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, 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 B, Xiong H, Jiang X, Ling F. SEMI-SUPERVISED OBJECT RECOGNITION USING STRUCTURE KERNEL. Proc Int Conf Image Proc. 2012 :2157-2160.
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, 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, 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, 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 .
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, Mohammed N, Chen R. Differentially private genome data dissemination through top-down specialization. BMC Med Inform Decis Mak. 2014 ;14 Suppl 1:S2.
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, 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.
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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, 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 .
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 .
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 .
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 .
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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Numano F, Shimizu C, Jimenez-Fernandez S, Vejar M, Oharaseki T, Takahashi K, Salgado A, Tremoulet AH, Gordon JB, Burns JC, et al. Galectin-3 is a marker of myocardial and vascular fibrosis in Kawasaki disease patients with giant aneurysms. Int J Cardiol. 2015 ;201:429-37.
Norman G, Kolodziejczyk J, Ramirez E, Hekler E. How to Deliver Physical Activity Messages. In: ACSM’s Behavioral Aspects of Physical Activity & Exercise. ACSM’s Behavioral Aspects of Physical Activity & Exercise. American College of Sports Medicine; 2014.
Nodora JN, Komenaka IK, Bouton ME, Ohno-Machado L, Schwab R, Kim HE, Farcas C, Perez G, M Martinez E. Biospecimen Sharing Among Hispanic Women in a Safety-Net Clinic: Implications for the Precision Medicine Initiative. Journal of the National Cancer Institute. 2016 .
Nguyen NH, Khera R, Ohno-Machado L, Sandborn WJ, Singh S. Annual Burden and Costs of Hospitalization for High-Need, High-Cost Patients with Chronic Gastrointestinal and Liver Diseases. Clinical Gastroenterology and Hepatology. 2018 .
Natarajan L, Pu M, Messer K. Exact statistical tests for the intersection of independent lists of genes. Ann Appl Stat. 2012 ;6(2):521-541.
Nadkarni PM, Ohno-Machado L, Chapman WW. Natural language processing: an introduction. J Am Med Inform Assoc. 2011 ;18(5):544-51.
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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 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 Y, Jiang X, Wang S, Xiong H, Ohno-Machado L. VERTIcal Grid lOgistic regression (VERTIGO). J Am Med Inform Assoc. 2015 .
Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy preserving RBF kernel support vector machine. Biomed Res Int. 2014 ;2014:827371.
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 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 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.
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-T, Kim H-E, Ohno-Machado L. Blockchain distributed ledger technologies for biomedical and health care applications. Journal of the American Medical Informatics Association. 2018 .
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 H-E, Jiang X, Kim J, Ohno-Machado L. Trends in biomedical informatics: most cited topics from recent years. J Am Med Inform Assoc. 2011 ;18 Suppl 1:i166-70.
Kim J, Levy E, Ferbrache A, Stepanowsky P, Farcas C, Wang S, Brunner S, Bath T, Wu Y, Ohno-Machado L. MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. Bioinformatics. 2014 .
Kim J, Patel K, Jung H, Kuo WP, Ohno-Machado L. AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. BMC Bioinformatics. 2011 ;12:75.
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.

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