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2017
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 .
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 .
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.
Yung CK, O'Connor BD, Yakneen S, Zhang J, Ellrott K, Kleinheinz K, Miyoshi N, Raine KM, Royo R, Saksena GB, et al. Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments. biorxiv. 2017 .
Wang M, Ji Z, Wang S, Kim J, Yang H, Jiang X, Ohno-Machado L. Mechanisms to Protect the Privacy of Families When Using the Transmission Disequilibrium Test in Genome-Wide Association Studies. Bioinformatics. 2017 .
Bonomi L, Jiang X. A Mortality Study for ICU Patients Using Bursty Medical Events. Data Engineering (ICDE), 2017 IEEE 33rd International Conference. 2017 .
Dulai PS, Singh S, Ohno-Machaco L, Sandborn WJ. Population Health Management for Inflammatory Bowel Disease. Gastroenterology. 2017 .
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 .
2016
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 .
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 .
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 .
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.
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 .
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 .
Shi E, Chmielecki J, Tang CM, Wang K, Heinrich MC, Kang G, Corless CL, Hong D, Fero KE, Murphy JD, et al. FGFR1 and NTRK3 actionable alterations in "Wild-Type" gastrointestinal stromal tumors. 2016 .
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 .
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 .
Wang S, Zhang Y, Dai W, Lauter K, Kim M, Tang Y, Xiong H, Jiang X. HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS. Bioinformatics. 2016 ;32(2):211-8.
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 .
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.
Wang S, Wang L, Afef D, Rathi L, Shen L, Jiang X, Wang W. PALME : PAtients Like My gEnome Server Backend MongoDB database. In: AMIA Summit on Translational Bioinformatics. AMIA Summit on Translational Bioinformatics. ; 2016.
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 .
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).
Tang H, Jiang X, Wang X, Wang S, Sofia H, Fox D, Lauter K, Malin B, Telenti A, Xiong L, et al. Protecting genomic data analytics in the cloud: state of the art and opportunities. BMC Medical Genomics. 2016 ;9(63).
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 .
Shi H, Jiang C, Dai W, Jiang X, Tang Y, Ohno-Machado L. Secure Multi-pArty Computation Grid LOgistic REgression (SMAC-GLORE). BMC Medical Informatics and Decision Making. 2016 .
2015
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.
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.
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).
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.
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 .
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.
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.
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.
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 .
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.
Song S, Chaudhuri K, Sarwate AD. Learning from Data with Heterogeneous Noise using SGD. In: 18th International Conference on Artificial Intelligence and Statistics (AISTATS). 18th International Conference on Artificial Intelligence and Statistics (AISTATS). ; 2015.
Tremoulet AH, Dutkowski J, Sato Y, Kanegaye JT, Ling XB, Burns JC. Novel data-mining approach identifies biomarkers for diagnosis of Kawasaki disease. Pediatr Res. 2015 ;78(5):547-53.
Wang S, Jiang X, Fox D, L O-M. Preserving genome privacy in research studies. In: Medical Data Privacy Handbook. Medical Data Privacy Handbook. Springer; 2015.
Mohammed N, Wang S, Chen R, Jiang X. Private Genome Data Dissemination. In: Medical Data Privacy Handbook. Medical Data Privacy Handbook. Springer; 2015.
Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L. Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015 .
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 .
Meeker D, Jiang X, Matheny ME, Farcas C, D'Arcy M, Pearlman L, Nookala L, Day ME, Kim KK, Kim H, et al. A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research. J Am Med Inform Assoc. 2015 ;22(6):1187-95.
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.
Li Y, Jiang X, Wang S, Xiong H, Ohno-Machado L. VERTIcal Grid lOgistic regression (VERTIGO). J Am Med Inform Assoc. 2015 .
2014
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 .
Ross MK, Wei W, Ohno-Machado L. "Big data" and the electronic health record. Yearb Med Inform. 2014 ;9(1):97-104.
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.
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.
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.
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.
Kinsella M, Patel A, Bafna V. The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 ;42(13):8231-42.
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.
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.
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.
Norman G, Kolodziejczyk J, Ramirez E, Hekler E. How to Deliver Physical Activity Messages. In: ACSM’s Behavioral Aspects of Physical Activity & Exercise. ACSM’s Behavioral Aspects of Physical Activity & Exercise. American College of Sports Medicine; 2014.
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.
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.
Chaudhuri K, Hsu D, Song S. The Large Margin Mechanism for Differentially Private Maximization. Neural Information Processing Systems (NIPS). 2014 .
Lin J, Jain S, Sun X, Liu V, Sato YZ, Jimenez-Fernandez S, Newfield RS, Pourfarzib R, Tremoulet AH, Gordon JB, et al. Lipoprotein Particle Concentrations in Children and Adults following Kawasaki Disease. J Pediatr. 2014 ;165(4):727-31.
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.
Gan Z, Wang J, Salomonis N, Stowe JC, Haddad GG, McCulloch AD, Altintas I, Zambon AC. MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. BMC Bioinformatics. 2014 ;15(1):69.
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 .
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.
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.
Stepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L. Prediction of MicroRNA Precursors Using Parsimonious Feature Sets. Cancer Inform. 2014 ;13(Suppl 1):95-102.
Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy preserving RBF kernel support vector machine. Biomed Res Int. 2014 ;2014:827371.
Ohno-Machado L, Agha Z, Bell DS, Dahm L, Day ME, Doctor JN, Gabriel D, Kahlon MK, Kim KK, Hogarth M, et al. pSCANNER: patient-centered Scalable National Network for Effectiveness Research. J Am Med Inform Assoc. 2014 ;21(4):621-6.
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.
Yu F, Ji Z. Scalable privacy-preserving data sharing methodology for genome-wide association studies: an application to iDASH healthcare privacy protection challenge. BMC Med Inform Decis Mak. 2014 ;14 Suppl 1:S3.
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.
Wang S, Jiang X, Chen F, Cui L, Cheng S. Streamlined Genome Sequence Compression using Distributed Source Coding. Cancer Inform. 2014 ;13(Suppl 1):123-31.
Farcas C, Farcas E, Krueger I. Successful Cyberinfrastructures for E-Health. In: Economics Driven Software Architecture. Economics Driven Software Architecture. Elsvevier; 2014.
Kim H, Ohno-Machado L, Oh J, Jiang X. Trends in publication of nursing informatics research. AMIA Annu Symp Proc. 2014 ;2014:805-14.
Gan Z, Stowe JC, McCulloch A, Zambon AC. Using Kepler for tool integration in microarray analysis workflows. Procedia Computer Science. 2014 .
Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, et al. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol. 2014 ;15(2):R36.
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.

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