Journal of Biomedical Informatics, Volume 40

Volume 40, Number 1, February 2007

Bio*Medical Informatics

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  Peter Tarczy-Hornoch, Mia K. Markey, John A. Smith, Tadaaki Hiruki:
  Bio*Medical informatics and genomic medicine: Research and training. 1-4

Methodological Review

• 
  Brenton Louie, Peter Mork, Fernando Martín-Sánchez, Alon Y. Halevy, Peter Tarczy-Hornoch:
  Data integration and genomic medicine. 5-16

Research Papers

• 
  Raúl Alonso-Calvo, Victor Maojo, Holger Billhardt, Fernando Martín-Sánchez, Miguel García-Remesal, David Pérez-Rey:
  An agent- and ontology-based system for integrating public gene, protein, and disease databases. 17-29
• 
  Nicholas Sioutos, Sherri de Coronado, Margaret W. Haber, Frank W. Hartel, Wen-Ling Shaiu, Lawrence W. Wright:
  NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information. 30-43
• 
  Mark A. Hoffman:
  The genome-enabled electronic medical record. 44-46
• 
  Douglas R. Mitchell, Joyce A. Mitchell:
  Status of clinical gene sequencing data reporting and associated risks for information loss. 47-54

Training in Biomedical Informatics

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  Russ B. Altman, Teri E. Klein:
  Biomedical informatics training at Stanford in the 21st century. 55-58
• 
  Stephen B. Johnson, Richard A. Friedman:
  Bridging the gap between biological and clinical informatics in a graduate training program. 59-66
• 
  Michael D. Kane, Jeffrey L. Brewer:
  An information technology emphasis in biomedical informatics education. 67-72
• 
  Mark Gerstein, Dov Greenbaum, Kei-Hoi Cheung, Perry L. Miller:
  An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective. 73-79

Volume 40, Number 2, April 2007

• 
  Sameer Malhotra, Desmond A. Jordan, Edward H. Shortliffe, Vimla L. Patel:
  Workflow modeling in critical care: Piecing together your own puzzle. 81-92
• 
  Jorge R. Herskovic, M. Sriram Iyengar, Elmer V. Bernstam:
  Using hit curves to compare search algorithm performance. 93-99
• 
  Steven E. Labkoff, William A. Yasnoff:
  A framework for systematic evaluation of health information infrastructure progress in communities. 100-105
• 
  S. Trent Rosenbloom, Adrienne N. Crow, Jennifer Urbano Blackford, Kevin B. Johnson:
  Cognitive factors influencing perceptions of clinical documentation tools. 106-113
• 
  Yasunori Yamamoto, Toshihisa Takagi:
  Biomedical knowledge navigation by literature clustering. 114-130
• 
  Ray L. Somorjai, Brion Dolenko, Marina Mandelzweig:
  Direct classification of high-dimensional data in low-dimensional projected feature spaces - Comparison of several classification methodologies. 131-138
• 
  Szymon Nowakowski, Jerzy Tiuryn:
  A new approach to the assessment of the quality of predictions of transcription factor binding sites. 139-149
• 
  Hong Yu, Won Kim, Vasileios Hatzivassiloglou, W. John Wilbur:
  Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. 150-159
• 
  Markus Brameier, Carsten Wiuf:
  Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. 160-173
• 
  Janet F. E. Penz, Adam B. Wilcox, John F. Hurdle:
  Automated identification of adverse events related to central venous catheters. 174-182

Methodological Review

• 
  Li Zhou, George Hripcsak:
  Temporal reasoning with medical data - A review with emphasis on medical natural language processing. 183-202

Volume 40, Number 3, June 2007

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  Boris A. Galitsky, Sergei O. Kuznetsov, Dmitry V. Vinogradov:
  Applying hybrid reasoning to mine for associative features in biological data. 203-220
• 
  Silvia Alayón, Richard Robertson, Simon K. Warfield, Juan Ruiz-Alzola:
  A fuzzy system for helping medical diagnosis of malformations of cortical development. 221-235
• 
  Hong Yu, Minsuk Lee, David R. Kaufman, John W. Ely, Jerome A. Osheroff, George Hripcsak, James J. Cimino:
  Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians. 236-251
• 
  Olga Brazhnik, John F. Jones:
  Anatomy of data integration. 252-269
• 
  P. Karina Tulipano, Ying Tao, William S. Millar, Pat Zanzonico, Katherine Kolbert, Hua Xu, Hong Yu, Lifeng Chen, Yves A. Lussier, Carol Friedman:
  Natural language processing and visualization in the molecular imaging domain. 270-281
• 
  David A. Dorr, Spencer S. Jones, Adam B. Wilcox:
  A framework for information system usage in collaborative care. 282-287
• 
  Ted Pedersen, Serguei V. S. Pakhomov, Siddharth Patwardhan, Christopher G. Chute:
  Measures of semantic similarity and relatedness in the biomedical domain. 288-299
• 
  Michael Bada, Lawrence Hunter:
  Enrichment of OBO ontologies. 300-315
• 
  Martijn J. Schuemie, Barend Mons, Marc Weeber, Jan A. Kors:
  Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification. 316-324
• 
  Qing T. Zeng, Juan Pablo Pratt, Jane Pak, Dino Ravnic, Harold Huss, Steven J. Mentzer:
  Feature-guided clustering of multi-dimensional flow cytometry datasets. 325-331
• 
  Umberto Giani, G. Brascio, Dario Bruzzese, Carmine Garzillo, S. Vigilante:
  Emotional and cognitive information processing in web-based medical education. 332-342
• 
  Hui Cao, George Hripcsak, Marianthi Markatou:
  A statistical methodology for analyzing co-occurrence data from a large sample. 343-352

Methodological Review

• 
  Chunhua Weng, John H. Gennari, Douglas B. Fridsma:
  User-centered semantic harmonization: A case study. 353-364

Volume 40, Number 4, August 2007

Public Health Informatics

• 
  Rita Kukafka, William A. Yasnoff:
  Public health informatics. 365-369

Methodological Review

• 
  David L. Buckeridge:
  Outbreak detection through automated surveillance: A review of the determinants of detection. 370-379

Book Review

• 
  Sharib A. Khan:
  Handbook of Biosurveillance, M.M. Wagner, A.W. Moore, R.M. Aryel (Eds.). Elsevier Inc. ISBN-13: 978-0-12-369378-5. 380-381

Research Articles

• 
  Shannon A. Sims, Laverne A. Snow, Christina A. Porucznik:
  Surveillance of methadone-related adverse drug events using multiple public health data sources. 382-389
• 
  Wilson W. Odero, Joseph K. Rotich, Constantin T. Yiannoutsos, Tom Ouna, William M. Tierney:
  Innovative approaches to application of information technology in disease surveillance and prevention in Western Kenya. 390-397
• 
  Rita Kukafka, Jessica S. Ancker, Connie V. Chan, John Chelico, Sharib A. Khan, Selasie Mortoti, Karthik Natarajan, Kempton Presley, Kayann Stephens:
  Redesigning electronic health record systems to support public health. 398-409
• 
  Debra Revere, Anne M. Turner, Ann Madhavan, Neil Rambo, Paul F. Bugni, Ann Marie Kimball, Sherrilynne S. Fuller:
  Understanding the information needs of public health practitioners: A literature review to inform design of an interactive digital knowledge management system. 410-421
• 
  Jacqueline Merrill, Suzanne Bakken, Maxine L. Rockoff, Kristine Gebbie, Kathleen M. Carley:
  Description of a method to support public health information management: Organizational network analysis. 422-428
• 
  Toomas Timpka, Magnus Bång, Tom Delbanco, Janet Walker:
  Information infrastructure for inter-organizational mental health services: An actor network theory analysis of psychiatric rehabilitation. 429-437
• 
  Nada Lavrac, Marko Bohanec, Aleksander Pur, Bojan Cestnik, Marko Debeljak, Andrej Kobler:
  Data mining and visualization for decision support and modeling of public health-care resources. 438-447

Letters to the Editor

• 
  Ronald N. Kostoff:
  Validating discovery in literature-based discovery. 448-450
• 
  Wanda Pratt, Meliha Yetisgen-Yildiz:
  Response to ''Validating discovery in literature-based discovery". 450-452

Volume 40, Number 5, October 2007

• 
  Xin Li, Hsinchun Chen, Zan Huang, Hua Su, Jesse D. Martinez:
  Global mapping of gene/protein interactions in PubMed abstracts: A framework and an experiment with P53 interactions. 453-464
• 
  Mohammad R. Akbarzadeh-Totonchi, Majid Moshtagh-Khorasani:
  A hierarchical fuzzy rule-based approach to aphasia diagnosis. 465-475
• 
  Dorota Formanowicz, Andrea Sackmann, Piotr Formanowicz, Jacek Blazewicz:
  Petri net based model of the body iron homeostasis. 476-485
• 
  Giorgio Leonardi, Silvia Panzarasa, Silvana Quaglini, Mario Stefanelli, Wil M. P. van der Aalst:
  Interacting agents through a web-based health serviceflow management system. 486-499
• 
  Chaeyoung Lee, Jungdae Park:
  Estimation of epistasis among finite polygenic loci for complex traits with a mixed model using Gibbs sampling. 500-506
• 
  Ohad Young, Yuval Shahar, Yair Liel, Eitan Lunenfeld, Guy Bar, Erez Shalom, Susana B. Martins, Laszlo T. Vaszar, Tal Marom, Mary K. Goldstein:
  Runtime application of Hybrid-Asbru clinical guidelines. 507-526
• 
  Kaei Hiroi, Keisuke Ido, Woosung Yang, Jun Nakaya:
  Interface analysis between GSVML and HL7 version 3. 527-538
• 
  Brian Hazlehurst, Carmit K. McMullen, Paul N. Gorman:
  Distributed cognition in the heart room: How situation awareness arises from coordinated communications during cardiac surgery. 539-551
• 
  Shizhu Zang, Ruifang Guo, Liang Zhang, Youyong Lu:
  Integration of statistical inference methods and a novel control measure to improve sensitivity and specificity of data analysis in expression profiling studies. 552-560
• 
  Yue Wang, Michael Halper, Hua Min, Yehoshua Perl, Yan Chen, Kent A. Spackman:
  Structural methodologies for auditing SNOMED. 561-581

Methodological Review

• 
  Philip R. O. Payne, Eneida A. Mendonça, Stephen B. Johnson, Justin Starren:
  Conceptual knowledge acquisition in biomedicine: A methodological review. 582-602

Book Review

• 
  Andrea Califano:
  Hui-Huang Hsu, Advanced Data Mining Technologies in Bioinformatics, Editors: Idea Group Publishing, pp 239. 603-604

Volume 40, Number 6, December 2007

Intelligent Data Analysis in Biomedicine

• 
  John H. Holmes, Niels Peek:
  Intelligent data analysis in biomedicine. 605-608

Special Issue Articles

• 
  Marion Verduijn, Niels Peek, Peter M. J. Rosseel, Evert de Jonge, Bas A. de Mol:
  Prognostic Bayesian networks: I: Rationale, learning procedure, and clinical use. 609-618
• 
  Marion Verduijn, Peter M. J. Rosseel, Niels Peek, Evert de Jonge, Bas A. de Mol:
  Prognostic Bayesian networks: II: An application in the domain of cardiac surgery. 619-630
• 
  Birgit Lessmann, Tim W. Nattkemper, Volkmar H. Hans, Andreas Degenhard:
  A method for linking computed image features to histological semantics in neuropathology. 631-641
• 
  Garrick L. Wallstrom, William R. Hogan:
  Unsupervised clustering of over-the-counter healthcare products into product categories. 642-648
• 
  Tudor Toma, Ameen Abu-Hanna, Robert-Jan Bosman:
  Discovery and inclusion of SOFA score episodes in mortality prediction. 649-660
• 
  Janez Demsar, Gregor Leban, Blaz Zupan:
  FreeViz - An intelligent multivariate visualization approach to explorative analysis of biomedical data. 661-671
• 
  Thomas Guyet, Catherine Garbay, Michel Dojat:
  Knowledge construction from time series data using a collaborative exploration system. 672-687
• 
  Michael E. Matheny, Frederic S. Resnic, Nipun Arora, Lucila Ohno-Machado:
  Effects of SVM parameter optimization on discrimination and calibration for post-procedural PCI mortality. 688-697
• 
  Eleftherios Panteris, Stephen Swift, Annette M. Payne, Xiaohui Liu:
  Mining pathway signatures from microarray data and relevant biological knowledge. 698-706
• 
  Junbai Wang:
  A new framework for identifying combinatorial regulation of transcription factors: A case study of the yeast cell cycle. 707-725
• 
  Losiana Nayak, Rajat K. De:
  An algorithm for modularization of MAPK and calcium signaling pathways: Comparative analysis among different species. 726-749
• 
  Valentin Dinu, Hongyu Zhao, Perry L. Miller:
  Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis. 750-760
• 
  Lucia Sacchi, Cristiana Larizza, Paolo Magni, Riccardo Bellazzi:
  Precedence Temporal Networks to represent temporal relationships in gene expression data. 761-774
• 
  Pritha Mahata, Kaushik Mahata:
  Selecting differentially expressed genes using minimum probability of classification error. 775-786

Methodological Review

• 
  Riccardo Bellazzi, Blaz Zupan:
  Towards knowledge-based gene expression data mining. 787-802

Volume 40, Number 6, Supplement, December 2007

Developing Common Methods for Evaluating Health Information Exchange
Guest Editorial

• 
  George Hripcsak:
  Developing common methods for evaluating health information exchange. S1-S2

Special Supplement Articles

• 
  George Hripcsak, Rainu Kaushal, Kevin B. Johnson, Joan S. Ash, David W. Bates, Rachel Block, Mark E. Frisse, Lisa M. Kern, Janet Marchibroda, J. Marc Overhage, Adam B. Wilcox:
  The United Hospital Fund meeting on evaluating health information exchange. S3-S10
• 
  Janet Marchibroda:
  Health information exchange policy and evaluation. S11-S16
• 
  Lisa M. Kern, Rainu Kaushal:
  Health information technology and health information exchange in New York State: New initiatives in implementation and evaluation. S17-S20
• 
  Kevin B. Johnson, Cynthia S. Gadd:
  Playing smallball: Approaches to evaluating pilot health information exchange systems. S21-S26
• 
  Mark E. Frisse, Rodney L. Holmes:
  Estimated financial savings associated with health information exchange and ambulatory care referral. S27-S32
• 
  Joan S. Ash, Kenneth P. Guappone:
  Qualitative evaluation of health information exchange efforts. S33-S39
• 
  David C. Kaelber, David W. Bates:
  Health information exchange and patient safety. S40-S45
• 
  Jason S. Shapiro:
  Evaluating public health uses of health information exchange. S46-S49