Journal of Biomedical Informatics, Volume 44

Volume 44, Number 1, February 2011

Guest Editorial

• 
  Barry Smith, Richard H. Scheuermann:
  Ontologies for clinical and translational research: Introduction. 3-7

Original Research

• 
  Mathias Brochhausen, Andrew D. Spear, Cristian Cocos, Gabriele Weiler, Luis Martín, Alberto Anguita, Holger Stenzhorn, Evangelia Daskalaki, Fatima Schera, Ulf Schwarz, Stelios Sfakianakis, Stephan Kiefer, Martin Doerr, Norbert M. Graf, Manolis Tsiknakis:
  The ACGT Master Ontology and its applications - Towards an ontology-driven cancer research and management system. 8-25
• 
  William R. Hogan:
  Towards an ontological theory of substance intolerance and hypersensitivity. 26-34
• 
  Albert Goldfain, Barry Smith, Lindsay G. Cowell:
  Towards an ontological representation of resistance: The case of MRSA. 35-41
• 
  Pantelis Topalis, Emmanuel Dialynas, Elvira Mitraka, Elena Deligianni, Inga Siden-Kiamos, Christos Louis:
  A set of ontologies to drive tools for the control of vector-borne diseases. 42-47
• 
  Y. Megan Kong, Carl Dahlke, Qun Xiang, Yu Qian, David R. Karp, Richard H. Scheuermann:
  Toward an ontology-based framework for clinical research databases. 48-58
• 
  Dennis G. Thomas, Rohit V. Pappu, Nathan A. Baker:
  NanoParticle Ontology for cancer nanotechnology research. 59-74
• 
  Alexander D. Diehl, Alison Deckhut Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, Timothy A. Gondré-Lewis, Anna Maria Masci, Terrence F. Meehan, Penelope A. Morel, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard H. Scheuermann, Q. Alison Yao, Martin S. Zand, Christopher J. Mungall:
  Hematopoietic cell types: Prototype for a revised cell ontology. 75-79
• 
  Christopher J. Mungall, Michael Bada, Tanya Z. Berardini, Jennifer I. Deegan, Amelia Ireland, Midori A. Harris, David P. Hill, Jane Lomax:
  Cross-product extensions of the Gene Ontology. 80-86
• 
  Christopher J. Mungall, Colin R. Batchelor, Karen Eilbeck:
  Evolution of the Sequence Ontology terms and relationships. 87-93
• 
  Michael Bada, Lawrence Hunter:
  Desiderata for ontologies to be used in semantic annotation of biomedical documents. 94-101

Applications

• 
  Marianne Shaw, Landon Fridman Detwiler, Natalya Fridman Noy, James F. Brinkley, Dan Suciu:
  vSPARQL: A view definition language for the semantic web. 102-117
• 
  Montserrat Batet, David Sánchez, Aïda Valls:
  An ontology-based measure to compute semantic similarity in biomedicine. 118-125
• 
  Bernardo Gonçalves, Giancarlo Guizzardi, José Gonçalves Pereira Filho:
  Using an ECG reference ontology for semantic interoperability of ECG data. 126-136
• 
  Jessica D. Tenenbaum, Patricia L. Whetzel, Kent Anderson, Charles D. Borromeo, Ivo D. Dinov, Davera Gabriel, Beth A. Kirschner, Barbara Mirel, Timothy D. Morris, Natasha Fridman Noy, Csongor Nyulas, David Rubenson, Paul R. Saxman, Harpreet Singh, Nancy Whelan, Zach Wright, Brian D. Athey, Michael J. Becich, Geoffrey S. Ginsburg, Mark A. Musen, Kevin A. Smith, Alice F. Tarantal, Daniel L. Rubin, Peter Lyster:
  The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. 137-145
• 
  John H. Gennari, Maxwell Lewis Neal, Michal Galdzicki, Daniel L. Cook:
  Multiple ontologies in action: Composite annotations for biosimulation models. 146-154
• 
  Pinar Wennerberg, Klaus U. Schulz, Paul Buitelaar:
  Ontology modularization to improve semantic medical image annotation. 155-162

Methodological Review

• 
  Kaihong Liu, William R. Hogan, Rebecca S. Crowley:
  Natural Language Processing methods and systems for biomedical ontology learning. 163-179

Volume 44, Number 2, April 2011

Regular Articles

• 
  Timothy W. Bickmore, Daniel Schulman, Candace L. Sidner:
  A reusable framework for health counseling dialogue systems based on a behavioral medicine ontology. 183-197
• 
  Adinda Freudenthal, Thomas Stüdeli, Pablo Lamata, Eigil Samset:
  Collaborative co-design of emerging multi-technologies for surgery. 198-215
• 
  Parviz Owlia, M. Vasei, B. Goliaei, I. Nassiri:
  Normalized impact factor (NIF): An adjusted method for calculating the citation rate of biomedical journals. 216-220
• 
  Emily H. Chan, Robyn Tamblyn, Katia M. L. Charland, David L. Buckeridge:
  Outpatient physician billing data for age and setting specific syndromic surveillance of influenza-like illnesses. 221-228
• 
  Bin Han, Lihua Li, Yan Chen, Lei Zhu, Qi Dai:
  A two step method to identify clinical outcome relevant genes with microarray data. 229-238
• 
  Samson W. Tu, Mor Peleg, Simona Carini, Michael Bobak, Jessica Ross, Daniel L. Rubin, Ida Sim:
  A practical method for transforming free-text eligibility criteria into computable criteria. 239-250
• 
  Serguei V. S. Pakhomov, Ted Pedersen, Bridget T. McInnes, Genevieve B. Melton, Alexander Ruggieri, Christopher G. Chute:
  Towards a framework for developing semantic relatedness reference standards. 251-265
• 
  Monica M. Horvath, Stephanie Winfield, Steve Evans, Steve Slopek, Howard Shang, Jeffrey M. Ferranti:
  The DEDUCE Guided Query tool: Providing simplified access to clinical data for research and quality improvement. 266-276
• 
  Yonggang Cao, Feifan Liu, Pippa Simpson, Lamont D. Antieau, Andrew S. Bennett, James J. Cimino, John W. Ely, Hong Yu:
  AskHERMES: An online question answering system for complex clinical questions. 277-288
• 
  Alexander C. Yu, James J. Cimino:
  A comparison of two methods for retrieving ICD-9-CM data: The effect of using an ontology-based method for handling terminology changes. 289-298
• 
  Felipe Mancini, Fernando Sequeira Sousa, Fábio Oliveira Teixeira, Alex Esteves Jaccoud Falcão, Anderson Diniz Hummel, Thiago Martini da Costa, Pável Pereira Calado, Luciano Vieira de Araújo, Ivan Torres Pisa:
  Use of Medical Subject Headings (MeSH) in Portuguese for categorizing web-based healthcare content. 299-309
• 
  Aurélie Névéol, Rezarta Islamaj Dogan, Zhiyong Lu:
  Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction. 310-318
• 
  Tim Van den Bulcke, Paul Vanden Broucke, Viviane Van Hoof, Kristien Wouters, Seppe vanden Broucke, Geert Smits, Elke Smits, Sam Proesmans, Toon Van Genechten, François Eyskens:
  Data mining methods for classification of Medium-Chain Acyl-CoA dehydrogenase deficiency (MCADD) using non-derivatized tandem MS neonatal screening data. 319-325
• 
  Wen-Shan Jian, Hsyien-Chia Wen, Jeremiah Scholl, Syed Abdul Shabbir, Peisan Lee, Chien-Yeh Hsu, Yu-Chuan Li:
  The Taiwanese method for providing patients data from multiple hospital EHR systems. 326-332
• 
  Bradley A. Malin, Steve Nyemba, John Paulett:
  Learning relational policies from electronic health record access logs. 333-342
• 
  Leonardo Lezcano, Miguel-Ángel Sicilia, Carlos Rodríguez-Solano:
  Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules. 343-353
• 
  Ning Kang, Erik M. van Mulligen, Jan A. Kors:
  Comparing and combining chunkers of biomedical text. 354-360
• 
  Lorenzo Beretta, Alessandro Santaniello:
  Implementing ReliefF filters to extract meaningful features from genetic lifetime datasets. 361-369

Book Review

• 
  Graciela Gonzalez:
  Biomedical Informatics in Translational Research, Hai Hu, Richard J. Mural, Michael N. Liebman (Eds.). Artech House (2008). 370-371

Methodological Review

• 
  Remko van der Togt, Piet J. M. Bakker, Monique W. M. Jaspers:
  A framework for performance and data quality assessment of Radio Frequency IDentification (RFID) systems in health care settings. 372-383

Corrigendum

• 
  Vimla L. Patel, Riccardo Bellazzi, Silvana Quaglini:
  Corrigendum to "In Memoriam: 'Professor Mario Stefanelli (1945-2010)'" [J Biomed Inform (2010) 859-60]. 384

Volume 44, Number 3, June 2011

In Memoriam

• 
  Kazuhiko Ohe, Michio Kimura:
  Shigekoto Kaihara (1937-2011). 385-386

Guest Editorial

• 
  Vimla L. Patel, Kanav Kahol, Timothy G. Buchman:
  Biomedical Complexity and Error. 387-389

Special Issue Articles

• 
  René Amalberti, Dan Benhamou, Yves Auroy, Laurent Degos:
  Adverse events in medicine: Easy to count, complicated to understand, and complex to prevent. 390-394
• 
  Matthew C. Holtman:
  Paradoxes of professionalism and error in complex systems. 395-401
• 
  Anton E. Lawson, Erno S. Daniel:
  Inferences of clinical diagnostic reasoning and diagnostic error. 402-412
• 
  Vimla L. Patel, Trevor Cohen, Tripti Murarka, Joanne Olsen, Srujana Kagita, Sahiti Myneni, Timothy G. Buchman, Vafa Ghaemmaghami:
  Recovery at the edge of error: Debunking the myth of the infallible expert. 413-424
• 
  Kanav Kahol, Mithra Vankipuram, Vimla L. Patel, Marshall L. Smith:
  Deviations from protocol in a complex Trauma environment: Errors or innovations? 425-431
• 
  Mithra Vankipuram, Kanav Kahol, Trevor Cohen, Vimla L. Patel:
  Toward automated workflow analysis and visualization in clinical environments. 432-440
• 
  Thomas George Kannampallil, Zhe Li, Min Zhang, Trevor Cohen, David J. Robinson, Amy Franklin, Jiajie Zhang, Vimla L. Patel:
  Making sense: Sensor-based investigation of clinician activities in complex critical care environments. 441-454
• 
  Loubna Bouarfa, Pieter P. Jonker, Jenny Dankelman:
  Discovery of high-level tasks in the operating room. 455-462
• 
  Alexander Turchin, Oliver D. James, Eric D. Godlewski, Maria Shubina, Christopher M. Coley, Tejal K. Gandhi, Carol A. Broverman:
  Effectiveness of interruptive alerts in increasing application functionality utilization: A controlled trial. 463-468
• 
  Amy Franklin, Ying Liu, Zhe Li, Vickie Nguyen, Todd R. Johnson, David J. Robinson, Nnaemeka Okafor, Brent King, Vimla L. Patel, Jiajie Zhang:
  Opportunistic decision making and complexity in emergency care. 469-476
• 
  Avi Parush, Chelsea Kramer, Tara Foster-Hunt, Kathryn Momtahan, Aren Hunter, Benjamin Sohmer:
  Communication and team situation awareness in the OR: Implications for augmentative information display. 477-485
• 
  Carla M. Pugh, Susan Santacaterina, Debra A. DaRosa, Richard E. Clark:
  Intra-operative decision making: More than meets the eye. 486-496

Methodological Review

• 
  Christa E. Bartos, Brian S. Butler, Rebecca S. Crowley:
  Ranked Levels of Influence model: Selecting influence techniques to minimize IT resistance. 497-504

Book Review

• 
  Thomas George Kannampallil:
  Handbook of Human Factors in Medical Device Design, Matthew B. Weinger, Michael E. Wiklund, Daryle J. Gardner-Bonneau (Eds.). CRC Press, New York, NY (2010). 844 pp., ISBN-10: 0805856277. 505-506

Volume 44, Number 4, August 2011

Regular Articles

• 
  Liang-Chih Yu, Chien-Lung Chan, Chao-Cheng Lin, I-Chun Lin:
  Mining association language patterns using a distributional semantic model for negative life event classification. 509-518
• 
  Juan C. Caicedo, Fabio A. González, Eduardo Romero:
  Content-based histopathology image retrieval using a kernel-based semantic annotation framework. 519-528
• 
  B. Chandra, Manish Gupta:
  An efficient statistical feature selection approach for classification of gene expression data. 529-535
• 
  Yue W. Webster, Ernst R. Dow, Jacob Koehler, Ranga Chandra Gudivada, Mathew J. Palakal:
  Leveraging health social networking communities in translational research. 536-544
• 
  Laurie Faisandier, Vincent Bonneterre, Régis De Gaudemaris, Dominique J. Bicout:
  Occupational exposome: A network-based approach for characterizing Occupational Health Problems. 545-552
• 
  Christos D. Melas, Leonidas A. Zampetakis, Anastasia Dimopoulou, Vassilis Moustakis:
  Modeling the acceptance of clinical information systems among hospital medical staff: An extended TAM model. 553-564
• 
  Fulvia Ferrazzi, Felix B. Engel, Erxi Wu, Annie P. Moseman, Isaac S. Kohane, Riccardo Bellazzi, Marco Ramoni:
  Inferring cell cycle feedback regulation from gene expression data. 565-575
• 
  Xiangming Mu, Hohyon Ryu, Kun Lu:
  Supporting effective health and biomedical information retrieval and navigation: A novel facet view interface evaluation. 576-586
• 
  Lawrence D. Fu, Yindalon Aphinyanaphongs, Lily Wang, Constantin F. Aliferis:
  A comparison of evaluation metrics for biomedical journals, articles, and websites in terms of sensitivity to topic. 587-594
• 
  Ickwon Choi, Brian J. Wells, Changhong Yu, Michael W. Kattan:
  An empirical approach to model selection through validation for censored survival data. 595-606
• 
  Chia-Hung Wei, Yue Li, Pai Jung Huang:
  Mammogram retrieval through machine learning within BI-RADS standards. 607-614
• 
  Maria C. Albertini, Fabiola Olivieri, Raffaella Lazzarini, Francesca Pilolli, Francesco Galli, Giorgio Spada, Augusto Accorsi, Maria R. Rippo, Antonio D. Procopio:
  Predicting microRNA modulation in human prostate cancer using a simple String IDentifier (SID1.0). 615-620
• 
  Luca-Dan Serbanati, Fabrizio L. Ricci, Gregorio Mercurio, Andrei Vasilateanu:
  Steps towards a digital health ecosystem. 621-636
• 
  Francisco Azuaje, Huiru Zheng, Anyela Camargo, Haiying Wang:
  Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease. 637-647
• 
  Murat Sariyar, Andreas Borg, Klaus Pommerening:
  Controlling false match rates in record linkage using extreme value theory. 648-654
• 
  Paul A. Harris, Jonathan A. Swafford, Terri L. Edwards, Minhua Zhang, Shraddha S. Nigavekar, Tonya R. Yarbrough, Lynda D. Lane, Tara Helmer, Laurie A. Lebo, Gail Mayo, Daniel R. Masys, Gordon R. Bernard, Jill M. Pulley:
  StarBRITE: The Vanderbilt University Biomedical Research Integration, Translation and Education portal. 655-662
• 
  Gyemin Lee, William Finn, Clayton Scott:
  Statistical file matching of flow cytometry data. 663-676
• 
  Salvador Tortajada, Elies Fuster-García, Javier Vicente, Pieter Wesseling, Franklyn A. Howe, Margarida Julià-Sapé, Ana-Paula Candiota, Daniel Monleón, Àngel Moreno-Torres, Jesús Pujol, John R. Griffiths, Alan Wright, Andrew Peet, M. Carmen Martínez-Bisbal, Bernardo Celda, Carles Arús, Montserrat Robles, Juan Miguel García-Gómez:
  Incremental Gaussian Discriminant Analysis based on Graybill and Deal weighted combination of estimators for brain tumour diagnosis. 677-687
• 
  Joshua Feblowitz, Adam Wright, Hardeep Singh, Lipika Samal, Dean F. Sittig:
  Summarization of clinical information: A conceptual model. 688-699

Commentaries

• 
  Reza Khajouei, Leila Ahmadian, Monique W. M. Jaspers:
  Methodological concerns in usability evaluation of software prototypes. 700-701
• 
  Adem Karahoca, Dilek Karahoca, Erkan Bayraktar, Ekrem Tatoglu:
  Response to "Commentary: 'Methodological concerns in usability evaluation of software prototypes' by Khajouei et al.". 702-703

Methodological Review

• 
  Sarah A. Collins, Daniel M. Stein, David K. Vawdrey, Peter D. Stetson, Suzanne Bakken:
  Content overlap in nurse and physician handoff artifacts and the potential role of electronic health records: A systematic review. 704-712

Volume 44, Number 5, October 2011

• 
  Kenneth J. Turner, Alex Gillespie, Lynne J. McMichael:
  Rigorous development of prompting dialogues. 713-727
• 
  Brian E. Chapman, Sean Lee, Hyunseok Peter Kang, Wendy Webber Chapman:
  Document-level classification of CT pulmonary angiography reports based on an extension of the ConText algorithm. 728-737
• 
  Laila Cure, José Zayas-Castro, Peter J. Fabri:
  Clustering-based methodology for analyzing near-miss reports and identifying risks in healthcare delivery. 738-748
• 
  David Sánchez, Montserrat Batet:
  Semantic similarity estimation in the biomedical domain: An ontology-based information-theoretic perspective. 749-759
• 
  Arnaud Sallaberry, Nicolas Pecheur, Sandra Bringay, Mathieu Roche, Maguelonne Teisseire:
  Sequential patterns mining and gene sequence visualization to discover novelty from microarray data. 760-774
• 
  Ray L. Somorjai, Brion Dolenko, Aleksander E. Nikulin, W. Roberson, N. Thiessen:
  Class proximity measures - Dissimilarity-based classification and display of high-dimensional data. 775-788
• 
  Isabel Segura-Bedmar, Paloma Martínez, César de Pablo-Sánchez:
  Using a shallow linguistic kernel for drug-drug interaction extraction. 789-804
• 
  Jung-Wei Fan, Carol Friedman:
  Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies. 805-814
• 
  Maciej A. Mazurowski, Joseph Y. Lo, Brian P. Harrawood, Georgia D. Tourassi:
  Mutual information-based template matching scheme for detection of breast masses: From mammography to digital breast tomosynthesis. 815-823
• 
  Cao D. Nguyen, Katheleen J. Gardiner, Krzysztof J. Cios:
  Protein annotation from protein interaction networks and Gene Ontology. 824-829
• 
  Han Zhang, Marcelo Fiszman, Dongwook Shin, Christopher M. Miller, Graciela Rosemblat, Thomas C. Rindflesch:
  Degree centrality for semantic abstraction summarization of therapeutic studies. 830-838
• 
  Harsh Dweep, Carsten Sticht, Priyanka Pandey, Norbert Gretz:
  miRWalk - Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes. 839-847
• 
  Daehyun Kim, Balaji Polepalli Ramesh, Hong Yu:
  Automatic figure classification in bioscience literature. 848-858
• 
  Di Zhao, Chunhua Weng:
  Combining PubMed knowledge and EHR data to develop a weighted bayesian network for pancreatic cancer prediction. 859-868
• 
  Catalina Martínez-Costa, Marcos Menárguez Tortosa, Jesualdo Tomás Fernández-Breis:
  Clinical data interoperability based on archetype transformation. 869-880
• 
  Bader Aljaber, David Martínez, Nicola Stokes, James Bailey:
  Improving MeSH classification of biomedical articles using citation contexts. 881-896

Methodological Reviews

• 
  Heather A. Taylor, Dori Sullivan, Cydney Mullen, Constance M. Johnson:
  Implementation of a user-centered framework in the development of a web-based health information database and call center. 897-908
• 
  Karen Marie Lyng, Birgitte Seierøe Pedersen:
  Participatory design for computerization of clinical practice guidelines. 909-918

Volume 44, Number 6, December 2011

• 
  Theodosios Theodosiou, Ioannis S. Vizirianakis, Lefteris Angelis, Athanasios Tsaftaris, Nikos Darzentas:
  MeSHy: Mining unanticipated PubMed information using frequencies of occurrences and concurrences of MeSH terms. 919-926
• 
  Zhihui Luo, Meliha Yetisgen-Yildiz, Chunhua Weng:
  Dynamic categorization of clinical research eligibility criteria by hierarchical clustering. 927-935
• 
  Cyril Dalmasso, Philippe Broët:
  Detection of chromosomal abnormalities using high resolution arrays in clinical cancer research. 936-942
• 
  Thomas George Kannampallil, Guido F. Schauer, Trevor Cohen, Vimla L. Patel:
  Considering complexity in healthcare systems. 943-947
• 
  Reza Khajouei, Linda W. P. Peute, Arie Hasman, Monique W. M. Jaspers:
  Classification and prioritization of usability problems using an augmented classification scheme. 948-957
• 
  Jeremiah Scholl, Syed Abdul Shabbir, Luai Awad Ahmed:
  A case study of an EMR system at a large hospital in India: Challenges and strategies for successful adoption. 958-967
• 
  Andreas Holzinger, Primoz Kosec, Gerold Schwantzer, Matjaz Debevc, Rainer Hofmann-Wellenhof, Julia Frühauf:
  Design and development of a mobile computer application to reengineer workflows in the hospital and the methodology to evaluate its effectiveness. 968-977
• 
  Blaine Reeder, Anne M. Turner:
  Scenario-based design: A method for connecting information system design with public health operations and emergency management. 978-988
• 
  Adrian Benton, Lyle H. Ungar, Shawndra Hill, Sean Hennessy, Jun Mao, Annie Chung, Charles E. Leonard, John H. Holmes:
  Identifying potential adverse effects using the web: A new approach to medical hypothesis generation. 989-996
• 
  Giuseppe Milani, Corrado Masciullo, Cinzia Sala, Riccardo Bellazzi, Iwan Buetti, Giorgio Pistis, Michela Traglia, Daniela Toniolo, Cristiana Larizza:
  Computer-based genealogy reconstruction in founder populations. 997-1003
• 
  Hai Hu, Mick Correll, Leonid Kvecher, Michelle Osmond, Jim Clark, Anthony Bekhash, Gwendolyn Schwab, De Gao, Jun Gao, Vladimir Kubatin, Craig D. Shriver, Jeffrey Hooke, G. Larry Maxwell, Albert J. Kovatich, Jonathan G. Sheldon, Michael N. Liebman, Richard J. Mural:
  DW4TR: A Data Warehouse for Translational Research. 1004-1019
• 
  José Antonio Miñarro-Giménez, Mikel Egaña Aranguren, Rodrigo Martínez-Béjar, Jesualdo Tomás Fernández-Breis, Marisa Madrid:
  Semantic integration of information about orthologs and diseases: The OGO system. 1020-1031
• 
  Feifan Liu, Lamont D. Antieau, Hong Yu:
  Toward automated consumer question answering: Automatically separating consumer questions from professional questions in the healthcare domain. 1032-1038
• 
  Marco Stuit, Hans Wortmann, Nick B. Szirbik, Jan Roodenburg:
  Multi-View Interaction Modelling of human collaboration processes: A business process study of head and neck cancer care in a Dutch academic hospital. 1039-1055
• 
  Jiajie Zhang, Muhammad F. Walji:
  TURF: Toward a unified framework of EHR usability. 1056-1067
• 
  Hua Xu, Samir AbdelRahman, Yanxin Lu, Joshua C. Denny, Son Doan:
  Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences. 1068-1075
• 
  Hoon Jin, Han-Chul Lee, Sung Sup Park, Yong-Su Jeong, Seon-Young Kim:
  Serum cancer biomarker discovery through analysis of gene expression data sets across multiple tumor and normal tissues. 1076-1085
• 
  Yijia Zhang, Hongfei Lin, Zhihao Yang, Yanpeng Li:
  Neighborhood hash graph kernel for protein-protein interaction extraction. 1086-1092
• 
  Jian Xing, Howard S. Burkom, Jerome I. Tokars:
  Method selection and adaptation for distributed monitoring of infectious diseases for syndromic surveillance. 1093-1101

Methodological Reviews

• 
  Samantha Kleinberg, George Hripcsak:
  A review of causal inference for biomedical informatics. 1102-1112
• 
  Jiaping Zheng, Wendy Webber Chapman, Rebecca S. Crowley, Guergana K. Savova:
  Coreference resolution: A review of general methodologies and applications in the clinical domain. 1113-1122

Volume 44, Number Supplement-1, December 2011

AMIA Joint Summits on Translational Science - 2011

• 
  Indra Neil Sarkar, Philip R. O. Payne:
  The joint summits on translational science: Crossing the translational chasm. S1-S2

Summit on Translational Bioinformatics (TBI)

• 
  Indra Neil Sarkar:
  Selected Papers from the 2011 Summit on Translational Bioinformatics. S3-S4
• 
  Terrence F. Meehan, Christopher J. Carr, Jeremy J. Jay, Carol J. Bult, Elissa J. Chesler, Judith A. Blake:
  Autism candidate genes via mouse phenomics. S5-S11
• 
  Mickaël Fabrègue, Sandra Bringay, Pascal Poncelet, Maguelonne Teisseire, Beatrice Orsetti:
  Mining microarray data to predict the histological grade of a breast cancer. S12-S16
• 
  Philip Ganchev, David Malehorn, William L. Bigbee, Vanathi Gopalakrishnan:
  Transfer learning of classification rules for biomarker discovery and verification from molecular profiling studies. S17-S23
• 
  Suresh K. Bhavnani, Sundar Victor, William J. Calhoun, William W. Busse, Eugene Bleecker, Mario Castro, Hyunsu Ju, Regina Pillai, Numan Oezguen, Gowtham Bellala, Allan R. Brasier:
  How cytokines co-occur across asthma patients: From bipartite network analysis to a molecular-based classification. S24-S30
• 
  Paea LePendu, Mark A. Musen, Nigam H. Shah:
  Enabling enrichment analysis with the Human Disease Ontology. S31-S38
• 
  David Ruau, Michael Mbagwu, Joel T. Dudley, Vijay Krishnan, Atul J. Butte:
  Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. S39-S43
• 
  Matthew Scotch, Indra Neil Sarkar, Changjiang Mei, Robert Leaman, Kei-Hoi Cheung, Pierina Ortiz, Ashutosh Singraur, Graciela Gonzalez:
  Enhancing phylogeography by improving geographical information from GenBank. S44-S47
• 
  Van Anh Tran, Nathan Johnson, Susan Redline, Guo-Qiang Zhang:
  OnWARD: Ontology-driven web-based framework for multi-center clinical studies. S48-S53

Summit on Clinical Research Informatics (CRI)

• 
  Philip R. O. Payne, Peter J. Embí, Michael G. Kahn:
  Selected Papers from the 2011 Summit on Clinical Research Informatics. S54-S55
• 
  Tara Borlawsky, Omkar Lele, Philip R. O. Payne:
  Research-IQ: Development and evaluation of an ontology-anchored integrative query tool. S56-S62
• 
  Sasikiran Kandula, Qing Zeng-Treitler, Lingji Chen, William L. Salomon, Bruce E. Bray:
  A bootstrapping algorithm to improve cohort identification using structured data. S63-S68
• 
  Risa B. Myers, Jorge R. Herskovic:
  Probabilistic techniques for obtaining accurate patient counts in Clinical Data Warehouses. S69-S77
• 
  Guoqian Jiang, Harold R. Solbrig, Christopher G. Chute:
  Quality evaluation of cancer study Common Data Elements using the UMLS Semantic Network. S78-S85
• 
  Stephen Luther, Donald J. Berndt, Dezon Finch, Matthew Richardson, Edward Hickling, David Hickam:
  Using statistical text mining to supplement the development of an ontology. S86-S93
• 
  Abdennaji El Fadly, Bastien Rance, Noël Lucas, Charles N. Mead, Gilles Chatellier, Pierre-Yves Lastic, Marie-Christine Jaulent, Christel Daniel:
  Integrating clinical research with the Healthcare Enterprise: From the RE-USE project to the EHR4CR platform. S94-S102
• 
  Joshua D. Franklin, Alicia F. Guidry, James F. Brinkley:
  A partnership approach for Electronic Data Capture in small-scale clinical trials. S103-S108