Faculty

Yalini Senathirajah, PhD

Directory Listing Information
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

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.

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.

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

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.
426 Bridgeside Point II
450 Technology Dr
Pittsburgh, PA 15219
412-383-4458

  Assistant Professor, Department of Biomedical Informatics

Publications: 

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

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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.
Room 531
5607 Baum Blvd
Pittsburgh
PA
15206
412-648-9037
Assistant Professor, Department of Biomedical Informatics

University of Pittsburgh School of Medicine

Curriculum Vitae

Publications: 

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  [Available on 2018-06-01]  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. PubMed PMID: 28092517. doi: 10.1109/TPAMI.2016.2646685.

Batmanghelich N, Saeedi A, Narasimhan K, Gershman S. 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.

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. PMID: 26886973 DOI: 10.1109/TMI.2016.2527784

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. PubMed Central 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. PMID: 21791408 PMCID: PMC3402718 DOI: 10.1109/TMI.2011.2162961

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

Directory Listing Information
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: 

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 [Available on 2018-08-01].

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.

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 [Available on 2018-05-01].

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.

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.

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. J Immigr Minor Health. 2017 Apr 12. doi: 10.1007/s10903-017-0582-8. [Epub ahead of print.] PMID: 28405871.

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 [Available on 2018-12-01].

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.

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

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: 

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 Jan 12. pii: jbc.M117.789503. doi: 10.1074/jbc.M117.789503. [Epub ahead of print]. 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

Fuchiang (Rich) Tsui, PhD

Directory Listing Information
Tsui, Fu-Chiang (Rich)
Clinical informatics, public health informatics, biosurveillance, mobile healthcare, machine learning, (big) data mining, artificial intelligence, natural language processing, precision medicine, data warehouse, time series analysis, signal processing, and large real-time production systems.
Dr. Tsui is Assistant Professor of Biomedical Informatics, Intelligent Systems, and Bioengineering. He is Associate Director of RODS Laboratory.
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
Biomedical Informatics Training Program Core Faculty, University of Pittsburgh School of Medicine
Publications: 

Aronis JM, Millett NE, Wagner MM, Tsui F, Ye Y, Ferraro JP, Haug PJ, Gesteland PH, Cooper GF. A Bayesian system to detect and characterize overlapping outbreaks. J Biomed Inform. 2017 Sep;73:171-181. doi: 10.1016/j.jbi.2017.08.003. Epub 2017 Aug 7. PMID: 28797710. PMC5604259.

Posada JD, Barda AJ, Shi L, Xue D, Ruiz V, Kuan PH, Ryan ND, Tsui FR. Predictive Modeling for Classification of Positive Valence System Symptom Severity from Initial Psychiatric Evaluation Records. J Biomed Inform. 2017Nov; 75S:S94-S104. doi: 10.1016/j.jbi.2017.05.019. Epub 2017 May 29. PMID: 28571784. PMCID: PMC5705330. 

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.

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)

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.

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

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.

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.

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

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.

Que, J., & Tsui, F.-C. (2012). Spatial and Temporal Algorithm Evaluation for Detecting Over-The-Counter Thermometer Sale Increases during 2009 H1N1 Pandemic. Online Journal of Public Health Informatics, 4(1), ojphi.v4i1.3915. http://doi.org/10.5210/ojphi.v4i1.3915 PMID: 23569624 PMCID: PMC3615801

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

Que, J., & Tsui, F.-C. (2011). Rank-based spatial clustering: an algorithm for rapid outbreak detection. Journal of the American Medical Informatics Association : JAMIA, 18(3), 218–224. http://doi.org/10.1136/amiajnl-2011-000137 PMID: 21486881 PMCID: PMC3078668

Rexit R, Tsui FC, Espino JU, Wesaratchakit S, Ye Y, Chrysanthis PK. Using a distributed search engine to identify optimal product sets for use in an outbreak detection system. International Workshop on Collaborative Big Data (C-Big 2012); 2012 Oct 14 - 17; Pittsburgh, PA. 2014 Oct. 560-66.

Wu TS, Shih FY, Yen MY, Wu JS, Lu SW, Chang KC, Hsiung C, Chou JH, Chu YT, Chang H, Chiu CH, Tsui FCWagner 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, and 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.

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

Tsui FC, Espino JU, Wagner MM, Gesteland P, Ivanov O, Olszewski RT, Liu Z, Zeng X, Chapman W, Wong WK, Moore A. (2002). Data, network, and application: technical description of the Utah RODS Winter Olympic Biosurveillance System. Proceedings of the AMIA Symposium, 815–819. PMID: 12463938 PMCID: PMC2244477

Wagner MM, Tsui FC, Espino JU, Dato VM, Sittig DF, Caruana RA, McGinnis LF, Deerfield DW, Druzdzel MJ, Fridsma DB. The emerging science of very early detection of disease outbreaks. J Public Health Manag Pract. 2001 Nov;7(6):51-9. PMID: 11710168

Tsui FC, Wagner MM, Dato V, Chang CC. Value of ICD-9 coded chief complaints for detection of epidemics. Proceedings / AMIA ... Annual Symposium. AMIA Symposium. 2001;711-5. PMID: 11825278 PMCID: PMC2243339

Tsui FC, Wagner MM, Wilbright W, Tse A, Hogan WR. A feasibility study of two methods for end-user configuration of a clinical event monitor. Proceedings / AMIA ... Annual Symposium. AMIA Symposium. 1999;975-8.  PMID: 10566506 PMCID: PMC2232807

Tsui FC, Li C, Sun M, Sclabassi RJ. "Acquiring, Modeling and Predicting Intracranial Pressure in the Intensive Care Unit,". Biomedical Engineering, Applications, Basis, and Communications. 1996;8(6):566-578.

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

Uma Chandran, PhD, MSIS

Directory Listing Information
Chandran, Uma
Genomic data mining, Next Generation Sequencing data analysis, Integrative analysis of The Cancer Genome Atlas Project (TCGA), Development of computing infrastructure for large genomics datasets
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
Research Associate Professor, Biomedical Informatics
Co-Director, Cancer Boinformatics Services, UPMC Hillman Cancer Center
Publications: 

Eshbach ML, Sethi R, Avula R, Lamb J, Hollingshead DJ, Finegold DN, Locker J, Chandran UR, Weisz OA. The Transcriptome of the Didelphis virginiana Opossum Kidney OK Proximal Tubule Cell Line. Am J Physiol Renal Physiol. 2017 Sep 1;313(3):F585-F595. doi: 10.1152/ajprenal.00228.2017. Epub 2017 Jun 14. PubMed PMID: 28615248. PMC ID: PMC 5625107.

Andersen CL, Sikora MJ, Boisen MM, Ma T, Christie A, Tseng G, Park Y, Luthra S, Chandran U, Haluska P, Mantia-Smaldone GM, Odunsi K, McLean K, Lee AV, Elishaev E, Edwards RP, Oesterreich S. Active Estrogen Receptor-alpha Signaling in Ovarian Cancer Models and Clinical Specimens. Clin Cancer Res. 2017 Jul 15;23(14):3802-3812. doi: 10.1158/1078-0432.CCR-16-1501. Epub 2017 Jan 10. PubMed PMID: 28073843. PMC ID: PMC5503796.

Frahm KA, Waldman JK, Luthra S, Rudine AC, Monaghan-Nichols AP, Chandran UR, DeFranco DB. A Comparison of the Sexually Dimorphic Dexamethasone Transcriptome in Mouse Cerebral Cortical and Hypothalamic Embryonic Neural Stem Cells. Mol Cell Endocrinol. 2017 May 26. pii: S0303-7207(17)30295-2. doi: 10.1016/j.mce.2017.05.026. [Epub ahead of print] Review. PubMed PMID: 28554804. PMCID: PMC5702594.

Pascal LE, Masoodi KZ, Liu J, Qiu X, Song Q, Wang Y, Zang Y, Yang T, Wang Y, Rigatti LH, Chandran U, Colli LM, Vencio RZN, Lu Y, Zhang J, Wang Z. Conditional deletion of ELL2 induces murine prostate intraepithelial neoplasia. J Endocrinol. 2017 Nov;235(2):123-136. doi: 10.1530/JOE-17-0112. PMID: 28870994.

Ramaswamy S, Walker WH, Aliberti P, Sethi R, Marshall GR, Smith A, Nourashrafeddin S, Belgorosky A, Chandran UR, Hedger MP, Plant TM. The testicular transcriptome associated with spermatogonia differentiation initiated by gonadotrophin stimulation in the juvenile rhesus monkey (Macaca mulatta). Hum Reprod. 2017 Oct 1;32(10):2088-2100. doi: 10.1093/humrep/dex270. PMID: 28938749.

Puri P, Little-Ihrig L, Chandran U, Law NC, Hunzicker-Dunn M, Zeleznik AJ. Protein Kinase A: A Master Kinase of Granulosa Cell Differentiation. Sci Rep. 2016 Jun 21;6:28132. doi: 10.1038/srep28132. PMID: 27324437. PMCID: PMC4914995.

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. 2015:14(12):1884-92. http://doi.org/10.1080/15384101.2015.1036203 PMID: 25927284. PMCID: PMC4614952.

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 Res. 2016 Mar 1;76(5):1031-43. doi: 10.1158/0008-5472.CAN-15-2001 PMID:26676749. PMCID: PMC4775348.

Chandran UR, Medvedeva OP, Barmada MM, Blood PD, Chakka A, Luthra S, Ferreira A, Wong KF, Lee AV, Zhang Z, Budden R, Scott JR, Berndt A, Berg JM, Jacobson RS. TCGA Expedition: A Data Acquisition and Management System for TCGA Data. PLoS One. 2016 Oct 27;11(10):e0165395. doi: 10.1371/journal.pone.0165395. eCollection 2016. PMID: 27788220. PMCID: PMC5082933.

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. Mol Endocrinol. 2016 Jan;30(1):144-54. doi: 10.1210/me.2015-1258. PMID: 26606517. PMCID: PMC4695633.

Chandran UR, Luthra S, Santana-Santos L, Mao P, Kim SH, Minata M, Li J, Benos PV, DeWang M, Hu B, Cheng SY, Nakano I, Sobol RW. Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells. Genom Data. 2015 Sep 1;5:333-336.http://doi.org/10.1016/j.gdata.2015.07.007. PMID: 26251826. PMCID: PMC4523279.

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. The molecular landscape of premenopausal breast cancer. Breast Cancer Res. 2015 Aug 7;17:104. http://doi.org/10.1186/s13058-015-0618-8. PMID: 26251034. PMCID: PMC4531812.

Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS. Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PLoS One. 2015 June 26;10(6):e0131166. http://doi.org/10.1371/journal.pone.0131166. eCollection 2015. PMID: 26115441. PMCID: PMC4483235.

Manohar R, Li Y, Fohrer H, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E. Identification of a candidate stem cell in human gallbladder. Stem Cell Res. 2015 May;14(3):258-69. http://doi.org/10.1016/j.scr.2014.12.003. Epub 2015 Feb 7. PMID: 25765520. PMCID: PMC4439375.

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.

Peffer ME, Chandran UR, Luthra S, Volonte D, Galbiati F, Garabedian MJ, Monaghan AP, DeFranco DB. Caveolin-1 regulates genomic action of the glucocorticoid receptor in neural stem cells. Mol Cell Biol. 2014 Jul;34(14):2611-23. doi: https://doi.org/10.1128/MCB.01121-13. PMID: 24777604. PMCID: PMC4097667.

Sikora MJ, Cooper KL, Bahreini A, Luthra S, Wang G, Chandran UR, Davidson NE, Dabbs DJ, Welm AL, Oesterreich S. Invasive lobular carcinoma cell lines are characterized by unique estrogen-mediated gene expression patterns and altered tamoxifen response. Cancer Res. 2014 Mar 1;74(5):1463-74. doi: http://doi.org/10.1158/0008-5472.CAN-13-2779. PMID: 24425047. PMCID: PMC3955299.

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. doi: 10.1016/j.ygyno.2013.04.017. Epub 2013 Apr 17. PMID: 23603370.

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.

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. doi: 10.1073/pnas.1221478110. Epub 2013 May 6. PMID: 23650391. PMCID: PMC3666732.

Krill-Burger JM, Lyons MA, Kelly LA, Sciulli CM, Petrosko P, Chandran UR, Kubal MD, Bastacky SI, Parwani AV, Dhir R, LaFramboise WA. Renal cell neoplasms contain shared tumor type-specific copy number variations. Am J Pathol. 2012 Jun; 180(6):2427-39. doi: 10.1016/j.ajpath.2012.01.044. Epub 2012 Apr 3. PMID: 22483639. PMCID: PMC3378847.

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.

McDade K, Day RS, Chandran U, Lisovich A. Optimal Probeset Filtering Using Proteomic-Transcriptomic Correlations. In: Proceedings of the AMIA Joint Summit on Translational Science; 2012 Mar 19-21; San Francisco, CA.

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

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. doi: 10.1186/1741-7015-10-157. PMID: 23216991. PMCID: PMC3566965.

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

Manohar R, Komori J, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E. Identification and expansion of a unique stem cell population from adult mouse gallbladder. Hepatology. 2011 Nov; 54(5):1830-41. PMID: 21793026. PMCID: PMC3205206 doi: 10.1002/hep.24568

Lisovich A, Chandran UR, Lyons-Weiler MA, LaFramboise WA, Brown AR, Jakacki RI, Pollack IF, Sobol RW. (2011). A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples. BMC Med Genomics. 2011 Jan 26;4:14. http://doi.org/10.1186/1755-8794-4-14. PMID: 21269491. PMCID: PMC3041647.

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

Chang G, Xu S, Dhir R, Chandran U, O'Keefe DS, Greenberg NM, Gingrich JR. Hypoexpression and epigenetic regulation of candidate tumor suppressor gene CADM-2 in human prostate cancer. Clin Cancer Res. 2010 Nov 15; 16(22):5390-401. Epub 2010 Nov 9. PMID: 21062931. PMCID: PMC3541035. doi: 10.1158/1078-0432.CCR-10-1461.

AEscamilla-Hernandez, R., Little-Ihrig, L., Orwig, K. E., Yue, J., Chandran, U., & Zeleznik, A. J. (2008). Constitutively Active Protein Kinase A Qualitatively Mimics the Effects of Follicle-Stimulating Hormone on Granulosa Cell Differentiation. Molecular Endocrinology, 22(8), 1842–1852. http://doi.org/10.1210/me.2008-0103 PMID: 18535249 PMCID: PMC2725770

Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP, Parwani AV, Sciulli CM, Li J, Chandran UR, Bastacky SI, Dhir R. Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Modern Pathology : An Official JouCopyrnal of The United States and Canadian Academy of Pathology, Inc. 2008 May;21(5):599-608.  PMID: 18246049 DOI: 10.1038/modpathol.2008.20

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

Chandran UR, Lyons-Weiler J, Sciulli C, Monzon FA. Informatics requirements of a high throughput genomics laboratory. AMIA Summit on Translational Bioinformatics. 2008;(0).

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

Chiosea S, Jelezcova E, Chandran U, Luo J, Mantha G, Sobol RW, Dacic S. Overexpression of Dicer in precursor lesions of lung adenocarcinoma. Cancer research. 2007 Mar 1;67(5):2345-50. PMID: 17332367 DOI: 10.1158/0008-5472.CAN-06-3533

Kelavkar UP, Harya NS, Hutzley J, Bacich DJ, Monzon FA, Chandran U, Dhir R, O'Keefe DS. DNA methylation paradigm shift: 15-lipoxygenase-1 upregulation in prostatic intraepithelial neoplasia and prostate cancer by atypical promoter hypermethylation. Prostaglandins & other lipid mediators. 2007 Jan;82(1):185-97. PMID: 17164146 DOI: 10.1016/j.prostaglandins.2006.05.015

Kelavkar, U., Lin, Y., Landsittel, D., Chandran, U., & Dhir, R. (2006). The yin and yang of 15-lipoxygenase-1 and delta-desaturases: Dietary omega-6 linoleic acid metabolic pathway in prostate. Journal of Carcinogenesis, 5, 9. http://doi.org/10.1186/1477-3163-5-9 PMID: 16566819 PMCID: PMC1440856

Chiosea S, Jelezcova E, Chandran U, Acquafondata M, McHale T, Sobol RW, Dhir R. Up-regulation of dicer, a component of the MicroRNA machinery, in prostate adenocarcinoma. The American journal of pathology. 2006 Nov;169(5):1812-20. PMID 17071602 PMCID: PMC1780192

Shah UZ, Dhir R, Gollin SM, Chandran UR, Lewis D, Acquafondata M, Pflug BR. Fatty Acid Synthase Gene Expression Amplification in Prostate Adenocarcinoma. Hum Pathol. 2006;4(0):401-409.

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

Chandran UR, DeFranco DB. Regulation of gonadotropin-releasing hormone gene transcription. Behavioural Brain Research. 1999;105(0):29-36. PMID: 10553688

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

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.

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

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.

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.

Chen J, Liu Y, Lu S, Sze S, Zhang F. Iterative Expansion and Color Coding: An Improved Algorithm for 3D-Matching. ACM Transactions on Algorithms. 2012; 8(1):6.

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.

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.

Chen J, Feng Q, Liu Y, Lu S, Wang J. Improved Deterministic Algorithms for Weighted Matching and Packing Problems. Theoretical Computer Science; 2011: 412(23):2503-2512.

Chen J, Lu S. Improved Parameterized Set Splitting Problem: A Probabilistic Approach. Algorithmica. 2009; 54 (4):472-489.

Chen J, Kneis J, Lu S, Mölle D, Richter S, Rossmanith P, Sze S, Zhang F. Randomized divide-and-conquer: Improved path, matching, and packing algorithm. SIAM Journal on Computing. 2009; 38 (6):2526-2547.

Chen J, Liu Y, Lu S. An improved parameterized algorithm for the minimum node mutiway cut problem. Algorithmica. 2009:55(1):1-13.

Chen J, Fomin F, Liu Y, Lu S, Villanger Y. Improved Algorithms for the Feedback Vertex Set Problems. Journal of Computer and System Science. 2008;74(7):1188-1198.

Chen J, Liu Y, Lu S, O’Sullivan B, Razgon I. A Fixed-Parameter Algorithm for the Directed Feedback Vertex Set Problem. Journal of the ACM. 2008; 55(5):21.

Lu S, Zhang F, Chen J, Sze S. Finding Pathway Structures in Protein Interaction Networks. Algorithmica. 2007:48(4):363-74.

Chen J, Liu Y, Lu S. Directed Feedback Vertex Set Problem is FPT. Structure Theory and FPT Algorithmics for Graphs, Digraphs and Hypergraphs. 2007.

Chen J, Lu S, Sze SH, Zhang F. Improved Algorithms for Path, Matching, and Packing Problems. Proc SODA 2007. 18th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA); 2007 Jan 7-9; 298-307.



 

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