat A, Zahid M, Pu W, Watkins S, Grossfeld P, Murray SA, Porter GA Jr, Tsang M, Martin LJ, Benson DW, Aronow BJ, Lo CW. The complex genetics of hypoplastic left heart syndrome. Nat Genet. 2017 Jul;49(7):1152-1159. doi: 10.1038/ng.3870. Epub 2017 May 22. PMID: 28530678.

Malavia TA, Chaparala S, Wood J, Chowdari K, Prasad KM, McClain L, Jegga AG, Ganapathiraju MK, Nimgaonkar VL. Generating Testable Hypotheses for Schizophrenia and Rheumatoid Arthritis Pathogenesis by Integrating Epidemiological, Genomic and Protein Interaction Data. NPJ Schizophr. Feb 24;3:11. doi: 10.1038/s41537-017-0010-z. eCollection 2017. PMID: 28560257. PMCID: PMC5441529.

Ganapathiraju MK, Thahir M, Handen A, Sarkar SN, Sweet RA, Nimgaonkar VL, Loscher CE, Bauer EM, Chaparala S: Schizophrenia interactome with 504 novel protein–protein interactions. Npj Schizophrenia 2016, 2:16012. Link to Publication


Li Y, Klena NT, Gabriel GC, Liu X, Kim AJ, Lemke K, Chen Y, Chatterjee B, Devine W, Damerla RR, Chang C, Yagi H, San Agustin JT, Thahir M, Anderton S, Lawhead C, Vescovi A, Pratt H, Morgan J, Haynes L, Smith CL, Eppig JT, Reinholdt L, Francis R, Leatherbury L, Ganapathiraju MK, Tobita K, Pazour GJ, Lo CW. Global genetic analysis in mice unveils central role for cilia in congenital heart disease. Nature. 2015 Mar 25. doi: 10.1038/nature14269. [Epub ahead of print] PubMed PMID: 25807483.

Handen A, Ganapthiraju MK. LENS: web-based lens for enrichment and network studies of human proteins. BMC Medical Genomics. 2015;8(Suppl 4):S2. doi:10.1186/1755-8794-8-S4-S2.
 
Roth A, Subramanian S, Ganapathiraju MK. Towards extracting supporting information about predicted protein-protein interactions. IEEE/ACM Trans Comput Biol Bioinform. 2015 Dec 7. [Epub ahead of print] PubMed PMID: 26672046.
 

A. Gupta, H. Wang and M. Ganapathiraju, "Learning structure in gene expression data using deep architectures, with an application to gene clustering," Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on, Washington, DC, 2015, pp. 1328-1335. doi: 10.1109/BIBM.2015.7359871

Jianzhong Zhu, Yugen Zhang, Arundhati Ghosh, Rolando A. Cuevas, Adriana Forero, Jayeeta Dhar, Mikkel Søes Ibsen, Jonathan Leo Schmid-Burgk, Tobias Schmidt, Madhavi K. Ganapathiraju, Takashi Fujita, Rune Hartmann, Sailen Barik, Veit Hornung, Carolyn B. Coyne, Saumendra N. Sarkar. Antiviral Activity of Human OASL Protein Is Mediated by Enhancing Signaling of the RIG-I RNA Sensor. Immunity. 2014 June 19; 40(6): 936–948.

Kuppuswamy U, Ananthasubramanian S, Wang Y, Balakrishnan N, Ganapathiraju MK. Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions. Algorithms Mol Biol. 2014 Apr 3;9(1):10. doi: 10.1186/1748-7188-9-10. PMID: 24708602

Ganapathiraju MK, Orii N. Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics. Gigascience. 2013 Aug 30;2(1):11. doi: 10.1186/2047-217X-2-11. PMID: 24001106

Giorgio E, Rolyan H, Kropp L, Chakka AB, Yatsenko S, Gregorio ED, Lacerenza D, Vaula G, Talarico F, Mandich P, Toro C, Pierre EE, Labauge P, Capellari S, Cortelli P, Vairo FP, Miguel D, Stubbolo D, Marques LC, Gahl W, Boespflug-Tanguy O, Melberg A, Hassin-Baer S, Cohen OS, Pjontek R, Grau A, Klopstock T, Fogel B, Meijer I, Rouleau G, Bouchard JP, Ganapathiraju M, Vanderver A, Dahl N, Hobson G, Brusco A, Brussino A, Padiath QS. Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression. Human mutation. 2013 May 3. PMID:23649844.

Thahir M, Sharma T, Ganapathiraju MK. An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction. BMC Proceedings 2012, 6(Suppl 7):S2.

Osmanbeyoglu HU, Ganapathiraju MK. N-gram analysis of 970 microbial organisms reveals presence of biological language models. BMC Bioinformatics. 2011; 12 (1):12. PMCID: PMC3027111. PMID: 21219653.

Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK. Active machine learning for transmembrane helix prediction. BMC Bioinformatics. 2010; 11:S58. PMCID: PMC3009531. PMID: 20122233.

Roger S. Day, ScD

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Day, Roger S.
Day leads the Educational Resource for Tumor Heterogeneity, and continues the evolution of the Oncology Thinking Cap computer modeling facility. These projects use stochastic models of tumor growth to help cancer researchers do thought experiments about cancer biology and treatment, with the goal of improving translational research resources. Interpreting dose information from disease-free survival curves in adjuvant breast cancer treatment; tracking genetic evolution of breast cancers through molecular studies of individual cells in tumor cell samples and through modeling. Statistical modeling of events and effects in biology and medicine, development of methods more effective than the usual linear modeling.
Associate Professor Day leads development of the Oncology Thinking Cap computer modeling facility, which uses stochastic models of tumor growth to help researchers do thought experiments about cancer biology and treatment.
Room 532
5607 Baum Boulevard
Pittsburgh, PA 15206
412-624-3253
412-624-5310
Associate Professor
Department of Biomedical Informatics
University of Pittsburgh School of Medicine
Publications: 

Day RS. Want a letter? You write it for me. Science. 2016 Jan 8;351(6269):198. PMID: 26744407 DOI: 10.1126/science.351.6269.198

Archer KJ, Dobbin K, Biswas S, Day RS, Wheeler DC, Wu H. (2015). Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes. Cancer Informatics, 14 (Suppl 2), 247–251. PMID: 26380548. PMCID: PMC4559198. DOI: 10.4137/CIN.S32525.

Day RS. What Tumor Dynamics Modeling Can Teach us About Exploiting the Stem-Cell View for Better Cancer Treatment. Cancer Informatics. 2015 Feb 24;14(Suppl 2):25-36. doi: 10.4137/CIN.S17294. eCollection 2015. PMID: 25780337PMCID: PMC434585.

McDade KK, Chandran U, Day RSImproving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Inform. 2015 Dec 16;14:149-61. doi: 10.4137/CIN.S33076. eCollection 2015. PMID: 26715829. PMCID: PMC4686346.

Day RS, McDade KK. (2013). A decision theory paradigm for evaluating identifier mapping and filtering methods using data integration. BMC Bioinformatics, 14, 223.  PMID: 23855655 PMCID: PMC3734162 DOI: 10.1186/1471-2105-14-223

Risinger JI, Allard J, Chandran U, Day R, Chandramouli GV, Miller C, Zahn C, Oliver J, Litzi T, Marcus C, Dubil E, Byrd K, Cassablanca Y, Becich M, Berchuck A, Darcy KM, Hamilton CA, Conrads TP, Maxwell GL. Gene expression analysis of early stage endometrial cancers reveals unique transcripts associated with grade and histology but not depth of invasion. Front Oncol. 2013 Jun 17;3:139. doi: 10.3389/fonc.2013.00139. Print 2013. PMID: 23785665. PMCID: PMC3683664.

Day RS, McDade K, Grover H, Luthra S, Chandran U, Lisovich A. Bioinformatic Data Integration to Assess Data Preprocessing. In: Proceedings of the AMIA Joint Summit on Translational Science; 2012 Mar 19-21; San Francisco, CA.

Buch SC, Diergaarde B, Nukui T, Day RS, Siegfried JM, Romkes M, Weissfeld JL. (2012). Genetic variability in DNA repair and cell cycle control pathway genes and risk of smoking-related lung cancer. Molecular Carcinogenesis, 51 (Suppl 1), E11–E20.  PMID: 21976407 PMCID: PMC3289753 DOI: 10.1002/mc.20858.

Day RS, McDade KK, Chandran UR, Lisovich A, Conrads TP, Hood BL, Kolli VS, Kirchner D, Litzi T, Maxwell GL. Identifier mapping performance for integrating transcriptomics and proteomics experimental results. BMC Bioinformatics. 2011 May 27;12:213. http://doi.org/10.1186/1471-2105-12-213. PMID: 21619611 PMCID: PMC3124437

Zeng X, Hood BL, Zhao T, Conrads TP, Sun M, Gopalakrishnan V, Grover H, Day RS, Weissfeld JL, Siegfried JM, Bigbee WL. Lung Cancer Serum Biomarker Discovery Using Label Free Liquid Chromatography-Tandem Mass Spectrometry. J Thorac Oncol. 2011 Apr;6(4):725-34. PMCID:PMC3104087.

Wang M, Day RS.  Adaptive Bayesian design for phase I dose-finding trials using a joint model of response and toxicity.   2010 Jan.  J Bioppharm Stat. 20(1), 125-44.

Gregory Cooper, MD, PhD

Directory Listing Information
Cooper, Gregory F.
Dr. Cooper’s research interest is in application of decision theory, probability theory, and artificial intelligence to address biomedical informatics research questions, with a focus on causal modeling and discovery in medicine and biology, data mining of medical databases, application of Bayesian statistics in medicine, and biosurveillance.
Dr. Cooper is the Vice chair of the Department of Biomedical Informatics and Professor of Biomedical Informatics, Computational Biology, Computer Science, Information Science, and Intelligent Systems.
Professor, Department of Biomedical Informatics and of Intelligent Systems
Vice Chairman, Department of Biomedical Informatics
University of Pittsburgh School of Medicine
Publications: 

King AJ, Hochheiser H, Visweswaran S, Clermont G, Cooper GF. Eye-tracking for Clinical Decision Support: A Method to Capture Automatically What Physicians Are Viewing in the EMR. AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:512-521. eCollection 2017. PMID: 28815151. PMCID: PMC5543363.

Ferraro JP, Ye Y, Gesteland PH, Haug PJ, Tsui F-C, Cooper GF, Van Bree R, Ginter T, Nowalk AJ, Wagner MM. The effects of natural language processing on cross-institutional portability of influenza case detection for disease surveillance. Appl Clin Inform. 2017 May 31;8(2):560-580. doi:10.4338/ACI-2016-12-RA-0211. PubMed PMID: 28561130.

Ye Y, Wagner MM, Cooper GF, Ferraro JP, Su H, Gesteland PH, Haug PJ, Millett NE, Aronis JM, Nowalk AJ, Ruiz VM, López Pineda A, Shi L, Van Bree R, Ginter T, Tsui F. A study of the transferability of influenza case detection systems between two large healthcare systems. PLoS One. 2017 Apr 5;12(4):e0174970. doi: 10.1371/journal.pone.0174970. eCollection 2017. PMID: 28380048 PMCID: PMC5381795

Ding MQ, Chen L, Cooper GF, Young JD, Lu X. Precision Oncology Beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics. Mol Cancer Res. 2017 Nov 13. pii: molcanres.0378.2017. doi: 10.1158/1541-7786.MCR-17-0378. [Epub ahead of print] PMID: 29133589

Tsui F, Ye Y, Ruiz V, Cooper GF, Wagner MM. Automated influenza case detection for public health surveillance and clinical diagnosis using dynamic influenza prevalence method. J Public Health (Oxf). 2017 Oct 20:1-8. doi: 10.1093/pubmed/fdx141. [Epub ahead of print]. PMID: 29059331.

Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer Res. 206 Dec 1:76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. Epub 2016 Oct 10. PMID: 27758891. PMCID: PMC5165695.

Naeini Pakdaman M, Cooper GF. Binary classifier calibration using an ensemble of linear trend estimation. In: Proceedings of the 2016 SIAM International Conference on Data Mining (2016) May;2016:261-269. doi: 10:1137/1.9781611974348.30.  PMID: 28357159 PMCID: PMC5367639

Hill SM, et al. Inferring causal molecular networks: Empirical assessment through a community-based effort. Nature Methods (2016) Apr; 13(4):310-318. doi: 10.1038/nmeth.3773. PMID: 26901648 PMCID: PMC4854847

Naeini Pakdaman M, Cooper GF. Binary classifier calibration using an ensemble of near isotonic regression models. In: Proceedings of the IEEE International Conference on Data Mining (2016) Dec;2016:360-369.  doi: 10.1109/ICDM.2016.0047  PMID: 28316511 PMCID: PMC5351887

Hauskrecht M, Batal I, Hong C, Nguyen Q, Cooper GF, Visweswaran S, Clermont G. Outlier-based detection of unusual patient-management actions: An ICU study. Journal of Biomedical Informatics (2016) Oct 5  pii: S1532-0464(16)30135-6. doi: http://dx.doi.org/10.1016/j.jbi.2016.10.002. PMID: 27720983. PMCID: PMC5207478.

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team. The Center for causal discovery of biomedical knowledge from Big Data. J Am Med Inform Assoc. 2015 Nov;22(6): 1132-6. doi: 10.1093/jamia/ocv059. Epub 2015 Jul 2.  PMID: 26138794. PMCID: PMC5009908.

Visweswaran S, Ferreira A, Cooper GF. Personalized modeling for prediction with decision-path models. PLoS One. 2015 Jun 22;10(6):e0131022 PMID: 26098570 PMCID: PMC4476684.

Cooper GF, Villamarin R, Rich Tsui FC, Millett N, Espino JU, Wagner MM. A method for detecting and characterizing outbreaks of infectious disease from clinical reports. J Biomed Inform. 2015 Feb; 53:15-26.  doi: 10.1016/j.jbi.2014.08.011. Epub 2014 Aug 30.  PMID: 25181466. PMCID: PMC4441330.

López Pineda A, Ye Y, Visweswaran S, Cooper GF, Wagner MM, Tsui FR. Comparison of Machine Learning Classifiers for Influenza Detection from Emergency Department Free-text Reports. J Biomed Inform. 2015 Dec;58:60-69. doi: 10.1016/j.jbi.2015.08.019. Epub 2015 Sep 16. PMID: 26385375. PMCID: PMC4684714.

Sverchkov Y, Cooper GF. A Bayesian approach for identifying multivariate differences between groups. In: Proceedings of the International Symposium on Intelligent Data Analysis (2015). Adv Intell Data Anal. 2015 Oct;9385:275-285. Epub 2015 Nov 22.  PMCID: 27069983 PMCID: PMC4825814

King AJ, Cooper GF, Hochheiser H, Clermont G. Development and preliminary evaluation of a prototype of a learning electronic medical record system. AMIA Annu Symp Proc. 2015 Nov 5;2015:1967-75. eCollection 2015. PMID: 26958296 PMCID: PMC4765593.

Balasubramanian JB, Cooper GF, Visweswaran SGopalakrishnan V. Selective Model Averaging with Bayesian Rule Learning for Predictive Biomedicine. Proceedings of the AMIA 2014 Joint Summits in Translational Science (In Press); April 2014; San Francisco, CA, USA2014.

Jiang X, Cai B, Xue D, Lu X, Cooper GF, Neapolitan RE. A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets. Journal of the American Medical Informatics Association (2014). Oct;21(e2):e312-9. doi: 10.1136/amiajnl-2013-002358. Epub 2014 Apr 15. PMID: 24737607. PMC4173174.

Pineda AL, Tsui FC, Visweswaran S, Cooper GF. (2013). Detection of Patients with Influenza Syndrome Using Machine-Learning Models Learned from Emergency Department Reports. Online Journal of Public Health Informatics, 5(1), e41.

Montefusco DJ, Chen L, Matmati N, Lu S, Newcomb B, Cooper GF, Hannun YA, Lu X. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses. Sci Signal. 2013 Oct 29;6(299): rs14. doi: 10.1126/scisignal.2004515. PMID: 24170935. PMC3974757.

Sverchkov Y, Visweswaran S, Clermont G, Hauskrecht M, Cooper GF. A multivariate probabilistic method for comparing two clinical datasets. In: Proceedings of the ACM International Health Informatics Symposium (2012) 795-800.

Jiang X, Neapolitan RE, Barmada M, Visweswaran S, Cooper GF. A fast algorithm for learning epistatic genomic relationships. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2010) 341-345. PMID: 21346997. PMC3041370.

Jiang X, Cooper GF. Modeling the Temporal Trend of the Daily Severity of an Outbreak using Bayesian Networks. In: Holmes DE, Jain LC, editors. Innovations in Bayesian Networks of Studies in Computational Intelligence. NY: Springer-Verlag, 2008.

Cooper GF.  A diagnostic method that uses causal knowledge and linear programming in the application of Bayes' formula. Computer Methods and Programs in Biomedicine 22 (1986) 223–237. PMID: 3519071

 

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