1. BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features Tsai, Richard; Chou, Wen-Chi; Su, Ying-Shan; Lin, Yu-Chun; Sung, Cheng-Lung; Dai, Hong-Jie; Yeh, Irene; Ku, Wei; Sung, Ting-Yi; Hsu, Wen-Lian 2007 Articles Entropy (Information theory)--Mathematical modelsBiomedical engineering--ResearchBioinformaticsBiomedical engineering
2. ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding Margolin, Adam; Palomero Vazquez, M. Teresa; Ferrando, Adolfo A.; Califano, Andrea; Stolovitzky, Gustavo 2007 Articles BioinformaticsGene regulatory networksHuman genetics--VariationGeneticsBiology
3. Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen Kolokotronis, Sergios-Orestis; MacPhee, Ross; Greenwood, Alex D. 2007 Articles Evolution (Biology)DNA--ResearchMitochondrial DNABioinformaticsCytology
4. Distributed Augmented Reality with 3D Lung Dynamics - A Planning Tool Concept Hamza-Lup, Felix G.; Santhanam, Anand P.; Imielinska, Celina Z.; Meeks, Sanford; Rolland, Jannick P. 2007 Conference Objects Diagnostic imagingBioinformaticsBiomedical engineering
5. Evaluation of high-throughput functional categorization of human disease genes Chen, James L.; Liu, Yang; Sam, Lee T.; Li, Jianrong; Lussier, Yves 2007 Articles Medical geneticsBioinformaticsGeneticsPathology
6. Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes Makita, Yuko; de Hoon, Michiel; Danchin, Antoine 2007 Articles Bacillus subtilis--GeneticsProkaryotes--GeneticsBayesian statistical decision theoryBioinformatics
7. Model based analysis of real-time PCR data from DNA binding dye protocols Alvarez, Mariano Javier; Vila-Ortiz, Guillermo; Salibe, Mariano; Podhajcer, Osvaldo; Pitossi, Fernando 2007 Articles Polymerase chain reactionMessenger RNABioinformaticsGenetics
8. Modeling Air-flow in the Tracheobronchial Tree using Computational Fluid Dynamics Kaya, Ilhan; Santhanam, Anand P.; Imielinska, Celina Z.; Rolland, Jannick 2007 Conference Objects Biomedical engineeringBioinformaticsBiomechanics
9. Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base Skrabanek, Lucy; Murcia, Marta; Bouvier, Michel; Devi, Lakshmi; George, Susan; Lohse, Martin; Milligan, Graeme; Neubig, Richard; Palczewski, Krzysztof; Parmentier, Marc; Pin, Jean-Philippe; Vriend, Gerrit; Javitch, Jonathan A.; Campagne, Fabien; Filizola, Marta 2007 Articles OligomerizationCell receptorsBioinformaticsCytology
10. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition Melvin, Iain; Ie, Eugene; Kuang, Rui; Weston, Jason; Noble, William; Leslie, Christina 2007 Articles Proteins--StructureProtein foldingComputational biologyProteomicsBioinformatics
11. Symmetry Based Multi-modality Registration of the Brain Imagery Liu, Xin; Imielinska, Celina Z.; Laine, Andrew F.; D'Ambrosio, Anthony Louis 2007 Conference Objects Diagnostic imagingBioinformaticsNeurosciences
12. Using contextual and lexical features to restructure and validate the classification of biomedical concepts Fan, Jung-Wei; Xu, Hua; Friedman, Carol 2007 Articles Biology--SemioticsUMLSBioinformaticsBiomedical engineering
13. A classification-based framework for predicting and analyzing gene regulatory response Kundaje, Anshul; Middendorf, Manuel; Wiggins, Chris H.; Shah, Mihir; Freund, Yoav; Leslie, Christina 2006 Articles BioinformaticsGenetics
14. ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context Margolin, Adam A.; Nemenman, Ilya; Basso, Katia; Wiggins, Chris H.; Stolovitzky, Gustavo Alejandro; Favera, Riccardo Dalla; Califano, Andrea 2006 Articles BioinformaticsCytology
15. BAMarray™: Java software for Bayesian analysis of variance for microarray data Ishwaran, Hemant; Rao, J. Sunil; Kogalur, Udaya B. 2006 Articles DNA microarrays--Data processingJava (Computer program language)BioinformaticsBayesian statistical decision theoryStatisticsInformation technology
16. Detecting transcriptionally active regions using genomic tiling arrays Halasz, Gabor; van Batenburg, Marinus F.; Perusse, Joelle; Hua, Sujun; Lu, Xiang-Jun; White, Kevin P.; Bussemaker, Harmen J. 2006 Articles Genetic transcriptionDNA probesGenomicsDNA microarraysGeneticsBioinformatics
17. DWARF – a data warehouse system for analyzing protein families Fischer, Markus; Thai, Quan; Grieb, Melanie; Pleiss, Jürgen 2006 Articles Proteins--Data processingProtein engineeringBioengineering--Data processingData warehousingBioinformatics
18. Dynamics of semiflexible polymers in a flow field Munk, Tobias; Hallatschek, Oskar; Wiggins, Chris H.; Frey, Erwin 2006 Articles MathematicsBioinformatics
19. Enhanced Techniques for Asymmetry Quantification in Brain Imagery Liu, Xin; Imielinska, Celina Z.; Rosiene, Joel; Connolly Jr., E. Sander; D'Ambrosio, Anthony Louis 2006 Conference Objects BioinformaticsNeurosciencesDiagnostic imaging
20. Exploring supervised and unsupervised methods to detect topics in biomedical text Lee, Minsuk; Wang, Weiqing; Yu, Hong 2006 Articles Natural language processing (Computer science)Cluster analysisInformation storage and retrieval systems--ScienceMachine learningBioinformaticsComputer science