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2013
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.
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.
Henderson L, Bortone DS, Lim C, Zambon AC. Classic Broken Cell and Newer Live Cell Methods for Cell Cycle Assessment. Am J Physiol Cell Physiol. 2013.
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.
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.
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.
Wang S, Jiang X, Cui L, Cheng S, Ohno-Machado L. EXpectation Propagation based LOgistic REgRession (EXPLORER): Distributed Privacy Preserving Online Model Learning. Journal of Biomedical Informatics. 2013.
Jiang X, Ji Z, Wang S, Mohammed N, Cheng S, Ohno-Machado L. Privacy preserving data publishing through component analysis, Transaction on Data Privacy. 2013.
Kim S, Medvedev P, Paton TA, Bafna V. REPREVER: Resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Research. 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.
Kozanitis CK, Heiberg A, Varghese G, Bafna V. Using Genome Query Language (GQL) to uncover genetic variation. Bioinformatics. 2013.
2012
Cui L, Wang S, Jiang X, Cheng S. Adaptive Distributed Video Coding with Correlation Estimation using Expectation Propagation. SPIE Optics + Photonics. 2012.
Pu M, Hayashi T, Cottam H, Mulvaney J, Arkin M, Corr M, Carson D, Messer K. Analysis of high-throughput screening assays using cluster enrichment. Stat Med. 2012;31(30):4175-89.
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.
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.
Dasgupta S. Consistency of nearest neighbor classification under selective sampling. 25th Annual Conference on Learning Theory. 2012.
Chaudhuri K, Hsu D. Convergence Rates for Differentially Private Statistical Estimation. 29th International Conference on Machine Learning. 2012.
Yamazaki KG, Gonzalez E, Zambon AC. Crosstalk Between the Renin-Angiotensin System and the Advance Glycation End Product Axis in the Heart: Role of the Cardiac Fibroblast. J Cardiovasc Transl Res. 2012.
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.
Vinterbo S. Differentially Private Projected Histograms: Construction and Use for Prediction. European Conference on Machine Learning . 2012.
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.
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.
Burns JC, Newburger JW. Genetics insights into the pathogenesis of Kawasaki disease. Circ Cardiovasc Genet. 2012;5(3):277-8.
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.
Silgard E, Tharp M, Reeves R, Calvitti A, Chapman WW, Mulkar-Mehta R. A Hybrid System for Temporal Relation Determination in Medical Discharge Summaries. Sixth i2b2 Shared Task and Workshop. 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.
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. .
Chaudhuri K, Sarwate AD, Sinha K. Near-Optimal Algorithms for Differentially-Private Principal Components. Neural Information Processing Systems (NIPS). 2012.
Grando MA, Schwab R, Boxwala A, Alipanah N. Ontological approach for the management of informed consent permissions. 2nd IEEE Conference on Healthcare informatics, Imaging, and Systems Biology. 2012.
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.
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.
Menon AK, Jiang X, Vembu S, Elkan C, Ohno-Machado L. Predicting accurate probabilities with a ranking loss. 29th International Conference on Machine Learning. 2012.
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.
Vinterbo SA, Sarwate AD, Boxwala AA. Protecting count queries in study design. J Am Med Inform Assoc. 2012.
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.
von Muhlen M, Ohno-Machado L. Reviewing social media use by clinicians. J Am Med Inform Assoc. 2012;19(5):777-81.
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.
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.
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.
Wang B, Xiong H, Jiang X, Ling F. Semi-supervised object recognition using structure kernel. International Conference on Image Processing (ICIP) IEEE . 2012.
Zhu Q, Xiong H, Jiang X. Shape-oriented graph cuts and graph matching feedback for silhouette tracking. Visual Communications and Image Processing . 2012.
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.
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.
Zou KH, Liu A, Bandos AI, Ohno-Machado L, Rockette HE. Statistical Evaluation of Diagnostic Performance: Topics in Roc Analysis. In: Boca Raton; 2012. p. 223.
Natarajan L, Pu M, Messer K. Statistical Tests for the Intersection of Independent Lists of Genes: Sensitivity, FDR, and Type I Error Control. The Annals of Applied Statistics. 2012;6(2):521-541.
Ohno-Machado L. To share or not to share: that is not the question. Sci Transl Med. 2012;4(165):165cm15.
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.
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.
Jiang X, Osl M, Kim J, Ohno-Machado L. Calibrating predictive model estimates to support personalized medicine. J Am Med Inform Assoc. 2011.
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.
Chaudhuri K, Monteleoni C, Sarwate AD. Differentially Private Empirical Risk Minimization. J Mach Learn Res. 2011;12:1069-1109.
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
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.
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.
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.
Nadkarni PM, Ohno-Machado L, Chapman WW. Natural language processing: an introduction. J Am Med Inform Assoc. 2011;18(5):544-51.
Chapman WW, Nadkarni PM, Hirschman L, D'Avolio LW, Savova GK, Uzuner O. Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions. J Am Med Inform Assoc. 2011;18(5):540-3.
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.
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.
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.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.
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.
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.
2010
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.
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
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.
Chaudhuri K, Hsu D. Sample Complexity Bounds for Differentially Private Learning. 24th Annual Conference on Learning Theory. 2010.