Journal: Journal of Biomedical Informatics

Volume 42, Issue 6

979 -- 989Richard D. Boyce, Carol Collins, John Horn, Ira Kalet. Computing with evidence: Part I: A drug-mechanism evidence taxonomy oriented toward confidence assignment
990 -- 1003Richard D. Boyce, Carol Collins, John Horn, Ira Kalet. Computing with evidence: Part II: An evidential approach to predicting metabolic drug-drug interactions
1004 -- 1012Sookyung Hyun, Stephen B. Johnson, Peter D. Stetson, Suzanne Bakken. Development and evaluation of nursing user interface screens using multiple methods
1013 -- 1021Matteo Paoletti, Gianna Camiciottoli, Eleonora Meoni, Francesca Bigazzi, Lucia Cestelli, Massimo Pistolesi, Carlo Marchesi. Explorative data analysis techniques and unsupervised clustering methods to support clinical assessment of Chronic Obstructive Pulmonary Disease (COPD) phenotypes
1022 -- 1028Rajat K. De, Anupam Ghosh. Interval based fuzzy systems for identification of important genes from microarray gene expression data: Application to carcinogenic development
1029 -- 1034George Ölund, Anders Brinne, Pontus Lindqvist, Jan-Eric Litton. Unleashing genotypes in epidemiology - A novel method for managing high throughput information
1035 -- 1045Hua Min, Frank J. Manion, Elizabeth Goralczyk, Yu-Ning Wong, Eric Ross, J. Robert Beck. Integration of prostate cancer clinical data using an ontology
1046 -- 1055Serhan Tatar, Ilyas Cicekli. Two learning approaches for protein name extraction
1056 -- 1064Sheena Xin Liu. Symmetry and asymmetry analysis and its implications to computer-aided diagnosis: A review of the literature

Volume 42, Issue 5

757 -- 759Wendy Webber Chapman, K. Bretonnel Cohen. Current issues in biomedical text mining and natural language processing
760 -- 772Dina Demner-Fushman, Wendy Webber Chapman, Clement J. McDonald. What can natural language processing do for clinical decision support?
773 -- 780Son Doan, Ai Kawazoe, Mike Conway, Nigel Collier. Towards role-based filtering of disease outbreak reports
781 -- 789Joshua C. Denny, Lisa Bastarache, Elizabeth Ann Sastre, Anderson Spickard III. Tracking medical students clinical experiences using natural language processing
790 -- 800Grace Yuet-Chee Chung. Towards identifying intervention arms in randomized controlled trials: Extracting coordinating constructions
801 -- 813Marcelo Fiszman, Dina Demner-Fushman, Halil Kilicoglu, Thomas C. Rindflesch. Automatic summarization of MEDLINE citations for evidence-based medical treatment: A topic-oriented evaluation
814 -- 823Aurélie Névéol, Sonya E. Shooshan, Susanne M. Humphrey, James G. Mork, Alan R. Aronson. A recent advance in the automatic indexing of the biomedical literature
824 -- 830Lam C. Tsoi, Ravi Patel, Wenle Zhao, W. Jim Zheng. Text-mining approach to evaluate terms for ontology development
831 -- 838Zhiyong Lu, W. John Wilbur. Improving accuracy for identifying related PubMed queries by an integrated approach
839 -- 851Henk Harkema, John N. Dowling, Tyler Thornblade, Wendy Webber Chapman. ConText: An algorithm for determining negation, experiencer, and temporal status from clinical reports
852 -- 865Laura Rimell, Stephen Clark. Porting a lexicalized-grammar parser to the biomedical domain
866 -- 872Man Lan, Chew Lim Tan, Jian Su. Feature generation and representations for protein-protein interaction classification
873 -- 886Ira Goldstein, Özlem Uzuner. Specializing for predicting obesity and its co-morbidities
887 -- 894Hui Yang, John A. Keane, Casey M. Bergman, Goran Nenadic. Assigning roles to protein mentions: The case of transcription factors
895 -- 904Larry H. Smith, W. John Wilbur. The value of parsing as feature generation for gene mention recognition
905 -- 911Sujan Kumar Saha, Sudeshna Sarkar, Pabitra Mitra. Feature selection techniques for maximum entropy based biomedical named entity recognition
912 -- 922Mei-Yu Hsiao, Chien-Chung Chen, Jyh-Horng Chen. Using UMLS to construct a generalized hierarchical concept-based dictionary of brain functions for information extraction from the fMRI literature
923 -- 936Agnieszka Mykowiecka, Malgorzata Marciniak, Anna Kupsc. Rule-based information extraction from patients clinical data
937 -- 949Anni Coden, Guergana K. Savova, Igor L. Sominsky, Michael A. Tanenblatt, James J. Masanz, Karin Schuler, James W. Cooper, Wei Guan, Piet C. de Groen. Automatically extracting cancer disease characteristics from pathology reports into a Disease Knowledge Representation Model
950 -- 966Angus Roberts, Robert J. Gaizauskas, Mark Hepple, George Demetriou, Yikun Guo, Ian Roberts, Andrea Setzer. Building a semantically annotated corpus of clinical texts
967 -- 977C. Cano, Thomas Monaghan, A. Blanco, Dennis P. Wall, Leonid Peshkin. Collaborative text-annotation resource for disease-centered relation extraction from biomedical text

Volume 42, Issue 4

581 -- 592David R. Kaufman, Jenia Pevzner, Martha Rodriguez, James J. Cimino, Susana Ebner, Lesley Fields, Vilma Moreno, Christina McGuiness, Ruth S. Weinstock, Steven Shea, Justin Starren. Understanding workflow in telehealth video visits: Observations from the IDEATel project
593 -- 604Kanav Kahol, Mithra Vankipuram, Marshall L. Smith. Cognitive simulators for medical education and training
605 -- 611Dominik Lutter, Thomas Langmann, Peter Ugocsai, C. Moehle, E. Seibold, W. D. Splettstoesser, Peter Gruber, Elmar Wolfgang Lang, Gerd Schmitz. Analyzing time-dependent microarray data using independent component analysis derived expression modes from human macrophages infected with F. tularensis holartica
612 -- 623Julie Bourbeillon, Catherine Garbay, Françoise Giroud. Mass data exploration in oncology: An information synthesis approach
624 -- 632Christian Fiegl, Carsten Pontow. Online scheduling of pick-up and delivery tasks in hospitals
633 -- 643Meliha Yetisgen-Yildiz, Wanda Pratt. A new evaluation methodology for literature-based discovery systems
644 -- 653Eugenia G. Giannopoulou, Spiros D. Garbis, Antonia Vlahou, Sofia Kossida, George Lepouras, Elias S. Manolakos. Proteomic Feature Maps: A new visualization approach in proteomics analysis
654 -- 666Hong-Qiang Wang, Hau-San Wong, Hailong Zhu, Timothy T. C. Yip. A neural network-based biomarker association information extraction approach for cancer classification
667 -- 677Ayse P. Gurses, Yan Xiao, Peter Fu-Ming Hu. User-designed information tools to support communication and care coordination in a trauma hospital
678 -- 684L. Y. Tanaka, Jorge R. Herskovic, M. Sriram Iyengar, Elmer V. Bernstam. Sequential result refinement for searching the biomedical literature
685 -- 691Bing Liu 0002, Jiuyong Li, Anna Tsykin. Discovery of functional miRNA-mRNA regulatory modules with computational methods
692 -- 701Louise Deléger, Magnus Merkel, Pierre Zweigenbaum. Translating medical terminologies through word alignment in parallel text corpora
702 -- 709Eric S. Hall, Mollie R. Poynton, Scott P. Narus, Spencer S. Jones, R. Scott Evans, Michael W. Varner, Sidney N. Thornton. Patient-level analysis of outcomes using structured labor and delivery data
710 -- 720Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha. @Note: A workbench for Biomedical Text Mining
721 -- 725Melanie Osl, Stephan Dreiseitl, F. Cerqueira, Michael Netzer, Bernhard Pfeifer, Christian Baumgartner. Demoting redundant features to improve the discriminatory ability in cancer data
726 -- 735Zhiping Wang, Seongho Kim, Sara K. Quinney, Yingying Guo, Stephen D. Hall, Luis Mateus Rocha, Lang Li. Literature mining on pharmacokinetics numerical data: A feasibility study
736 -- 747Mor Peleg, Judith Somekh, Dov Dori. A methodology for eliciting and modeling exceptions
748 -- 755Rashmi Kandwal, P. K. Garg, R. D. Garg. Health GIS and HIV/AIDS studies: Perspective and retrospective

Volume 42, Issue 3

407 -- 411James Geller, Yehoshua Perl, Michael Halper, Ronald Cornet. Special Issue on Auditing of Terminologies
413 -- 425Xinxin Zhu, Jung-Wei Fan, David M. Baorto, Chunhua Weng, James J. Cimino. A review of auditing methods applied to the content of controlled biomedical terminologies
426 -- 439Lowell Vizenor, Olivier Bodenreider, Alexa T. McCray. Auditing associative relations across two knowledge sources
440 -- 451Fleur Mougin, Olivier Bodenreider, Anita Burgun. Analyzing polysemous concepts from a clinical perspective: Application to auditing concept categorization in the UMLS
452 -- 467Yan Chen, Huanying Helen Gu, Yehoshua Perl, James Geller. Structural group-based auditing of missing hierarchical relationships in UMLS
468 -- 489C. Paul Morrey, James Geller, Michael Halper, Yehoshua Perl. The Neighborhood Auditing Tool: A hybrid interface for auditing the UMLS
490 -- 493Geraldine Wade, S. Trent Rosenbloom. The impact of SNOMED CT revisions on a mapped interface terminology: Terminology development and implementation issues
494 -- 503David M. Baorto, Li Li, James J. Cimino. Practical experience with the maintenance and auditing of a large medical ontology
504 -- 517Guoqian Jiang, Jyotishman Pathak, Christopher G. Chute. Formalizing ICD coding rules using Formal Concept Analysis
518 -- 529Werner Ceusters. Applying evolutionary terminology auditing to the Gene Ontology
530 -- 539Sherri de Coronado, Lawrence W. Wright, Gilberto Fragoso, Margaret W. Haber, Elizabeth A. Hahn-Dantona, Francis W. Hartel, Sharon L. Quan, Tracy Safran, Nicole Thomas, Lori Whiteman. The NCI Thesaurus quality assurance life cycle
540 -- 549Ira J. Kalet, Jose L. V. Mejino, Vania Wang, Mark Whipple, James F. Brinkley. Content-specific auditing of a large scale anatomy ontology
550 -- 557Huanying Helen Gu, Duo Wei, Jose L. V. Mejino Jr., Gai Elhanan. Relationship auditing of the FMA ontology
558 -- 570Olivier Bodenreider, Lee B. Peters. A graph-based approach to auditing RxNorm
571 -- 580James J. Cimino, Terry F. Hayamizu, Olivier Bodenreider, Brian Davis, Grace A. Stafford, Martin Ringwald. The caBIG terminology review process

Volume 42, Issue 2

199 -- 200Edward H. Shortliffe, Andrea Califano, Lawrence Hunter. New JBI emphasis on translational bioinformatics
203 -- 218Efrat German, Akiva Leibowitz, Yuval Shahar. An architecture for linking medical decision-support applications to clinical databases and its evaluation
219 -- 227Ingrid Petric, Tanja Urbancic, Bojan Cestnik, Marta Macedoni-Luksic. Literature mining method RaJoLink for uncovering relations between biomedical concepts
228 -- 236Saliha Durmus Tekir, Kazim Yalçin Arga, Kutlu Ö. Ülgen. Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network
237 -- 250Kenneth J. Turner. Abstraction and analysis of clinical guidance trees
251 -- 261John Lakoumentas, John Drakos, Marina Karakantza, George Nikiforidis, George Sakellaropoulos. Bayesian clustering of flow cytometry data for the diagnosis of B-Chronic Lymphocytic Leukemia
262 -- 271Suzhen Wang, Jielai Xia, Lili Yu, Chanjuan Li, Li Xu, Liang Zheng. Realization of simulations for blinded internal pilot study based on web
272 -- 286Itay Segal, Yuval Shahar. A distributed system for support and explanation of shared decision-making in the prenatal testing domain
287 -- 295Sangeeta B. English, Shou-Ching Shih, Marco Ramoni, Lois E. Smith, Atul J. Butte. Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR
296 -- 307Gloria Díaz, Fabio A. González, Eduardo Romero. A semi-automatic method for quantification and classification of erythrocytes infected with malaria parasites in microscopic images
308 -- 316Bilal A. Ahmed, Michael E. Matheny, Phillip L. Rice, John R. Clarke, Omolola Ogunyemi. A comparison of methods for assessing penetrating trauma on retrospective multi-center data
317 -- 326Geva Vashitz, Joachim Meyer, Yisrael Parmet, Roni Peleg, Dan Goldfarb, Avi Porath, Harel Gilutz. Defining and measuring physicians responses to clinical reminders
327 -- 333Meredith Nahm, Jiajie Zhang. Operationalization of the UFuRT methodology for usability analysis in the clinical research data management domain
334 -- 346Adam Wright, David W. Bates, Blackford Middleton, Tonya Hongsermeier, Vipul Kashyap, Sean M. Thomas, Dean F. Sittig. Creating and sharing clinical decision support content with Web 2.0: Issues and examples
347 -- 355Dominikus Herzberg, Nicola Marsden, Peter Kübler, Corinna Leonhardt, Sabine Thomanek, Hartmut Jung, Annette Becker. Specifying computer-based counseling systems in health care: A new approach to user-interface and interaction design
356 -- 364L. M. Taft, R. Scott Evans, C. R. Shyu, M. J. Egger, N. Chawla, J. A. Mitchell, Sidney N. Thornton, B. Bray, Michael W. Varner. Countering imbalanced datasets to improve adverse drug event predictive models in labor and delivery
365 -- 376Bill Andreopoulos, Aijun An, Xiaogang Wang, Dirk Labudde. Efficient layered density-based clustering of categorical data
377 -- 381Paul A. Harris, Robert Taylor, Robert Thielke, Jonathon Payne, Nathaniel Gonzalez, Jose G. Conde. Research electronic data capture (REDCap) - A metadata-driven methodology and workflow process for providing translational research informatics support
382 -- 389Martti Tolvanen, Pauli J. Ojala, Petri Törönen, Heidi Anderson, Jukka Partanen, Hannu Turpeinen. Interspliced transcription chimeras: Neglected pathological mechanism infiltrating gene accession queries?
390 -- 405Trevor Cohen, Dominic Widdows. Empirical distributional semantics: Methods and biomedical applications

Volume 42, Issue 1

1 -- 10Sandro Tognazzo, Bovo Emanuela, Fiore Anna Rita, Guzzinati Stefano, Monetti Daniele, Stocco Cramen Fiorella, Zambon Paola. Probabilistic classifiers and automated cancer registration: An exploratory application
11 -- 21Robert Moskovitch, Yuval Shahar. Vaidurya: A multiple-ontology, concept-based, context-sensitive clinical-guideline search engine
22 -- 31Xingwei Wang, Bin Zheng, Shibo Li, John J. Mulvihill, Marc C. Wood, Hong Liu. Automated classification of metaphase chromosomes: Optimization of an adaptive computerized scheme
32 -- 40Jun Wang, Xiaobo Zhou, Fuhai Li, Pamela Bradley, Shih-Fu Chang, Norbert Perrimon, Stephen T. C. Wong. An image score inference system for RNAi genome-wide screening based on fuzzy mixture regression modeling
41 -- 52Yan Chen, Huanying Gu, Yehoshua Perl, James Geller, Michael Halper. Structural group auditing of a UMLS semantic type s extent
53 -- 58John M. Paulett, Curtis P. Langlotz. Improving language models for radiology speech recognition
59 -- 65Qi Shen, Wei-Min Shi, Wei Kong. New gene selection method for multiclass tumor classification by class centroid
66 -- 73Blanca Gallego, Vitali Sintchenko, Qinning Wang, Lester Hiley, Gwendolyn L. Gilbert, Enrico W. Coiera. Biosurveillance of emerging biothreats using scalable genotype clustering
74 -- 81Luis Tari, Chitta Baral, Seungchan Kim. Fuzzy c-means clustering with prior biological knowledge
82 -- 89Guilherme Del Fiol, Peter J. Haug. Classification models for the prediction of clinicians information needs
90 -- 99Xia Jiang, Garrick L. Wallstrom, Gregory F. Cooper, Michael M. Wagner. Bayesian prediction of an epidemic curve
100 -- 112Xiaoming Wang, Lili Liu, James Fackenthal, Shelly Cummings, Oluwatobi I. Olopade, Kisha Hope, Jonathan C. Silverstein, Olufunmilayo I. Olopade. Translational integrity and continuity: Personalized biomedical data integration
113 -- 122Petra Kralj Novak, Nada Lavrac, Dragan Gamberger, Antonija Krstacic. CSM-SD: Methodology for contrast set mining through subgroup discovery
123 -- 139Spencer S. Jones, R. Scott Evans, Todd L. Allen, Alun Thomas, Peter J. Haug, Shari J. Welch, Gregory L. Snow. A multivariate time series approach to modeling and forecasting demand in the emergency department
140 -- 149Costas P. Exarchos, Costas Papaloukas, Themis P. Exarchos, Anastassios N. Troganis, Dimitrios I. Fotiadis. Prediction of cis/trans isomerization using feature selection and support vector machines
150 -- 164Catalina Martínez-Costa, Marcos Menárguez Tortosa, Jesualdo Tomás Fernández-Breis, José Alberto Maldonado. A model-driven approach for representing clinical archetypes for Semantic Web environments
165 -- 175Mor Peleg, Nuaman Asbeh, Tsvi Kuflik, Mitchell Schertz. Onto-clust - A methodology for combining clustering analysis and ontological methods for identifying groups of comorbidities for developmental disorders
176 -- 197Vimla L. Patel, Nicole A. Yoskowitz, José F. Arocha, Edward H. Shortliffe. Cognitive and learning sciences in biomedical and health instructional design: A review with lessons for biomedical informatics education