Journal of Biomedical Informatics, Volume 42

Volume 42, Number 1, February 2009

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  Sandro Tognazzo, Bovo Emanuela, Fiore Anna Rita, Guzzinati Stefano, Monetti Daniele, Stocco Cramen Fiorella, Zambon Paola:
  Probabilistic classifiers and automated cancer registration: An exploratory application. 1-10
• 
  Robert Moskovitch, Yuval Shahar:
  Vaidurya: A multiple-ontology, concept-based, context-sensitive clinical-guideline search engine. 11-21
• 
  Xingwei Wang, Bin Zheng, Shibo Li, John J. Mulvihill, Marc C. Wood, Hong Liu:
  Automated classification of metaphase chromosomes: Optimization of an adaptive computerized scheme. 22-31
• 
  Jun 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. 32-40
• 
  Yan Chen, Huanying Gu, Yehoshua Perl, James Geller, Michael Halper:
  Structural group auditing of a UMLS semantic type's extent. 41-52
• 
  John M. Paulett, Curtis P. Langlotz:
  Improving language models for radiology speech recognition. 53-58
• 
  Qi Shen, Wei-Min Shi, Wei Kong:
  New gene selection method for multiclass tumor classification by class centroid. 59-65
• 
  Blanca Gallego, Vitali Sintchenko, Qinning Wang, Lester Hiley, Gwendolyn L. Gilbert, Enrico W. Coiera:
  Biosurveillance of emerging biothreats using scalable genotype clustering. 66-73
• 
  Luis Tari, Chitta Baral, Seungchan Kim:
  Fuzzy c-means clustering with prior biological knowledge. 74-81
• 
  Guilherme Del Fiol, Peter J. Haug:
  Classification models for the prediction of clinicians' information needs. 82-89
• 
  Xia Jiang, Garrick L. Wallstrom, Gregory F. Cooper, Michael M. Wagner:
  Bayesian prediction of an epidemic curve. 90-99
• 
  Xiaoming 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. 100-112
• 
  Petra Kralj Novak, Nada Lavrac, Dragan Gamberger, Antonija Krstacic:
  CSM-SD: Methodology for contrast set mining through subgroup discovery. 113-122
• 
  Spencer 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. 123-139
• 
  Costas 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. 140-149
• 
  Catalina Martínez-Costa, Marcos Menárguez Tortosa, Jesualdo Tomás Fernández-Breis, José Alberto Maldonado:
  A model-driven approach for representing clinical archetypes for Semantic Web environments. 150-164
• 
  Mor 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. 165-175

Methodological Review

• 
  Vimla 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. 176-197

Volume 42, Number 2, April 2009

Editorial

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  Edward H. Shortliffe, Andrea Califano, Lawrence Hunter:
  New JBI emphasis on translational bioinformatics. 199-200

Regular Articles

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  Efrat German, Akiva Leibowitz, Yuval Shahar:
  An architecture for linking medical decision-support applications to clinical databases and its evaluation. 203-218
• 
  Ingrid Petric, Tanja Urbancic, Bojan Cestnik, Marta Macedoni-Luksic:
  Literature mining method RaJoLink for uncovering relations between biomedical concepts. 219-227
• 
  Saliha Durmus Tekir, Kazim Yalçin Arga, Kutlu Ö. Ülgen:
  Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network. 228-236
• 
  Kenneth J. Turner:
  Abstraction and analysis of clinical guidance trees. 237-250
• 
  John Lakoumentas, John Drakos, Marina Karakantza, George Nikiforidis, George Sakellaropoulos:
  Bayesian clustering of flow cytometry data for the diagnosis of B-Chronic Lymphocytic Leukemia. 251-261
• 
  Suzhen Wang, Jielai Xia, Lili Yu, Chanjuan Li, Li Xu, Liang Zheng:
  Realization of simulations for blinded internal pilot study based on web. 262-271
• 
  Itay Segal, Yuval Shahar:
  A distributed system for support and explanation of shared decision-making in the prenatal testing domain. 272-286
• 
  Sangeeta 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. 287-295
• 
  Gloria Díaz, Fabio A. González, Eduardo Romero:
  A semi-automatic method for quantification and classification of erythrocytes infected with malaria parasites in microscopic images. 296-307
• 
  Bilal 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. 308-316
• 
  Geva Vashitz, Joachim Meyer, Yisrael Parmet, Roni Peleg, Dan Goldfarb, Avi Porath, Harel Gilutz:
  Defining and measuring physicians' responses to clinical reminders. 317-326
• 
  Meredith Nahm, Jiajie Zhang:
  Operationalization of the UFuRT methodology for usability analysis in the clinical research data management domain. 327-333
• 
  Adam 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. 334-346
• 
  Dominikus 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. 347-355
• 
  L. 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. 356-364
• 
  Bill Andreopoulos, Aijun An, Xiaogang Wang, Dirk Labudde:
  Efficient layered density-based clustering of categorical data. 365-376
• 
  Paul 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. 377-381
• 
  Martti Tolvanen, Pauli J. Ojala, Petri Törönen, Heidi Anderson, Jukka Partanen, Hannu Turpeinen:
  Interspliced transcription chimeras: Neglected pathological mechanism infiltrating gene accession queries? 382-389

Methodological Review

• 
  Trevor Cohen, Dominic Widdows:
  Empirical distributional semantics: Methods and biomedical applications. 390-405

Volume 42, Number 3, June 2009

Guest Editorial

• 
  James Geller, Yehoshua Perl, Michael Halper, Ronald Cornet:
  Special Issue on Auditing of Terminologies. 407-411

Methodological Review

• 
  Xinxin 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. 413-425

Research Papers

• 
  Lowell Vizenor, Olivier Bodenreider, Alexa T. McCray:
  Auditing associative relations across two knowledge sources. 426-439
• 
  Fleur Mougin, Olivier Bodenreider, Anita Burgun:
  Analyzing polysemous concepts from a clinical perspective: Application to auditing concept categorization in the UMLS. 440-451
• 
  Yan Chen, Huanying Helen Gu, Yehoshua Perl, James Geller:
  Structural group-based auditing of missing hierarchical relationships in UMLS. 452-467
• 
  C. Paul Morrey, James Geller, Michael Halper, Yehoshua Perl:
  The Neighborhood Auditing Tool: A hybrid interface for auditing the UMLS. 468-489
• 
  Geraldine Wade, S. Trent Rosenbloom:
  The impact of SNOMED CT revisions on a mapped interface terminology: Terminology development and implementation issues. 490-493
• 
  David M. Baorto, Li Li, James J. Cimino:
  Practical experience with the maintenance and auditing of a large medical ontology. 494-503
• 
  Guoqian Jiang, Jyotishman Pathak, Christopher G. Chute:
  Formalizing ICD coding rules using Formal Concept Analysis. 504-517
• 
  Werner Ceusters:
  Applying evolutionary terminology auditing to the Gene Ontology. 518-529
• 
  Sherri 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. 530-539
• 
  Ira J. Kalet, José L. V. Mejino Jr., Vania Wang, Mark Whipple, James F. Brinkley:
  Content-specific auditing of a large scale anatomy ontology. 540-549
• 
  Huanying Helen Gu, Duo Wei, José L. V. Mejino Jr., Gai Elhanan:
  Relationship auditing of the FMA ontology. 550-557
• 
  Olivier Bodenreider, Lee B. Peters:
  A graph-based approach to auditing RxNorm. 558-570
• 
  James J. Cimino, Terry F. Hayamizu, Olivier Bodenreider, Brian Davis, Grace A. Stafford, Martin Ringwald:
  The caBIG terminology review process. 571-580

Volume 42, Number 4, August 2009

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  David 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. 581-592
• 
  Kanav Kahol, Mithra Vankipuram, Marshall L. Smith:
  Cognitive simulators for medical education and training. 593-604
• 
  Dominik 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. 605-611
• 
  Julie Bourbeillon, Catherine Garbay, Françoise Giroud:
  Mass data exploration in oncology: An information synthesis approach. 612-623
• 
  Christian Fiegl, Carsten Pontow:
  Online scheduling of pick-up and delivery tasks in hospitals. 624-632
• 
  Meliha Yetisgen-Yildiz, Wanda Pratt:
  A new evaluation methodology for literature-based discovery systems. 633-643
• 
  Eugenia G. Giannopoulou, Spiros D. Garbis, Antonia Vlahou, Sofia Kossida, George Lepouras, Elias S. Manolakos:
  Proteomic Feature Maps: A new visualization approach in proteomics analysis. 644-653
• 
  Hong-Qiang Wang, Hau-San Wong, Hailong Zhu, Timothy T. C. Yip:
  A neural network-based biomarker association information extraction approach for cancer classification. 654-666
• 
  Ayse P. Gurses, Yan Xiao, Peter Fu-Ming Hu:
  User-designed information tools to support communication and care coordination in a trauma hospital. 667-677
• 
  Len Y. Tanaka, Jorge R. Herskovic, M. Sriram Iyengar, Elmer V. Bernstam:
  Sequential result refinement for searching the biomedical literature. 678-684
• 
  Bing Liu, Jiuyong Li, Anna Tsykin:
  Discovery of functional miRNA-mRNA regulatory modules with computational methods. 685-691
• 
  Louise Deléger, Magnus Merkel, Pierre Zweigenbaum:
  Translating medical terminologies through word alignment in parallel text corpora. 692-701
• 
  Eric 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. 702-709
• 
  Anália 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. 710-720
• 
  Melanie Osl, Stephan Dreiseitl, F. Cerqueira, Michael Netzer, Bernhard Pfeifer, Christian Baumgartner:
  Demoting redundant features to improve the discriminatory ability in cancer data. 721-725
• 
  Zhiping 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. 726-735
• 
  Mor Peleg, Judith Somekh, Dov Dori:
  A methodology for eliciting and modeling exceptions. 736-747

Methodological Review

• 
  Rashmi Kandwal, P. K. Garg, R. D. Garg:
  Health GIS and HIV/AIDS studies: Perspective and retrospective. 748-755

Volume 42, Number 5, October 2009

Guest Editorial

• 
  Wendy Webber Chapman, K. Bretonnel Cohen:
  Current issues in biomedical text mining and natural language processing. 757-759

Methodological Review

• 
  Dina Demner-Fushman, Wendy Webber Chapman, Clement J. McDonald:
  What can natural language processing do for clinical decision support? 760-772

Research Papers

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

Volume 42, Number 6, December 2009

• 
  Richard D. Boyce, Carol Collins, John R. Horn, Ira Kalet:
  Computing with evidence: Part I: A drug-mechanism evidence taxonomy oriented toward confidence assignment. 979-989
• 
  Richard D. Boyce, Carol Collins, John R. Horn, Ira Kalet:
  Computing with evidence: Part II: An evidential approach to predicting metabolic drug-drug interactions. 990-1003
• 
  Sookyung Hyun, Stephen B. Johnson, Peter D. Stetson, Suzanne Bakken:
  Development and evaluation of nursing user interface screens using multiple methods. 1004-1012
• 
  Matteo 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. 1013-1021
• 
  Rajat K. De, Anupam Ghosh:
  Interval based fuzzy systems for identification of important genes from microarray gene expression data: Application to carcinogenic development. 1022-1028
• 
  George Ölund, Anders Brinne, Pontus Lindqvist, Jan-Eric Litton:
  Unleashing genotypes in epidemiology - A novel method for managing high throughput information. 1029-1034
• 
  Hua Min, Frank J. Manion, Elizabeth Goralczyk, Yu-Ning Wong, Eric A. Ross, J. Robert Beck:
  Integration of prostate cancer clinical data using an ontology. 1035-1045
• 
  Serhan Tatar, Ilyas Cicekli:
  Two learning approaches for protein name extraction. 1046-1055

Methodological Review

• 
  Sheena Xin Liu:
  Symmetry and asymmetry analysis and its implications to computer-aided diagnosis: A review of the literature. 1056-1064