Publications

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Wu Y, Jiang X, Ohno-Machado L. Preserving Institutional Privacy in Distributed binary Logistic Regression. AMIA Annu Symp Proc. 2012 ;2012:1450-8.
Wu Y, Jiang X, Kim J, Ohno-Machado L. Grid Binary LOgistic REgression (GLORE): building shared models without sharing data. J Am Med Inform Assoc. 2012 .
Wu Y, Jiang X, Kim J, Ohno-Machado L. I-spline Smoothing for Calibrating Predictive Models. AMIA Summits Transl Sci Proc. 2012 ;2012:39-46.
Wu W, Dasgupta S, Ramirez EE, Peterson C, Norman GJ. Classification accuracies of physical activities using smartphone motion sensors. J Med Internet Res. 2012 ;14(5):e130.
Wu Y, Jiang X, Wang S, Jiang W, Li P, Ohno-Machado L. Grid multi-category response logistic models. BMC Med Inform Decis Mak. 2015 ;15:10.
Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L. Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015 .
Wang S, Jiang X, Ji Z, El-Kareh R, Choi J, Kim H. When you can't tell when it hurts: a preliminary algorithm to assess pain in patients who can't communicate. AMIA Annu Symp Proc. 2013 ;2013:1429-37.
Wang S, Mohammed N, Chen R. Differentially private genome data dissemination through top-down specialization. BMC Med Inform Decis Mak. 2014 ;14 Suppl 1:S2.
Wang B, Xiong H, Jiang X, Ling F. SEMI-SUPERVISED OBJECT RECOGNITION USING STRUCTURE KERNEL. Proc Int Conf Image Proc. 2012 :2157-2160.
Wang S, Wang L, Afef D, Rathi L, Shen L, Jiang X, Wang W. PALME : PAtients Like My gEnome Server Backend MongoDB database. In: AMIA Summit on Translational Bioinformatics. AMIA Summit on Translational Bioinformatics. ; 2016.
Wang S, Jiang X, Chen F, Cui L, Cheng S. Streamlined Genome Sequence Compression using Distributed Source Coding. Cancer Inform. 2014 ;13(Suppl 1):123-31.
Wang S, Zhang Y, Dai W, Lauter K, Kim M, Tang Y, Xiong H, Jiang X. HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS. Bioinformatics. 2016 ;32(2):211-8.
Wang S, Kim J, Jiang X, Brunner SF, Ohno-Machado L. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda. BMC Med Genomics. 2014 ;7 Suppl 1:S9.
Wang S, Cui L, Que J, Choi D-H, Jiang X, Cheng S, Xie L. A Randomized Response Model For Privacy Preserving Smart Metering. IEEE Trans Smart Grid. 2012 ;3(2):1317-1324.
Wang S, Jiang X, Singh S, Marmor R, Bonomi L, Fox D, Dow M, Ohno-Machado L. Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States. 2016 .
Wang S, Bonomi L, Dai W, Chen F, Cheung C, Bloss CS, Jiang X, Cheng S. Big Data Privacy in Biomedical Research. IEEE Transactions on Big Data. 2016 .
Wang S, Jiang X, Fox D, L O-M. Preserving genome privacy in research studies. In: Medical Data Privacy Handbook. Medical Data Privacy Handbook. Springer; 2015.
Wang S, Jiang X, Wu Y, Cui L, Cheng S, Ohno-Machado L. EXpectation Propagation LOgistic REgRession (EXPLORER): Distributed privacy-preserving online model learning. J Biomed Inform. 2013 ;46(3):480-96.
Wang S, Wang X, Jiang X, Tang H, Bu D, Carey K, Dyke SOM, Fox D, Jiang C, Lauter K, et al. A community effort to protect genomic data sharing, collaboration and outsourcing. NPJ Genomic Medicine. 2017 ;2.
Wang M, Ji Z, Wang S, Kim J, Yang H, Jiang X, Ohno-Machado L. Mechanisms to Protect the Privacy of Families When Using the Transmission Disequilibrium Test in Genome-Wide Association Studies. Bioinformatics. 2017 .
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Stepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L. Prediction of MicroRNA Precursors Using Parsimonious Feature Sets. Cancer Inform. 2014 ;13(Suppl 1):95-102.
South BR, Mowery D, Suo Y, Leng J, Ferrández Ó, Meystre SM, Chapman WW. Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text. J Biomed Inform. 2014 ;50:162-72.
Song S, Chaudhuri K, Sarwate AD. Learning from Data with Heterogeneous Noise using SGD. In: 18th International Conference on Artificial Intelligence and Statistics (AISTATS). 18th International Conference on Artificial Intelligence and Statistics (AISTATS). ; 2015.
Shimizu C, Sood A, Lau HD, Oharaseki T, Takahashi K, Krous HF, Campman S, Burns JC. Cardiovascular pathology in 2 young adults with sudden, unexpected death due to coronary aneurysms from Kawasaki disease in childhood. Cardiovasc Pathol. 2015 .
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW, et al. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011 ;4(1):16-25.
Shimizu C, Kim J, Stepanowsky P, Trinh C, Lau HD, Akers JC, Chen C, Kanegaye JT, Tremoulet A, Ohno-Machado L, et al. Differential expression of miR-145 in children with Kawasaki disease. PLoS One. 2013 ;8(3):e58159.
Shimizu C, Oharaseki T, Takahashi K, Kottek A, Franco A, Burns JC. The role of TGF-β and myofibroblasts in the arteritis of Kawasaki disease. Hum Pathol. 2012 .
Shimizu C, Eleftherohorinou H, Wright VJ, Kim J, Alphonse MP, Perry JC, Cimaz R, Burgner D, Dahdah N, Hoang LT, et al. Genetic Variation in the SLC8A1 Calcium Signaling Pathway Is Associated with Susceptibility to Kawasaki Disease and Coronary Artery Abnormalities. 2016 .
Shi E, Chmielecki J, Tang CM, Wang K, Heinrich MC, Kang G, Corless CL, Hong D, Fero KE, Murphy JD, et al. FGFR1 and NTRK3 actionable alterations in "Wild-Type" gastrointestinal stromal tumors. 2016 .
Shi H, Jiang C, Dai W, Jiang X, Tang Y, Ohno-Machado L. Secure Multi-pArty Computation Grid LOgistic REgression (SMAC-GLORE). BMC Medical Informatics and Decision Making. 2016 .
Sarwate AD, Chaudhuri K. Signal Processing and Machine Learning with Differential Privacy: Algorithms and challenges for continuous data. IEEE Signal Process Mag. 2013 ;30(5):86-94.
Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011 ;18(4):354-7.
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Myslín M, Zhu S-H, Chapman W, Conway M. Using twitter to examine smoking behavior and perceptions of emerging tobacco products. J Med Internet Res. 2013 ;15(8):e174.
von Muhlen M, Ohno-Machado L. Reviewing social media use by clinicians. J Am Med Inform Assoc. 2012 ;19(5):777-81.
Mohammed N, Wang S, Chen R, Jiang X. Private Genome Data Dissemination. In: Medical Data Privacy Handbook. Medical Data Privacy Handbook. Springer; 2015.
Mohammed N, Jiang X, Chen R, Fung BCM, Ohno-Machado L. Privacy-preserving heterogeneous health data sharing. J Am Med Inform Assoc. 2012 .
Menon AKrishna, Jiang XJ, Vembu S, Elkan C, Ohno-Machado L. Predicting accurate probabilities with a ranking loss. Mach Learn Int Conf Mach Learn. 2012 ;2012:703-710.
Menon AKrishna, Jiang X, Kim J, Vaidya J, Ohno-Machado L. Detecting Inappropriate Access to Electronic Health Records Using Collaborative Filtering. Mach Learn. 2014 ;95(1):87-101.
Mehta SR, Vinterbo SA, Little SJ. Ensuring Privacy in the Study of Pathogen Genetics in the 21st Century. The Lancet Infectious Diseases. 2014 .
Meeker D, Jiang X, Matheny ME, Farcas C, D'Arcy M, Pearlman L, Nookala L, Day ME, Kim KK, Kim H, et al. A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research. J Am Med Inform Assoc. 2015 ;22(6):1187-95.
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Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K. On the design of clone-based haplotyping. Genome Biol. 2013 ;14(9):R100.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011 ;12 Suppl 1:S24.
Lin J, Jain S, Sun X, Liu V, Sato YZ, Jimenez-Fernandez S, Newfield RS, Pourfarzib R, Tremoulet AH, Gordon JB, et al. Lipoprotein Particle Concentrations in Children and Adults following Kawasaki Disease. J Pediatr. 2014 ;165(4):727-31.
Li P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L. HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. J Am Med Inform Assoc. 2014 ;21(2):363-73.
Li Y, Jiang X, Wang S, Xiong H, Ohno-Machado L. VERTIcal Grid lOgistic regression (VERTIGO). J Am Med Inform Assoc. 2015 .
Li P, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X. DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique. PLoS One. 2013 ;8(11):e80377.
Li H, Xiong K, Jiang X, Liu J. Differentially private histogram publication for dynamic datasets: An adaptive sampling approach. In: 24th ACM International Conference on Information and Knowledge Management (CIKM). 24th ACM International Conference on Information and Knowledge Management (CIKM). ; 2015.
Li Z, Chao T-C, Chang K-Y, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM. The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A. 2014 ;111(3):1002-7.
Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy preserving RBF kernel support vector machine. Biomed Res Int. 2014 ;2014:827371.
Levy E, Marty R, Calderón VGárate, Woo B, Dow M, Armisen R, Carter H, Harismendy O. Immune DNA signature of T-cell infiltration in breast tumor exomes. Sci Rep. 2016 ;6:30064.
Lee A, Shimizu C, Oharaseki T, Takahashi K, Daniels LB, Kahn A, Adamson R, Dembitsky W, Gordon JB, Burns JC. Role of TGF-β Signaling in Remodeling of Non-coronary Artery Aneurysms in Kawasaki diseaseβ. Pediatr Dev Pathol. 2015 .
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010 ;43(5):709-15.
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Kuo T, Kim H, Ohno-Machado L. Blockchain distributed ledger technologies for biomedical and health care applications. Journal of the American Medical Informatics Association. 2017 .
Kuo T, Rao P, Maehara C, Doan S, Chaparro J, Day M, Farcas C, Ohno-Machado L, Hsu C. Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. 2016 .
Kozono D, Li J, Nitta M, Sampetrean O, Gonda D, Kushwaha DS, Merzon D, Ramakrishnan V, Zhu S, Zhu K, et al. Dynamic epigenetic regulation of glioblastoma tumorigenicity through LSD1 modulation of MYC expression. Proceedings of the National Academy of Sciences. 2015 .
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011 ;18(3):401-13.
Kozanitis C, Heiberg A, Varghese G, Bafna V. Using Genome Query Language to uncover genetic variation. Bioinformatics. 2013 .
Kinsella M, Patel A, Bafna V. The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 ;42(13):8231-42.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011 ;27(8):1068-75.
Kim S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 .
Kim J, Grillo JM, Boxwala AA, Jiang X, Mandelbaum RB, Patel BA, Mikels D, Vinterbo SA, Ohno-Machado L. Anomaly and Signature Filtering Improve Classifier Performance For Detection Of Suspicious Access To EHRs. AMIA Annu Symp Proc. 2011 ;2011:723-31.
Kim S, Jeong K, Bhutani K, Lee JH, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol. 2013 ;14(8):R90.
Kim J, Shimizu C, Kingsmore SF, Veeraraghavan N, Levy E, Santos AMRibeiro Do, Yang H, Flatley J, Hoang LT, Hibberd ML, et al. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. 2017 .
Kim H, Ohno-Machado L, Oh J, Jiang X. Trends in publication of nursing informatics research. AMIA Annu Symp Proc. 2014 ;2014:805-14.
Kim S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 ;29(8):1076-7.
Kim H, El-Kareh R, Goel A, Vineet F, Chapman WW. An approach to improve LOINC mapping through augmentation of local test names. J Biomed Inform. 2011 .
Kim H, Chung H, Wang S, Jiang X, Choi J. SAPPIRE: a prototype mobile tool for pressure ulcer risk assessment. Stud Health Technol Inform. 2014 ;201:433-40.

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