Faculty

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

 

Michael J. Becich, MD, PhD

Directory Listing Information
Becich, Michael J.
bioinformatics; biological markers; computational biology; computer communication networks; computer-assisted instruction; diagnostic imaging; gene expression regulation, neoplastic; imaging informatics; informatics; laboratories, hospital; medical informatics; next generation sequencing; pathology; translational research; personalized medicine
Dr. Becich is a Professor of Biomedical Informatics, Pathology, Clinical/Translational Sciences, Information Sciences/Telecommunications. He is the Chair of the Department of Biomedical Informatics and Associate Vice-Chancellor for the Health Sciences.
Room 521
5607 Baum Boulevard
Pittsburgh
PA
15206-3701
412-648-9244
412-624-5310
412-606-6453
http://www.dbmi.pitt.edu/person/michael-j-becich-md-phd
Chairman and Distinguished University Professor, Department of Biomedical Informatics
Professor of Pathology, Information Sciences, Telecommunications and Clinical/Translational Sciences
Associate Vice Chancellor for Informatics in the Health Sciences
Director, Center for Commercial Application (CCA) of Healthcare Data
Associate Director for Cancer Institute (UPCI)
Associate Director, Clinical and Translational Science Institute (CTSI)
University of Pittsburgh School of Medicine
Publications: 

Luthra S, Chandran U, Diergaarde B, Becich M, Lee AV, Neumann CA. Expression of reactive species related genes is associated with patient survival in luminal B breast cancer. Free Radic Biol Med. 2018 Mar 12. pii: S0891-5849(18)30114-X. doi: 10.1016/j.freeradbiomed.2018.03.011. [Epub ahead of print]. PMID: 2954507.

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.

King AJ, Fisher AM, Becich MJ, Boone DN. Computer Science, Biology and Biomedical Informatics academy: Outcomes from 5 years of Immersing High-school Students into Informatics Research. J Pathol Inform. 2017 Feb 28;8:2. doi: 10.4103/2153-3539.201110. eCollection 2017. PMID: 28400991 PMC ID: 5359992.

De Rienzo A, Cook RW, Wilkinson J, Gustafson CE, Amin W, Johnson CE, Oelschlager KM, Maetzold DJ, Stone JF, Feldman MD, Becich MJ, Yeap BY, Richards WG, Bueno R. Validation of a Gene Expression Test for Mesothelioma Prognosis in Formalin-Fixed Paraffin-Embedded Tissues. J Mol Diagn. 2017 Jan;19(1):65-71. doi: 10.1016/j.jmoldx.2016.07.011. Epub 2016 Nov 15. Pub Med PMID: 27863259. PMCID: PMC5225306.

Uppal R, Mandava G, Romagnoli KM, King AJ, Draper AJ, Handen AL, Fisher AM, Becich MJ, Dutta-Moscato J. How can we improve Science, Technology, Engineering, and Math education to encourage careers in Biomedical and Pathology Informatics? J Pathol Inform. 2016 Jan 29;7:2. doi: 10.4103/2153-3539.175375. eCollection 2016. PMID: 26955500. PMCID: PMC4763503.

Jacobson RS, Becich MJ, Bollag RJ, Chavan G, Dhir R, Corrigan J, Feldman M, Ganguly A, Gaudioso C, Legowski E, Maihle N, Mitchell K, Murphy M, Sakthivel M, Tseytlin E, Weaver J. A Federated Network for Translational Cancer Research Using Clinical Data and Biospecimens. Cancer Res. 2015;75(24):5194-201.doi: 10.1158/0008-5472.CAN-15-1973. Review. PMID: 26670560 PMCID: PMC4683415.

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.

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.

Amin W, Tsui FC, Borromeo C, Chang CH, Espino JU, Ford D, Hwang W, Kapoor W, Lehmann H, Martich GD, Morton S, Paranjape A, Shirey W, Sorensen A, Becich MJ, Hess R. PaTH: towards a learning health system in the Mid-Atlantic region. J Am Med Inform Assoc. 2014;21(4):63-6 doi: 10.1136/amiajnl-2014-002759. Epub 2014 May 12. PMID: 24821745. PMCID: PMC4078296.

Amin W, Srinivasan M, Song SY, Parwani AV, Becich MJUse of automated image analysis in evaluation of mesothelioma Tissue Microarray (TMA) from National Mesothelioma Virtual Bank. Pathol Res Pract. 2014 Feb;210(2):79-82. doi: 10.1016/j.prp.2013.09.002. Epub 2013 Nov 14. PMID: 24359722.

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.

Park S, Parwani AV, Aller RD, Banach L, Becich MJ, Borkenfeld S, Carter AB, Friedman BA, Rojo MG, Georgiou A, Kayser G, Kayser K, Legg M, Naugler C, Sawai T, Weiner H, Winsten D, Pantanowitz L. The history of pathology informatics: A global perspective. J Pathol Inform. 2013 May 30;4:7. doi: 10.4103/2153-3539.112689. Print 2013. PMID: 23869286. PMCID: PMC3714902.

Amin W, Parwani A, Melamed J, Flores R, Pennathur A, Valdivieso F, Whelan N, Landreneau R, Luketich J, Feldman M, Pass H, Becich MJNational Mesothelioma Virtual Bank: A Platform for Collaborative Research and Mesothelioma Biobanking Resource to Support Translational Research. Lung Cancer International, Volume 2013, Article ID 765748.

Gullapalli RR, Desai KV, Santana-Santos L, Kant JA, Becich MJNext generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. J Pathol Inform. 2012;3:40. doi: 10.4103/2153-3539.103013. Epub 2012 Oct 31. PMID:  23248761

Bartholow TL, Chandran UR, Becich MJ, Parwani AV. Immunohistochemical profiles of claudin-3 in primary and metastatic prostatic adenocarcinoma. Diagn Pathol. 2011 Jan 21;6:12. PMID: 21255442. PMCID: PMC3033791. doi: 10.1186/1746-1596-6-12

Amin W, Singh H, Pople AK, Winters S, Dhir R, Parwani AV, Becich MJ. A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research. Journal of Pathology Informatics. 2010 Aug 10; 1.12. PMID: 20922029. PMCID: PMC2941965. doi: 10.4103/2153-3539.68314

Amin W, Parwani A, Schmandt L, Mohanty S, Farhat G, Pople A, Winters S, Whelan N, Schneider A, Milnes J, Valdivieso F, Feldman M, Pass H, Dhir R, Melamed J, Becich M. National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research. BMC cancer. 2008 Aug; 8(1): 236. PMID: 18700971. PMCID: PMC2533341

Yin M, Bastacky S, Chandran U, Becich MJ, Dhir R. Prevalence of incidental prostate cancer in the general population: a study of healthy organ donors. The Journal of Urology. 2008 Mar;179(3):892-5; discussion 895. PMID: 18207193 DOI: 10.1016/j.juro.2007.10.057

Mohanty S, Mistry A, Amin W, Parwani A, Pople A, Schmandt L, Winters S, Milliken E, Kim P, Whelan N, Farhat G, Melamed J, Taioli E, Dhir R, Pass H, Becich M. The development and deployment of Common Data Elements for tissue banks for translational research in cancer - an emerging standard based approach for the Mesothelioma Virtual Tissue Bank. BMC cancer 2008 Apr; 8(8): 91. PMID: 18397527. PMCID: PMC2329649

Chandran UR, Ma C, Dhir R, Bisceglia M, Lyons-Weiler J, Liang W, Michalopoulos GK, Becich MJ, Monzon FA. Gene expression profiles of metastatic prostate cancer reveals disregulation of specific molecular pathways. BMC Cancer. 2007;7(0):64. PMID: 17430594 PMCID: PMC1865555

Chandran UR, Dhir R, Ma C, Michalopoulos G, Becich M, Gilbertson J. (2005). Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer, 5, 45. http://doi.org/10.1186/1471-2407-5-45 PMID: 15892885 PMCID: PMC1173092

Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer cell. 2005 Nov;8(5):393-406. PMID: 16286247

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