Faculty

Jonathan C. Silverstein, MD, MS, FACS, FACMI

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Silverstein, Jonathan
Clinical Informatics Imaging/Visualization/Virtual Reality Vocabularies Virtual Organizations Learning Health Systems Oncology Informatics
Department of Biomedical Informatics
Chief Research Informatics Officer, Department of Biomedical Informatics
Visiting Professor of Biomedical Informatics
University of Pittsburgh School of Medicine
Room 433
5607 Baum Boulevard, Suite 500
Pittsburgh, PA
412-624-8950
Selected Publications: 

Gitelis ME, Kaczynski A, Shear T, Deshur M, Beig M, Sefa M, Silverstein J, Ujiki M. Increasing compliance with the World Health Organization Surgical Safety Checklist-A regional health system's experience.  Am J Surg. 2017; 214(1):7-13.  PMID: 27692671 PMCID: PMC4429500 DOI: 10.1016/j.amjsurg.2016.07.024

Cheng Q, Juen J, Bellam S, Fulara N, Close D, Silverstein JC, Schatz B. Predicting Pulmonary Function from Phone Sensors. Telemed J E Health [Internet]. 2017 Mar 16; Available from: http://dx.doi.org/10.1089/tmj.2017.0008 PMID: 28300524

Cheng Q, June J, Bellam S, Fulara N, Close D, Silverstein JC, Schatz B.  Classification Models for Pulmonary Function using Motion Analysis from Phone Sensors.  AMIA Annu Symp Proc. 2016; :401-410.  PMC5333291

Friedman CP, Allee NJ, Delaney BC, Flynn AJ, Silverstein JC, Sullivan K, Young KA.  The science of Learning Health Systems: Foundations for a new journal. Learning Health Systems. 2017 January; 1(1):1. doi: 10.1002/lrh2.10020

McCray AT, Glaser J, Koppel R, Langlotz CP, Silverstein J. Health IT vendors and the academic community: The 2014 ACMI debate. J Biomed Inform. 2016 Apr;60:365-75. doi: 10.1016/j.jbi.2016.03.003. Epub 2016 Mar 8. PMID: 26968349

Baldridge AS, Pacheco JA, Aufox SA, Kim KY, Silverstein JC, Denham W, Hungness E, Smith ME, Allen NB, Greenland P, Rasmussen-Torvik LJ.  Factors Associated With Long-Term Weight Loss Following Bariatric Surgery Using 2 Methods for Repeated Measures Analysis.  Am J Epidemiol. 2015 Aug 1;182(3):235-43.  PMID: 26093003 PMCID: PMC4517695 DOI: 10.1093/aje/kwv039

Zhu Y, Xu Y, Helseth DL Jr, Gulukota K, Yang S, Pesce LL, Mitra R, Müller P, Sengupta S, Guo W, Silverstein JC, Foster I, Parsad N, White KP, Ji Y.  Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data. J Natl Cancer Inst. 2015 May 8;107(8). pii: djv129. PMID: 25956356 PMCID: PMC4554190 DOI: 10.1093/jnci/djv129

Rasmussen-Torvik LJ, Baldridge AS, Pacheco JA, Aufox SA, Kim KY, Silverstein JC, Denham EW, Hungness E, Smith ME, Greenland P.  rs4771122 Predicts Multiple Measures of Long-Term Weight Loss After Bariatric Surgery. Obes Surg. 2015 Nov;25(11):2225-9.  PMID: 26337695 PMCID: PMC4598314 DOI: 10.1007/s11695-015-1872-7

Maraganore DM, Frigerio R, Kazmi N, Meyers SL, Sefa M, Walters SA, Silverstein JC. Quality improvement and practice-based research in neurology using the electronic medical record. Neurol Clin Pract. 2015 Oct;5(5):419–429. PMCID: PMC4634157

Solomonides A, Goel S, Hynes D, Silverstein JC, Hota B, Trick W, Angulo F, Price R, Sadhu E, Zelisko S, Fischer J, Furner B, Hamilton A, Phua J, Brown W, Hohmann SF, Meltzer D, Tarlov E, Weaver FM, Zhang H, Concannon T, Kho A.  Patient-Centered Outcomes Research in Practice: The CAPriCORN Infrastructure. Stud Health Technol Inform. 2015;216:584-8. PMID: 26262118

Cherenfant J, Talamonti MS, Hall CR, Thurow TA, Gage MK, Stocker SJ, Lapin B, Wang E, Silverstein JC, Mangold K, Odeleye M, Kaul KL, Lamzabi I, Gattuso P, Winchester DJ, Marsh RW, Roggin KK, Bentrem DJ, Baker MS, Prinz RA. Comparison of tumor markers for predicting outcomes after resection of nonfunctioning pancreatic neuroendocrine tumors. Surgery. 2014 Dec;156(6):1504-10; discussion 1510-1. PMID: 25456943 DOI: 10.1016/j.surg.2014.08.043

Erik S. Wright, PhD, MS

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Wright, Erik
Dr. Wright's research integrates comparative genomics and experimental evolution to tackle the problem of antibiotic resistance. Although antibiotics have been used by microorganisms for eons, it remains unclear how these organisms have mitigated the rise of antibiotic resistance in their competitors. Dr. Wright studies the strategies that naturally antibiotic-producing bacteria have evolved to discourage the build-up of resistance, and how some bacteria have adapted to overcome antibiotics while paying a minimal price for resistance. The goal of this research is to develop new strategies for treating pathogens in the clinic, ultimately turning the tide against increasing antibiotic resistance.
Dr. Wright is interested in combatting infectious disease by better understanding how microorganisms evolve.

  Assistant Professor, Department of Biomedical Informatics

426 Bridgeside Point II
450 Technology Dr
Pittsburgh, PA 15219
412-383-4458
Selected Publications: 

Wright ES., Getting my feet wet., Science. 2017 Apr 7;356(6333):106. doi: 10.1126/science.356.6333.106. PMID: 28386014

Kayhan Batmanghelich

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Batmanghelich, Kayhan
Building efficient inference and computational tools to elucidate the statistical connections between imaging, genomics, and medical health records, to improve our understanding of human diseases.
Assistant Professor, Department of Biomedical Informatics

University of Pittsburgh School of Medicine

Curriculum Vitae

Room 531
5607 Baum Blvd
Pittsburgh
PA
15206
412-648-9037
Selected Publications: 

N. Batmanghelich, A. Saeedi, K. Narasimhan, S. Gershman, Nonparametric Spherical Topic Modeling with Word Embeddings. Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics (ACL), pp 537-542, 2016. arXiv:1604.00126

N. Batmanghelich, A. Dalca, G. Quon, M. Sabuncu, P. Golland, Probabilistic Modeling of Imaging, Genetics and the Diagnosis. IEEE Transactions on Medical Imaging (TMI), pp 1765-1779, 2016.  PMID: 26886973 DOI: 10.1109/TMI.2016.2527784

N. Batmanghelich, A. Saeedi, M. Cho, R. Jose, P. Golland, Generative Method to Discover Genetically Driven Image Biomarkers. International Conference on Information Processing in Medical Imaging (IPMI), LNCS 9123, pp 30-42, 2015. PMID: 26221665 PMCID: PMC4527679

C. Wachinger, N. Batmanghelich, P. Golland, M. Reuter, BrainPrint in the Computer-Aided Diagnosis of Alzheimer's Disease. Challenge on Computer-Aided Diagnosis of Dementia. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2014.

N. Batmanghelich, M. Cho, R. Jose, P. Golland, Spherical Topic Models for Imaging Phenotype Discovery in Genetic Studies. Workshop on Bayesian and Graphical Models for Biomedical imaging, International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS 8677, pp 107-117, 2014.

N. Batmanghelich, A. Dalca, M. Sabuncu, P. Golland, Joint Modeling of Imaging and Genetics. International Conference on Information Processing in Medical Imaging (IPMI), LNCS 7917, pp 766-777, 2013. PMID: 24684016 PMCID: PMC3979537

L. Bloy, M. Ingalhalikar, N. Batmanghelich, An integrated Framework for High Angular Resolution Diffusion Imaging-Based Investigation of Structural Connectivity. Brain Connectivity, 2(2), pp 69-19, 2012. doi:  10.1089/brain.2011.0070 PMCID: PMC3380149

N. Batmanghelich, B. Taskar, C. Davatzikos, Generative-Discriminative Basis Learning for Medical Imaging. IEEE Transactions on Medical Imaging (TMI), 31(1), pp 51-69, 2012. PMID: 21791408 PMCID: PMC3402718 DOI: 10.1109/TMI.2011.2162961

Y. Ghanbari, L. Bloy, N. Batmanghelich, R. Verma, Dominant Component Analysis of Electro-physiological Connectivity Network. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pp 231-238, 2012. PMID: 23286135 PMCID: PMC4029114

N. Batmanghelich, D. Ye, B. Taskar, C. Davatzikos, Disease Classification and Prediction via semi-supervised Dimensionality Reduction. IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI), pp 1086-1090, 2011. DOI: 10.1109/ISBI.2011.5872590

C. Davatzikos, P. Bhatt, L. Shaw, N. Batmanghelich, J. Trojanowski, Prediction of MCI Conversion via MRI, CSF Biomarkers, and Pattern Classification. Neurobiology of Aging, 32(12), pp 2322.e192322.e27, 2010. PMID: 20594615 PMCID: PMC2951483 DOI: 10.1016/j.neurobiolaging.2010.05.023

N. Batmanghelich, B. Taskar, C. Davatzikos, Regularized Tensor Factorization for Multi-Modality Medical Image Classification. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pp 17-24, 2011. PMID: 22003679

N. Batmanghelich, A. Gooya, B. Taskar, C. Davatzikos, Application of Trace-Norm and Low-Rank Matrix Decomposition for Computational Anatomy. IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA), Computer Vision and Pattern Recognition Workshops (CVPRW), pp 146-153, 2010. DOI: 10.1109/CVPRW.2010.5543596

N. Batmanghelich, B. Taskar, C. Davatzikos, A General and Unifying Framework for Feature Construction, in Image-Based Pattern Classification. International Conference on Information Processing in Medical Imaging (IPMI), LNCS 5636, pp 423-434, 2009. PMID: 19694282

N. Batmanghelich, R. Verma, On Non-linear Characterization of Tissue Abnormality by Constructing Disease Manifolds. IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA), Computer Vision and Pattern Recognition Workshops (CVPRW), pp 1-8, 2008. DOI: 10.1109/CVPRW.2008.4563027

Y. Fan, N. Batmanghelich, C. Clark, C. Davatzikos, Spatial Patterns of Brain Atrophy in MCI Patients, Identified via High-dimensional Pattern Classification, Predict Subsequent Cognitive Decline. NeuroImage, 39(4), pp 1731-43, 2008. PMID: 18053747 PMCID: PMC2861339 DOI: 10.1016/j.neuroimage.2007.10.031

H. Shariatpanahi, N. Batmanghelich, A. Kermani, M. Ahmadabadi, H. Soltanian-Zadeh, Distributed Behavior-based Multi-agent System for Automatic Segmentation of Brain MR Images. International Joint Conference on Neural Networks (IJCNN), pp 4535-4542, 2006. DOI: 10.1109/IJCNN.2006.247079

M. Karimi, N. Batmanghelich, H. Soltanian-Zadeh, C. Lucas, A 3-D Deformable Surface Method for Automatic Hippocampus-Amygdala Complex Segmentation. IEEE Nuclear Science Symposium Conference Record, 6, pp 3725-3729, 2004.DOI: 10.1109/NSSMIC.2004.1466690

N. Batmanghelich, H. Soltanian-Zadeh, B. Aarabi, Knowledge-based Segmentation: Using Simultaneous Shape Priori and Histogram Information to Segment Brain Structures. IASTED Conference on Signal and Image Processing, pp 15-17, 2005.

Douglas Landsittel, PhD

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Landsittel, Douglas
Department of Biomedical Informatics

Educational Interests

Professor of Biomedical Informatics, Biostatistics, and Clinical and Translational Science
Director of Biostatistics, Starzl Transplant Institute
Program Director, Expanding National Capacity in PCOR through Training
Core Faculty, Comparative Effectiveness Research Center
Dr. Landsittel is a professor and biostatistician whose research focuses on the intersection of biomarker studies and causal inference methods, with applications in transplant, occupational, and comparative effectiveness research.
Room 536
5607 Baum Boulevard, Suite 500
Pittsburgh, PA
412-624-0270
Selected Publications: 

Thurston RC, Chang Y, Barinas-Mitchell E, Jennings R, von Känel R, Landsittel DP, Matthews KA. Physiologically assessed hot flashes and endothelial function among midlife women. In Press. Menopause. PMID: 28399007  PMCID: PMC5524590 [Available on 2018-08-01] DOI: 10.1097/GME.0000000000000857

Hughes AM, Patterson PD, Weaver MD, Gregory ME, Sonesh SC, Landsittel D, Krackhardt D, Hostler D, Lazzara EH, Wang X, Vena J, Salas E, Yealy DM. Teammate familiarity, teamwork, and risk of workplace injury in EMS teams. In Press. Journal of Emergency Nursing. PMID: 28366241 DOI: 10.1016/j.jen.2016.11.007

Kline TL, Korfiatis P, Edwards ME, Bae KT, Yu A, Chapman AB, Mrug M, Grantham JJ, Landsittel D, Bennett WM, Flessner MF, King BF, Harris PC, Torres VE, Erickson BJ. Image Texture Features Predict Renal Function Decline in Autosomal Dominant Polycystic Kidney Disease Patients. In Press. Kidney International.  PMID: 28532709  DOI: 10.1016/j.kint.2017.03.026

Thurston RC, Chang Y, Mitchell EB, von Känel R, Jennings JR, Santoro N, Landsittel DP, Matthews KA. Child abuse and neglect and subclinical cardiovascular disease among midlife women. Psychosomatic medicine, 2017;79(4), 441-449. PMID: 27763988 PMCID: PMC5477855 [Available on 2018-05-01] DOI: 10.1097/PSY.0000000000000400

Rosenberger EM, DeVito Dabbs AJ, DiMartini AF, Landsittel DP, Pilewski JM, Dew MA. Long-Term Clinical Impact of a Mobile Health Intervention for Self-Management in Lung Transplant Recipients. In Press. American Journal of Transplantation, 2017;17(5):1286–1293. DOI: 10.1111/ajt.14062

Sentell T, Shen C, Landsittel D, Mays MH, Southerland J, Henriques-Forsythe M, Taira DA. Racial/ethnic differences in those accompanying Medicare patients to the doctor: Insights from the 2013 Medicare Current Beneficiary's Survey. In Press. Journal of Immigrant and Minority Health. PMID: 28405871 DOI: 10.1007/s10903-017-0582-8

Shen C, Landsittel D, Irazabal MV, Yu ASL, Chapman AB, Mrug M, Grantham JJ, Bae KT, Bennett WM, Flessner MF, Torres VE. Performance of equations to estimate glomerular filtration rate in a longitudinal study of Autosomal Dominant Polycystic Kidney Disease. American Journal of Kidney Disease, 2017;69(3):482-484. PubMed: 28027795  PMC: PMC5497695  DOI: 10.1053/j.ajkd.2016.10.021

Cherukuri A, Salama AD, Carter CR, Landsittel D, Arumugakani G, Clark B, Rothstein DM and Baker RJ. Reduced Human Transitional B cell T1/T2 Ratio Is Associated with Subsequent Deterioration in Renal Allograft Function. Kidney International. 2017;91(1):183-195. PMID: 28029430 DOI: 10.1016/j.kint.2016.08.028

Liapis H, Gaut JP, Klein C, Bagnasco S, Kraus E, Farris AB, Honsova E, Perkowska-Ptasinska A, David D, Goldberg J, Smith M, Mengel M, Haas M, Seshan S, Pegas KL, Horwedel T, Paliwa Y,  Gao X,  Landsittel D, Randhawa P. Banff histopathological consensus criteria for pre-implantation kidney biopsies. In Press. American Journal of Transplantation. 2017;17(1):140-150. PMID: 27333454 DOI: 10.1111/ajt.13929

Taira DA, Shen C, Henriques-Forsythe M, Landsittel D, Mays MH, Sentell T, Southerland J. Access to Medications for Medicare Enrollees Related to Race/Ethnicity: Results from the 2013 Medicare Current Beneficiary Survey. In Press. Research in Social and Administrative Pharmacy. PMID: 27914950 PMCID: PMC5500432 [Available on 2018-05-23] DOI: 10.1016/j.sapharm.2016.10.021

Donald P. Taylor, Ph.D., M.B.A.

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Taylor, Donald P.
Mechanisms of breast cancer metastatic latency through computational models and human 3D-perfused micro-scale tissue bioreactors.

Donald P. Taylor, PhD, MBA, is assistant vice chancellor for commercial translation in the health sciences; codirector of the Center for Commercial Applications of Healthcare Data and of the Clinical and Translational Science Institute; associate director of the Center for Medical Innovation; associate professor of biomedical informatics and of plastic surgery, School of Medicine; and associate professor of bioengineering, Swanson School of Engineering.

Assistant Vice Chancellor for Commercial Translation in the Health Sciences
Associate Professor, Department of Biomedical Informatics
Co-Director, Center for Commercial Applications of Healthcare Data
Co-Director, Clinical and Translational Science Institute, Innovation Core
Associate Director, Center for Medical Innovation
Associate Professor, Bioengineering
Associate Professor, Plastic Surgery
Faculty, McGowan Institute for Regenerative Medicine
University of Pittsburgh School of Medicine
Room 514
5607 Baum Boulevard
Pittsburgh, PA 15206
412-648-9324

David Boone, PhD

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Boone, David
Development and implementation of STEM outreach programs -Insulin-like Growth Factor 1 (IGF1) signaling in breast cancer -Regulation and function of long noncoding RNAs (lncRNAs) -Transcription and transcriptomics -Breast cancer biology
Department of Biomedical Informatics
Assistant Professor, Director of CoSBBI
Executive Director of the UPCI Academy
Department of Biomedical Informatics
University of Pittsburgh School of Medicine
Dr. Boone is an Assistant Professor of Biomedical Informatics and Director of the CoSBBI Summer Academy
Room 414
5607 Baum Boulevard
Pittsburgh
PA
412-648-7231
Selected Publications: 

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 [serial online] 2017 [cited 2017 Mar 1];8:2. Available from: http://www.jpathinformatics.org/text.asp?2017/8/1/2/201110

Nayak S, Harrington E, Boone DN, Hartmaier R, Pathiraja, T, Cooper K, Fine J, Sanfilippo J, Davidson N, Lee AV, Dabbs D, and Oesterreich S. A Role for Histone H2B Variants in Endocrine Resistant Breast Cancer. Hormones and Cancer. 2015  PUBMED 26113056

Farabaugh SM, Boone DN, and Lee AV. Role of IGF1R in breast cancer subtypes, stemness, and lineage differentiation.  Frontiers in Endocrinology. 2015. PUBMED 25964777

Zhang Q, Spears E, Boone DN, Li Z, Gregory M, and Hann S.  Domain specific c-Myc ubiquitylation controls c-Myc transcriptional and apoptotic activitysPNAS. 2012; 110(3):978-83. PUBMED 23277542

Boone DN and Lee AV. Targeting the Insulin-like Growth Factor Receptor: Developing Biomarkers from Gene Expression Profiling. Critical Reviews in Oncogenesis.  2012;17(2):161-73. PUBMED 22471706

Boone DN and Hann SR. The Myc-ARF-Egr1 Pathway: Unleashing Myc’s Apoptotic Power.  Cell Cycle.  2011 Jul1;10(13):2043-4.  PMC3234342

Boone DN, Qi Y, Li Z, and Hann S. Egr1 mediates p53-independent c-Myc-induced apoptosis via a noncanonical ARF-dependent transcriptional mechanism. PNAS. 2011 Jan 11;108(2):632-7.  PUBMED 21187408

Zhaoliang Li, Boone D, and Hann S.  Nucleophosmin interacts directly with c-Myc and controls c-Myc-induced hyperproliferation and transformationPNAS.  2008 Dec 2;105(48):18794-9. PUBMED 19033198

van Rheede T, Bastiaans T, Boone D, Hedges SB, de Jong W, and Madsen O.  2006. The platypus is in its place: nuclear genes and indels confirm the sister group relation of monotremes and therians. Mol. Biol. Evol. 23:587-597. PMID:19033198

Fuchiang (Rich) Tsui, PhD

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Tsui, Fu-Chiang (Rich)

Primary Appointment: 

Associate Professor, Department of Biomedical Informatics
Associate Professor of Intelligent Systems
Associate Professor of Bioengineering
Associate Professor of Clinical and Translational Science
Associate Director, RODS Laboratory
Dr. Tsui is Assistant Professor of Biomedical Informatics, Intelligent Systems, and Bioengineering. He is Associate Director of RODS Laboratory.
Room 437L
5607 Baum Blvd.
Pittsburgh
PA
15260
412-648-7182
412-648-9118

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

Arturo López Pineda, Ye Ye, Shyam Visweswaran, Gregory F. Cooper, Michael M. Wagner, Fuchiang Rich Tsui. Comparison of Machine Learning Classifiers for Influenza Detection from Emergency Department Free-text Reports. Journal of Biomedical Informatics. Available online 16 September 2015, ISSN 1532-0464. PMID: 26385375

http://dx.doi.org/10.1016/j.jbi.2015.08.019.(http://www.sciencedirect.com/science/article/pii/S1532046415001872)

Cooper, G. F., Villamarin, R., Tsui, F.-C. (Rich), Millett, N., Espino, J. U., & Wagner, M. M. (2015). A Method for Detecting and Characterizing Outbreaks of Infectious Disease from Clinical Reports. Journal of Biomedical Informatics, 53, 15–26. http://doi.org/10.1016/j.jbi.2014.08.011 PMID: 25181466 PMCID: PMC4441330

Rexit R, Tsui FC, Espino JU, Chrysanthis PK, Wesaratchakit S, Ye Y. An analytics appliance for identifying (near) optimal over-the-counter medicine products as health indicators for influenza surveillance. J Manager Infor Systems. 2015;48:151-63.

Draper AJ, Ye Y, Ruiz VM, Patterson C, Urbach A, Palmer F, Wang S, Somboonna M, Tsui F.-C., Using laboratory data for prediction of 30-day hospital readmission of pediatric seizure patients, Conference Proceedings, American Medical Informatics Association, Washington DC, Nov. 2014 (Distinguished award)

Tsui F-C, Adaptive Hospital Readmission Prediction System (AHRPS), Innovation in Healthcare Technology 2014, Pittsburgh, Feb. 14, 2014

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 Sept:21(5):815-823. (2014 Jan 9. doi: 10.1136/amiajnl-2013-001934. Epub ahead of print. PubMed PMID: 24406261.  PMCID:PMC in Process: Available on 09/01/2015.

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, PMID: 24821745 PMCID: PMC4078296

Lu S, Ye Y, Tsui FC, Liu X, Hwa R. Feature Selection for 30-Day Heart Failure Readmission Prediction Using Clinical Drug Data. NIPS workshop on Machine Learning for Clinical Data Analysis and Healthcare; 2013 Dec 10.

Lu S., Ye Y., Tsui F.-C., Su H., Rexit R., Wesaratchakit S., Hwa R., "Domain ontology-based feature reduction for high dimensional drug data and its application to 30-day heart failure readmission prediction," Collaborative Computing: Networking, Applications and Worksharing (Collaboratecom), 2013 9th International Conference Conference on, Austin, TX, 2013, pp. 478-484.

Villamarín R, Cooper G, Wagner M, Tsui FC, Espino JU. A method for estimating from thermometer sales the incidence of diseases that are symptomatically similar to influenza. Journal of Biomedical Informatics. 2013 Jun;46(3):444-57. PMID: 23501015 PMCID: PMC4609543

Pineda, A. L., Tsui, F.-C., Visweswaran, S., & Cooper, G. F. (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.

Liu TY, Sanders JL, Tsui FC, Espino JU, Dato VM, Suyama J. Association of over-the-counter pharmaceutical sales with influenza-like-illnesses to patient volume in an urgent care setting. PloS one. 2013;8(3):e59273. PMID: 23555647 PMCID: PMC3605458

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

Pages

Uma Chandran, PhD, MSIS

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Chandran, Uma
Dr. Chandran's interests include genomic data mining, Next Generation Sequencing data analysis, integrative analysis of The Cancer Genome Atlas Project (TCGA) and development of computing infrastructure for large genomics datasets
Room 513
5607 Baum Boulevard
Pittsburgh, PA 15206
412-648-9326

Concha-Benavente F, Srivastava RM, Trivedi S, Lei Y, Chandran U, Seethala RR, Freeman GJ, Ferris RL. Identification of the Cell-Intrinsic and -Extrinsic Pathways Downstream of EGFR and IFNy That Induce PD-L1 Expression in Head and Neck Cancer. Cancer Research. 2016 Mar 1;76(5):1031-43. PMID:26676749.

Frahm KA, Peffer ME, Zhang JY, Luthra S, Chakka AB, Couger MB, Chandran UR, Monaghan AP, DeFranco DB. Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells. Molecular Endocrinology (Baltimore, Md.). 2016 Jan;30(1):144-54. PMID: 26606517

Gau DM, Lesnock JL, Hood BL, Bhargava R, Sun M, Darcy K, Luthra S, Chandran U, Conrads TP, Edwards RP, Kelley JL, Krivak TC, Roy P. (2015). BRCA1 deficiency in ovarian cancer is associated with alteration in expression of several key regulators of cell motility – A proteomics study. Cell Cycle, 14(12), 1884–1892. http://doi.org/10.1080/15384101.2015.1036203 PMID: 25927284 PMCID: PMC4614952

McDade KK, Chandran U, Day RS. Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Informatics, 2015. PMID: 26715829 PMCID: PMC4686346

McDade, K. K., Chandran, U., & Day, R. S. (2015). Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Informatics, 14, 149–161.  PMID: 26715829 PMCID: PMC4686346 DOI: 10.4137/CIN.S33076

Chandran, U. R., Luthra, S., Santana-Santos, L., Mao, P., Kim, S.-H., Minata, M., Li J, Benos PV, DeWang M, Hu B, Cheng SY, Nakano I, Sobol RW. (2015). Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells. Genomics Data, 5, 333–336. http://doi.org/10.1016/j.gdata.2015.07.007 PMID: 26251826 PMCID: PMC4523279

Manohar R, Li Y, Fohrer H, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E.  (2015). Identification of a candidate stem cell in human gallbladder. Stem Cell Research, 14(3), 258–269. http://doi.org/10.1016/j.scr.2014.12.003  PMID:  25765520 PMCID: PMC4439375

Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS. (2015). Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PLoS ONE, 10(6), e0131166. http://doi.org/10.1371/journal.pone.0131166 PMID: 26115441 PMCID: PMC4483235

Liao S, Hartmaier RJ, McGuire KP, Puhalla SL, Luthra S, Chandran UR, Ma T, Bhargava R, Modugno F, Davidson NE, Benz S, Lee AV, Tseng GC, Oesterreich S. (2015). The molecular landscape of premenopausal breast cancer. Breast Cancer Research : BCR, 17(1), 104. http://doi.org/10.1186/s13058-015-0618-8 PMID: 26251034 PMCID: PMC4531812

Sikora MJ, Cooper KL, Bahreini A, Luthra S, Wang G, Chandran UR, Davidson NE, Dabbs DJ, Welm AL, Oesterreich S. (2014). Invasive lobular carcinoma cell lines are characterized by unique estrogen-mediated gene expression patterns and altered tamoxifen response. Cancer Research, 74(5), 1463–1474. http://doi.org/10.1158/0008-5472.CAN-13-2779 PMID: 24425047 PMCID: PMC3955299

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. PMID: 23785665. PMCID: PMC3683664. doi: 10.3389/fonc.2013.00139

Maxwell GL, Allard J, Gadisetti CV, Litzi T, Casablanca Y, Chandran U, Darcy KM, Levine DA, Berchuck A, Hamilton CA, Conrads TP, Risinger JI. Transcript expression in endometrial cancers from Black and White patients. Gynecol Oncol. 2013 Jul; 130(1):169-73. PMID: 23603370. doi: 10.1016/j.ygyno.2013.04.017

Mao P, Joshi K, Li J, Kim SH, Li P, Santana-Santos L, Luthra S, Chandran UR, Benos PV, Smith L, Wang M, Hu B, Cheng SY, Sobol RW, Nakano I. Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3. Proc Natl Acad Sci U S A. 2013 May 21;110(21):8644-9. PMID: 23650391. PMCID: PMC3666732. doi: 10.1073/pnas.1221478110

LaFramboise WA, Dhir R, Kelly LA, Petrosko P, Krill-Burger JM, Sciulli CM, Lyons-Weiler MA, Chandran UR, Lomakin A, Masterson RV, Marroquin OC, Mulukutla SR, McNamara DM. Serum protein profiles predict coronary artery disease in symptomatic patients referred for coronary angiography. BMC Med. 2012 Dec 5; 10:157. PMID: 23216991. PMCID: PMC3566965. doi: 10.1186/1741-7015-10-157

Li J, Luthra S, Wang XH, Chandran UR, Sobol RW. Transcriptional profiling reveals elevated Sox2 in DNA polymerase ß null mouse embryonic fibroblasts. Am J Cancer Res. 2012; 2(6):699-713. Epub 2012 Nov 20. PMID: 23226616. PMCID: PMC3512183

Pages

Songjian Lu, PhD

Directory Listing Information
Lu, Songjian
Using computational method to search for driver somatic genome alterations, such as somatic mutations, copy number alterations, that are related to cancer development. Formulating the biological problems into graph or statistical problems. Designing efficient exact algorithms for the hard computational problems.

Publications

 

Assistant Professor, Department of Biomedical Informatics
University of Pittsburgh School of Medicine
Room 512
5607 Baum Boulevard
Pittsburgh, PA 15206
412-648-9543
412-624-5310
Selected Publications: 

Lu, S., Jin, B., Cowart, LA., and Lu, X (2013) From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data. PLoS One 8(4): e61134  PMID: 23637789 PMCID: PMC3634064

Gerald Douglas, PhD

Directory Listing Information
Douglas, Gerald
Health informatics in medically underserved populations, eHealth policy/strategy, Financial models of health information systems, Global health informatics, Quality improvement, Human-computer interaction, and Point-of-care computing
Dr. Douglas is an Assistant Professor focusing on Health Informatics for the Underserved.
Assistant Professor, Department of Biomedical Informatics
Assistant Professor of Health Policy & Management
Director of Center for Health Informatics for the Underserved
University of Pittsburgh School of Medicine
Room 519
5607 Baum Boulevard
Pittsburgh, PA 15206
412-648-9323
Selected Publications: 

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

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

Landis-Lewis, Z., Brehaut, J. C., Hochheiser, H., Douglas, G. P., & Jacobson, R. S. (2015). Computer-supported feedback message tailoring: theory-informed adaptation of clinical audit and feedback for learning and behavior change. Implementation Science, 10(1), 1.

Driessen J, Cioffi M, Alide N, Landis-Lewis Z, Gamadzi G, Gadabu OJ, Douglas G. Modeling return on investment for an electronic medical record system in Lilongwe, Malawi. Journal of the American Medical Informatics Association: JAMIA. 2012 Nov 9. PMCID: PMC3721156. PMID: 23144335.

Gadabu OJ, Munthali CV, Zacharaiah R, Gudmund-Hinderaker S, Jahn A, Twea H, Gondwe A, Mumba S, Lungu M, Malisita K, Mhango E, Makombe SD, Tenthani L, Mwalwanda L, Moyo C, Douglas GP, Landis-Lewis Z, Chimbwandira F. Is transcription of data on antiretroviral treatment from electronic to paper-based registers reliable in Malawi? Public Health Action. 2011 Sep; 1 (1):10-12(3).

Allain TJ, van Oosterhout JJ, Douglas GP, Joukes S, Gadabu OJ, Darts C, Kapur A, Harries AD. Applying lessons learnt from the ‘DOTS’ Tuberculosis Model to monitoring and evaluating persons with diabetes mellitus in Blantyre, Malawi. Tropical medicine & international health : TM & IH. 2011 Jun 27; 16 (9):1077-84. PMID: 21702868.

Landis-Lewis Z, Mello-Thoms C, Gadabu OJ, Gillespie M, Douglas GP, Crowley RS. The Feasibility of Automating Audit and Feedback for ART Guideline Adherence in Malawi. J Am Med Inform Assoc. 2011 May 12; 18 (6):868-74. PMCID: PMC3197989. PMID: 21565857.

Douglas GP, Gadabu OJ, Joukes S, Mumba S, McKay MV, et al. Using touchscreen electronic medical record systems to support and monitor national scale-up of antiretroviral therapy in Malawi.PLoS Med. 2010 Aug 10;7(8). pii: e1000319. doi: 10.1371/journal.pmed.1000319. PMCID: PMC2919419

Waters E, Rafter J, Douglas GP, Bwanali M, Jazayeri D, et al. Experience Implementing a Point-of-Care Electronic Medical Record System for Primary Care in Malawi. Medinfo 2010. In Press. PMID: 20841657

Landis Lewis Z, Douglas GP, Monaco V. Touchscreen task efficiency and learnability in an electronic medical record at the point-of-care. Medinfo 2010. In Press. PMID: 20841658

Douglas GPEngineering an EMR system in the developing world: necessity is the mother of invention. PhD dissertation. Pittsburgh (PA): University of Pittsburgh; 2009.

Waters E, Rafter J, Maganga RT, Fraser HSF, Douglas GP, et al. Integration of a touchscreen system for patient registration and primary care data collection with OpenMRS at Neno district hospital, Malawi. AMIA Annu Symp Proc 2009;107.

Fraser HS, Allen C, Bailey C, Douglas G, Shin S, Blaya J. Information systems for patient follow-up and chronic management of HIV and tuberculosis: a life-saving technology in resource-poor areas. Journal of medical Internet research. 2007; 9 (4):e29. PMCID: PMC2223184. PMID: 17951213.

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