Publications

Export 180 results:
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, 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.
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 .
Chaudhuri K, Hsu D. Sample Complexity Bounds for Differentially Private Learning. JMLR Workshop Conf Proc. 2011 ;2011:155-186.
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, et al. 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.
2012
Cui L, Wang S, Jiang X, Cheng S. Adaptive Distributed Video Coding with Correlation Estimation using Expectation Propagation. Proc SPIE. 2012 ;8499.
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 .
Farcas C, Krueger I, Balac N, Chapman B, Ohno-Machado L. iDASH CyberInfrastructure: Mastering the Bits. In: NSF Towards a Shared Cyberinfrastructure Workshop 2012. NSF Towards a Shared Cyberinfrastructure Workshop 2012. ; 2012.
Farcas C, Krueger I, Balac N, Ohno-Machado L. iDASH CyberInfrastructure: The Nuts and Bolts. In: NSF Towards a Shared Cyberinfrastructure Workshop 2012. NSF Towards a Shared Cyberinfrastructure Workshop 2012. ; 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.
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, Krüger I. Policy Driven Development: Flexible Policy Insertion for Large Scale Systems. Proc IEEE Int Symp Policies Distrib Syst Netw. 2012 ;2012:17-24.
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 .
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. Proc Int Conf Image Proc. 2012 :2157-2160.
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 .
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.
Dai W, Xiong H, Jiang X, Ohno-Machado L. An Adaptive Difference Distribution-based Cod-ing with Hierarchical Tree Structure for DNA Sequence Compression. IEEE Data Compression Conference. 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.
Farcas C, Balac N, Ohno-Machado L. Biomedical CyberInfrastructure Challenges. Extreme Science and Engineering Discovery Environment: Gateway to Discovery. 2013 .
Grando A, Schwab R. Building and evaluating an ontology-based tool for reasoning about consent permission. AMIA Annu Symp Proc. 2013 ;2013:514-23.
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.
Ogata S, Tremoulet AH, Sato Y, Ueda K, Shimizu C, Sun X, Jain S, Silverstein L, Baker AL, Tanaka N, et al. Coronary artery outcomes among children with Kawasaki disease in the United States and Japan. Int J Cardiol. 2013 .
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.
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.
Ji Z, Elkan C. Differential privacy based on importance weighting. Mach Learn. 2013 ;93(1):163-183.
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.
Chapman WW, Hillert D, Velupillai S, Kvist M, Skeppstedt M, Chapman BE, Conway M, Tharp M, Mowery DL, Deleger L. Extending the NegEx lexicon for multiple languages. Stud Health Technol Inform. 2013 ;192:677-81.
Burns JC, Song Y, Bujold M, Shimizu C, Kanegaye JT, Tremoulet AH, Franco A. Immune-monitoring in Kawasaki disease patients treated with infliximab and intravenous immunoglobulin. Clin Exp Immunol. 2013 .
Feupe SF, Frias PF, Mednick SC, McDevitt EA, Heintzman ND. Nocturnal continuous glucose and sleep stage data in adults with type 1 diabetes in real-world conditions. J Diabetes Sci Technol. 2013 ;7(5):1337-45.
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, 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 .
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 .
Kim S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 .
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.
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.
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.
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.
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.
Yan S, Jiang X, Chen Y. Text Mining Driven Drug-Drug Interaction Detection. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2013 :349-355.
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.
Kozanitis C, Heiberg A, Varghese G, Bafna V. Using Genome Query Language to uncover genetic variation. Bioinformatics. 2013 .
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.
Kim S, Jeong K, Bhutani K, Lee JH, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol. 2013 ;14(8):R90.
Jiang W, Li P, Wang S, Wu Y, Xue M, Ohno-Machado L, Jiang X. WebGLORE: A Webservice for Grid LOgistic REgression. Bioinformatics. 2013 .
Kim S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 ;29(8):1076-7.
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.
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.
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.

Pages