Publications

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Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, et al. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet. 2013 ;93(3):452-62.
Dubchak I, Munoz M, Poliakov A, Salomonis N, Minovitsky S, Bodmer R, Zambon AC. Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. Bioinformatics. 2013 ;29(16):2059-61.
Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, et al. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol. 2014 ;15(2):R36.
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 .
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.
Kim S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 ;29(8):1076-7.
Jiang W, Li P, Wang S, Wu Y, Xue M, Ohno-Machado L, Jiang X. WebGLORE: A Webservice for Grid LOgistic REgression. Bioinformatics. 2013 .
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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 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.
Han D, Wang S, Jiang C, Jiang X, Kim H-E, Sun J, Ohno-Machado L. Trends in biomedical informatics: automated topic analysis of JAMIA articles. J Am Med Inform Assoc. 2015 ;22(6):1153-63.
Ogata S, Shimizu C, Franco A, Touma R, Kanegaye JT, Choudhury BP, Naidu NN, Kanda Y, Hoang LT, Hibberd ML, et al. Treatment response in kawasaki disease is associated with sialylation levels of endogenous but not therapeutic intravenous immunoglobulin G. PLoS One. 2013 ;8(12):e81448.
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.
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.
Ohno-Machado L. To share or not to share: that is not the question. Sci Transl Med. 2012 ;4(165):165cm15.
Yan S, Jiang X, Chen Y. Text Mining Driven Drug-Drug Interaction Detection. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2013 :349-355.
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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.
Farcas C, Farcas E, Krueger I. Successful Cyberinfrastructures for E-Health. In: Economics Driven Software Architecture. Economics Driven Software Architecture. Elsvevier; 2014.
Dai W, Xiong H, Jiang X, Chen CWen. Structured Set Intra Prediction With Discriminative Learning in a Max-Margin Markov Network for High Efficiency Video Coding. IEEE Trans Circuits Syst Video Technol. 2013 ;23(11):1941-1956.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011 ;12 Suppl 1:S24.
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.
Zou KH, Liu A, Bandos AI, Ohno-Machado L, Rockette HE. Statistical Evaluation of Diagnostic Performance: Topics in Roc Analysis. In: Boca Raton: CRC Press; 2012. p. 223.
Chaudhuri K, Viterbo S. A Stability-based Validation Procedure for Differentially Private Machine Learning. In: Neural Information Processing Systems (NIPS) Conference. Neural Information Processing Systems (NIPS) Conference. ; 2013.
Jiang X, Osl M, Kim J, Ohno-Machado L. Smooth isotonic regression: a new method to calibrate predictive models. AMIA Joint Summit on Translational Science. 2011 ;2011:16-20.
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.
Bell EA, Ohno-Machado L, M Grando A. Sharing my health data: a survey of data sharing preferences of healthy individuals. AMIA Annu Symp Proc. 2014 ;2014:1699-708.
Ohno-Machado L. Sharing data for the public good and protecting individual privacy: informatics solutions to combine different goals. J Am Med Inform Assoc. 2013 ;20(1):1.
Gardner J, Xiong L, Xiao Y, Gao J, Post AR, Jiang X, Ohno-Machado L. SHARE: system design and case studies for statistical health information release. J Am Med Inform Assoc. 2012 .
Zhu Q, Xiong H, Jiang X. Shape-oriented graph cuts and graph matching feedback for silhouette tracking. Visual Communications and Image Processing . 2012 .
Hinske LC, Heyn J, Galante PAF, Ohno-Machado L, Kreth S. Setting up an intronic miRNA database. Methods Mol Biol. 2013 ;936:69-76.
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.
Wang B, Xiong H, Jiang X, Ling F. SEMI-SUPERVISED OBJECT RECOGNITION USING STRUCTURE KERNEL. Proc Int Conf Image Proc. 2012 :2157-2160.
Berty HL, Simon M, Chapman BE. A semi-automated quantification of pulmonary artery dimensions in computed tomography angiography images. AMIA Annu Symp Proc. 2012 ;2012:36-42.
Jiang X, Kim J, Wu Y, Wang S, Ohno-Machado L. Selecting cases for whom additional tests can improve prognostication. AMIA Annu Symp Proc. 2012 ;2012:1260-8.
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 .
Burns JC, Herzog L, Fabri O, Tremoulet AH, Rodó X, Uehara R, Burgner D, Bainto E, Pierce D, Tyree M, et al. Seasonality of Kawasaki disease: a global perspective. PLoS One. 2013 ;8(9):e74529.
Yu F, Ji Z. Scalable privacy-preserving data sharing methodology for genome-wide association studies: an application to iDASH healthcare privacy protection challenge. BMC Med Inform Decis Mak. 2014 ;14 Suppl 1:S3.
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.
Chaudhuri K, Hsu D. Sample Complexity Bounds for Differentially Private Learning. JMLR Workshop Conf Proc. 2011 ;2011:155-186.
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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 .
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 .
von Muhlen M, Ohno-Machado L. Reviewing social media use by clinicians. J Am Med Inform Assoc. 2012 ;19(5):777-81.
Kim S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 .
Jiang X, Tse K, Wang S, Doan S, Kim H, Ohno-Machado L. Recent trends in biomedical informatics: a study based on JAMIA articles. J Am Med Inform Assoc. 2013 .
Dulai PS, Singh S, Jiang X, Peerani F, Narula N, Chaudrey K. The Real-World Effectiveness and Safety of Vedolizumab for Moderate-Severe Crohn’s Disease: Results From the US VICTORY Consortium. The American Journal of Gastroenterology. 2016 .
Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010 ;26(22):2856-62.
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, 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.
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Ohno-Machado L, Agha Z, Bell DS, Dahm L, Day ME, Doctor JN, Gabriel D, Kahlon MK, Kim KK, Hogarth M, et al. pSCANNER: patient-centered Scalable National Network for Effectiveness Research. J Am Med Inform Assoc. 2014 ;21(4):621-6.
Tang H, Jiang X, Wang X, Wang S, Sofia H, Fox D, Lauter K, Malin B, Telenti A, Xiong L, et al. Protecting genomic data analytics in the cloud: state of the art and opportunities. BMC Medical Genomics. 2016 ;9(63).
Vinterbo SA, Sarwate AD, Boxwala AA. Protecting count queries in study design. J Am Med Inform Assoc. 2012 .
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 .
Jiang X, Sarwate AD, Ohno-Machado L. Privacy technology to support data sharing for comparative effectiveness research: a systematic review. Med Care. 2013 ;51(8 Suppl 3):S58-65.
Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy preserving RBF kernel support vector machine. Biomed Res Int. 2014 ;2014:827371.
Jiang X, Ji Z, Wang S, Mohammed N, Cheng S, Ohno-Machado L. Privacy preserving data publishing through component analysis, Transaction on Data Privacy. Transaction on Data Privacy. 2013 .
Chen F, Wang S, Jiang X, Ding S, Lu Y, Kim J, Sahinalp S, Shimizu C, Burns J, Wright V, et al. PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryp-tion through Software guard extensionS. 2016 ;33(16).
Wu Y, Jiang X, Ohno-Machado L. Preserving Institutional Privacy in Distributed binary Logistic Regression. AMIA Annu Symp Proc. 2012 ;2012:1450-8.
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.
Feng C, Dow M, Ding S, Lu Y, Jiang X, Tang H, Wan S. PREMIX: PRivacy-preserving EstiMation of Individual admixture. 2016 .
Farhan W, Wang Z, Huang Y, Wang S, Wang F, Jiang X. A Predictive Model for Medical Events Based on Contextual Embedding of Temporal Sequences. 2016 .
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.
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.
Chen F, S W, Mohammed N, Cheng S. PRECISE: PRivacy-prEserving Cloud-assisted quality Improvement Service in hEalthcare. In: Translational Bioinformatics Conference. Translational Bioinformatics Conference. ; 2014.
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010 ;11:533.
Dulai PS, Singh S, Ohno-Machaco L, Sandborn WJ. Population Health Management for Inflammatory Bowel Disease. Gastroenterology. 2017 .
Dulai PS, Singh S, Ohno-Machado L, Sandborn WJ. Population Health Management for Inflammatory Bowel Disease. Gastroenterology. 2018 .
Demchak B, Krüger I. Policy Driven Development: Flexible Policy Insertion for Large Scale Systems. Proc IEEE Int Symp Policies Distrib Syst Netw. 2012 ;2012:17-24.
Doan S, Lin K-W, Conway M, Ohno-Machado L, Hsieh A, Feupe SF, Garland A, Ross MK, Jiang X, Farzaneh S, et al. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. J Am Med Inform Assoc. 2013 .
Jiang X, Boxwala AA, El-Kareh R, Kim J, Ohno-Machado L. A patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision support. J Am Med Inform Assoc. 2012 ;19(e1):e137-e144.
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.

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