Journal of Biomedical Informatics, Volume 43

Volume 43, Number 1, February 2010

• 
  Georgios Papachristoudis, Sotiris Diplaris, Pericles A. Mitkas:
  SoFoCles: Feature filtering for microarray classification based on Gene Ontology. 1-14
• 
  Yonghong Peng, Zhi Qing Wu, Jianmin Jiang:
  A novel feature selection approach for biomedical data classification. 15-23
• 
  Scott L. DuVall, Richard A. Kerber, Alun Thomas:
  Extending the Fellegi-Sunter probabilistic record linkage method for approximate field comparators. 24-30
• 
  Hai-Tao Zheng, Charles Borchert, Hong-Gee Kim:
  GOClonto: An ontological clustering approach for conceptualizing PubMed abstracts. 31-40
• 
  Vojtech Huser, Scott P. Narus, Roberto A. Rocha:
  Evaluation of a flowchart-based EHR query system: A case study of RetroGuide. 41-50
• 
  Nadezhda Sazonova, Edward Sazonov, E. James Harner:
  Algorithm for haplotype resolution and block partitioning for partial XOR-genotype data. 51-59
• 
  Ashis Jalote-Parmar, Petra Badke-Schaub, Wajid Ali, Eigil Samset:
  Cognitive processes as integrative component for developing expert decision-making systems: A workflow centered framework. 60-74
• 
  Nabyl Tejani, Timothy R. Dresselhaus, Matthew B. Weinger:
  Development of a hand-held computer platform for real-time behavioral assessment of physicians and nurses. 75-80
• 
  Huawen Liu, Lei Liu, Huijie Zhang:
  Ensemble gene selection by grouping for microarray data classification. 81-87
• 
  Zhihao Yang, Hongfei Lin, Yanpeng Li:
  BioPPISVMExtractor: A protein-protein interaction extractor for biomedical literature using SVM and rich feature sets. 88-96
• 
  Xiaoli Wang, Daniel Zeng, Holly Seale, Su Li, He Cheng, Rongsheng Luan, Xiong He, Xinghuo Pang, Xiangfeng Dou, Quanyi Wang:
  Comparing early outbreak detection algorithms based on their optimized parameter values. 97-103
• 
  Elmer V. Bernstam, Jack W. Smith, Todd R. Johnson:
  What is biomedical informatics? 104-110
• 
  Yaron Denekamp, Mor Peleg:
  TiMeDDx - A multi-phase anchor-based diagnostic decision-support model. 111-124
• 
  Ely Edison Matos, Fernanda Campos, Regina M. M. Braga, Daniele Palazzi:
  CelOWS: An ontology based framework for the provision of semantic web services related to biological models. 125-136
• 
  Magnus Irestig, Toomas Timpka:
  Towards responsible system development in health services: A discourse analysis study of design conflict resolution tactics. 137-143
• 
  Thusitha De Silva Mabotuwana, Jim Warren:
  ChronoMedIt - A computational quality audit framework for better management of patients with chronic conditions. 144-158

Methodological Review

• 
  Richard J. Holden, Ben-Tzion Karsh:
  The Technology Acceptance Model: Its past and its future in health care. 159-172

Volume 43, Number 2, April 2010

• 
  Catherine Blake:
  Beyond genes, proteins, and abstracts: Identifying scientific claims from full-text biomedical articles. 173-189
• 
  Xiao Hu, Peng Xu, Shaozhi Wu, Shadnaz Asgari, Marvin Bergsneider:
  A data mining framework for time series estimation. 190-199
• 
  Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch:
  Measuring prediction capacity of individual verbs for the identification of protein interactions. 200-207
• 
  Andigoni Malousi, Ioanna Chouvarda, Vassilis Koutkias, Sofia Kouidou, Nicos Maglaveras:
  SpliceIT: A hybrid method for splice signal identification based on probabilistic and biological inference. 208-217
• 
  Jonathan P. DeShazo, Anne M. Turner:
  An interactive and user-centered computer system to predict physician's disease judgments in discharge summaries. 218-223
• 
  Adem Karahoca, Erkan Bayraktar, Ekrem Tatoglu, Dilek Karahoca:
  Information system design for a hospital emergency department: A usability analysis of software prototypes. 224-232
• 
  Yang Liu, Mark Junjie Li, Yiu-ming Cheung, Pak Chung Sham, Michael K. Ng:
  SKM-SNP: SNP markers detection method. 233-239
• 
  Trevor Cohen, Roger W. Schvaneveldt, Dominic Widdows:
  Reflective Random Indexing and indirect inference: A scalable method for discovery of implicit connections. 240-256
• 
  Ioannis K. Valavanis, George M. Spyrou, Konstantina S. Nikita:
  A similarity network approach for the analysis and comparison of protein sequence/structure sets. 257-267
• 
  Philip Brown, Sylvia Halász, Colin R. Goodall, Dennis G. Cochrane, Peter Milano, John R. Allegra:
  The ngram chief complaint classifier: A novel method of automatically creating chief complaint classifiers based on international classification of diseases groupings. 268-272
• 
  Linda Peelen, Nicolette de Keizer, Evert de Jonge, Robert-Jan Bosman, Ameen Abu-Hanna, Niels Peek:
  Using hierarchical dynamic Bayesian networks to investigate dynamics of organ failure in patients in the Intensive Care Unit. 273-286
• 
  María Adela Grando, Mor Peleg, David Glasspool:
  A goal-oriented framework for specifying clinical guidelines and handling medical errors. 287-299
• 
  Connie V. Chan, David R. Kaufman:
  A technology selection framework for supporting delivery of patient-oriented health interventions in developing countries. 300-306
• 
  Evanthia E. Tripoliti, Dimitrios I. Fotiadis, Maria Argyropoulou, George Manis:
  A six stage approach for the diagnosis of the Alzheimer's disease based on fMRI data. 307-320
• 
  Kevin B. Johnson, Yun-Xian Ho, Cather Marie Cala, Coda L. Davison:
  Showing Your Work: Impact of annotating electronic prescriptions with decision support results. 321-325
• 
  Jon D. Duke, Xiaochun Li, Shaun J. Grannis:
  Data visualization speeds review of potential adverse drug events in patients on multiple medications. 326-331
• 
  Raj Ashar, Sheri Lewis, David L. Blazes, Jean-Paul Chretien:
  Applying information and communications technologies to collect health data from remote settings: A systematic assessment of current technologies. 332-341

Methodological Review

• 
  Arnon Rosenthal, Peter Mork, Maya Hao Li, Jean Stanford, David Koester, Patti Reynolds:
  Cloud computing: A new business paradigm for biomedical information sharing. 342-353

Volume 43, Number 3, June 2010

Guest Editorial

• 
  Yves A. Lussier, Atul J. Butte, Lawrence Hunter:
  Current methodologies for translational bioinformatics. 355-357

Special Issue Articles

• 
  David P. Chen, Alexander A. Morgan, Atul J. Butte:
  Validating pathophysiological models of aging using clinical electronic medical records. 358-364
• 
  Xin Liu, Ya-Pu Zhao:
  Simulated pathogenic conformational switch regions matched well with the biochemical findings. 365-375
• 
  Xinan Yang, Yong Huang, Matthew G. Crowson, Jianrong Li, Michael L. Maitland, Yves A. Lussier:
  Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data. 376-384
• 
  James L. Chen, Lee T. Sam, Yong Huang, Younghee Lee, Jianrong Li, Yang Liu, H. Rosie Xing, Yves A. Lussier:
  Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. 385-396
• 
  Rosalia Maglietta, Angela Distaso, Ada Piepoli, Orazio Palumbo, Massimo Carella, Annarita D'Addabbo, Sayan Mukherjee, Nicola Ancona:
  On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers. 397-406
• 
  Terry H. Shen, Peter Tarczy-Hornoch, Landon Detwiler, Eithon Cadag, Christopher S. Carlson:
  Evaluation of probabilistic and logical inference for a SNP annotation system. 407-418
• 
  Alberto Riva, Angelo Nuzzo, Mario Stefanelli, Riccardo Bellazzi:
  An automated reasoning framework for translational research. 419-427
• 
  Jeffrey Kriseman, Christopher Busick, Szabolcs Szelinger, Valentin Dinu:
  BING: Biomedical informatics pipeline for Next Generation Sequencing. 428-434
• 
  Young Soo Song, Hye Won Lee, Yu Rang Park, Do Kyoon Kim, Jaehyun Sim, Hyunseok Peter Kang, Ju Han Kim:
  TMA-TAB: A spreadsheet-based document for exchange of tissue microarray data based on the tissue microarray-object model. 435-441
• 
  Elizabeth S. Chen, Indra Neil Sarkar:
  MeSHing molecular sequences and clinical trials: A feasibility study. 442-450

Methodological Review

• 
  Chunhua Weng, Samson W. Tu, Ida Sim, Rachel L. Richesson:
  Formal representation of eligibility criteria: A literature review. 451-467

Volume 43, Number 4, August 2010

• 
  Gianluca Colombo, Daniele Merico, Giorgio Boncoraglio, Flavio De Paoli, John Ellul, Giuseppe Frisoni, Zoltán Nagy, Aad van der Lugt, István Vassányi, Marco Antoniotti:
  An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case. 469-484
• 
  Norman E. Fenton, Martin Neil:
  Comparing risks of alternative medical diagnosis using Bayesian arguments. 485-495
• 
  Christos Argyropoulos, Antonis Daskalakis, George Nikiforidis, George Sakellaropoulos:
  Background adjustment of cDNA microarray images by Maximum Entropy distributions. 496-509
• 
  Nancy C. Baker, Bradley M. Hemminger:
  Mining connections between chemicals, proteins, and diseases extracted from Medline annotations. 510-519
• 
  Beatriz Pérez, Ivan Porres:
  Authoring and verification of clinical guidelines: A model driven approach. 520-536
• 
  Fatma Betül Kavun Özbayraktar, Kutlu Ö. Ülgen:
  Drug target identification in sphingolipid metabolism by computational systems biology tools: Metabolic control analysis and metabolic pathway analysis. 537-549
• 
  Wenyuan Li, Min Xu, Xianghong Jasmine Zhou:
  Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets. 550-559
• 
  Anindya Bhattacharya, Rajat K. De:
  Average correlation clustering algorithm (ACCA) for grouping of co-regulated genes with similar pattern of variation in their expression values. 560-568
• 
  Feng Chen, Yi-Ping Phoebe Chen:
  Exploring the ncRNA-ncRNA patterns based on bridging rules. 569-577
• 
  Tudor Toma, Robert-Jan Bosman, Arno Siebes, Niels Peek, Ameen Abu-Hanna:
  Learning predictive models that use pattern discovery - A bootstrap evaluative approach applied in organ functioning sequences. 578-586
• 
  Dina Demner-Fushman, James G. Mork, Sonya E. Shooshan, Alan R. Aronson:
  UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. 587-594
• 
  Xiaoyan Wang, Herbert S. Chase, Marianthi Markatou, George Hripcsak, Carol Friedman:
  Selecting information in electronic health records for knowledge acquisition. 595-601
• 
  Sarada S. Panchanathan, Diana B. Petitti, Douglas B. Fridsma:
  The development and validation of a simulation tool for health policy decision making. 602-607
• 
  Chintan Patel, James J. Cimino:
  A network-theoretic approach for decompositional translation across Open Biological Ontologies. 608-612
• 
  Ivan Stajduhar, Bojana Dalbelo Basic:
  Learning Bayesian networks from survival data using weighting censored instances. 613-622
• 
  Dympna O'Sullivan, Szymon Wilk, Wojtek Michalowski, Ken Farion:
  Automatic indexing and retrieval of encounter-specific evidence for point-of-care support. 623-631
• 
  R. S. Mans, Nick C. Russell, Wil M. P. van der Aalst, Piet J. M. Bakker, Arnold J. Moleman, Monique W. M. Jaspers:
  Proclets in healthcare. 632-649

Methodological Review

• 
  Xuezhong Zhou, Yonghong Peng, Baoyan Liu:
  Text mining for traditional Chinese medical knowledge discovery: A survey. 650-660

Volume 43, Number 5, October 2010

• 
  Mithra Vankipuram, Kanav Kahol, Alex McLaren, Sethuraman Panchanathan:
  A virtual reality simulator for orthopedic basic skills: A design and validation study. 661-668
• 
  Shyam Visweswaran, Derek C. Angus, Margaret Hsieh, Lisa A. Weissfeld, Donald Yealy, Gregory F. Cooper:
  Learning patient-specific predictive models from clinical data. 669-685
• 
  Sooyoung Yoo, Jinwook Choi:
  On the query reformulation technique for effective MEDLINE document retrieval. 686-693
• 
  Vidya Vasuki, Trevor Cohen:
  Reflective random indexing for semi-automatic indexing of the biomedical literature. 694-700
• 
  Ameen Abu-Hanna, Barry Nannings, Dave Dongelmans, Arie Hasman:
  PRIM versus CART in subgroup discovery: When patience is harmful. 701-708
• 
  Ronilda Lacson, Erik Pitzer, Jihoon Kim, Pedro A. F. Galante, Christian Hinske, Lucila Ohno-Machado:
  DSGeo: Software tools for cross-platform analysis of gene expression data in GEO. 709-715
• 
  Nathan C. Hulse, Grant M. Wood, Peter J. Haug, Marc S. Williams:
  Deriving consumer-facing disease concepts for family health histories using multi-source sampling. 716-724
• 
  Guocai Chen, Jim Warren, Patricia Riddle:
  Semantic Space models for classification of consumer webpages on metadata attributes. 725-735
• 
  Catalina Martínez-Costa, Marcos Menárguez Tortosa, Jesualdo Tomás Fernández-Breis:
  An approach for the semantic interoperability of ISO EN 13606 and OpenEHR archetypes. 736-746
• 
  Hersh Sagreiya, Russ B. Altman:
  The utility of general purpose versus specialty clinical databases for research: Warfarin dose estimation from extracted clinical variables. 747-751
• 
  Alistair Miles, Jun Zhao, Graham Klyne, Helen White-Cooper, David M. Shotton:
  OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster. 752-761
• 
  Mark Stevenson, Yikun Guo:
  Disambiguation of ambiguous biomedical terms using examples generated from the UMLS Metathesaurus. 762-773
• 
  Ljiljana Trtica-Majnaric, Marijana Zekic-Susac, Natasa Sarlija, Branko Vitale:
  Prediction of influenza vaccination outcome by neural networks and logistic regression. 774-781
• 
  Jan Horsky, Kerry McColgan, Justine E. Pang, Andrea J. Melnikas, Jeffrey A. Linder, Jeffrey L. Schnipper, Blackford Middleton:
  Complementary methods of system usability evaluation: Surveys and observations during software design and development cycles. 782-790
• 
  Jacob Barhak, Deanna J. M. Isaman, Wen Ye, Donghee Lee:
  Chronic disease modeling and simulation software. 791-799
• 
  Ghasem Mahdevar, Javad Zahiri, Mehdi Sadeghi, Abbas Nowzari-Dalini, Hayedeh Ahrabian:
  Tag SNP selection via a genetic algorithm. 800-804
• 
  Ann Kristin Rotegaard, Cornelia M. Ruland:
  Patient centeredness in terminologies: Coverage of health assets concepts in the International Classification of Nursing Practice. 805-811
• 
  Francisco Azuaje, Yvan Devaux, Melanie Vausort, Céline Yvorra, Daniel R. Wagner:
  Transcriptional networks characterize ventricular dysfunction after myocardial infarction: A proof-of-concept investigation. 812-819
• 
  Haiyan Hu:
  Mining patterns in disease classification forests. 820-827

Commentaries

• 
  Elmer V. Bernstam, William R. Hersh, Ida Sim, David Eichmann, Jonathan C. Silverstein, Jack W. Smith, Michael J. Becich:
  Unintended consequences of health information technology: A need for biomedical informatics. 828-830
• 
  John Fox, David Glasspool, Vivek Patkar, Mark Austin, Liz Black, Matthew South, Dave Robertson, Charles Vincent:
  Delivering clinical decision support services: There is nothing as practical as a good theory. 831-843

Methodological Review

• 
  Stefan V. Pantazi:
  Unsupervised grammar induction and similarity retrieval in medical language processing using the Deterministic Dynamic Associative Memory (DDAM) model. 844-857

Volume 43, Numbers 5-Supplement-1, October 2010

Guest Editorial

• 
  Kevin B. Johnson:
  Project HealthDesign: Advancing the vision of consumer-clinician-computer collaborations. S1-S2

Introduction

• 
  Patricia Flatley Brennan, Stephen Downs, Gail R. Casper:
  Project HealthDesign: Rethinking the power and potential of personal health records. S3-S5

Special Supplement Articles

• 
  Michael Hogarth, Kathy Hajopoulos, Meg Young, Neil Cowles, John Churin, Bethany Hornthal, Laura Esserman:
  The Communication and Care Plan: A novel approach to patient-centered clinical information systems. S6-S8
• 
  Peter Chira, Lisa Nugent, Kimberly Miller, Tina Park, Sean Donahue, Amit Soni, Diane Nugent, Christy Sandborg:
  Living Profiles: Design of a health media platform for teens with special healthcare needs. S9-S12
• 
  George Ferguson, Jill Quinn, Cecilia Horwitz, Mary D. Swift, James F. Allen, Lucian Galescu:
  Towards a Personal Health Management Assistant. S13-S16
• 
  Stephanie J. Fonda, Richard J. Kedziora, Robert A. Vigersky, Sven-Erik Bursell:
  Evolution of a web-based, prototype Personal Health Application for diabetes self-management. S17-S21
• 
  Katie A. Siek, Stephen E. Ross, Danish Ullah Khan, Leah M. Haverhals, Steven R. Cali, Jane Meyers:
  Colorado Care Tablet: The design of an interoperable Personal Health Application to help older adults with multimorbidity manage their medications. S22-S26
• 
  Jason Slagle, Jeffry S. Gordon, Christopher E. Harris, Coda L. Davison, DeMoyne K. Culpepper, Patti Scott, Kevin B. Johnson:
  MyMediHealth - Designing a next generation system for child-centered medication management. S27-S31
• 
  Roger Luckmann, Amin Vidal:
  Design of a handheld electronic pain, treatment and activity diary. S32-S36
• 
  Lynne T. Harris, James Tufano, Tung Le, Courtney Rees, Ginny A. Lewis, Alison B. Evert, Jan Flowers, Carol Collins, James Hoath, Irl B. Hirsch, Harold I. Goldberg, James D. Ralston:
  Designing mobile support for glycemic control in patients with diabetes. S37-S40
• 
  Barbara L. Massoudi, Murrey G. Olmsted, Yuying Zhang, Ruth Ann Carpenter, Carolyn E. Barlow, Rachel Huber:
  A web-based intervention to support increased physical activity among at-risk adults. S41-S45
• 
  Walter V. Sujansky, Samuel A. Faus, Ethan Stone, Patricia Flatley Brennan:
  A method to implement fine-grained access control for personal health records through standard relational database queries. S46-S50
• 
  Reid Cushman, A. Michael Froomkin, Anita Cava, Patricia Abril, Kenneth W. Goodman:
  Ethical, legal and social issues for personal health records and applications. S51-S55

Volume 43, Number 6, December 2010

In Memoriam

• 
  Vimla L. Patel, Riccardo Bellazzi, Silvana Quaglini:
  Professor Mario Stefanelli (1945-2010). 859-860

Regular Articles

• 
  Joris van de Klundert, Pascal Gorissen, Stef Zeemering:
  Measuring clinical pathway adherence. 861-872
• 
  Eithon Cadag, Peter Tarczy-Hornoch:
  Supporting retrieval of diverse biomedical data using evidence-aware queries. 873-882
• 
  Leila Ahmadian, Ronald Cornet, Nicolette de Keizer:
  Facilitating pre-operative assessment guidelines representation using SNOMED CT. 883-890
• 
  Adam Wright, Elizabeth S. Chen, Francine L. Maloney:
  An automated technique for identifying associations between medications, laboratory results and problems. 891-901
• 
  Roxana Dánger, Isabel Segura-Bedmar, Paloma Martínez Fernández, Paolo Rosso:
  A comparison of machine learning techniques for detection of drug target articles. 902-913
• 
  Jonathan S. Schildcrout, Melissa A. Basford, Jill M. Pulley, Daniel R. Masys, Dan M. Roden, Deede Wang, Christopher G. Chute, Iftikhar J. Kullo, David Carrell, Peggy L. Peissig, Abel N. Kho, Joshua C. Denny:
  An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records. 914-923
• 
  Songhua Xu, Michael Krauthammer:
  A new pivoting and iterative text detection algorithm for biomedical images. 924-931
• 
  Jesse M. Engreitz, Bernie J. Daigle Jr., Jonathan J. Marshall, Russ B. Altman:
  Independent component analysis: Mining microarray data for fundamental human gene expression modules. 932-944
• 
  Stefan Wuchty, Alice Zhang, Jennifer Walling, Susie Ahn, Aiguo Li, Martha Quezado, Carl Oberholtzer, Jean-Claude Zenklusen, Howard A. Fine:
  Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. 945-952
• 
  Shashank Agarwal, Hong Yu:
  Detecting hedge cues and their scope in biomedical text with conditional random fields. 953-961
• 
  Yonggang Cao, James J. Cimino, John W. Ely, Hong Yu:
  Automatically extracting information needs from complex clinical questions. 962-971
• 
  Mark Stevenson, Yikun Guo:
  Disambiguation in the biomedical domain: The role of ambiguity type. 972-981
• 
  Simon Horsburgh, Pauline Norris, Gordon Becket, Peter Crampton, Bruce Arroll, Jacqueline Cumming, Peter Herbison, Gerald Sides:
  The Equity in Prescription Medicines Use Study: Using community pharmacy databases to study medicines utilisation. 982-987
• 
  Gai Elhanan, Kuo-Chuan Huang, Yehoshua Perl:
  Source authenticity in the UMLS - A case study of the Minimal Standard Terminology. 988-997
• 
  Helena F. Deus, Diogo F. Veiga, Pablo R. Freire, John N. Weinstein, Gordon B. Mills, Jonas S. Almeida:
  Exposing the cancer genome atlas as a SPARQL endpoint. 998-1008
• 
  Adrien Coulet, Nigam H. Shah, Yael Garten, Mark A. Musen, Russ B. Altman:
  Using text to build semantic networks for pharmacogenomics. 1009-1019
• 
  Jahiruddin, Muhammad Abulaish, Lipika Dey:
  A concept-driven biomedical knowledge extraction and visualization framework for conceptualization of text corpora. 1020-1035
• 
  Tae Youn Kim, Amy Coenen, Nicholas R. Hardiker:
  A quality improvement model for healthcare terminologies. 1036-1043