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 ..
Classic Broken Cell and Newer Live Cell Methods for Cell Cycle Assessment. Am J Physiol Cell Physiol. 2013 ..
Cloud Computing and Architecture
Policy Driven Development: Flexible Policy Insertion for Large Scale Systems. Proc IEEE Int Symp Policies Distrib Syst Netw. 2012 ;2012:17-24..
Data Analysis and Compression
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..
AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data. Bioinformatics. 2014 ..
Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015 ..
HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. J Am Med Inform Assoc. 2014 ;21(2):363-73..
DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique. PLoS One. 2013 ;8(11):e80377..
GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda. BMC Med Genomics. 2014 ;7 Suppl 1:S9..
Data Modeling and Integration
An approach to improve LOINC mapping through augmentation of local test names. J Biomed Inform. 2011 ..
Demographic Identification:Variable Extraction Resource (DIVER). 2nd IEEE Conference on Healthcare informatics, Imaging, and Systems Biology. 2012 ..
WebGLORE: A Webservice for Grid LOgistic REgression. Bioinformatics. 2013 ..
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. J Am Med Inform Assoc. 2013 .
Influences of Architectural and Implementation Choices on CyberInfrastructure Quality – A Case Study. In: Software Quality Assurance. Software Quality Assurance. Elsevier; 2015..
PALME : PAtients Like My gEnome Server Backend MongoDB database. In: AMIA Summit on Translational Bioinformatics. AMIA Summit on Translational Bioinformatics. ; 2016..
iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2011 .
To share or not to share: that is not the question. Sci Transl Med. 2012 ;4(165):165cm15..
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..
Recent trends in biomedical informatics: a study based on JAMIA articles. J Am Med Inform Assoc. 2013 ..
pSCANNER: patient-centered Scalable National Network for Effectiveness Research. J Am Med Inform Assoc. 2014 ;21(4):621-6.
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.
Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cells. BMC Res Notes. 2011 ;4:381..
AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. BMC Bioinformatics. 2011 ;12:75..
Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011 ;18(4):354-7..
Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011 ;12:467..
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011 ;27(8):1068-75..
Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011 ;18(3):401-13..
A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010 ;11:533..
DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010 ;43(5):709-15..
Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011 ;12 Suppl 1:S24..
RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010 ;26(22):2856-62..
Setting up an intronic miRNA database. Methods Mol Biol. 2013 ;936:69-76..
An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proc Natl Acad Sci U S A. 2013 ;110(14):5546-51..
Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 ..
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..
Using Genome Query Language to uncover genetic variation. Bioinformatics. 2013 ..
Nucleotide sequence alignment using sparse coding and belief propagation. Conf Proc IEEE Eng Med Biol Soc. 2013 ;2013:588-91..
Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet. 2013 ;93(3):452-62.
An Adaptive Difference Distribution-based Cod-ing with Hierarchical Tree Structure for DNA Sequence Compression. IEEE Data Compression Conference. 2013 ..
Using Kepler for tool integration in microarray analysis workflows. Procedia Computer Science. 2014 ..
MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. BMC Bioinformatics. 2014 ;15(1):69..
Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 ;29(8):1076-7..
Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol. 2013 ;14(8):R90..
On the design of clone-based haplotyping. Genome Biol. 2013 ;14(9):R100..
Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol. 2014 ;15(2):R36.
MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. Bioinformatics. 2014 ..
The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 ;42(13):8231-42..
BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. J Transl Med. 2015 ;13:122..
Abstractions for Genomics. Commun ACM. 2013 ;56(1):83-93..
Streamlined Genome Sequence Compression using Distributed Source Coding. Cancer Inform. 2014 ;13(Suppl 1):123-31..
Shape-oriented graph cuts and graph matching feedback for silhouette tracking. Visual Communications and Image Processing . 2012 ..
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..
A semi-automated quantification of pulmonary artery dimensions in computed tomography angiography images. AMIA Annu Symp Proc. 2012 ;2012:36-42..
SEMI-SUPERVISED OBJECT RECOGNITION USING STRUCTURE KERNEL. Proc Int Conf Image Proc. 2012 :2157-2160..
Biomedical CyberInfrastructure Challenges. Extreme Science and Engineering Discovery Environment: Gateway to Discovery. 2013 ..
Successful Cyberinfrastructures for E-Health. In: Economics Driven Software Architecture. Economics Driven Software Architecture. Elsvevier; 2014..
iDASH CyberInfrastructure: Mastering the Bits. In: NSF Towards a Shared Cyberinfrastructure Workshop 2012. NSF Towards a Shared Cyberinfrastructure Workshop 2012. ; 2012..
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)
Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011 ;4(1):16-25.
Genetics insights into the pathogenesis of Kawasaki disease. Circ Cardiovasc Genet. 2012 ;5(3):277-8..
The role of TGF-β and myofibroblasts in the arteritis of Kawasaki disease. Hum Pathol. 2012 ..
Differential expression of miR-145 in children with Kawasaki disease. PLoS One. 2013 ;8(3):e58159.
Immune-monitoring in Kawasaki disease patients treated with infliximab and intravenous immunoglobulin. Clin Exp Immunol. 2013 ..
Coronary artery outcomes among children with Kawasaki disease in the United States and Japan. Int J Cardiol. 2013 .
Treatment response in kawasaki disease is associated with sialylation levels of endogenous but not therapeutic intravenous immunoglobulin G. PLoS One. 2013 ;8(12):e81448.
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..
Lipoprotein Particle Concentrations in Children and Adults following Kawasaki Disease. J Pediatr. 2014 ;165(4):727-31.
Seasonality of Kawasaki disease: a global perspective. PLoS One. 2013 ;8(9):e74529.
Role of TGF-β Signaling in Remodeling of Non-coronary Artery Aneurysms in Kawasaki diseaseβ. Pediatr Dev Pathol. 2015 ..
Fine specificities of natural regulatory T cells after IVIG therapy in patients with Kawasaki disease. Autoimmunity. 2015 ;48(3):181-8..
Cardiovascular pathology in 2 young adults with sudden, unexpected death due to coronary aneurysms from Kawasaki disease in childhood. Cardiovasc Pathol. 2015 ..
Natural Language Processing
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..
Natural language processing: an introduction. J Am Med Inform Assoc. 2011 ;18(5):544-51..
Extending the NegEx lexicon for multiple languages. Stud Health Technol Inform. 2013 ;192:677-81..
Using twitter to examine smoking behavior and perceptions of emerging tobacco products. J Med Internet Res. 2013 ;15(8):e174..
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..
Natural language processing in biomedicine: a unified system architecture overview. Methods Mol Biol. 2014 ;1168:275-94..
Text Mining Driven Drug-Drug Interaction Detection. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2013 :349-355..
Patient Centered Research
Calibrating predictive model estimates to support personalized medicine. J Am Med Inform Assoc. 2011 ..
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..
Ontological approach for the management of informed consent permissions. 2nd IEEE Conference on Healthcare informatics, Imaging, and Systems Biology. 2012 ..
Selecting cases for whom additional tests can improve prognostication. AMIA Annu Symp Proc. 2012 ;2012:1260-8..
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..
Building and evaluating an ontology-based tool for reasoning about consent permission. AMIA Annu Symp Proc. 2013 ;2013:514-23..
"Big data" and the electronic health record. Yearb Med Inform. 2014 ;9(1):97-104..
Sharing my health data: a survey of data sharing preferences of healthy individuals. AMIA Annu Symp Proc. 2014 ;2014:1699-708..
SAPPIRE: a prototype mobile tool for pressure ulcer risk assessment. Stud Health Technol Inform. 2014 ;201:433-40..
Physical Activity Monitoring (DBP3)
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..
Classification accuracies of physical activities using smartphone motion sensors. J Med Internet Res. 2012 ;14(5):e130..
Anomaly and Signature Filtering Improve Classifier Performance For Detection Of Suspicious Access To EHRs. AMIA Annu Symp Proc. 2011 ;2011:723-31..
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..
Protecting count queries in study design. J Am Med Inform Assoc. 2012 ..
Grid Binary LOgistic REgression (GLORE): building shared models without sharing data. J Am Med Inform Assoc. 2012 ..
Quantifying Fine-Grained Privacy Risk and Representativeness in Medical Data. 17th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 2011 ..
Diﬀerentially Private Projected Histograms: Construction and Use for Prediction. European Conference on Machine Learning . 2012 ..
Differentially Private Empirical Risk Minimization. J Mach Learn Res. 2011 ;12:1069-1109..
Near-Optimal Algorithms for Differentially-Private Principal Components. Neural Information Processing Systems (NIPS). 2012 ..
SHARE: system design and case studies for statistical health information release. J Am Med Inform Assoc. 2012 ..