Faculty
Sofia Triantafillou, PhD
Assistant Professor, Department of Biomedical Informatics
Research interests:
Developing causal discovery methods in the presence of latent variables, methods for integrative analysis of multiple experiments, modelling and application of causal discovery on neural and biological data.
View my Website
Hatice Ulku Osmanbeyoglu, PhD
Assistant Professor
Department of Biomedical Informatics
School of Medicine, University of Pittsburgh
UPMC Hillman Cancer Center
Yalini Senathirajah, PhD
Associate Professor, Department of Biomedical Informatics
University of Pittsburgh School of Medicine
Chung A, Seixas Z, Williams N, Senathirajah Y, Robbins R, Newsome Garcia V, Ravenell J, Jean-Louis G. Development of “Advancing People of Color in Clinical Trials Now!”: Web-Based Randomized Controlled Trial Protocol. JMIR Research Protocols 2020;9(7):e17589. DOI: 10.2196/17589
Subbian V, Solomonides A, Clarkson M, Rahimzadeh VN, Petersen C, Schreiber R, DeMuro PR, Dua P, Goodman KW, Kaplan B, Koppel R, Lehmann CU, Pan E, Senathirajah Y Ethics and Informatics in the Age of COVID-19: Challenges and Recommendations for Public Health Organization and Public Policy. Journal of the American Medical Informatics. 2020 Jul 28:ocaa188. doi: 0.1093/jamia/ocaa188. Online ahead of print. PMID: 32722749
Y. Senathirajah, S. Pelayo, Section Editors of the IMIA Yearbook Section on Human Factors and Organizational Issues. International Medical Informatics Association Yearbook 2020, 202 April 17;1:1-309
Pelayo S, Senathirajah Y. Human Factors and Sociotechnical Issues. Year Med Inform. 2019 Aug. doi: 10.1055/s-0039-1677927.
Robbins R, Senathirajah Y, Williams NJ, Hutchinson C, Rapoport DM, Allegrante DM, Allegrante JP, Cohall A, Rogers A, Ogedegbe O, Jean-Louis G. Developing a Tailored Website for Promoting Awareness about Obstructive Sleep Apnea (OSA) Among Blacks in Community-Based Settings. Health Commun. 2018 Jan 17:1-9. doi: 10.1080/10410236.2018.1423865. [Epub ahead of print]. PMID: 29338353.
Senathirajah Y, Wang J, Borycki E, Kushniruk A. Mapping the Electronic Health Record: A Method to Study Display Fragmentation. Stud Health Technol Inform. 2017 245:1138-1142. PMID: 29295280.
Senathirajah Y, Kaufman D, Bakken S. User-composable Electronic Health Record Improves Efficiency of Clinician Data Viewing for Patient Case Appraisal: A Mixed-Methods Study. EGEMS (Wash DC). 2016 May 2;4(1):1176. doi: 10.13063/2327-9214.1176. eCollection 2016. PMID: 27195306. PMCID: PMC4862763.
Roman LC, Ancker JS, Johnson SB, Senathirajah Y. Navigation in the electronic health record: A review of the safety and usability literature. J Biomed Inform. 2017 Mar;67:69-79. doi: 10.1016/j.jbi.2017.01.005. Epub 2017 Jan 11. Review. PMID: 28088527.
Kushniruk A, Senathirajah Y, Borycki E. Effective Usability Engineering in Healthcare: A Vision of Usable and Safer Healthcare IT. Stud Health Technol Inform. 2017;245:1066-1069. PMID: 29295265.
Kushniruk A, Senathirajah Y, Borycki E. Towards a Usability and Error "Safety Net": A Multi-Phased Multi-Method Approach to Ensuring System Usability and Safety. Stud Health Technol Inform. 2017;245:763-767. PMID: 29295201.
Borycki E, Senathirajah Y, Kushniruk AW. The Future of Mobile Usability, Workflow and Safety Testing. Stud Health Technol Inform. 2017;245:15-19. PMID: 29295043.
Sockolow P, Schug S, Zhu J, Smith TJ, Senathirajah Y, Bloom S. At-risk adolescents as experts in a new requirements elicitation procedure for the development of a smart phone psychoeducational trauma-informed care application. Inform Health Soc Care. 2017 Jan;42(1):77-96. Epub 2016 Jun 3. doi: 10.1080/17538157.2016.1177532. PMID: 27259373.
Borycki E, Dexheimer JW, Hullin Lucay Cossio C, Gong Y, Jensen S, Kaipio J, Kennebeck S, Kirkendall E, Kushniruk AW, Kuziemsky C, Marcilly R, Röhrig R, Saranto K, Senathirajah Y, Weber J, Takeda H. Methods for Addressing Technology-induced Errors: The Current State. Yearb Med Inform. 2016 Nov 10;(1):30-40. doi: 10.15265/IY-2016-029. Review. PMID: 27830228. PMCID: PMC5171580.
Kuziemsky CE, Nøhr C, Borycki EM, Kushniruk AW, Senathirajah Y. Understanding the Context of Patient Safety Through The Lenses of Three IMIA Working Groups. Stud Health Technol Inform. 2015;218:40615. PMID: 26262545.
Senathirajah Y. Safer Design - Composable EHRs and Mechanisms for Safety. Stu Health Technol Inform. 2015;218:40602. PMID: 2626532.
Senathirajah Y, Kaufman D, Bakken S. The clinician in the driver's seat: part 2 - intelligent uses of space in a drag/drop user-composable electronic health record. J Biomed Inform. 2014 Dec;52:177-88. doi: 10.1016/j.jbi.2014.09.008. Epub 2014 Oct 24. PMID: 25445921.
Senathirajah Y, Bakken S, Kaufman D. The clinician in the Driver's Seat: part 1 - a drag/drop user-composable electronic health record platform. J Biomed Inform. 2014 Dec;52:165-76. doi: 10.1016/j.jbi.2014.09.002. Epub 2014 Sep 18. PMID: 25240253.
Senathirajah Y, Kaufman D, Bakken S. Beyond copy and paste: clinician approaches to meeting information needs during note writing. Stud Health Technol Inform. 2014;205:599-603. PMID: 25160256.
Merrill J, Phillips A, Keeling J, Kaushal R, Senathirajah Y Effects of automated immunization registry reporting via an electronic health record deployed in community practice settings. Appl Clin Inform. 2013 Jun 12;4(2):267-75. doi: 10.4338/ACI-2013-02-CR-0009. Print 2013. PMID: 23874363. PMCID: PMC3716417.
Senathirajah Y, Kaufman D, Bakken S. Essential questions: accuracy, errors and user perceptions in a drag/drop user-composable electronic health record. Stud Health Technol Inform. 2013;194:181-7. PMID: 23941953.
Senathirajah Y, Bakken S. Visual clustering analysis of CIS logs to inform creation of a user-configurable Web CIS interface. Methods Inf Med. 2011;50(4):337-48. doi: 10.3414/ME09-01-0087. Epub 2011 Jun 21. PMID: 21691676.
Senathirajah Y, Bakken S. Important ingredients for health adaptive information systems. Stud Health Technol Inform. 2011;169:280-4. PMID: 21893757.
Senathirajah Y, Kaufman D, Bakken S. Cognitive Analysis of a Highly Configurable Web 2.0 EHR Interface. AMIA Annu Symp Proc. 2010 Nov 13;2010:732-6. PMID: 21347075. PMCID: PMC3041363.
Senathirajah Y, Bakken S. Architectural and usability considerations in the development of a Web 2.0-based EHR. Stud Health Technol Inform. 2009;143:315-21. PMID: 19380954.
Jonathan C. Silverstein, MD, MS, FACS, FACMI
Chief Research Informatics Officer, Health Sciences and Institute for Precision Medicine (IPM)
Professor, Department of Biomedical Informatics (DBMI), School of Medicine
Affiliate Scholar, Pitt Cyber
Fukushima M, Austin C, Sato N, Maruyama T, Navarro E, Rocca M, Demotes J, Haendel M, Volchenboum SL, Cowperthwaite M, Silverstein JC, Webb C, Sim I, Chase M, Speakman J, Augustine E, Ford DE, Kush R. The Global academic research organization network: Data sharing to cure diseases and enable learning health systems. Learn Health Sys. 2019 Dec 3;8. https://doi.org/10.1002/lrh2.10073, PMID: 31245596; PMCID: PMC6508835
HuBMAP Consortium (Writing Group: Snyder MP, Lin S, Posgai A, Atkinson M, Regev A, r Rood J, Rozenblatt-Rosen O, Gaffney L, Hupalowska A, Satija R, Gehlenborg G, Shendure J, Laskin J, Harbury P, Nystrom NA, C. Silverstein JC, Bar-Joseph Z, Zhang K, Börner K, Lin Y, Conroy R, Procaccini D, Roy AL, Pillai A, Brown M, Galis ZS.)The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. Nature Publishing Group; 2019 Oct 9; 574(7777):187–192. DOI: 10.1038/s41586-019-1629-x, PMID: 31597973; PMCID: PMC6800388.
Marquis-Gravel G, Roe MT., Turakhia MP., Boden W, Temple R, Sharma A, Hirshberg B, Slater P, Craft N, Stockbridge N, McDowell B, Waldstreicher J, Bourla A, Bansilal S, Wong JL., Meunier C, Kassahun H, Coran P, Bataille L, Patrick-Lake B, Hirsch B, Reites J, Mehta R, Muse ED., Chandross KJ., Silverstein JC., Silcox C, Overhage JM, Califf RM., Peterson ED. Technology-Enabled Clinical Trials: Transforming Medical Evidence Generation.. Circulation. American Heart Association; 2019 Oct 22;140(17):1426–1436. PMID: 31634011
Amin W, Linkov F, Landsittel DP, Silverstein JC, Bashara W, Gaudioso C, Feldman MD, Pass HI, Melamed J, Friedberg JS, Becich MJ. Factors influencing malignant mesothelioma survival: a retrospective review of the National Mesothelioma Virtual Bank cohort. F1000Res. 2018 Aug 3;7:1184. doi: 10.12688/f1000research.15512.3. PubMed PMID: 30410729; PubMed Central PMCID: PMC6198263.3.
Linkov F, Silverstein JC, Davis M, Crocker B, Hao D, Schneider A, Schwenk M, Winters S, Zelnis J, Lee AV, Becich MJ. Integration of Cancer Registry Data into the Text Information Extractio System: Leveraging the Structured Data Import Tool. J Pathol Inform. 2018 Dec 24;9:47. doi: 10.4103/jpi.jpi_38_18. eCollection 2018. PMID: 30662793. PMCID: PMC6319041.
Gitelis ME, Kaczynski A, Shear T, Deshur M, Beig M, Sefa M, Silverstein J, Ujiki M. Increasing compliance with the World Health Organization Surgical Safety Checklist-A regional health system's experience. Am J Surg. 2017; 214(1):7-13. PMID: 27692671 PMCID: PMC4429500 DOI: 10.1016/j.amjsurg.2016.07.024
Cheng Q, June J, Bellam S, Fulara N, Close D, Silverstein JC, Schatz B. Classification Models for Pulmonary Function using Motion Analysis from Phone Sensors. 2017 Feb 10;2016:401-410. eCollection 2016. PMID: 28269835. PMC5333291.
Cheng Q, Juen J, Bellam S, Fulara N, Close D, Silverstein JC, Schatz B. Predicting Pulmonary Function from Phone Sensors. Telemed J E Health. 2017 Nov;23(11):913-919. doi: 10.1089/tmj.2017.0008. Epub 2017 Mar 16. PMID: 28300524. PMCID: PMC5684658.
Friedman CP, Allee NJ, Delaney BC, Flynn AJ, Silverstein JC, Sullivan K, Young KA. The science of Learning Health Systems: Foundations for a new journal. Learning Health Systems. 2017 January; 1(1):1. doi: 10.1002/lrh2.10020
McCray AT, Glaser J, Koppel R, Langlotz CP, Silverstein J. Health IT vendors and the academic community: The 2014 ACMI debate. J Biomed Inform. 2016 Apr;60:365-75. doi: 10.1016/j.jbi.2016.03.003. Epub 2016 Mar 8. PMID: 26968349
Baldridge AS, Pacheco JA, Aufox SA, Kim KY, Silverstein JC, Denham W, Hungness E, Smith ME, Allen NB, Greenland P, Rasmussen-Torvik LJ. Factors Associated With Long-Term Weight Loss Following Bariatric Surgery Using 2 Methods for Repeated Measures Analysis. Am J Epidemiol. 2015 Aug 1;182(3):235-43. PMID: 26093003 PMCID: PMC4517695 DOI: 10.1093/aje/kwv039
Zhu Y, Xu Y, Helseth DL Jr, Gulukota K, Yang S, Pesce LL, Mitra R, Müller P, Sengupta S, Guo W, Silverstein JC, Foster I, Parsad N, White KP, Ji Y. Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data. J Natl Cancer Inst. 2015 May 8;107(8). pii: djv129. PMID: 25956356 PMCID: PMC4554190 DOI: 10.1093/jnci/djv129
Rasmussen-Torvik LJ, Baldridge AS, Pacheco JA, Aufox SA, Kim KY, Silverstein JC, Denham EW, Hungness E, Smith ME, Greenland P. rs4771122 Predicts Multiple Measures of Long-Term Weight Loss After Bariatric Surgery. Obes Surg. 2015 Nov;25(11):2225-9. PMID: 26337695 PMCID: PMC4598314 DOI: 10.1007/s11695-015-1872-7
Maraganore DM, Frigerio R, Kazmi N, Meyers SL, Sefa M, Walters SA, Silverstein JC. Quality improvement and practice-based research in neurology using the electronic medical record. Neurol Clin Pract. 2015 Oct;5(5):419–429. PMCID: PMC4634157
Solomonides A, Goel S, Hynes D, Silverstein JC, Hota B, Trick W, Angulo F, Price R, Sadhu E, Zelisko S, Fischer J, Furner B, Hamilton A, Phua J, Brown W, Hohmann SF, Meltzer D, Tarlov E, Weaver FM, Zhang H, Concannon T, Kho A. Patient-Centered Outcomes Research in Practice: The CAPriCORN Infrastructure. Stud Health Technol Inform. 2015;216:584-8. PMID: 26262118
Cherenfant J, Talamonti MS, Hall CR, Thurow TA, Gage MK, Stocker SJ, Lapin B, Wang E, Silverstein JC, Mangold K, Odeleye M, Kaul KL, Lamzabi I, Gattuso P, Winchester DJ, Marsh RW, Roggin KK, Bentrem DJ, Baker MS, Prinz RA. Comparison of tumor markers for predicting outcomes after resection of nonfunctioning pancreatic neuroendocrine tumors. Surgery. 2014 Dec;156(6):1504-10; discussion 1510-1. PMID: 25456943 DOI: 10.1016/j.surg.2014.08.043
Erik S. Wright, PhD, MS
Assistant Professor, Department of Biomedical Informatics
Erik Scott Wright. RNAconTest: Comparing tools for non-coding RNA multiple sequence alignment based on structural consistency. RNA. 2020 Jan 31. pii: rna.073015.119. doi: 10.1261/rna.073015.119
Birer C, Wright ES. Capturing the complex interplay between drugs and the intestinal microbiome. Clin Pharmacol Ther. 2019 May 18. doi: 10.1002/cpt.1505. [Epub ahead of print] PubMed PMID: 31102465.
Murali A, Bhargava A, Wright ES. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome. 2018 Aug 9;6(1):140. doi: 10.1186/s40168-018-0521-5. PMID: 30092815. PMCID: PMC6085705.
Wright ES, Baum DA. Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow. BMC Genomics. 2018 Oct 3;19(1):724. doi: 10.1186/s12864-018-5099-6. PubMed PMID: 30285620. PMCID: PMC6171291.
Wright ES, Vetsigian KH. Stochastic exits from dormancy give rise to heavy-tailed distributions of descendants in bacterial populations. bioRxiv. 2018 January 11. http://doi.org/10.1101/246629
Wright ES. Getting my feet wet. Science. 2017 Apr 7;356(6333):106. doi: 10.1126/science.356.6333.106. PMID: 28386014.
Wright ES, Vetsigian KH. DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures. Bioinformatics. 2016 May 15;32(10):1565-7. doi: 10.1093/bioinformatics/btw047. Epub 2016 Jan 23. PMID: 26803162.
Wright ES, Vetsigian KH. Inhibitory interactions promote frequent bistability among competing bacteria. Nat Commun. 2016 Apr 21;7:11274. doi: 10.1038/ncomms11274. PMID: 27097658. PMCID: PMC4844671.
Wright ES, Vetsigian KH. Quality filtering of Illumina index reads mitigates sample cross-talk. BMC Genomics. 2016 Nov 4;17(1):876. doi: 10.1186/s12864-016-3217-x. PMID: 27814679. PMCID: PMC5097354.
Wright ES. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics. 2015 Oct 6;16:322. doi: 10.1186/s12859-015-0749-z. PMID: 26445311. PMCID: PMC4595117.
Wright ES, Yilmaz LS, Corcoran AM, Ökten HE, Noguera DR. Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification. Appl Environ Microbiol. 2014 Aug;80(16):5124-33. doi: 10.1128/AEM.01685-14. Epub 2014 Jun 13. PMID: 24928876. PMCID: PMC4135741.
Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR. Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates. Environ Microbiol. 2014 May;16(5):1354-65. doi: 10.1111/1462-2920.12259. Epub 2013 Sep 24. PMID: 24750536.
Noguera DR, Wright ES, Camejo P, Yilmaz LS. Mathematical tools to optimize the design of oligonucleotide probes and primers. Appl Microbiol Biotechnol. 2014 Dec;98(23):9595-608. doi: 10.1007/s00253-014-6165-x. Epub 2014 Oct 31. Review. PMID: 25359473.
Wright ES, Yilmaz LS, Noguera DR. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol. 2012 Feb;78(3):717-25. doi: 10.1128/AEM.06516-11. Epub 2011 Nov 18. PMID: 22101057. PMCID: PMC3264099.
Kayhan Batmanghelich, PhD
University of Pittsburgh School of Medicine
Yu K, Visweswaran S, Batmanghelich K. Semi-Supervised Hierarchical Drug Embedding in Hyperbolic Space. arXiv 1 June 2020. arXiv.org. arXiv:2006.00986
Mingming Gong, Yanwu Xu, Chuyuan Li, Kun Zhang, Kayhan Batmanghelich. Twin Auxiliary Classifiers GAN. 33rd Conference on Neural Information Processing Systems (NeurIPS 2019), Vancouver, Canada
Singla S, Gong M, Ravanbakhsh S, Sciurba F, Poszos B, Batmanghelich KN. Subject2Vec: Generative-Discriminative Approach from a Set of Image Patches to a Vector. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI). 2018: 502-510. doi: 10.1007/978-3-030-00928-1_57. PubMed PMID: 30895278. PMCID: PMC6422035.
Fu H, Gong M, Wang C, Batmanghelich K, Tao D. Deep Ordinal Regression Network for Monocular Depth Estimation. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2018 Jun;2018:2002-2011. doi: 10.1109/CVPR.2018.00214. Epub 2018 Dec 17. PubMed PMID: 31274971. PMCID: PMC6607900.
Huisman, SMH, Mahfouz A, Batmanghelich NK, Lelieveldt BPF, Reinders MJT on behalf of for the Alzheimer's Disease Neuroimaging Initiative. A structural equation model for imaging genetics using spatial transcriptomics. Brain Inf. (2018) 5:13. PMID: 30390165. doi: https://doi.org/10.1186/s40708-018-0091-0.
Schabdach J, Wells S, Cho M, Batmanghelich N. A Likelihood-Free Approach for Characterizing Heterogeneous Diseases in Large-Scale Studies. International Conference on Information Processing in Medical Imaging (IPMI). 2017 Jun 25; 170-183. PMID:29129964. PMCID: PMC5679301. doi: 10.1007/978-3-319-59050-9_14
Freifeld O, Haubert S, Fisher J III, Batmanghelich N, Transformations Based on Continuous Piecewise-Affine Velocity Fields. IEEE Trans Pattern Anal Mach Intell. 2017 Dec;39(12):2496-2509. Epub 2017 Jan 1. doi: 10.1109/TPAMI.2016.2646685. PubMed PMID: 28092517. PMCID: PMC5889303.
Batmanghelich N, Saeedi A, Narasimhan K, Gershman S. Nonparametric Spherical Topic Modeling with Word Embeddings. Proc Conf Assoc Comput Linguist Meet. 2016 Aug; 2016: 537-542. pp 537-542, 2016. doi: 10.18653/v1/P16-2087. PMID: 30636838. PMCID: PMC6327958.
Batmanghelich N, Dalca A, Quon G, Sabuncu M, Golland P. Probabilistic Modeling of Imaging, Genetics and the Diagnosis. IEEE Transactions on Medical Imaging (TMI), pp 1765-1779, 2016. doi: 10.1109/TMI.2016.2527784. PMID: 26886973. PMCID: PMC5364030.
Batmanghelich N, Saeedi A, Estepar RJ, Cho M, Wells S. Inferring Disease Status by non-Parametric Probabalistic Embedding. Medical Computer Vision and Bayesian and Graphical Models for Biomedical Imaging. 2016 Oct 21; 49-57.
Binder P, Batmanghelich N, Estepar R, Golland P. Unsupervised Discovery of Emphysema Subtypes in a Large Clinical Cohort. Machine Learning in Medical Imaging: 7th International Workshop, MLMI 2016, Held in Conjunction with MICCAI 2016, Athens, Greece, October 17, 2016, Proceedings. 2016 Oct;10019:180-187. doi: 10.1007/978-3-319-47157-0_22. Epub 2016 Oct 1. PubMed PMID: 28232959. PMCID: PMC5317320.
Batmanghelich N, Saeedi A, Cho M, Jose R, Golland P. Generative Method to Discover Genetically Driven Image Biomarkers. International Conference on Information Processing in Medical Imaging (IPMI), LNCS 9123, pp 30-42, 2015. PMID: 26221665. PMCID: PMC4527679.
Wachinger C, Batmanghelich N, Golland P, Reuter M. BrainPrint in the Computer-Aided Diagnosis of Alzheimer's Disease. Challenge on Computer-Aided Diagnosis of Dementia. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2014.
Bloy L, Ingalhalikar M, Batmanghelich N. An integrated Framework for High Angular Resolution Diffusion Imaging-Based Investigation of Structural Connectivity. Brain Connectivity, 2(2), pp 69-19, 2012. doi: 10.1089/brain.2011.0070 PMCID: PMC3380149.
Batmanghelich N, Taskar B, Davatzikos C. Generative-Discriminative Basis Learning for Medical Imaging. IEEE Transactions on Medical Imaging (TMI), 31(1), pp 51-69, 2012. doi: 10.1109/TMI.2011.2162961. PMID: 21791408. PMCID: PMC3402718.
Batmanghelich N, Ye D, Taskar B, Davatzikos C. Disease Classification and Prediction via semi-supervised Dimensionality Reduction. IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI), pp 1086-1090, 2011. doi: 10.1109/ISBI.2011.5872590
Davatzikos C, Bhatt P, Shaw L, Batmanghelich N, Trojanowski J. Prediction of MCI Conversion via MRI, CSF Biomarkers, and Pattern Classification. Neurobiology of Aging, 32(12), pp 2322.e192322.e27, 2010. PMID: 20594615 PMCID: PMC2951483 DOI: 10.1016/j.neurobiolaging.2010.05.023
Batmanghelich N, Gooya A, Taskar B, Davatzikos C. Application of Trace-Norm and Low-Rank Matrix Decomposition for Computational Anatomy. IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA), Computer Vision and Pattern Recognition Workshops (CVPRW), pp 146-153, 2010. doi: 10.1109/CVPRW.2010.5543596
Batmanghelich N, Verma R. On Non-linear Characterization of Tissue Abnormality by Constructing Disease Manifolds. IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA), Computer Vision and Pattern Recognition Workshops (CVPRW), pp 1-8, 2008. doi: 10.1109/CVPRW.2008.4563027
Fan Y, Batmanghelich N, Clark C, Davatzikos C. Spatial Patterns of Brain Atrophy in MCI Patients, Identified via High-dimensional Pattern Classification, Predict Subsequent Cognitive Decline. NeuroImage, 39(4), pp 1731-43, 2008. PMID: 18053747 PMCID: PMC2861339 DOI: 10.1016/j.neuroimage.2007.10.031
Shariatpanahi H, Batmanghelich N, Kermani A, Ahmadabadi M, Soltanian-Zadeh H. Distributed Behavior-based Multi-agent System for Automatic Segmentation of Brain MR Images. International Joint Conference on Neural Networks (IJCNN), pp 4535-4542, 2006. doi: 10.1109/IJCNN.2006.247079
Karimi M, Batmanghelich N, Soltanian-Zadeh H, Lucas C. A 3-D Deformable Surface Method for Automatic Hippocampus-Amygdala Complex Segmentation. IEEE Nuclear Science Symposium Conference Record, 6, pp 3725-3729, 2004. doi: 10.1109/NSSMIC.2004.1466690
David Boone, PhD
Sreekumar S, Levine KM, Sikora MJ, Chen J, Tasdemir N, Carter D, Dabbs DJ, Meier C, Basudan A, Boone D, McAuliffe PF, Jankowitz RC, Lee AV, Atkinson JM, Oesterreich S. Differential regulation and targeting of estrogen receptor α turnover in invasive lobular breast carcinoma. Endocrinology 2020 Jul 1;bqaa109.
doi: 10.1210/endocr/bqaa109. PMID: 32609836
Gau D, Vignaud L, Allen A, Guo Z, Sahel J, Boone D, Koes D, Guillonneau X, Roy P. Disruption of profilin1 function suppresses developmental and pathological retinal neovascularization. Journal of Biological Chemistry 2020 Jul 10;295(28):9618-9629.
doi: 10.1074/jbc.RA120.012613. PMID 32444495
Boone DN, Warburton A, Som S, Lee AV. SNHG7 is a IncRNA oncogene controlled by Insulin-like Growth Factor signaling through a negative feedback loop to tightly regulate proliferation. Scientific Reports 2020; 22 May 2020. Doi: 10.1038/s41598-020-65109-7
PMID: 3244795 PMCID: PMC7244715
Nagle AM, Levine KM, Tasdemir N, Scott JA, Burlbaugh K, Kehm JW, Katz TA, Boone DN, Jacobsen BM, Atkinson JM, Oesterreich S, Lee AV. Loss of E-cadherin enhances IGF1-IGF1R pathway activation and sensitizes breast cancers to anti-IGF1R/InsR inhibitors. Clin Cancer Res. 2018 Jun 25. pii: clincanres.0279.2018. doi: 10.1158/1078-0432.CCR-18-0279. [Epub ahead of print]. PMID: 29941485.
Chen J, Nagle AM, Wang YF, Boone DN, Lee AV. Controlled dimerization of insulin-like grown factor-1 and insulin receptors reveal shared and distinct activities of holo and hybrid receptors. J Biol Chem. 2018 Mar 9;293(10):3700-3709. doi: 10.1074/jbc.M117.789503. Epub 2018 Jan 12. PMID: 23990302.
Warburton AJ, Boone DN. Insights of Global Analyses of Long Noncoding RNAs in Breast Cancer. Curr Pathobiol Rep. 2017 Mar;5(1):23-34. doi: 10.1007/s40139-017-0122-1. Epub 2017 Jan 23. PubMed PMID: 28616363. PubMed Central PMCID: PMC5467540.
King AJ, Fisher AM, Becich MJ, Boone DN. Computer Science, Biology and Biomedical Informatics academy: Outcomes from 5 years of Immersing High-school Students into Informatics Research. J Pathol Inform. 2017 Feb 28;8:2. doi: 10.4103/2153-3539.201110. eCollection 2017. PMID: 28400991 PMC ID: 5359992.
Nayak S, Harrington E, Boone DN, Hartmaier R, Pathiraja, T, Cooper K, Fine J, Sanfilippo J, Davidson N, Lee AV, Dabbs D, and Oesterreich S. A Role for Histone H2B Variants in Endocrine Resistant Breast Cancer. Hormones and Cancer. 2015 PUBMED 26113056
Farabaugh SM, Boone DN, and Lee AV. Role of IGF1R in breast cancer subtypes, stemness, and lineage differentiation. Frontiers in Endocrinology. 2015. PUBMED 25964777
Zhang Q, Spears E, Boone DN, Li Z, Gregory M, and Hann S. Domain specific c-Myc ubiquitylation controls c-Myc transcriptional and apoptotic activitys. PNAS. 2012; 110(3):978-83. PUBMED 23277542
Boone DN and Lee AV. Targeting the Insulin-like Growth Factor Receptor: Developing Biomarkers from Gene Expression Profiling. Critical Reviews in Oncogenesis. 2012;17(2):161-73. PUBMED 22471706
Boone DN and Hann SR. The Myc-ARF-Egr1 Pathway: Unleashing Myc’s Apoptotic Power. Cell Cycle. 2011 Jul1;10(13):2043-4. PMC3234342
Boone DN, Qi Y, Li Z, and Hann S. Egr1 mediates p53-independent c-Myc-induced apoptosis via a noncanonical ARF-dependent transcriptional mechanism. PNAS. 2011 Jan 11;108(2):632-7. PUBMED 21187408
Zhaoliang Li, Boone D, and Hann S. Nucleophosmin interacts directly with c-Myc and controls c-Myc-induced hyperproliferation and transformation. PNAS. 2008 Dec 2;105(48):18794-9. PUBMED 19033198
van Rheede T, Bastiaans T, Boone D, Hedges SB, de Jong W, and Madsen O. 2006. The platypus is in its place: nuclear genes and indels confirm the sister group relation of monotremes and therians. Mol. Biol. Evol. 23:587-597. PMID:19033198
Uma Chandran, PhD, MSIS
Kevin Louis, Camila Macedo, Elodie Bailly, Louis Lau, Bala Ramaswami, Marilyn Marrari, Douglas Landsittel, Alexander Chang, Uma Chandran, Paul Fadakar, Masaki Yamada, Geetha Chalasani, Parmjeet Randhawa, Adriana Zeevi, Harinder Singh, Carmen Lefaucheur, Diana Metes. Coordinated Circulating T Follicular Helper and Activated B Cell Responses Underlie the Onset of Antibody-Mediated Rejection in Kidney Transplantation. Journal of the American Society of Nephrology, 2020 Jul 28;ASN.2020030320. doi: 10.1681/ASN.2020030320
Wang Z, Pascal LE, Chandran UR, Chaparala S, Lv S, Ding H, Qi L, Wang Z. ELL2 Is Required for the Growth and Survival of AR-Negative Prostate Cancer Cells. Cancer Management and Research 2020 Jun 10;12:4411-4427. doi: 10.2147/CMAR.S248854. PMID: 32606936 PMCID: PMC7294050
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 RS. Improving 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
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. Cancer Res. 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 S, Lu 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 S, Lu, 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
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 GP. Engineering 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.