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Bafna V, Deutsch A, Heiberg A, Kozanitis C, Ohno-Machado L, Varghese G. Abstractions for Genomics: Or, which way to the Genomic Information Age?. Communications of the ACM. 2013.\par \par Zakov S, Kinsella M, Bafna V. An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proc Natl Acad Sci U S A. 2013;110(14):5546-51.\par \par 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.\par \par Menon A, Jiang X, Kim J, Vaidya J, Ohno-Machado L. Detecting Inappropriate Access to Electronic Health Records Using Collaborative Filtering. Machine Learning for Science and Society. 2013.\par \par Shimizu C, Kim J, Stepanowsky P, Trinh C, Lau HD, Akers JC, Chen C, Kanegaye JT, Tremoulet A, Ohno-Machado L. Differential expression of miR-145 in children with Kawasaki disease. PLoS One. 2013;8(3):e58159.\par \par Kim S, Medvedev P, Paton TA, Bafna V. REPREVER: Resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Research. 2013.\par \par Hinske LC, Heyn J, Galante PAF, Ohno-Machado L, Kreth S. Setting up an intronic miRNA database. Methods Mol Biol. 2013;936:69-76.\par \par Kozanitis CK, Heiberg A, Varghese G, Bafna V. Using Genome Query Language (GQL) to uncover genetic variation. Bioinformatics. 2013.\par \par Hsieh A, Doan S, Conway M, Lin KW, Kim H. Demographic Identification:Variable Extraction Resource (DIVER). 2nd IEEE Conference on Healthcare informatics, Imaging, and Systems Biology. 2012.\par \par 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.\par \par 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.\par \par 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.\par \par Norman G, Kolodziejczyk J, Ramirez E, Hekler E. Methods for Delivering Physical Activity Messages. In: Behavioral Aspects of Exercise. Behavioral Aspects of Exercise. ; 2012. p. .\par \par 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.\par \par Demchak B, Krueger I. Policy Driven Development: Flexible Policy Insertion for Large Scale Systems. IEEE International Symposium on Policies for Distributed Systems and Networks. 2012.\par \par Shimizu C, Oharaseki T, Takahashi K, Kottek A, Franco A, Burns JC. The role of TGF-? and myofibroblasts in the arteritis of Kawasaki disease. Hum Pathol. 2012.\par \par 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.\par \par Kroll JE, Galante PAF, Ohara DT, Navarro FCP, Ohno-Machado L, de Souza SJ. SPLOOCE: A new portal for the analysis of human splicing variants. RNA Biol. 2012;9(11):1339-43.\par \par 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.\par \par 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.\par \par 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.\par \par Jiang X, Osl M, Kim J, Ohno-Machado L. Calibrating predictive model estimates to support personalized medicine. J Am Med Inform Assoc. 2011.\par \par Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.\par \par Ohno-Machado L, Bafna V, Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, Day ME, Farcas C, Heintzman ND, Jiang X. iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2011.\par \par Kamberov YG, Kim J, Mazitschek R, Kuo WP, Whitman M. Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cells. BMC Res Notes. 2011;4:381.\par \par 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.\par \par 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.\par \par Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.\par \par 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.\par \par 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.\par \par 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.\par \par Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.\par \par }