Faculty

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: 

Butterfield LH, Vujanovic L, Santos PM, Maurer DM, Gambotto A, Lohr J, Li C, Waldman J, Chandran U, Lin Y, Lin H, Tawbi HA, Tarhini AA, Kirkwood JM. Multiple antigen-engineered DC vaccines with or without IFNα to promote antitumor immunity in melanoma. J Immunother Cancer. 2019 Apr 24;7(1):113. doi: 10.1186/s40425-019-0552-x. PubMed PMID: 31014399.

Faden DL, Concha-Benavente F, Chakka AB, McMichael EL, Chandran U, Ferris RL. Immunogenomic correlates of response to cetuximab monotherapy in head and neck squamous cell carcinoma. Head Neck. 2019 Mar 4. doi: 10.1002/hed.25726. [Epub ahead of print]. PMID: 30828910.

Liu Q, Dwyer GK, Zhao Y, Li H, Mathews LR, Chakka AB, Chandran UR, Demetris JA, Alcorn JF, Robinson KM, Ortiz LA, Pitt B, Thomson AW, Fan MH, BIlliar TR, Turnquist HR. IL-33-mediated IL-13 secretion by ST2+ Treg controls inflammation after lung injury. JCI Insight. 2019 Feb 19. pii: 123919. doi: 10.1172/jci.insight.123919. Epub ahead of print. PMID: 20779711.

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. 2018 Aug 15;471:42-50.. doi: 10.1016/j.mce.2017.05.026. PubMed PMID: 28554804. PMCID: PMC5702594.

Carson RA, Rudine AC, Tally SJ, Franks AL, Frahm KA, Waldman JK, Silswal N, Burale S, Phan JV, Chandran UR, Monaghan AP, DeFranco DB. Statins impact primary embryonic mouse neural stem cell survival, cell death, and fate through distinct mechanisms. PLoS One. 2018 May 8;13(5):e0196387. doi: 10.1371/journal.pone.0196387. eCollection 2018. PMID: 29738356.

Cao C, Wu H, Vasilatos SN, Chandran U, Qin Y, Wan Y, Oesterrich S, Davidson NE, Huang Y. HDAC5-LSD1 Axis Regulates Antineoplastic Effect of Natural HDAC Inhibitor Sulforaphane in Human Breast Cancer Cells. Int J Cancer. 2018 Sep 15;143(6):1388-1401. doi: 10.1005/ijc.31419. Epub 2018 Apr 20. PMID 29633255. PMCID: PMC6105499 [Available on 2019-09-15]

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

Aliberti P, Sethi R, Belgorosky A, Chandran UR, Plant TM, Walker WH. Gonadotrophin-mediated miRNA expression in testis at onset of puberty in rhesus monkey; predictions on regulation of thyroid hormone activity and DLK1-DIO3 locus. Mol Hum Reprod. 2018 Dec 24. doi: 10.1093/molehr/gay054. [Epub ahead of print]. PMID: 30290698.

Martin JM, Avula R, Nowalk MP, Lin CJ, Horne WT, Chandran UR, Nagg JP, Zimmerman RK, Cole KS, Alcorn JF. Inflammatory Mediator Expression Associated WIth Antibody Response Induced by Live Attenuated vs Inactivated Influenza Virus in Children. Open Forum Infect Dis. 2018 Oct 24;5(11):ofy277. doi: 10.1093/ofid/ofy277. eCollection 2018 Nov. PMID: 30515427. PMCID: PMC6262113.

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.

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

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

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.

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 KE, Yue J, Chandran U, Zeleznik AJ. (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 Journal 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, 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.

Chandran UR, Warren BS, Baumann CT, Hager GL, DeFranco DB. The glucocorticoid receptor is tethered to DNA-bound Oct-1 at the mouse GnRH distal negative glucocorticoid response element. J. Biol. Chem. 1999;274(0):2372-2378. PMID: 9891005.

Attardi B, Tsujii T, Friedman R, Zeng Z, Roberts JL, Dellovade T, Pfaff D, Chandran UR, DeFranco DB. Glucocorticoid repression of gonadotropin-releasing hormone gene expression and secretion in morphologically distinct subpopulations of GT1-7 cells. Mol. Cell. Endocrinol. 1997;131(0):241-255. PMID: 9296383.

Chandran UR, Attardi B, Friedman R, Zheng ZW, Roberts JL, DeFranco DB. Glucocorticoid repression of the mouse gonadotropin-releasing hormone gene is mediated by promoter elements that are recognized by heteromeric complexes containing glucocorticoid receptor. J. Biol. Chem.. 1996;271(0):20412-20420. PMID: 8702778

Chandran UR, Attardi B, Friedman R, Dong KW, Roberts JL, DeFranco DB. Glucocorticoid receptor-mediated repression of gonadotropin-releasing hormone promoter activity in GT1 hypothalamic cell lines. Endocrinol. 1994;134(0):1467-1474. PMID: 8119188.

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: 

Y. Xue, G. Cooper, C. Cai, S. Lu, B. Hu, X. Ma, and X. Lu. Tumour-specific Causal Inference Discovers Distinct Disease Mechanisms Underlying Cancer Subtypes. Scientific Reports; 2019 Sep 13;9(1):13225. doi: 10.1038/s41598-019-48318-7; PMID: 31519988​

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang JQ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Comput Biol, 2019 Jul 15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. [Epub ahead of print] PMID: 31276486; PMCID: PMC6650088.

Liang L, Chen V, Zhu K, Fan X, Lu X, Lu S. Integrating data and knowledge to identify functional modules of genes: a multilayer approach. BMC Bioinformatics. 2019 May 2;20(1):225. doi: 10.1186/s12859-019-2800-y. PubMed PMID: 31046665

M. Minata, A. Audia, J. Shi, S. Lu, J. Bernstock, M. Pavlyukov, A. Das, S.Kim, Y. Shin, Y. Lee, H. Koo, K. Snigdha, I. Waghmare, X. Guo, A. Mohyeldin, D. Gallego-Perez, J. Wang, D. Chen, P. Cheng, F. Mukheef, M. Contreras, J.Reyes, B. Vaillant, E.Sulman, S. Cheng, J. Markert, B.Tannous, X. Lu, M. Kango-Singh, L J. Lee, D. Nam, I. Nakano, K.Bhat. Phenotypic Plasticity of Invasive Edge Glioma Stem-like Cells in Response to Ionizing Radiation. Cell Reports; 2019; 26(7); PMID:30759398.​

X. Fan, S. Zhang *, S. Zhang, K. Zhu, S. Lu*. Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information. BMC Bioinformatics; 2019; 20(87); PMID: 30782113.​

X. Wang, M. O'Brien, J. Yu, L. Liang, Q. Zhang, S. Lu, X. An, J. McDyer, R. Mallampalli. Prolonged cold-ischemia induces necroptotic cell death after experimental  lung transplantation. American Journal of Respiratory Cell and Molecular Biology; 2019; PMID: 30742487.​

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

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

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

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

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.



 

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.
Room 519
5607 Baum Boulevard
Pittsburgh
PA
15206
412-648-9323
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
Publications: 

Mtonga TM, Choonara FE, Espino JU, Kachaje C, Kapundi K, Mengezi TE, Mumba SL, Douglas GP. Design and implementation of a clinical Laboratory Information System in a Low Resource Setting. African Journal of Laboratory Medicine.  2019 October 28; 8(1). https://doi.org/10.4102/ajlm.v8i1/841

Fisher AM, Mtonga TM, Espino JU, Jonkman LJ, Connor SE, Cappella NK, Douglas GP. User-centered design and usability testing of RxMAGIC: a prescription management and general inventory control system for free clinic dispensaries. BMC Health Serv Res. 2018 Sep 10;18(1):703. doi: 10.1186/s12913-018-3517-8. PMID: 30200939. PMCID: PMC6131751.

Gadabu OJ, Ben-Smith A, Douglas GP, Chirwa-Nasasara K, Manjomo RC, Harries AD, Dambula I, Kang'oma S, Chiumia T, Chinsinga FB. Scaling up electronic village registers for measuring vital statistics in rural villages in Malawi. Public Health Action. 2018 Jun 21;8(2):79-84. doi: 10.5588/pha.17.0116. PMID: 29946524. PMCID: PMC6012956.

Camacho J, Medina Ch. AM, Landis-Lewis Z, Douglas G, Boyce R. Comparing a Mobile Decision Support System Versus the Use of Printed Materials for the Implementation of an Evidence-Based Recommendation: Protocol for Qualitative Evaluation. JMIR Res Protoc 2018;7(4):e104. doi: 10.2196/resprot.9827. PMID: 29653921. PMCID: PMC5924374.

Mtonga T, Abaye M, Rosko SC, Douglas GP. A comparative usability study of two touchscreen clinical workstations for use in low resource settings. Journal of Health Informatics in Africa 2018;5(2). https://doi.org/10.12856/JHIA-2018-v5-i2-209

Ogoe HA, Asamani JA, Hochheiser H, Douglas GP. Assessing Ghana's eHealth Workforce: implications for planning and training. Human Resources for Health. 2018 Nov 27;16(1):65. doi: https://doi.org/10.1186/s12960-018-0330-8. PMID: 30482223. PMCID: PMC6260724.

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. PMID: 27687973. PMCID: PMC5043635.

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

Landis-Lewis Z, Brehaut JC, Hochheiser H, Douglas GP, Jacobson RS. (2015). Computer-supported feedback message tailoring: theory-informed adaptation of clinical audit and feedback for learning and behavior change. Implementation Science. 2015 Jan 25; 10(12). doi: 10.1186/s13012-014-0203-z.

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.

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

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.

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

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.

Xinghua Lu, MD, PhD, MS

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

Young JD, Andrews B, Cooper GF, Lu X. Learning Latent Causal Structures with a Redundant Input Neural Network. arXiv:2003.13135v1 29 Mar 2020.

 

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang JQ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Comput Biol, 2019 Jul 15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. [Epub ahead of print] PMID: 31276486; PMCID: PMC6650088.

Liang L, Chen V, Zhu K, Fan X, Lu X, Lu S. Integrating data and knowledge to identify functional modules of genes: a multilayer approach. BMC Bioinformatics. 2019 May 2;20(1):225. doi: 10.1186/s12859-019-2800-y. PubMed PMID: 31046665

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

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

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

Ding MQ, Chen L, Cooper GF, Young JD, Lu X. Precision Oncology Beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics. Mol Cancer Res. 2018 Feb;16(2):269-278. doi: 10.1158/1541-7786.MCR-17-0378. Epub 2017 Nov 13. PMID: 29133589. PMCID: PMC5821274.

Jin Q, Dhingra B, Cohen WW, Lu X. Attention MeSH: Simple, Effective and Interpretable Automatic MeSH Indexer. 

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

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

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

Cooper G, Cai C, Lu X. Tumor-specific Causal Inference (TCI): A Bayesian Method for Identifying Causative Genome Alterations within Individual Tumors. bioRxiv (2017). Doi: https://doi.org/10.1101/225631.

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

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

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

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

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

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

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

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

Cai C, Chen L, Jiang X, Lu X. Modeling Signal Transduction from Protein Phosphorylation to Gene Expression. Cancer Inform. 2014 Oct 13; 13(Suppl 1): 59-67. doi: 10.4137/CIN.S13883. eCollection 2014. PMID: 25392684. PMCID: PMC4216050.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Xia Jiang, PhD

Directory Listing Information
Jiang, Xia
Application of AI, Machine Learning, and Bayesian Networks in biomedical domain, clinical informatics, causal learning, prediction and decision support, biomarker/risk factors discovery via learning from data, design and development of computational methods/algorithms, and cancer and translational informatics.
Dr. Jiang's research focuses on developing novel algorithms/systems that improve the computational efficiency of high-dimensional data analysis, and network modeling of cancer genome data.
Room 518
5607 Baum Boulevard
Pittsburgh
PA
15206
412-648-9310
Associate Professor, Department of Biomedical Informatics
University of Pittsburgh School of Medicine
Faculty, Pitt Intelligent Systems Program
Faculty, CMU-Pitt Computational and Systems Biology PhD Program
Publications: 

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang JQ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Comput Biol, 2019 Jul 15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. [Epub ahead of print] PMID: 31276486; PMCID: PMC6650088.

Zeng Z, Jiang X, Li X, Wells A, Luo Y, Neapolitan RE. Conjugated equine estrogen and medroxyprogesterone acetate are associated with decreased risk of breast cancer relative to bioidentical hormone therapy and controls. PLoS One. 2018 May 16;13(5):e0197064. doi: 10.1371/journal.pone.0197064. eCollection 2018. PMID: 29768475. PMCID: PMC5955567.

Zeng Z, Espino S, Roy A, Li X, Khan SA, Clare SE, Jiang X, Neapolitan R, Luo Y. Using natural language processing and machine learning to identify breast cancer local recurrence. BMC Bioinformatics. 2018 Dec 28:19(Suppl 17):498. doi: 10.1186/s12859-018-2466-x. PMID: 30591037. PMCID: PMC6309052.

Neapolitan RE, Jiang X. Artifical intelligence: With an Introduction to Machine Learning, Second Edition. Chapman & Hall/CRC Artifical Intelligence and Robotics Series.Textbook. 2018.

Lee S, Jiang X. Modeling miRNA-mRNA interactions that cause phenotypic abnormality in breast cancer patients. PLOS One.2017 Aug 9;12(8):e1082666. doi: 10.1371/journal.pone.0182666. eCollection 2017. PMID: 28793339. PMCID: PMC5549916.

Neapolitan RE, Jiang X. Defining and Discovering Interactive Causes. In Holmes D and Jain L, editors. Advances in Biomedical Informatics, pp 53-78. Springer, October 2017.

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

Tenenbaum JD, Avillach P, Benhan-Hutchins M, Breitenstein MK, Crowgey EL, Hoffman MA, Jiang X, Madhavan S, Mattison JE, Nagarajan R, Ray B, Shin D, Visweswaran S, Zhao Z, Freimuth RR. An informatics research agenda to support precision medicine: seven key areas. J Am Med Inform Assoc. 2016 Jul;23(4):791-5. doi: 10.1093/jamia/ocv213. Epub 2016 Apr 23. PMID: 27107452. PMCID: PMC4926738.

Zeng Z, Jiang X, Neapolitan R. Discovering causal interactions using Bayesian network scoring and information gain. BMC Bioinformatics. 2016 May 26;17(1):221. doi: 10.1186/s12859-016-1084-8. PMID: 27230078. PMCID: PMC4880828.

Hill SM, Heiser LM, Cokelaer T, Jiang X, et. al. Inferring causal molecular networks: empirical assessment through a community-bsed effort. Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22. PMID: 26901648. PMCID: PMC4854847.

Cai B, Jiang X. Computational methods for ubiquination site prediction using physicochemical properties of protein sequences. BMC Bioinformatics. 2016 Mar 3;17:116. doi: 10.1186/s12859-016-0959-z. PMID: 26940649. PMCID: PMC4778322.

Neapolitan RE, Jiang X. The Bayesian Network Story. In Hajek A and Hitchcock C (Eds.): The Oxford Handbook of Probability and Philosophy. Oxford University Press, 2016.

Neapolitan R, Horvath CM, Jiang X. Pan-cancer analysis of TCGA data reveals notable signaling pathways. BMC Cancer. 2015 Jul 14;15:516. doi: 10.1186/s12885-015-1484-6. PMID: 26169172. PMCID: PMC4501083.

Jiang X, Neapolitan RE. LEAP: biomarker inference through learning and evaluating association patterns. Genet Epidemiol. 2015 Mar;39(3):173-184. doi: 10.1002/gepi.21889. PMID: 25677188. PMCID: PMC4366363.

Neapolitan RE, Jiang X. Study of integrated heterogeneous data reveals prognostic power of gene expression for breast cancer survival. PLoS ONE. 2015 Feb 27;10(2):e0117658. DOI: 10.1371/journal.pone.0117658. PMID: 25723490. PMCID: PMC4344205.

Jiang X, Jao J, Neapolitan R. Learning predictive interactions using information gain and Bayesian network scoring. PLoS ONE. 2015 Dec 1;10(12): e0143247. doi:10.1371/journal.pone.0143247. PMID: 26624895. PMCID: PMC4666609.

Jiang X, Neapolitan RE. Evaluation of a two-stage framework for prediction using big genomic data. Brief Bioinform. 2015 Nov;16(6):912-21. doi: 10.1093/bib/bbv010. Epub 2015 Mar 18. PMID: 25788325. PMCID: PMC4652616.

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

Neapolitan RE, Xue D, Jiang X. Modeling the Altered Expression Levels of Genes on Signaling Pathways in Tumors as Causal Bayesian Networks. Cancer Inform. 2014 May 15; 13:77-84. doi: 10.4137/CIN.S13578. PMID: 24932098. PMCID: PMC4051800.

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

Cai B, Jiang X. A novel artificial neural network method for biomedical prediction based on matrix pseudo-inversion. J Biomed Inf. 2014 Apr;48:114-21. doi: 10.1016/j.jbi.2013.12.009. Epub 2013 Dec 18. PMID: 24361387. PMCID: PMC4004678.

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

Cai B, Jiang X. Revealing Biological Pathways Implicated in Lung Cancer from TCGA Gene Expression Data using Gene Set Enrichment Analysis. Cancer Inform. 2014 Dec 1;13(Suppl 1):113-21. doi: 10.4137/CIN.S13882. eCollection 2014. PMID: 25520551. PMCID: PMC4251186.

Jiang X, Chen R, Cheng S, Shen B, Xu R, Yi S. Computational advances in cancer informatics (a). Cancer Inform. 2014 Oct 13;13(Suppl 1):45-8. doi: 10.4137/CIN.S19243. eCollection 2014. PMID: 2548472. PMCID: PMC4216040.

Neapolitan R, Jiang X. Inferring Aberrant Signal Transduction Pathways in Ovarian Cancer from TCGA Data. Cancer Inform. 2014 Oct 13;13(Suppl 1): 29-36. doi: 10.4137/CIN.S13881. eCollection 2014. PMID: 25392681. PMCID: PMC4216062.

Cai C, Chen L, Jiang X, Lu X. Modeling Signal Transduction from Protein Phosphorylation to Gene Expression. Cancer Inform. 2014 Oct 13; 13(Suppl 1): 59-67. doi: 10.4137/CIN.S13883. eCollection 2014. PMID: 25392684. PMCID: PMC4216050.

Neapolitan RE, Jiang X. The Bayesian Network Story. In: Hajek A, Hitchcock C, editors. The Oxford Handbook of Probability and Philosophy. Oxford University Press, 2014.

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

Sverchkov Y, Jiang X, Cooper GF.  Spatial cluster detection using dynamic programming. BMC Medical Informatics & Decision Making 12:22(2012).  Doi:10.1186/1472-6947-12-22.  PMID: 22443103. PMC: PMC3403878.

Jiang X, Neapolitan RE. Mining pure, strict epistatic interactions from high-dimensional datasets: ameliorating the curse of dimensionality. PLoS ONE. 2012;7(10):e46771.doi: 10.1371/journal.pone.0046771. Epub 2012 Oct 12. PMID: 23071633. PMCID: PMC3470561.

Jiang X, Barmada MM, Cooper GF, Becich MJ. A Bayesian method for evaluating and discovering disease loci associations. PLoS ONE. 2011;6(8):e22075. doi: 101371/journal.pone.0022075. Epub 2011 Aug 10. PMID: 21853025. PMCID: PMC3154195.

Jiang X, Neapolitan RE, Barmada MM, Visweswaran S. Learning genetic epistasis using Bayesian network scoring criteria. BMC Bioinformatics 2011 Mar 31;12:89. doi: 10.1186/1471-2105-12-89. PMID: 21453508. PMCID: PMC3080825.

Jiang X, Visweswaran S, Neapolitan RE. Mining Epistatic Interactions from High-Dimensional Data Sets Using Bayesian Networks, in Holmes, D. and L. Jain (Eds.): Foundations and Intelligent Paradigms--3, Springer-Verlag, Berlin Heidelberg, 2011, DOI:10.1007/978-3-642-23151-3_9.

Jiang X, Barmada MM, Becich MJ. Evaluating de novo locus-disease discoveries in GWAS using the signal-to-noise ratio. AMIA Annu Symp Proc. 2011;2011:617-24. Epub 2011 Oct 22. PMID: 22195117. PMCID: PMC3243170.

Jiang X, Cooper GF. A Bayesian spatio-temporal method for disease outbreak detection. Journal of the American Medical Informatics Association 17 (2010) 462-471. PMID: 20595315PMC2995651.

Jiang X, Barmada MM, Visweswaran S. Identifying genetic Interactions in genome-wide data using Bayesian networks. Genet Epidemiol. 2010 Sep;34(6):575-81. doi: 10.1002/gepi.20514. PMID: 20568290. PMCID: PMC3931553.

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

Jiang X, Cooper G. Joint SNP analysis using a breast cancer GWAS data set. In: Proceedings of Cancer Informatics Workshop. Cancer Informatics Workshop; 2010; Cambridge UK 2010.

Jiang X, Neill DB, Cooper GF. On the robustness of Bayesian network based spatial event surveillance. International Journal of Approximate Reasoning, 51 (2010) p 224-239.  http://dx.doi.org/10.1016/j.ijar.2009.01.001.

Jiang X, Neill DB, Cooper GF.  A Bayesian network model for spatial event surveillance. International Journal of Approximate Reasoning (2010) 51:224-239.  doi: ttp://dx.doi.org/10.1016/j.ijar.2009.01.001.

Jiang X, Cooper GF.  A real-time temporal Bayesian architecture for event surveillance and its application to patient-specific multiple disease outbreak detection. Data Mining and Knowledge Discovery (2010). DOI: 10.1007/s10618-009-0151-4.  

Jiang X, Wallstrom G, Cooper GF, Wagner MM. Bayesian prediction of an epidemic curve. J Biomed Inform. 2009 Feb; 42(1):90-9. doi: 10.1016/j.jbi.2008.05.013. Epub 2008 Jun 13.  PMID: 18593605.  

Jiang X, Neill DB, Cooper GF.  Generalized AMOC curves for evaluation and improvement of event surveillance. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2009) 281-285. PMID: 20351865. PMC2815453.

Neill DB, Cooper GF, Das K, Jiang X, Schneider J. Bayesian Networks Scan Statistics for Multivariate Pattern Detection. In: Glaz J, Pozdnyakov V, Wallenstein S, editors. Scan Statistics - Methods and Applications. Birkhauser, 2009.

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

Jiang X, Cooper GF. A temporal method for outbreak detection using a Bayesian networks. In: Proceedings of the International Symposium on Disease Surveillance. 5(2) 105, 2008.

Jiang X. A Bayesian Network Model for Spatio-temporal Event Surveillance. University of Pittsburgh (PhD Thesis), 2008.

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

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

Jiang X, Cooper GF. A recursive algorithm for spatial cluster detection. In: Proceedings of the Fall Symposium of the American Medical Informatics Association (2007) 369-373. PMID:  18693860PMC2655859.

Jiang X. A Bayesian Network for Estimating and Predicting Epicurves. Advances in Disease Surveillance. 2007; 2:15.

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

Jiang X, Wallstrom GL. A Bayesian Network for Outbreak Detection and Prediction. 21st Association for the Advancement of Artificial Intelligence (AAAI) Conference. 2006:1155-60.

Richard Boyce, PhD

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

Villa Zapata, L., Hansten, P.D., Horn, J.R. et al. Evidence of Clinically Meaningful Drug–Drug Interaction With Concomitant Use of Colchicine and Clarithromycin. Drug Saf (2020). https://doi.org/10.1007/s40264-020-00930-7

Grizzle AJ, Hines LE, Malone DC, Kravchenko O, Hochheiser H, Boyce RD. Testing the face validity and inter-rater agreement of a simple approach to drug-drug interaction evidence assessment. J Biomed Inform. 2020 Jan;101:103355. doi: 10.1016/j.jbi.2019.103355. Epub 2019 Dec 12. PMID: 31838211; DOI: 10.1016/j.jbi.2019.103355.

Nguyen BP, Reese T, Decker S, Malone D, Boyce RD, Beyan O. Implementation of Clinical Decision Support Services to Detect Potential Drug-Drug Interaction Using Clinical Quality Language.

Stud Health Technol Inform. 2019 Aug 21;264:724-728. doi: 10.3233/SHTI190318. PubMed PMID: 31438019.

Grizzle AJ, Horn J, Collins C, Schneider J, Malone DC, Stottlemyer B, Boyce RD. Identifying Common Methods Used by Drug Interaction Experts for Finding Evidence About Potential Drug-Drug Interactions: Web-Based Survey. J Med Internet Res. 2019 Jan 4;21(1):e11182. doi:10.2196/11182. PMID: 30609981.

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

Camacho J, Medina Ch. AM, Landis-Lewis Z, Douglas G, Boyce R. Comparing a Mobile Decision Support System Versus the Use of Printed Materials for the Implementation of an Evidence-Based Recommendation: Protocol for Qualitative Evaluation. JMIR Res Protoc 2018;7(4):e104. doi: 10.2196/resprot.9827. PMID: 29653921. PMCID: PMC5924374.

Boyce RD, Ragueneau-Majlessi I, Yu J, Tay-Sontheimer J, Kinsella C, Chou E, Brochhausen M, Judkins J, Guffort BT, Pinkleton BE, Cooney R, Paine MF, McCune JS. Developing User Personas to Aid in the Design of a User-Centered Natural Product-Drug Interaction Information Resource for Researchers. AMIA Annu Symp Proc. 2018 Dec 5;2018:279-287. eCollection 2018. PMID: 30815066. PMCID: PMC6371317.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


Conference Papers and Presentations at National and Local Meetings:

 

Michael M. Wagner, MD, PhD

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

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

Millett NE, Aronis JM, Wagner MM, Tsui F, Ye Y, Ferrar JP, Huag PJ, Gesteland PH, Cooper GF. The design and evaluation of a Bayesian System for detecting and characterizing outbreaks of influenza. Online Journal of Public Health Informatics, 11(2) (2019). Doi: https://doi.org/10.1101/435727.

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

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

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

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

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

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

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

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

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

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

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

Jiang X, Wallstrom G, Cooper GF, Wagner MM. Bayesian prediction of an epidemic curve. J Biomed Inform. 2009 Feb; 42(1):90-9. doi: 10.1016/j.jbi.2008.05.013. Epub 2008 Jun 13.  PMID: 18593605.  

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

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

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

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

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

 

Current Research Projects and Collaborations

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

Shyam Visweswaran, MD, PhD

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

Associate Professor, Department of Biomedical Informatics

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

Director of Clinical Informatics, Department of Biomedical Informatics

Director of the Data Enabled Clinical Informatics Center (DECIC)

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

Biomedical Informatics Training Program Core Faculty

University of Pittsburgh School of Medicine

Publications: 

Seymour CW, Kennedy JN, Wang S, Chang CH, Elliott CF, Xu Z, Berry S, Clermont G, Cooper G, Gomez H, Huang DT, Kellum JA, Mi Q, Opal SM, Talisa V, van der Poll T, Visweswaran S, Vodovotz Y, Weiss JC, Yealy DM, Yende S, Angus DC. Derivation, Validation, and Potential Treatment Implications of Novel Clinical Phenotypes for Sepsis. Journal of the American Medical Association ( 2019). doi:10.1001/jama.2019.5791. PMID: 31104070 PMCID: PMC6537818

Trivedi G, Hong C, Dadashzadeh ER, Handzel RM, Hochheiser H, Visweswaran S. Identifying incidental findings from radiology reports of trauma patients: An evaluation of automated feature representation methods. International Journal of Medical Informatics. 2019 Sept 129; 81-7. DOI: 10.1016/j.ijmedinf.2019.05.021 PMID:31445293 PMCID: PMC 6717529

King A, Cooper GF, Clermont G, Hochheiser H, Hauskrecht M, Sittig DF, Visweswaran S. Using machine learning to selectively highlight patient information. Journal of Biomedical Informatics.  2019; Oct 29;100:103327. DOI: 1016/j.jbi.2019.103329. PMID: 31676461; PMCID: PMC6932869 [Available on 2020-12-01].

 

Trivedi G, Dadashzadeh ER, Handzel RM, Chapman WW, Visweswaran S, Hochheiser H. Interactive NLP in clinical care: Identifying incidental findings in radiology reports. Applied Clinical Informatics. 2019 10:04 doi:10.1055/s-0039.1695791. PMID: 31286058 PMCID: PMC6727024

Strobl EV, Spirtes PL, Visweswaran S.  Estimating and Controlling the False Discovery Rate of the PC Algorithm Using Edge-Specific P-Values.  AMC Transactions on Intelligent Systems and Technology. 2019 Oct 10:10(5):46.

Mohammadamin Tajgardoon, Malarkodi J. Samayamuthu, Luca Calzoni, Shyam Visweswaran.  Patient-Specific Explanations for Predictions of Clinical OutcomesApplied Clinical Informatics (ACI) Journal.  2019; 03(02): e88-e97. DOI: 10.1055/s-0039-1697907.

Jabbari F, Viswewaran S, Cooper GF. Instance-Specific Bayesian Network Structure Learning. Proceedings of the International Conference on Probabilistic Graphical Models (2018) Sep;72:169-180.  PMID: 30775723. PMCID: PMC6376975.

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

King AJ, Cooper GF, Hochheiser H, Clermont G, Hausrecht M, Visweswaran S. Using Machine Learning to Predict the Information Seeking Behavior of Clinicians Using an Electronic Medical Record System. AMIA Annual Symp Proc. 2018 Dec 5;2018:673-682. eCollection 2018. PubMed PMID: 30815109. PMCID: PMC6371238.

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

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

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

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

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

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

Tenenbaum JD, Avillach P, Benhan-Hutchins M, Breitenstein MK, Crowgey EL, Hoffman MA, Jiang X, Madhavan S, Mattison JE, Nagarajan R, Ray B, Shin D, Visweswaran S, Zhao Z, Freimuth RR. An informatics research agenda to support precision medicine: seven key areas. J Am Med Inform Assoc. 2016 Jul;23(4):791-5. doi: 10.1093/jamia/ocv213. Epub 2016 Apr 23. PMID: 27107452. PMCID: PMC4926738.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Jiang X, Neapolitan RE, Barmada MM, Visweswaran S. Learning genetic epistasis using Bayesian network scoring criteria. BMC Bioinformatics 2011 Mar 31;12:89. doi: 10.1186/1471-2105-12-89. PMID: 21453508. PMCID: PMC3080825.

Jiang X, Visweswaran S, Neapolitan RE. Mining Epistatic Interactions from High-Dimensional Data Sets Using Bayesian Networks, in Holmes, D. and L. Jain (Eds.): Foundations and Intelligent Paradigms--3, Springer-Verlag, Berlin Heidelberg, 2011, DOI:10.1007/978-3-642-23151-3_9.

Jiang X, Barmada MM, Visweswaran S. Identifying genetic Interactions in genome-wide data using Bayesian networks. Genet Epidemiol. 2010 Sep;34(6):575-81. doi: 10.1002/gepi.20514. PMID: 20568290. PMCID: PMC3931553.

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

Harry Hochheiser, PhD

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

Zhou Yuan, Sean Finan, Jeremy Warner, Guergana Savova, Harry Hochheiser. Interactive Exploration of Longitudinal Cancer Patient Histories Extracted from Clinical Text. JCO Cancer Clinical Informatics  May 2020 DOI: 10.1200/CCI.19.00115 PMID: 32383981 PMCID In progress

Grizzle AJ, Hines LE, Malone DC, Kravchenko O, Hochheiser H, Boyce RD. Testing the face validity and inter-rater agreement of a simple approach to drug-drug interaction evidence assessment. J Biomed Inform. 2020 Jan;101:103355. doi: 10.1016/j.jbi.2019.103355. Epub 2019 Dec 12. PMID: 31838211; DOI: 10.1016/j.jbi.2019.103355.

Warner JL, Dymshyts D, Reich CG, Gurley MJ, Hochheiser H, Moldwin ZH, Belenkaya R,  Williams AE, Yang PC. HemOnc: A New Standard Vocabulary for Chemotherapy Regimen Representation in the OMOP Common Data Model. J Biomed Inform. 2019 Jun 22. doi: 10.1016/j.jbi.2019.103239 PMID:31238109; PMCID: PMC6697579 [Available on 2020-08-01].

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang JQ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Comput Biol, 2019 Jul 15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. [Epub ahead of print] PMID: 31276486; PMCID: PMC6650088.

Trivedi G, Hong C, Dadashzadeh ER, Handzel RM, Hochheiser H, Visweswaran S. Identifying incidental findings from radiology reports of trauma patients: An evaluation of automated feature representation methods. International Journal of Medical Informatics. 2019 Sept 129; 81-7. DOI: 10.1016/j.ijmedinf.2019.05.021 PMID:31445293 PMCID: PMC 6717529

Wu DTY, Chen AT, Manning JD, Levy-Fix G, Backonja U, Borland D, Caban JJ, Dowding DW, Hochheiser H, Kagan V, Kandaswamy S, Kumar M, Nunez A, Pan E, Gotz D. Evaluating visual analytics for health informatics applications: a systematic review from the American Medical Informatics Association Visual Analytics Working Group Task Force on Evaluation. J Am Med Inform Assoc. 2019 Apr 1;26(4):314-323. doi: 10.1093/jamia/ocy90. PubMed PMID: 30840080

King A, Cooper GF, Clermont G, Hochheiser H, Hauskrecht M, Sittig DF, Visweswaran S. Using machine learning to selectively highlight patient information. Journal of Biomedical Informatics.  2019; Oct 29;100:103327. DOI: 1016/j.jbi.2019.103329. PMID: 31676461; PMCID: PMC6932869 [Available on 2020-12-01].

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.

King AJ, Cooper GF, Hochheiser H, Clermont G, Hausrecht M, Visweswaran S. Using Machine Learning to Predict the Information Seeking Behavior of Clinicians Using an Electronic Medical Record System. AMIA Annual Symp Proc. 2018 Dec 5;2018:673-682. eCollection 2018. PubMed PMID: 30815109. PMCID: PMC6371238.

Ogoe HA, Asamani JA, Hochheiser H, Douglas GP. Assessing Ghana's eHealth Workforce: implications for planning and training. Human Resources for Health. 2018 Nov 27;16(1):65. doi: https://doi.org/10.1186/s12960-018-0330-8. PMID: 30482223. PMCID: PMC6260724.

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

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

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

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

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

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

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

Fisher A. Ding M, Hochheiser H, Douglas G. (2016) Measuring time utilization of pharmacists in the Birmingham Free Clinic dispensary. BMC Health Services Research 16(1-7) DOI: 10.1186/s12913-016-17. PMID: 27687973. PMCID: PMC5043635.

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

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

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

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

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

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

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

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

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

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

Landis-Lewis Z, Brehaut JC, Hochheiser H, Douglas GP, Jacobson RS. (2015). Computer-supported feedback message tailoring: theory-informed adaptation of clinical audit and feedback for learning and behavior change. Implementation Science. 2015 Jan 25; 10(12). doi: 10.1186/s13012-014-0203-z.

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

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

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

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

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

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

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

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

Osmanbeyoglu HU, Ganapathiraju MK. N-gram analysis of 970 microbial organisms reveals presence of biological language models. BMC Bioinformatics. 2011 Jan 10;12:12. doi: 10.1186/1471-2105-12-12. PubMed PMID: 21219653. PMCID: PMC3027111

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

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

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

Vanathi Gopalakrishnan, PhD

Directory Listing Information
Gopalakrishnan, Vanathi
Design and development of computational methods for solving clinically relevant biological problems, application of machine learning and data mining techniques to the analysis of proteomic data, prediction of protein sequence-structure-function relationships, and biomarker discovery from genotype-phenotype studies.
Dr. Gopalakrishnan is interested in the design and development of computational methods for solving clinically relevant biological problems.

Associate Professor of Biomedical Informatics

Associate Professor of Intelligent Systems
Associate Professor of Computational and Systems Biology

Associate Professor of Bioengineering
Director, PRoBE Laboratory for Pattern Recognition from Biomedical Evidence

Core Faculty Member, Biomedical Informatics Training Program
Faculty Member, Intelligent Systems Program
Faculty Member, Joint CMU-Pitt Program in Computational Biology
Faculty Member, Medical Scientist Training Program
Faculty Member, Cardiovascular Bioengineering Training Program
Co-Director of Bioengineering, Biotechnology and Innovation (BBI) Area of Concentration

School of Medicine

Co-Director of the Intelligent Systems Program, School of Computing and Information

 
Publications: 

Y Liu, J Manners, Y Bittar, SHY Chou, V Gopalakrishnan. Towards precision critical care management of blood pressure in hemorrhagic stroke patients using dynamic linear models.  PLoS One 2019;14(8): e0220283.

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

Balasubramanian JB, Gopalakrishnan V. Tunable structure priors for Bayesian rule learning for knowledge integrated biomarker discovery.World J Clin Oncol. 2018 Sep 14;9(5): 89-109. doi: 10.5306/wjco.v9.i5.98. PMID: 30254965. PMC ID: PMC6153126.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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