Publications

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Cloud Computing and Architecture
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.
Genomics
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 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.
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.
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011 ;12:467.
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.
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011 ;18(3):401-13.
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010 ;11:533.
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.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011 ;12 Suppl 1:S24.
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.
Hinske LC, Heyn J, Galante PAF, Ohno-Machado L, Kreth S. Setting up an intronic miRNA database. Methods Mol Biol. 2013 ;936:69-76.
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.
Kim S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 .
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.
Kozanitis C, Heiberg A, Varghese G, Bafna V. Using Genome Query Language to uncover genetic variation. Bioinformatics. 2013 .
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.
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.
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 .
Gan Z, Stowe JC, McCulloch A, Zambon AC. Using Kepler for tool integration in microarray analysis workflows. Procedia Computer Science. 2014 .
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 S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 ;29(8):1076-7.
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.
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.
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.
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 .
Kinsella M, Patel A, Bafna V. The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 ;42(13):8231-42.
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.
Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G. Abstractions for Genomics. Commun ACM. 2013 ;56(1):83-93.
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.
Infrastructure
Farcas C, Balac N, Ohno-Machado L. Biomedical CyberInfrastructure Challenges. Extreme Science and Engineering Discovery Environment: Gateway to Discovery. 2013 .
Farcas C, Farcas E, Krueger I. Successful Cyberinfrastructures for E-Health. In: Economics Driven Software Architecture. Economics Driven Software Architecture. Elsvevier; 2014.
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.
Kawasaki Disease (DBP1 & DBP4)
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.
Burns JC, Newburger JW. Genetics insights into the pathogenesis of Kawasaki disease. Circ Cardiovasc Genet. 2012 ;5(3):277-8.
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 .
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.
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 .
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 .
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.
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.
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.
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.
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 .
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.
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 .
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 .
Natural Language Processing
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.
Nadkarni PM, Ohno-Machado L, Chapman WW. Natural language processing: an introduction. J Am Med Inform Assoc. 2011 ;18(5):544-51.
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.
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.
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.
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.
Yan S, Jiang X, Chen Y. Text Mining Driven Drug-Drug Interaction Detection. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2013 :349-355.
Patient Centered Research
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, 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.
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, 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.
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.
Grando A, Schwab R. Building and evaluating an ontology-based tool for reasoning about consent permission. AMIA Annu Symp Proc. 2013 ;2013:514-23.
Ross MK, Wei W, Ohno-Machado L. "Big data" and the electronic health record. Yearb Med Inform. 2014 ;9(1):97-104.
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.
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.
Physical Activity Monitoring (DBP3)
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.
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.
Privacy Technology
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.
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.
Vinterbo SA, Sarwate AD, Boxwala AA. Protecting count queries in study design. J Am Med Inform Assoc. 2012 .
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 .
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 .
Vinterbo S. Differentially Private Projected Histograms: Construction and Use for Prediction. European Conference on Machine Learning . 2012 .
Chaudhuri K, Monteleoni C, Sarwate AD. Differentially Private Empirical Risk Minimization. J Mach Learn Res. 2011 ;12:1069-1109.
Chaudhuri K, Sarwate AD, Sinha K. Near-Optimal Algorithms for Differentially-Private Principal Components. Neural Information Processing Systems (NIPS). 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 .
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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