Volume 39, Number 1, February 2006

Phylogenetic Inferencing: Beyond Biology

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  Randolph A. Miller, Arie Hasman, Charles Safran, Reinhold Haux, Alexa T. McCray, Torgny Groth, Edward H. Shortliffe: On exemplary scientific conduct regarding submission of manuscripts to biomedical informatics journals. 1-2

Guest Editorial

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  Indra Neil Sarkar: Phylogenetics in the modern era. 3-5

Part I: Gathering and Organizing Data for Comparative Studies

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  Robert DeSalle: What's in a character? 6-17
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  Aloysius J. Phillips: Homology assessment and molecular sequence alignment. 18-33
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  John J. Wiens: Missing data and the design of phylogenetic analyses. 34-42

Part II: Inferring Data into Phylogenetic Trees

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  Griffin M. Weber, Lucila Ohno-Machado, Stuart M. Shieber: Representation in stochastic search for phylogenetic tree reconstruction. 43-50
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  Carolin Kosiol, Lee Bofkin, Simon Whelan: Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome. 51-61
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  Michael A. Charleston, Susan L. Perkins: Traversing the tangle: Algorithms and applications for cophylogenetic studies. 62-71

Part III: Assessing the Reliability of Phylogenetics

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  Mary G. Egan: Support versus corroboration. 72-85
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  Paul J. Planet: Tree disagreement: Measuring and testing incongruence in phylogenies. 86-102

Volume 39, Number 2, April 2006

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  Rita Noumeir: Radiology interpretation process modeling. 103-114
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  Xiaobo Zhou, Xinhua Cao, Zach Perlman, Stephen T. C. Wong: A computerized cellular imaging system for high content analysis in Monastrol suppressor screens. 115-125
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  Changwon Yoo, Gregory F. Cooper, Martin Schmidt: A control study to evaluate a computer-based microarray experiment design recommendation system for gene-regulation pathways discovery. 126-146
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  Ming Chen, Ralf Hofestädt: A medical bioinformatics approach for metabolic disorders: Biomedical data prediction, modeling, and systematic analysis. 147-159
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  Maged N. Kamel Boulos, Qiang Cai, Julian A. Padget, Gerard Rushton: Using software agents to preserve individual health data confidentiality in micro-scale geographical analyses. 160-170
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  Christian Baumgartner, Gábor Mátyás, Beat Steinmann, Martin Eberle, Jörg I. Stein, Daniela Baumgartner: A bioinformatics framework for genotype-phenotype correlation in humans with Marfan syndrome caused by FBN1 gene mutations. 171-183
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  Mor Peleg, Lily A. Gutnik, Vincenza Snow, Vimla L. Patel: Interpreting procedures from descriptive guidelines. 184-195
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  Wendy Webber Chapman, John N. Dowling: Inductive creation of an annotation schema for manually indexing clinical conditions from emergency department reports. 196-208
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  Yugyung Lee, James Geller: Semantic enrichment for medical ontologies. 209-226

Methodological Review

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  Hyunjin Shin, Mia K. Markey: A machine learning perspective on the development of clinical decision support systems utilizing mass spectra of blood samples. 227-248

Volume 39, Number 3, June 2006

Biomedical Ontologies

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  James J. Cimino, Barry Smith: Introduction: International Medical Informatics Association Working Group 6 and the 2005 Rome Conference. 249-251

Methodological Review

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  Alexander C. Yu: Methods in biomedical ontology. 252-266

Research Papers

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  Alexa T. McCray: Conceptualizing the world: Lessons from history. 267-273
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  Ingvar Johansson: Bioinformatics and biological reality. 274-287
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  Barry Smith: From concepts to clinical reality: An essay on the benchmarking of biomedical terminologies. 288-298
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  James J. Cimino: In defense of the Desiderata. 299-306
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  Anita Burgun: Desiderata for domain reference ontologies in biomedicine. 307-313
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  Judith A. Blake, Carol J. Bult: Beyond the data deluge: Data integration and bio-ontologies. 314-320
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  Christiane Fellbaum, Udo Hahn, Barry Smith: Towards new information resources for public health - From WordNet to MedicalWordNet. 321-332
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  Alan L. Rector, Jeremy Rogers, Thomas Bittner: Granularity, scale and collectivity: When size does and does not matter. 333-349
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  Stefan Schulz, Anand Kumar, Thomas Bittner: Biomedical ontologies: What part-of is and isn't. 350-361
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  Werner Ceusters, Barry Smith: Strategies for referent tracking in electronic health records. 362-378

Volume 39, Number 4, August 2006

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  Ghislain Bidaut, Frank J. Manion, Christophe Garcia, Michael F. Ochs: WaveRead: Automatic measurement of relative gene expression levels from microarrays using wavelet analysis. 379-388
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  Omolola Ogunyemi: Methods for reasoning from geometry about anatomic structures injured by penetrating trauma. 389-400
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  Zhuo Fang, Jiong Yang, Yixue Li, Qing-ming Luo, Lei Liu: Knowledge guided analysis of microarray data. 401-411
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  Mureen Allen, Leanne M. Currie, Suzanne Bakken, Vimla L. Patel, James J. Cimino: Heuristic evaluation of paper-based Web pages: A simplified inspection usability methodology. 412-423
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  Li Zhou, Genevieve B. Melton, Simon Parsons, George Hripcsak: A temporal constraint structure for extracting temporal information from clinical narrative. 424-439
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  Qiang Lu, Pei Hao, Vasa Curcin, Wei-Zhong He, Yuan-Yuan Li, Qing-ming Luo, Yike Guo, Yi-Xue Li: KDE Bioscience: Platform for bioinformatics analysis workflows. 440-450

Methodological Review

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  Michael E. Bales, Stephen B. Johnson: Graph theoretic modeling of large-scale semantic networks. 451-464

Volume 39, Number 5, October 2006

Dialog Systems for Health Communications

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  Timothy W. Bickmore, Toni Giorgino, Nancy Green, Rosalind W. Picard: Special issue on dialog systems for health communication. 465-467

Special Issue Articles

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  Jeffrey P. Migneault, Ramesh Farzanfar, Julie A. Wright, Robert H. Friedman: How to write health dialog for a talking computer. 468-481
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  Martin Beveridge, John Fox: Automatic generation of spoken dialogue from medical plans and ontologies. 482-499
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  James F. Allen, George Ferguson, Nate Blaylock, Donna K. Byron, Nathanael Chambers, Myroslava Dzikovska, Lucian Galescu, Mary D. Swift: Chester: Towards a personal medication advisor. 500-513
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  Fiorella de Rosis, Nicole Novielli, Valeria Carofiglio, Addolorata Cavalluzzi, Berardina De Carolis: User modeling and adaptation in health promotion dialogs with an animated character. 514-531
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  Robert C. Hubal, Ruth S. Day: Informed consent procedures: An experimental test using a virtual character in a dialog systems training application. 532-540
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  Ronilda C. Lacson, Regina Barzilay, William J. Long: Automatic analysis of medical dialogue in the home hemodialysis domain: Structure induction and summarization. 541-555

Methodological Review

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  Timothy W. Bickmore, Toni Giorgino: Health dialog systems for patients and consumers. 556-571

Volume 39, Number 6, December 2006

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  Silvia Alayón, J. I. Estévez, José F. Sigut, José L. Sánchez, Pedro A. Toledo: An evolutionary Michigan recurrent fuzzy system for nuclei classification in cytological images using nuclear chromatin distribution. 573-588
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  Stéphane M. Meystre, Peter J. Haug: Natural language processing to extract medical problems from electronic clinical documents: Performance evaluation. 589-599
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  Meliha Yetisgen-Yildiz, Wanda Pratt: Using statistical and knowledge-based approaches for literature-based discovery. 600-611
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  Radwan E. Abdel-Aal, Mona R. E. Abdel-Halim, Safa Abdel-Aal: Improving the classification of multiple disorders with problem decomposition. 612-625
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  Li Zhou, Ying Tao, James J. Cimino, Elizabeth S. Chen, Hongfang Liu, Yves A. Lussier, George Hripcsak, Carol Friedman: Terminology model discovery using natural language processing and visualization techniques. 626-636
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  Ilias Maglogiannis, Elias P. Zafiropoulos, Agapios N. Platis, Costas Lambrinoudakis: Risk analysis of a patient monitoring system using Bayesian Network modeling. 637-647
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  Jeffrey A. Linder, Alan F. Rose, Matvey B. Palchuk, Frank Chang, Jeffrey L. Schnipper, Joseph C. Chan, Blackford Middleton: Decision support for acute problems: The role of the standardized patient in usability testing. 648-655
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  Amy Berlin, Marco Sorani, Ida Sim: A taxonomic description of computer-based clinical decision support systems. 656-667
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  Quanzhi Li, Yi-fang Brook Wu: Identifying important concepts from medical documents. 668-679
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  Mollie R. Poynton, Anna M. McDaniel: Classification of smoking cessation status with a backpropagation neural network. 680-686
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  Ismail Abbas, Joan Rovira, Josep Casanovas: Validation by simulation of a clinical trial model using the standardized mean and variance criteria. 687-696
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  Genevieve B. Melton, Simon Parsons, Frances P. Morrison, Adam S. Rothschild, Marianthi Markatou, George Hripcsak: Inter-patient distance metrics using SNOMED CT defining relationships. 697-705
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  Hongwei Cai, Jielai Xia, Dezhong Xu, Donghuai Gao, Yongping Yan: A generic minimization random allocation and blinding system on web. 706-719

Methodological Review

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  Lily A. Gutnik, A. Forogh Hakimzada, Nicole A. Yoskowitz, Vimla L. Patel: The role of emotion in decision-making: A cognitive neuroeconomic approach towards understanding sexual risk behavior. 720-736