Publications

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Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G. Abstractions for Genomics. Commun ACM. 2013 ;56(1):83-93.
Bao L, Pu M, Messer K. AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data. Bioinformatics. 2014 .
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.
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.
Boland BS, Widjaja CE, Banno A, Zhang B, Kim SH, Stoven S, Peterson MR, Jones MC, Su HI, Crowe SE, et al. Immunodeficiency and Autoimmune Enterocolopathy Linked to NFAT5 Haploinsufficiency. The Journal of Immunology. 2015 .
Bonomi L, Jiang X. A Mortality Study for ICU Patients Using Bursty Medical Events. Data Engineering (ICDE), 2017 IEEE 33rd International Conference. 2017 .
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.
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.
Burns JC, Newburger JW. Genetics insights into the pathogenesis of Kawasaki disease. Circ Cardiovasc Genet. 2012 ;5(3):277-8.
Burns JC, Touma R, Song Y, Padilla RL, Tremoulet AH, Sidney J, Sette A, Franco A. Fine specificities of natural regulatory T cells after IVIG therapy in patients with Kawasaki disease. Autoimmunity. 2015 ;48(3):181-8.
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.
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 .
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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.
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.
Chaudhuri K, Hsu D. Sample Complexity Bounds for Differentially Private Learning. JMLR Workshop Conf Proc. 2011 ;2011:155-186.
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.
Chaudhuri K, Sarwate AD, Sinha K. Near-Optimal Algorithms for Differentially-Private Principal Components. Neural Information Processing Systems (NIPS). 2012 .
Chaudhuri K, Hsu D, Song S. The Large Margin Mechanism for Differentially Private Maximization. Neural Information Processing Systems (NIPS). 2014 .
Chaudhuri K, Hsu D. Convergence Rates for Differentially Private Statistical Estimation. 29th International Conference on Machine Learning. 2012 .
Chaudhuri K, Monteleoni C, Sarwate AD. Differentially Private Empirical Risk Minimization. J Mach Learn Res. 2011 ;12:1069-1109.
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.
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).
Cui L, Wang S, Jiang X, Cheng S. Adaptive Distributed Video Coding with Correlation Estimation using Expectation Propagation. Proc SPIE. 2012 ;8499.
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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 .
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.
Dasgupta S. Consistency of nearest neighbor classification under selective sampling. 25th Annual Conference on Learning Theory. 2012 .
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 .
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.
Doan S, Maehara CK, Chaparro JD, Lu S, Liu R, Graham A, Berry E, Hsu C-N, Kanegaye JT, Lloyd DD, et al. Building a Natural Language Processing Tool to Identify Patients with High Clinical Suspicion for Kawasaki Disease from Emergency Department Notes. Acad Emerg Med. 2016 .
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.
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 .
Dulai PS, Singh S, Ohno-Machaco L, Sandborn WJ. Population Health Management for Inflammatory Bowel Disease. Gastroenterology. 2017 .
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Farcas C, Farcas E, Krueger I. Successful Cyberinfrastructures for E-Health. In: Economics Driven Software Architecture. Economics Driven Software Architecture. Elsvevier; 2014.
Farcas C, Balac N, Ohno-Machado L. Biomedical CyberInfrastructure Challenges. Extreme Science and Engineering Discovery Environment: Gateway to Discovery. 2013 .
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.
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 E, Menarini M, Farcas C, Griswold W, Patrick K, Krueger I, Demchak B, Raab F, Yan Y, Ziftci C. Influences of Architectural and Implementation Choices on CyberInfrastructure Quality – A Case Study. In: Software Quality Assurance. Software Quality Assurance. Elsevier; 2015.
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 .
Feng C, Dow M, Ding S, Lu Y, Jiang X, Tang H, Wan S. PREMIX: PRivacy-preserving EstiMation of Individual admixture. 2016 .
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.
FitzHenry F, Resnic FS, Robbins SL, Denton J, Nookala L, Meeker D, Ohno-Machado L, Matheny ME. Creating a Common Data Model for Comparative Effectiveness with the Observational Medical Outcomes Partnership. Applied Clinical Informatics. 2015 ;6(3).
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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.
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 .
Hepler LN, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL. IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform. PLoS Comput Biol. 2014 ;10(9):e1003842.
Herberg JA, Kaforou M, Wright VJ, Shailes H, Eleftherohorinou H, Hoggart CJ, Cebey-López M, Carter MJ, Janes VA, Gormley S, et al. Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children. JAMA. 2016 ;316(8):835-45.
Hinske LC, Heyn J, Galante PAF, Ohno-Machado L, Kreth S. Setting up an intronic miRNA database. Methods Mol Biol. 2013 ;936:69-76.
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010 ;11:533.
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 .
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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.
Ji Z, Elkan C. Differential privacy based on importance weighting. Mach Learn. 2013 ;93(1):163-183.
Jiang X, Osl M, Kim J, Ohno-Machado L. Calibrating predictive model estimates to support personalized medicine. J Am Med Inform Assoc. 2011 .
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, 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.
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.
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.
Jiang W, Li P, Wang S, Wu Y, Xue M, Ohno-Machado L, Jiang X. WebGLORE: A Webservice for Grid LOgistic REgression. Bioinformatics. 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, 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.
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 .
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.
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.
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.
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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.
Kim H, Bell E, Kim J, Sitapati A, Ramsdell J, Farcas C, Friedman D, Feupe SF, Ohno-Machado L. iCONCUR: informed consent for clinical data and bio-sample use for research. 2016 .
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.
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 .
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 S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 .
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 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.
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 .
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 S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 ;29(8):1076-7.
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 .
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.
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.
Kinsella M, Patel A, Bafna V. The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 ;42(13):8231-42.
Kozanitis C, Heiberg A, Varghese G, Bafna V. Using Genome Query Language to uncover genetic variation. Bioinformatics. 2013 .
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011 ;18(3):401-13.
Kozono D, Li J, Nitta M, Sampetrean O, Gonda D, Kushwaha DS, Merzon D, Ramakrishnan V, Zhu S, Zhu K, et al. Dynamic epigenetic regulation of glioblastoma tumorigenicity through LSD1 modulation of MYC expression. Proceedings of the National Academy of Sciences. 2015 .
Kuo T, Kim H, Ohno-Machado L. Blockchain distributed ledger technologies for biomedical and health care applications. Journal of the American Medical Informatics Association. 2017 .
Kuo T, Rao P, Maehara C, Doan S, Chaparro J, Day M, Farcas C, Ohno-Machado L, Hsu C. Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. 2016 .
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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.
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 .
Levy E, Marty R, Calderón VGárate, Woo B, Dow M, Armisen R, Carter H, Harismendy O. Immune DNA signature of T-cell infiltration in breast tumor exomes. Sci Rep. 2016 ;6:30064.
Li H, Xiong K, Jiang X, Liu J. Differentially private histogram publication for dynamic datasets: An adaptive sampling approach. In: 24th ACM International Conference on Information and Knowledge Management (CIKM). 24th ACM International Conference on Information and Knowledge Management (CIKM). ; 2015.
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.
Li Z, Chao T-C, Chang K-Y, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM. The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A. 2014 ;111(3):1002-7.
Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy preserving RBF kernel support vector machine. Biomed Res Int. 2014 ;2014:827371.
Li Y, Jiang X, Wang S, Xiong H, Ohno-Machado L. VERTIcal Grid lOgistic regression (VERTIGO). J Am Med Inform Assoc. 2015 .
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.

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