Recent Publications

Nematollah (Kayhan) Batmanghelich, PhD

Fu H, Gong M, Wang Ch, Batmanghelich K, Tao D. Deep Ordinal Regression Network for Monocular Depth Estimation. Conference on Computer Vision and Pattern Recognition, to appear in CVPR 2018.

Yu X, Liu T, Gong M, Wang Ch, Batmanghelich K, Tao D. An Efficient and Provable Approach for Mixture Proportion Estimation Using Independent Assumption. Conference on Computer Vision and Pattern Recognition, to appear in CVPR 2018.

Michael Becich, MD, PhD

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 2018 Mar 12. PMID: 2954507.

David Boone, PhD

Chen J, Nagle AM, Wang YF, Boone DN, Lee AV. Controlled dimerization of insulin-like growth factor-1 and insulin receptors reveal shared and distinct activities of holo and hybrid receptors. J Biol Chem. 2018 Jan 12. pii: jbc. M117.789503. doi: 10.1074/jbc.M117.789503. Epub 2018 Jan 12. PMID: 29330302.

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.

Richard Boyce, PhD

Romagnoli KM, Boyce RD, Empey PE, Ning Y, Adams S, Hochheiser H. Design and evaluation of a pharmacogenomics information resource for pharmacists. J Am Med Inform Assoc. 2017 Jul 1;24(4):822-831. doi: 10.1093/jamia/ocx007. PMID: 28339805.

Le K, Chou E, Boyce RD, Albert SM. Potentially Harmful Medication Use and Decline in Health-Related Quality of Life among Community-Dwelling Older Adults. Drugs Real World Outcomes. 2017 Dec;4(4):257-264. doi: 10.1007/s40801- 017-0123-8. PMID: 29119486.

Utecht J, Brochhausen M, Judkins J, Schneider J, Boyce RD. Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation. Stud Health Technol Inform. 2017;245:960-964. PMID: 29295242. PMCID: PMC5765984.

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.

Natsiavas P, Boyce RD, Jaulent MC, Koutkias V. OpenPVSignal: Advancing Information Search, Sharing and Resuse on Pharmacovigilance Signals via FAIR Principles and Semantic Web Technologies. Front Pharmacol. 2018 Jun 26;9:609. doi: 10.3389/fphar.2018.00609. eCollection 2018. PMID: 29997499.

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.

Uma Chandran, PhD, MSIS

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. 8 8

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.

Pascal LE, Wang Y, Zhong M, Wang D, Chakka AB, Yang Z, Li F, Song Q, Rigatti LH, Chaparala S, Chandran U, Parwani AV, Wang Z. EAF2 and p53 Co-Regulate STAT3 Activation in Prostate Cancer. Neoplasia. 2018 Mar 5;20(4):351-363. doi: 10.1016/j.neo.2018.01.011. Epub 2018 Mar 6. PMID: 29518696.

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 2018 Mar 12. PMID: 2954507.

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 Apr 6. Doi: 10.1005/ijc.31419. Epub 2018 Apr 20. PMID 29633255.

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.

Gregory Cooper, MD, PhD

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

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.

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. 2017 Nov 13. pii: molcanres.0378.2017. doi: 10.1158/1541-7786.MCR-17-0378. Epub 2017 Nov 13. PMID: 29133589.

Naeini MP, Cooper GF. Binary Classifier Calibration Using an Ensemble of Piecewise Linear Regression Models. Knowl Inf Syst. 2018 Jan;54(1):151-170. doi: 10.1007/s10115-017-1133-2. Epub 2017 Nov 17. PMID: 29606784.

Andrews B, Ramsey J, Cooper GF. Scoring Bayesian Networks of Mixed Variables. Int J Data Sci Anal. 2018 Aug;6(1):3- 18. Doi: 10.1007/s41060-017-0085-7. Epub 2018 Jan 11. PMID: 30140730.

Gerald Douglas, PhD

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.

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.

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.

Vanathi Gopalakrishnan, PhD

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. 9 9

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): 98-109. doi: 10.5306/wjco.v9.i5.98.

Harry Hochheiser, PhD

Romagnoli KM, Boyce RD, Empey PE, Ning Y, Adams S, Hochheiser H. Design and evaluation of a pharmacogenomics information resource for pharmacists. J Am Med Inform Assoc. 2017 Jul 1;24(4):822-831. doi: 10.1093/jamia/ocx007. PMID: 28339805.

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.

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. 2018 Jan 1;25(1)87-87. doi: 10.1093/jamia/ocx070. PMID: 29016825.

Xia Jiang, PhD

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.

Neapolitan RE, Jiang X. Artificial Intelligence: With an Introduction to Machine Learning. 2nd ed. Boca Raton, FL: Chapman and Hall/CRC, 2018.

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.

Douglas Landsittel, PhD

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

Taira DA, Shen C, King M, Landsittel D, Mays MH, Sentell T, Southerland J. Access to medications for medicare enrollees related to race/ethnicity: Results from the 2013 Medicare Current Beneficiary Survey. Res Social Adm Pharm. 2017 Nov;13(6):1208-1213. doi: 10.1016/j.sapharm.2016.10.021. Epub 2016 Nov 23. PMID: 27914950. PMCID: PMC5500432.

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

Yu ASL, Shen C, Landsittel DP, Harris PC, Torres VE, Mrug M, Bae KT, Grantham JJ, Rahbari-Oskoui FF, Flessner MF, Bennett WM, Chapman AB; Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP). Baseline total kidney volume and the rate of kidney growth are associated with chronic kidney disease progression in Autosomal Dominant Polycystic Kidney Disease. Kidney Int. 2018 Mar;93(3):691-699. pii: S0085-2538(17)30785-8. doi: 10.1016/j.kint.2017.09.027. Epub 2017 Dec 28. PMID: 29290310.

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

Petrov AA, Traister RS, Crespo MM, Silveira FP, Xie M, Coffey K, Ensor CR, Landsittel D, Pilewski JM. A Prospective Observational Study of Hypogammaglobulinemia in the First Year After Lung Transplantation. Transplant Direct. 2018 Jul 12;4(8):e372. doi: 10.1097/TXD.0000000000000811. eCollection 2018 Aug. PMID: 30255132. 10 10 11 11

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

Sonjian Lu, PhD

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/s41598-017-09951-2. PMID: 28855549.

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.

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.

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 subtypespecific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma. Epigenetics. 2018 Jun 21. doi: 10.1080/15592294.2018.1469892. [Epub ahead of print]. PMID: 29927689.

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. 2018 Sep 12;13(9):e0203871. doi: 10.1371/journal.pone.0203871. eCollection 2018. PMID: 30208101.

Xinghua Lu, MD, PhD, MS

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/s41598-017-09951-2. PMID: 28855549.

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: PMC28984190.

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. 2017 Nov 13. pii: molcanres.0378.2017. doi: 10.1158/1541-7786.MCR-17-0378. Epub 2017 Nov 13. PMID: 29133589.

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.

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.

Chen L, Lu X. Making deep learning models transparent. Invited editorial article. Journal of Medical Artificial Intelligence. 19 July 2018. doi: 10.21037/jmai.2018.07.01.

Chen L, Lu X. Discover functional impact of microRNAs in cancer using a causal deep learning model. BMC Medical Genomics. 2018.

Jin Q, Dhingra B, Cohen W, Lu X. AttentionMeSH: Simple, Effective and Interpretable Automatic MeSH Indexer. Proceedings of Empirical Methods in Natural Language Processing. 2018.

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 subtypespecific 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.

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. 2018 Sep 12;13(9):e0203871. doi: 10.1371/journal.pone.0203871. eCollection 2018. PMID: 30208101.

Yalini Senathirajah, PhD

Robbins R, Senathirajah Y, Williams NJ, Hutchinson C, Rapoport 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.

Shyam Visweswaran, MD, PhD

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: 0.1093/bib/bbx157. [Epub ahead of print]. PMID: 29186302.

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. PMID: 29888097. PMCID: PMC5961808.

Michael M. Wagner, MD, PhD

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

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.

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. PMID: 29888097. PMCID: PMC5961808.

Erik S. Wright, PhD, MS

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

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