Publications

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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 .
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 .
Cui L, Wang S, Jiang X, Cheng S. Adaptive Distributed Video Coding with Correlation Estimation using Expectation Propagation. Proc SPIE. 2012 ;8499.
Raisaro JL, Tramer F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, et al. Addressing the Beacon Re-Identification Attacks: Quantification and Mitigation of Privacy. Journal of the American Medical Informatics Association. 2017 .
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.
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.
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 .
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Alakus H, Yost SE, Woo B, French R, Lin GY, Jepsen K, Frazer KA, Lowy AM, Harismendy O. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. J Transl Med. 2015 ;13:122.
Ross MK, Wei W, Ohno-Machado L. "Big data" and the electronic health record. Yearb Med Inform. 2014 ;9(1):97-104.
Wang S, Bonomi L, Dai W, Chen F, Cheung C, Bloss CS, Jiang X, Cheng S. Big Data Privacy in Biomedical Research. IEEE Transactions on Big Data. 2016 .
Farcas C, Balac N, Ohno-Machado L. Biomedical CyberInfrastructure Challenges. Extreme Science and Engineering Discovery Environment: Gateway to Discovery. 2013 .
Nodora JN, Komenaka IK, Bouton ME, Ohno-Machado L, Schwab R, Kim HE, Farcas C, Perez G, M Martinez E. Biospecimen Sharing Among Hispanic Women in a Safety-Net Clinic: Implications for the Precision Medicine Initiative. Journal of the National Cancer Institute. 2016 .
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 .
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 .
Grando A, Schwab R. Building and evaluating an ontology-based tool for reasoning about consent permission. AMIA Annu Symp Proc. 2013 ;2013:514-23.
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Jiang X, Osl M, Kim J, Ohno-Machado L. Calibrating predictive model estimates to support personalized medicine. J Am Med Inform Assoc. 2011 .
Shimizu C, Sood A, Lau HD, Oharaseki T, Takahashi K, Krous HF, Campman S, Burns JC. Cardiovascular pathology in 2 young adults with sudden, unexpected death due to coronary aneurysms from Kawasaki disease in childhood. Cardiovasc Pathol. 2015 .
Zhao Y, Wang X, Jiang X, Ohno-Machado L, Tang H. Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery. J Am Med Inform Assoc. 2015 ;22(1):100-8.
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 .
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.
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.
Wang S, Wang X, Jiang X, Tang H, Bu D, Carey K, Dyke SOM, Fox D, Jiang C, Lauter K, et al. A community effort to protect genomic data sharing, collaboration and outsourcing. NPJ Genomic Medicine. 2017 ;2.
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.
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011 ;18(3):401-13.
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 .
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 .
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).
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 .
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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 .
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.
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.
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.
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.
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.
Chaudhuri K, Monteleoni C, Sarwate AD. Differentially Private Empirical Risk Minimization. J Mach Learn Res. 2011 ;12:1069-1109.
Wang S, Mohammed N, Chen R. Differentially private genome data dissemination through top-down specialization. BMC Med Inform Decis Mak. 2014 ;14 Suppl 1:S2.
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.
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.
Vinterbo S. Differentially Private Projected Histograms: Construction and Use for Prediction. European Conference on Machine Learning . 2012 .
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.
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.
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.
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 .
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Kinsella M, Patel A, Bafna V. The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 ;42(13):8231-42.
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011 ;12:467.
Roozgard A, Barzigar N, Wang S, Jiang X, Cheng S. Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment. Cancer Inform. 2014 ;13(Suppl 1):159-65.
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 .
Mehta SR, Vinterbo SA, Little SJ. Ensuring Privacy in the Study of Pathogen Genetics in the 21st Century. The Lancet Infectious Diseases. 2014 .
South BR, Mowery D, Suo Y, Leng J, Ferrández Ó, Meystre SM, Chapman WW. Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text. J Biomed Inform. 2014 ;50:162-72.
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.
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.
Eguchi A, Lazaro RG, Wang J, Kim J, Povero D, Willliams B, Ho SB, Stärkel P, Schnabl B, Ohno-Machado L, et al. Extracellular vesicles released by hepatocytes from gastric infusion model of ALD contain a miRNA barcode that can be detected in blood. 2016 .
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Numano F, Shimizu C, Jimenez-Fernandez S, Vejar M, Oharaseki T, Takahashi K, Salgado A, Tremoulet AH, Gordon JB, Burns JC, et al. Galectin-3 is a marker of myocardial and vascular fibrosis in Kawasaki disease patients with giant aneurysms. Int J Cardiol. 2015 ;201:429-37.
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.
Shimizu C, Eleftherohorinou H, Wright VJ, Kim J, Alphonse MP, Perry JC, Cimaz R, Burgner D, Dahdah N, Hoang LT, et al. Genetic Variation in the SLC8A1 Calcium Signaling Pathway Is Associated with Susceptibility to Kawasaki Disease and Coronary Artery Abnormalities. 2016 .
Burns JC, Newburger JW. Genetics insights into the pathogenesis of Kawasaki disease. Circ Cardiovasc Genet. 2012 ;5(3):277-8.
Wang S, Jiang X, Singh S, Marmor R, Bonomi L, Fox D, Dow M, Ohno-Machado L. Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States. 2016 .
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, Wang S, Jiang W, Li P, Ohno-Machado L. Grid multi-category response logistic models. BMC Med Inform Decis Mak. 2015 ;15:10.
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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 .
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.
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 .
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.
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.
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 .
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 .
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.
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.
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.

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