Faculty

Sofia Triantafillou, PhD

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Triantafillou, Sofia
The Offices at Baum, 532
5607 Baum Blvd.
Pittsburgh
PA
15206
412-624-7198

Assistant Professor, Department of Biomedical Informatics

Research interests:

Developing causal discovery methods in the presence of latent variables, methods for integrative analysis of multiple experiments, modelling and application of causal discovery on neural and biological data.

Hatice Ulku Osmanbeyoglu, PhD

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Osmanbeyoglu, Hatice
Bioinformatics Specialties: Machine learning, information integration, knowledge discovery
Assistant Professor, Biomedical Informatics School of Medicine, University of Pittsburgh UPMC Hillman Cancer Center
UPMC Hillman Cancer Center G27c
5117 Centre Ave
Pittsburgh
PA
15232
412-623-7789
https://sites.google.com/view/haticeulkuosmanbeyoglu/

Assistant Professor
Department of Biomedical Informatics
School of Medicine, University of Pittsburgh
UPMC Hillman Cancer Center

 

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Yalini Senathirajah, PhD

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Senathirajah, Yalini
Clinical Informatics Global Health Informatics Interface Design
Department of Biomedical Informatics
Visiting Associate Professor, Department of Biomedical Informatics
Baum Room 515
5607 Baum Blvd.
Pittsburgh
PA
15206
347-619-4021

Visiting Associate Professor, Department of Biomedical Informatics
University of Pittsburgh School of Medicine

Publications: 

Robbins R, Senathirajah Y, Williams NJ, Hutchinson C, Rapoport DM, Allegrante DM, Allegrante JP, Cohall A, Rogers A, Ogedegbe O, Jean-Louis G. Developing a Tailored Website for Promoting Awareness about Obstructive Sleep Apnea (OSA) Among Blacks in Community-Based Settings. Health Commun. 2018 Jan 17:1-9. doi: 10.1080/10410236.2018.1423865. [Epub ahead of print]. PMID: 29338353.

Senathirajah Y, Wang J, Borycki E, Kushniruk A. Mapping the Electronic Health Record: A Method to Study Display Fragmentation. Stud Health Technol Inform. 2017 245:1138-1142. PMID: 29295280.

Senathirajah Y, Kaufman D, Bakken S. User-composable Electronic Health Record Improves Efficiency of Clinician Data Viewing for Patient Case Appraisal: A Mixed-Methods Study. EGEMS (Wash DC). 2016 May 2;4(1):1176. doi: 10.13063/2327-9214.1176. eCollection 2016. PMID: 27195306. PMCID: PMC4862763.

Roman LC, Ancker JS, Johnson SB, Senathirajah Y. Navigation in the electronic health record: A review of the safety and usability literature. J Biomed Inform. 2017 Mar;67:69-79. doi: 10.1016/j.jbi.2017.01.005. Epub 2017 Jan 11. Review. PMID: 28088527

Kushniruk A, Senathirajah Y, Borycki E. Effective Usability Engineering in Healthcare: A Vision of Usable and Safer Healthcare IT. Stud Health Technol Inform. 2017;245:1066-1069. PMID: 29295265.

Kushniruk A, Senathirajah Y, Borycki E. Towards a Usability and Error "Safety Net": A Multi-Phased Multi-Method Approach to Ensuring System Usability and Safety. Stud Health Technol Inform. 2017;245:763-767. PMID: 29295201.

Borycki E, Senathirajah Y, Kushniruk AW. The Future of Mobile Usability, Workflow and Safety Testing. Stud Health Technol Inform. 2017;245:15-19. PMID: 29295043.

Sockolow P, Schug S, Zhu J, Smith TJ, Senathirajah Y, Bloom S. At-risk adolescents as experts in a new requirements elicitation procedure for the development of a smart phone psychoeducational trauma-informed care application. Inform Health Soc Care. 2017 Jan;42(1):77-96. Epub 2016 Jun 3. doi: 10.1080/17538157.2016.1177532. PMID: 27259373.

Borycki E, Dexheimer JW, Hullin Lucay Cossio C, Gong Y, Jensen S, Kaipio J, Kennebeck S, Kirkendall E, Kushniruk AW, Kuziemsky C, Marcilly R, Röhrig R, Saranto K, Senathirajah Y, Weber J, Takeda H. Methods for Addressing Technology-induced Errors: The Current State. Yearb Med Inform. 2016 Nov 10;(1):30-40. doi: 10.15265/IY-2016-029. Review. PMID: 27830228. PMCID: PMC5171580.

Kuziemsky CE, Nøhr C, Borycki EM, Kushniruk AW, Senathirajah Y. Understanding the Context of Patient Safety Through The Lenses of Three IMIA Working Groups. Stud Health Technol Inform. 2015;218:40615. PMID: 26262545.

Senathirajah Y. Safer Design - Composable EHRs and Mechanisms for Safety. Stu Health Technol Inform. 2015;218:40602. PMID: 2626532.

Senathirajah Y, Kaufman D, Bakken S. The clinician in the driver's seat: part 2 - intelligent uses of space in a drag/drop user-composable electronic health record. J Biomed Inform. 2014 Dec;52:177-88. doi: 10.1016/j.jbi.2014.09.008. Epub 2014 Oct 24. PMID: 25445921.

Senathirajah Y, Bakken S, Kaufman D. The clinician in the Driver's Seat: part 1 - a drag/drop user-composable electronic health record platform. J Biomed Inform. 2014 Dec;52:165-76. doi: 10.1016/j.jbi.2014.09.002. Epub 2014 Sep 18. PMID: 25240253.

Senathirajah Y, Kaufman D, Bakken S. Beyond copy and paste: clinician approaches to meeting information needs during note writing. Stud Health Technol Inform. 2014;205:599-603. PMID: 25160256.

Merrill J, Phillips A, Keeling J, Kaushal R, Senathirajah Y Effects of automated immunization registry reporting via an electronic health record deployed in community practice settings. Appl Clin Inform. 2013 Jun 12;4(2):267-75. doi: 10.4338/ACI-2013-02-CR-0009. Print 2013. PMID: 23874363. PMCID: PMC3716417.

Senathirajah Y, Kaufman D, Bakken S. Essential questions: accuracy, errors and user perceptions in a drag/drop user-composable electronic health record. Stud Health Technol Inform. 2013;194:181-7. PMID: 23941953.

Senathirajah Y, Bakken S. Visual clustering analysis of CIS logs to inform creation of a user-configurable Web CIS interface. Methods Inf Med. 2011;50(4):337-48. doi: 10.3414/ME09-01-0087. Epub 2011 Jun 21. PMID: 21691676.

Senathirajah Y, Bakken S. Important ingredients for health adaptive information systems. Stud Health Technol Inform. 2011;169:280-4. PMID: 21893757.

Senathirajah Y, Kaufman D, Bakken S. Cognitive Analysis of a Highly Configurable Web 2.0 EHR Interface. AMIA Annu Symp Proc. 2010 Nov 13;2010:732-6. PMID: 21347075. PMCID: PMC3041363.

Senathirajah Y, Bakken S. Architectural and usability considerations in the development of a Web 2.0-based EHR. Stud Health Technol Inform. 2009;143:315-21. PMID: 19380954.

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
Room 433
5607 Baum Boulevard, Suite 500
Pittsburgh, PA
15206
412-624-8950

Chief Research Informatics Officer, Health Sciences and Institute for Precision Medicine (IPM)

Visiting Professor, Department of Biomedical Informatics (DBMI), School of Medicine

Affiliate Scholar, Pitt Cyber

Publications: 

Amin W, Linkov F, Landsittel DP, Silverstein JC, Bashara W, Gaudioso C, Feldman MD, Pass HI, Melamed J, Friedberg JS, Becich MJ. Factors influencing malignant mesothelioma survival: a retrospective review of the National Mesothelioma Virtual Bank cohort. F1000Res. 2018 Aug 3;7:1184. doi: 10.12688/f1000research.15512.3. PubMed PMID: 30410729; PubMed Central PMCID: PMC6198263.3.

Linkov F, Silverstein JC, Davis M, Crocker B, Hao D, Schneider A, Schwenk M, Winters S, Zelnis J, Lee AV, Becich MJ. Integration of Cancer Registry Data into the Text Information Extractio System: Leveraging the Structured Data Import Tool. J Pathol Inform. 2018 Dec 24;9:47. doi: 10.4103/jpi.jpi_38_18. eCollection 2018. PMID: 30662793. PMCID: PMC6319041.

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, June J, Bellam S, Fulara N, Close D, Silverstein JC, Schatz B.  Classification Models for Pulmonary Function using Motion Analysis from Phone Sensors.  2017 Feb 10;2016:401-410. eCollection 2016. PMID: 28269835PMC5333291.

Cheng Q, Juen J, Bellam S, Fulara N, Close D, Silverstein JC, Schatz B. Predicting Pulmonary Function from Phone Sensors. Telemed J E Health. 2017 Nov;23(11):913-919. doi: 10.1089/tmj.2017.0008. Epub 2017 Mar 16. PMID: 28300524. PMCID: PMC5684658.

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

Ann Donnelly, PhD

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Donnelly, Ann
Ann is a research specialist engaged in many of the lab's projects. Her primary research involves studying the role of compensatory mutations in the evolution of antibiotic resistance. Ann is particularly interested in understanding the challenges associated with restoring antibiotic sensitivity in multi-drug resistant pathogens.
Wright Lab
437 Bridgeside Point II
450 Technology Dr
Pittsburgh, PA 15219
412-383-0028 (lab)

Research Assistant Professor

PhD, Chemistry, Princeton University
BA, Chemistry,Drew University
 

Erik S. Wright, PhD, MS

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Wright, Erik
Erik's research integrates experimental and computational approaches 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. Erik studies the strategies that naturally antibiotic-producing bacteria have evolved to discourage the build-up of resistance, how we might employ similar tactics in the clinic, and how some pathogens have adapted to overcome antibiotics while paying a minimal price for resistance. The goal of this research is to develop new strategies for treating infectious disease, ultimately turning the tide against increasing antibiotic resistance.
Dr. Wright is interested in combatting infectious disease by better understanding how microorganisms evolve.
426 Bridgeside Point II
450 Technology Dr
Pittsburgh, PA 15219
412-383-4458

  Assistant Professor, Department of Biomedical Informatics

Publications: 

Birer C, Wright ES. Capturing the complex interplay between drugs and the intestinal microbiome. Clin Pharmacol Ther. 2019 May 18. doi: 10.1002/cpt.1505. [Epub ahead of print] PubMed PMID: 31102465

Murali A, Bhargava A, Wright ES. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome. 2018 Aug 9;6(1):140. doi: 10.1186/s40168-018-0521-5. PMID: 30092815. PMCID: PMC6085705.

Wright ES, Baum DA. Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow. BMC Genomics. 2018 Oct 3;19(1):724. doi: 10.1186/s12864-018-5099-6. PubMed PMID: 30285620. PMCID: PMC6171291.

Wright ES, Vetsigian KH. Stochastic exits from dormancy give rise to heavy-tailed distributions of descendants in bacterial populations. bioRxiv. 2018 January 11. http://doi.org/10.1101/246629

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

Wright ES, Vetsigian KH. DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures. Bioinformatics. 2016 May 15;32(10):1565-7. doi: 10.1093/bioinformatics/btw047. Epub 2016 Jan 23. PMID: 26803162.

Wright ES, Vetsigian KH. Inhibitory interactions promote frequent bistability among competing bacteria. Nat Commun. 2016 Apr 21;7:11274. doi: 10.1038/ncomms11274. PMID: 27097658. PMCID: PMC4844671.

Wright ES, Vetsigian KH. Quality filtering of Illumina index reads mitigates sample cross-talk. BMC Genomics. 2016 Nov 4;17(1):876. doi: 10.1186/s12864-016-3217-x. PMID: 27814679. PMCID: PMC5097354.

Wright ES. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics. 2015 Oct 6;16:322. doi: 10.1186/s12859-015-0749-z. PMID: 26445311. PMCID: PMC4595117.

Wright ES, Yilmaz LS, Corcoran AM, Ökten HE, Noguera DR. Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification. Appl Environ Microbiol. 2014 Aug;80(16):5124-33. doi: 10.1128/AEM.01685-14. Epub 2014 Jun 13. PMID: 24928876. PMCID: PMC4135741.

Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR. Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates. Environ Microbiol. 2014 May;16(5):1354-65. doi: 10.1111/1462-2920.12259. Epub 2013 Sep 24. PMID: 24750536.

Noguera DR, Wright ES, Camejo P, Yilmaz LS. Mathematical tools to optimize the design of oligonucleotide probes and primers. Appl Microbiol Biotechnol. 2014 Dec;98(23):9595-608. doi: 10.1007/s00253-014-6165-x. Epub 2014 Oct 31. Review. PMID: 25359473.

Wright ES, Yilmaz LS, Noguera DR. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol. 2012 Feb;78(3):717-25. doi: 10.1128/AEM.06516-11. Epub 2011 Nov 18. PMID: 22101057. PMCID: PMC3264099.

Kayhan Batmanghelich, PhD

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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

Publications: 

Singla S, Gong M, Ravanbakhsh S, Sciurba F, Poszos B, Batmanghelich KN. Subject2Vec: Generative-Discriminative Approach from a Set of Image Patches to a Vector. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI). 2018: 502-510. doi: 10.1007/978-3-030-00928-1_57. PubMed PMID: 30895278. PMCID: PMC6422035.

Fu H, Gong M, Wang C, Batmanghelich K, Tao D. Deep Ordinal Regression Network for Monocular Depth Estimation. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2018 Jun;2018:2002-2011. doi: 10.1109/CVPR.2018.00214. Epub 2018 Dec 17. PubMed PMID: 31274971. PMCID: PMC6607900.

Huisman, SMH, Mahfouz A, Batmanghelich NK, Lelieveldt BPF, Reinders MJT on behalf of for the Alzheimer's Disease Neuroimaging Initiative. A structural equation model for imaging genetics using spatial transcriptomics. Brain Inf. (2018) 5:13. PMID: 30390165. doi: https://doi.org/10.1186/s40708-018-0091-0.

Schabdach J, Wells S, Cho M, Batmanghelich N. A Likelihood-Free Approach for Characterizing Heterogeneous Diseases in Large-Scale Studies. International Conference on Information Processing in Medical Imaging (IPMI). 2017 Jun 25; 170-183. PMID:29129964. PMCID: PMC5679301. doi: 10.1007/978-3-319-59050-9_14

Freifeld O, Haubert S, Fisher J III, Batmanghelich N, Transformations Based on Continuous Piecewise-Affine Velocity Fields. IEEE Trans Pattern Anal Mach Intell. 2017 Dec;39(12):2496-2509. Epub 2017 Jan 1. doi: 10.1109/TPAMI.2016.2646685. PubMed PMID: 28092517. PMCID: PMC5889303.

Batmanghelich N, Saeedi A, Narasimhan K, Gershman S. Nonparametric Spherical Topic Modeling with Word Embeddings. Proc Conf Assoc Comput Linguist Meet. 2016 Aug; 2016: 537-542. pp 537-542, 2016. doi: 10.18653/v1/P16-2087. PMID: 30636838. PMCID: PMC6327958

Batmanghelich N, Dalca A, Quon G, Sabuncu M, Golland P. Probabilistic Modeling of Imaging, Genetics and the Diagnosis. IEEE Transactions on Medical Imaging (TMI), pp 1765-1779, 2016.  doi: 10.1109/TMI.2016.2527784. PMID: 26886973. PMCID: PMC5364030.

Batmanghelich N, Saeedi A, Estepar RJ, Cho M, Wells S. Inferring Disease Status by non-Parametric Probabalistic Embedding. Medical Computer Vision and Bayesian and Graphical Models for Biomedical Imaging. 2016 Oct 21; 49-57.

Binder P, Batmanghelich N, Estepar R, Golland P. Unsupervised Discovery of Emphysema Subtypes in a Large Clinical Cohort. Machine Learning in Medical Imaging: 7th International Workshop, MLMI 2016, Held in Conjunction with MICCAI 2016, Athens, Greece, October 17, 2016, Proceedings. 2016 Oct;10019:180-187. doi: 10.1007/978-3-319-47157-0_22. Epub 2016 Oct 1. PubMed PMID: 28232959. PMCID: PMC5317320.

Batmanghelich N, Saeedi A, Cho M, Jose R, Golland P. 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.

Wachinger C, Batmanghelich N, Golland P, Reuter M. 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.

Bloy L, Ingalhalikar M, Batmanghelich N. 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.

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

Batmanghelich N, Ye D, Taskar B, Davatzikos C. 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

Davatzikos C, Bhatt P, Shaw L, Batmanghelich N, Trojanowski J. 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

Batmanghelich N, Gooya A, Taskar B, Davatzikos C. 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

Batmanghelich N, Verma R. 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

Fan Y, Batmanghelich N, Clark C, Davatzikos C. 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

Shariatpanahi H, Batmanghelich N, Kermani A, Ahmadabadi M, Soltanian-Zadeh H. 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

Karimi M, Batmanghelich N, Soltanian-Zadeh H, Lucas C. 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

Douglas Landsittel, PhD

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Landsittel, Douglas
Department of Biomedical Informatics
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 523
5607 Baum Boulevard, Suite 500
Pittsburgh, PA
412-624-0270
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
Publications: 

Hayek SS, Landsittel DP, Wei C, Zeier M, Yu ASL, Torres VE, Roth S, Pao CS, Reiser J. Soluble Urokinase Plasminogen Activator Receptor and Decline in Kidney Function in Autosomal Dominant Polycystic Kidney Disease. J Am Soc Nephrol. 2019 Jun 6. doi: 10.1681/ASN.2018121227. [Epub ahead of print] PubMed PMID: 31171572.

Bae KT, Shen C, Landsittel DP, Zhao W, Wu Z, Tao C, Chapman AB, Torres VE, Yu ASL, Mrug M, Bennett B, Flessner MF, Harris PC. Growth pattern of kidney cyst number and volume in autosomal dominant polycystic kidney disease.  2019  Jun 7;14(6):823-833. doi: 10.2215/CJN.10360818. Epub 2019 May 14. PubMed PMID: 31088850.

Yu ASL, Shen C, Landsittel DP, Grantham JJ, Cook LT, Torres VE, Chapman AB, Bae KT, Mrug M, Harris PC, Rahbari-Oskoui FF, Flessner MF, Bennett WM. Long-term trajectory of kidney function in autosomal dominant polycystic kidney disease. Kidney Int. 2019 May;95(5):1253-1261. doi: 10.1016/j.kint.2018.12.023. Epub 2019 Mar 4. PubMed PMID: 30922668.

Macedo C, Hadi K, Walters J, Elinoff B, Marrai M, Zeevi A, Ramaswami B, Chalasani G, Landsittel D, Shields A, Alloway R, Woodle ES, Lakkis F, Metes D. Impact of Induction Therapy on Circulating T Helper Cells and Subsequent Donor-Specific Antibody Formation After Kidney Transplant. Kidney Int Rep. 2019 Mar;4(3):455-469. doi: 10.1016/j.ekir.2018.11.020. PubMed PMID: 30899873. PMCID: PMC6409398

Schnetz MP, Hochheiser HS, Danks DJ, Landsittel DP, Vogt KM, Ibinson JW, Whitehurst SL, McDermott SP, Duque MG, Kaynar AM. The triple variable index combines information generated over time from common monitoring variables to identify patients expressing distinct patterns of intraoperative physiology. BMC Med Res Methodol. 2019 Jan 14;19(1):17. doi: 10.1186/s12874-019-0660-9. PMID: 30642260. PMCID: PMC6332613.

Radovic A, Li Y, Landsittel D, Stein BD, Miller E. A Social Media Website (Supporting Our Valued Adolescents) to Support Treatment Uptake for Adolescents With Depression and/or Anxiety and Their Parents: Protocol for a Pilot Randomized Controlled Trial. JMIR Res Protoc. 2019 Jan 23;8(1):e12117. doi: 10.2196/12117. PMID: 30672741. PMCID: PMC6264211.

Petrov AA, Traister RS, Crespo MM, Silveira FP, Xie M, Coffey K, Ensor CR, Landsittel D, Pilewski JM.A Prospective Observational Study of Hypogammaglobulinemia in the First Year After Lung Transplantation. Transplant Direct. 2018 Jul 12;4(8):e372. doi: 10.1097/TXD.0000000000000811. eCollection 2018 Aug. PMID: 30255132. PMCID: PMC6092181.

Puttarajappa CM, Hariharan S, Humar A, Paliwal Y, Gao X, Cruz RJ, Ganoza AJ, Landsittel D, Bhattarai M, Sogawa H. Outcomes of Adult Intestinal Transplant Recipients Requiring Dialysis and Renal Transplantation. Transplant Direct. 2018 Jul 20;4(8):e377. doi: 10.1097/TXD.0000000000000815. eCollection 2018 Aug. PubMed PMID: 30255137. PMCID: PMC6092176

Shaikh N, Hoberman A, Hum SW, Alberty A, Muniz G, Kurs-Lasky M, Landsittel D, Shope T. Development and Validation of a Calculator for Estimating the Probability of Urinary Tract Infection in Young Febrile Children. JAMA Pediatr. 2018 Jun 1;172(6):550-556. doi: 10.1001/jamapediatrics.2018.0217. PMID: 29710324. PMCID: PMC6137527.

McKenzie KA, El Ters M, Torres VE, Harris PC, Chapman AB, Mrug M, Rabhari-Oskoui FF, Bae KT, Landsittel DP, Bennett WM, Yu ASL, Mahnken JD. Relationship between caffeine intake and autosomal dominant polycystic kidney disease progression: a retrospective analysis using the CRISP cohort. BMC Nephrol. 2018 Dec 27;19(1):378. doi: 10.1186/s12882-018-1182-0. PMID: 30591038. PMCID: PMC6307167.

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. Menopause. 2017 Aug;24(8):886-893. doi: 10.1097/GME.0000000000000857. PMID: 28399007  PMCID: PMC5524590.

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. J Emerg Nurs. 2017 Jul;43(4):339-346. doi: 10.1016/j.jen.2016.11.07. Epub 2017 Mar 30. PMID: 28366241.

Gao B, Long C, Lee W, Zhang Z, Gao X, Landisttel D, Ezzelarab M, Arares D, Liu Q, Cooper D, Hara H. Anti-Neu5Gc and anti-non-Neu5Gc antibodies in health humans. PLos One. 2017 Jul 17; 12(7):e0180768. doi: 10.1371/journal.pone.0180768. eCollection 2017. PMID: 28715486. PMCID: PMC 55134129.

Rosenberger EM, DeVito Dabbs AJ, DiMartini AF, Landsittel DP, Pilewski JM, Dew MA. Long-Term Follow-up of a Randomized Controlled Trial Evaluating a Mobile Health Intervention for Self-Management in Lung Transplant Recipients. Am J Transplant. 2017 May;17(5):1286–1293. doi: 10.1111/ajt.14062. Epub 2016 Oct 31. PMID: 27664940. PMCID: PMC5365382.

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; CRISP Investigators. Image Texture Features Predict Renal Function Decline in Autosomal Dominant Polycystic Kidney Disease Patients. Kidney Int. 2017 Nov;92(5):1206-1216. doi: 10.1016/j.kint.2017.03.026. Epub 2017 May 20. PMID: 28532709. PMCID: PMC5651185.

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. Psychosom Med. 2017 May;79(4): 441-449. doi: 10.1097/PSY.0000000000000400. PMID: 27763988 PMCID: PMC5477855.

Sentell TL, Shen C, Landsittel D, Mays MH, Southerland J, King MH, Taira DA. Racial/ethnic differences in those accompanying Medicare patients to the doctor: Insights from the 2013 Medicare Current Beneficiary's Survey. J Immigr Minor Health. 2018 Aug 20:20(4):776-783.  doi: 10.1007/s10903-017-0582-8. PMID: 28405871. PMCID: PMC5656534 [Available on 2019-08-01].

Shen C, Landsittel D, Irazabal MV, Yu ASL, Chapman AB, Mrug M, Grantham JJ, Bae KT, Bennett WM, Flessner MF, Torres VE. Performance of the CKD-EPI equation to estimate GFR in a longitudinal study of Autosomal Dominant Polycystic Kidney Disease. Am J Kidney Dis. 2017;69(3):482-484. doi: 10.1053/j.ajkd.2016.10.021. PMID:28027795.  PMCID: PMC5497695.

Taira DA, Seto BK, Davis JW, Seto TB, Landsittel D, Sumida WK. Examining Factors Associated With Nonadherence And Identifying Providers Caring For Nonadherent Subgroups. J Pharm Health Serv Res. 2017 Dec;8(4):247-253. doi: 10.1111/jphs.12193. Epub 2017 Aug 7. PMID:29151900. PMCID: PMC5690547.

Yu ASL, Shen C, Landsittel DP, Harris PC, Torres VE, Mrug M, Bae KT, Grantham JJ, Rahbari-Oskoui FF, Flessner MF, Bennett WM, Chapman AB; Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP). Baseline total kidney volume and the rate of kidney growth are associated with chronic kidney disease progression in Autosomal Dominant Polycystic Kidney Disease. Kidney Int. 2018 Mar; 93(3):691-699. doi: 10.1016/j.kint.2017.09.027. Epub 2017 Dec 28. PMID: 29290310. PMCID: PMC5826779.

Taira DA, Shen C, King M, Landsittel D, Mays MH, Sentell T, Southerland J. Access to medications for medicare enrolees related to race/ethnicity: Results from the 2013 Medicare Current Beneficiary Survey. Res Social Adm Pharm. 2017 Nov; 13(6): 1208-1213. doi: 10.1016/j.sapharm.2016-10-021. Epub 2016 Nov 23. PMID:27914950. PMC ID: PMC5500432.

Landsittel DP, Kessler L, Schmid CH, Marantz P, Suarez-Almazor ME Training in patient-centered outcomes research for specific researcher communities.  2017 Oct;1(5):278-284. doi: 10.1017/cts.2017.307. PMID: 29707248. PMCID: PMC5915813

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. Am J Transplant. 2017 Jan;17(1):140-150. doi: 10.1111/ajt.13929. Epub 2016 Jul 22. PMID: 27333454. PMCID: PMC6139430.

Educational Interests

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

Directory Listing Information
Taylor, Donald P.
Mechanisms of breast cancer metastatic latency through computational models and human 3D-perfused micro-scale tissue bioreactors.
Room 514
5607 Baum Boulevard
Pittsburgh, PA 15206
412-648-9324
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

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.

David Boone, PhD

Directory Listing Information
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
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
Assistant Professor, Director of CoSBBI
Executive Director of the UPCI Academy
Department of Biomedical Informatics
University of Pittsburgh School of Medicine
Publications: 

Nagle AM, Levine KM, Tasdemir N, Scott JA, Burlbaugh K, Kehm JW, Katz TA, Boone DN, Jacobsen BM, Atkinson JM, Oesterreich S, Lee AV. Loss of E-cadherin enhances IGF1-IGF1R pathway activation and sensitizes breast cancers to anti-IGF1R/InsR inhibitors. Clin Cancer Res. 2018 Jun 25. pii: clincanres.0279.2018. doi: 10.1158/1078-0432.CCR-18-0279. [Epub ahead of print]. PMID: 29941485.

Chen J, Nagle AM, Wang YF, Boone DN, Lee AV. Controlled dimerization of insulin-like grown factor-1 and insulin receptors reveal shared and distinct activities of holo and hybrid receptors. J Biol Chem. 2018 Mar 9;293(10):3700-3709. doi: 10.1074/jbc.M117.789503. Epub 2018 Jan 12. PMID: 23990302.

Warburton AJ, Boone DN. Insights of Global Analyses of Long Noncoding RNAs in Breast Cancer. Curr Pathobiol Rep. 2017 Mar;5(1):23-34. doi: 10.1007/s40139-017-0122-1. Epub 2017 Jan 23. PubMed PMID: 28616363. PubMed Central PMCID: PMC5467540.

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.

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

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