Publications

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2011
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 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.
Jiang X, Osl M, Kim J, Ohno-Machado L. Calibrating predictive model estimates to support personalized medicine. J Am Med Inform Assoc. 2011 .
Ohno-Machado L, Bafna V, Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, Day ME, Farcas C, Heintzman ND, Jiang X, et al. iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2011 .
Jiang X, El-Kareh R, Ohno-Machado L. Improving predictions in imbalanced data using pairwise expanded logistic regression. AMIA Annu Symp Proc. 2011 ;2011:625-34.
Nadkarni PM, Ohno-Machado L, Chapman WW. Natural language processing: an introduction. J Am Med Inform Assoc. 2011 ;18(5):544-51.
Jiang X, Cheng S, Ohno-Machado L. Quantifying Fine-Grained Privacy Risk and Representativeness in Medical Data. 17th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 2011 .
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.
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.
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.
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011 ;18(4):498-505.
2012
Que J, Jiang X, Ohno-Machado L. A collaborative framework for Distributed Privacy-Preserving Support Vector Machine learning. AMIA Annu Symp Proc. 2012 ;2012:1350-9.
Jiang X, Menon A, Wang S, Kim J, Ohno-Machado L. Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): An Algorithm for Joint Optimization of Discrimination and Calibration. PLoS One. 2012 ;7(11):e48823.
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.
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.
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.
Wu Y, Jiang X, Ohno-Machado L. Preserving Institutional Privacy in Distributed binary Logistic Regression. AMIA Annu Symp Proc. 2012 ;2012:1450-8.
Mohammed N, Jiang X, Chen R, Fung BCM, Ohno-Machado L. Privacy-preserving heterogeneous health data sharing. J Am Med Inform Assoc. 2012 .
von Muhlen M, Ohno-Machado L. Reviewing social media use by clinicians. J Am Med Inform Assoc. 2012 ;19(5):777-81.
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.
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 .
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.
Ohno-Machado L. To share or not to share: that is not the question. Sci Transl Med. 2012 ;4(165):165cm15.
2013
Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G. Abstractions for Genomics. Commun ACM. 2013 ;56(1):83-93.
Thawait SK, Kim J, Klufas RA, Morrison WB, Flanders AE, Carrino JA, Ohno-Machado L. Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis. AJR Am J Roentgenol. 2013 ;200(3):493-502.
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.
Jiang X, Ji Z, Wang S, Mohammed N, Cheng S, Ohno-Machado L. Differential-Private Data Publishing Through Component Analysis. Trans Data Priv. 2013 ;6(1):19-34.
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.
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.
Roozgard A, Barzigar N, Wang S, Jiang X, Ohno-Machado L, Cheng S. Nucleotide sequence alignment using sparse coding and belief propagation. Conf Proc IEEE Eng Med Biol Soc. 2013 ;2013:588-91.
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, 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.
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 .
Hinske LC, Heyn J, Galante PAF, Ohno-Machado L, Kreth S. Setting up an intronic miRNA database. Methods Mol Biol. 2013 ;936:69-76.
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.
Jiang W, Li P, Wang S, Wu Y, Xue M, Ohno-Machado L, Jiang X. WebGLORE: A Webservice for Grid LOgistic REgression. Bioinformatics. 2013 .
2014
Jiang X, Zhao Y, Wang X, Malin B, Wang S, Ohno-Machado L, Tang H. A community assessment of privacy preserving techniques for human genomes. BMC Med Inform Decis Mak. 2014 ;14 Suppl 1:S1.
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.
Ji Z, Jiang X, Wang S, Xiong L, Ohno-Machado L. Differentially private distributed logistic regression using private and public data. BMC Med Genomics. 2014 ;7 Suppl 1:S14.
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.
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.
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 .
Doan S, Conway M, Phuong TMinh, Ohno-Machado L. Natural language processing in biomedicine: a unified system architecture overview. Methods Mol Biol. 2014 ;1168:275-94.
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.
Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy preserving RBF kernel support vector machine. Biomed Res Int. 2014 ;2014:827371.
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.
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.
Kim H, Ohno-Machado L, Oh J, Jiang X. Trends in publication of nursing informatics research. AMIA Annu Symp Proc. 2014 ;2014:805-14.