Journal: Journal of Biomedical Informatics

Volume 46, Issue 6

0 -- 0Jennifer D'Souza, Vincent Ng. Classifying temporal relations in clinical data: A hybrid, knowledge-rich approach
0 -- 0Azadeh Nikfarjam, Ehsan Emadzadeh, Graciela Gonzalez. Towards generating a patient's timeline: Extracting temporal relationships from clinical notes
0 -- 0Prateek Jindal, Dan Roth. Extraction of events and temporal expressions from clinical narratives
0 -- 0Weiyi Sun, Anna Rumshisky, Özlem Uzuner. Annotating temporal information in clinical narratives
0 -- 0Yung-Chun Chang, Hong-Jie Dai, Johnny Chi-Yang Wu, Jian-Ming Chen, Richard Tzong-Han Tsai, Wen-Lian Hsu. TEMPTING system: A hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries
0 -- 0Özlem Uzuner, Amber Stubbs, Weiyi Sun. Chronology of your health events: Approaches to extracting temporal relations from medical narratives
0 -- 0Yu-Kai Lin, Hsinchun Chen, Randall A. Brown. MedTime: A temporal information extraction system for clinical narratives
0 -- 0Yao Cheng, Peter Anick, Pengyu Hong, Nianwen Xue. Temporal relation discovery between events and temporal expressions identified in clinical narrative
955 -- 956Alejandro Rodríguez González, Miguel Angel Mayer, Jesualdo Tomás Fernández-Breis. Biomedical information through the implementation of social media environments
957 -- 969Mark Merolli, Kathleen Gray, Fernando Martín-Sánchez. Health outcomes and related effects of using social media in chronic disease management: A literature review and analysis of affordances
970 -- 976Jacob B. Weiss, Eta S. Berner, Kevin B. Johnson, Dario A. Giuse, Barbara A. Murphy, Nancy M. Lorenzi. Recommendations for the design, implementation and evaluation of social support in online communities, networks, and groups
977 -- 984Alicia Martinez-Garcia, Alberto Moreno-Conde, Francisco Jódar-Sánchez, Sandra Leal, Carlos Parra. Sharing clinical decisions for multimorbidity case management using social network and open-source tools
985 -- 997Delroy Cameron, Gary A. Smith, Raminta Daniulaityte, Amit P. Sheth, Drashti Dave, Lu Chen, Gaurish Anand, Robert Carlson, Kera Z. Watkins, Russel Falck. PREDOSE: A semantic web platform for drug abuse epidemiology using social media
998 -- 1005Jina Huh, Meliha Yetisgen-Yildiz, Wanda Pratt. Text classification for assisting moderators in online health communities
1006 -- 1029Laia Subirats, Luigi Ceccaroni, Raquel Lopez-Blazquez, Felip Miralles, Alejandro García-Rudolph, José María Tormos. Circles of Health: Towards an advanced social network about disabilities of neurological origin
1030 -- 1043Dorota Formanowicz, Adam Kozak, Tomasz Glowacki, Marcin Radom, Piotr Formanowicz. Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets
1044 -- 1059Christopher E. Gillies, Mohammad-Reza Siadat, Nilesh V. Patel, George D. Wilson. A simulation to analyze feature selection methods utilizing gene ontology for gene expression classification
1060 -- 1067Riccardo Miotto, Silis Jiang, Chunhua Weng. eTACTS: A method for dynamically filtering clinical trial search results
1068 -- 1079Rasmus Rasmussen, André Kushniruk. Digital video analysis of health professionals' interactions with an electronic whiteboard: A longitudinal, naturalistic study of changes to user interactions
1080 -- 1087William Brown III, Po-Yin Yen, Marlene Rojas, Rebecca Schnall. Assessment of the Health IT Usability Evaluation Model (Health-ITUEM) for evaluating mobile health (mHealth) technology
1088 -- 1098Shaodian Zhang, Noemie Elhadad. Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts
1099 -- 1107Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu, Charles Sneiderman, Thomas C. Rindflesch. A methodology for extending domain coverage in SemRep
1108 -- 1115Pedro Lopes, José Luís Oliveira. An innovative portal for rare genetic diseases research: The semantic Diseasecard
1116 -- 1124Bridget T. McInnes, Ted Pedersen. Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text
1125 -- 1135Hamed Valizadegan, Quang Nguyen, Milos Hauskrecht. Learning classification models from multiple experts
1136 -- 1144Oladimeji Farri, Karen A. Monsen, Serguei V. S. Pakhomov, David S. Pieczkiewicz, Stuart M. Speedie, Genevieve B. Melton. Effects of time constraints on clinician-computer interaction: A study on information synthesis from EHR clinical notes
1145 -- 1151Riccardo Miotto, Chunhua Weng. Unsupervised mining of frequent tags for clinical eligibility text indexing

Volume 46, Issue 5

765 -- 773Carol Friedman, Thomas C. Rindflesch, Milton Corn. Natural language processing: State of the art and prospects for significant progress, a workshop sponsored by the National Library of Medicine
774 -- 781Aisling O'Driscoll, Jurate Daugelaite, Roy D. Sleator. 'Big data', Hadoop and cloud computing in genomics
782 -- 783Kenneth W. Goodman. Handbook of Analytic Philosophy of Medicine Series: Philosophy and Medicine, Vol 113. Kazem Sadegh-Zadeh (2012). XXXII, 1133 pp
784 -- 794Ali Anil Sinaci, Gokce Banu Laleci Erturkmen. A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains
795 -- 804Brent I. Fox, Joshua C. Hollingsworth, Michael D. Gray, Michael L. Hollingsworth, Juan Gao, Richard A. Hansen. Developing an expert panel process to refine health outcome definitions in observational data
805 -- 813Sanmitra Bhattacharya, Michael N. Cantor. Analysis of eligibility criteria representation in industry-standard clinical trial protocols
814 -- 821Kevin B. Johnson, Yun-Xian Ho, S. Andrew Spooner, Marvin Palmer, Stuart T. Weinberg. Assessing the reliability of an automated dose-rounding algorithm
822 -- 829Germain Forestier, Florent Lalys, Laurent Riffaud, D. Louis Collins, Jürgen Meixensberger, Shafik N. Wassef, Thomas Neumuth, Benoît Goulet, Pierre Jannin. Multi-site study of surgical practice in neurosurgery based on surgical process models
830 -- 836Nicole Gray Weiskopf, George Hripcsak, Sushmita Swaminathan, Chunhua Weng. Defining and measuring completeness of electronic health records for secondary use
837 -- 848Michael J. Rothman, Steven I. Rothman, Joseph Beals IV. Development and validation of a continuous measure of patient condition using the Electronic Medical Record
849 -- 856Prashanti Manda, Fiona M. McCarthy, Susan M. Bridges. Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO relationships
857 -- 868Thusitha De Silva Mabotuwana, Michael C. Lee, Eric Cohen-Solal. An ontology-based similarity measure for biomedical data - Application to radiology reports
869 -- 875Vijay Garla, Caroline Taylor, Cynthia Brandt. Semi-supervised clinical text classification with Laplacian SVMs: An application to cancer case management
876 -- 881Francesca Vitali, Francesca Mulas, Pietro Marini, Riccardo Bellazzi. Network-based target ranking for polypharmacological therapies
882 -- 893Cui Tao, Dezhao Song, Deepak K. Sharma, Christopher G. Chute. Semantator: Semantic annotator for converting biomedical text to linked data
894 -- 904Patrizia F. Stifanelli, Teresa Maria Creanza, Roberto Anglani, Vania C. Liuzzi, Sayan Mukherjee, Francesco P. Schena, Nicola Ancona. A comparative study of covariance selection models for the inference of gene regulatory networks
905 -- 913Barbara Sheehan, Lise E. Nigrovic, Peter S. Dayan, Nathan Kuppermann, Dustin W. Ballard, Evaline Alessandrini, Lalit Bajaj, Howard Goldberg, Jeffrey Hoffman, Steven R. Offerman, Dustin G. Mark, Marguerite Swietlik, Eric Tham, Leah Tzimenatos, David R. Vinson, Grant S. Jones, Suzanne Bakken. Informing the design of clinical decision support services for evaluation of children with minor blunt head trauma in the emergency department: A sociotechnical analysis
914 -- 920María Herrero-Zazo, Isabel Segura-Bedmar, Paloma Martínez, Thierry Declerck. The DDI corpus: An annotated corpus with pharmacological substances and drug-drug interactions
921 -- 928Jörn Lötsch, Alfred Ultsch. A machine-learned knowledge discovery method for associating complex phenotypes with complex genotypes. Application to pain
929 -- 939Myungjae Kwak, Gondy Leroy, Jesse D. Martinez, Jeffrey Harwell. Development and evaluation of a biomedical search engine using a predicate-based vector space model
940 -- 946Ke-Chun Huang, I-Jen Chiang, Furen Xiao, Chun-Chih Liao, Charles Chih-Ho Liu, Jau-Min Wong. PICO element detection in medical text without metadata: Are first sentences enough?
947 -- 954Jonathan Joe, George Demiris. Older adults and mobile phones for health: A review

Volume 46, Issue 4

575 -- 584Anne M. Turner, Blaine Reeder, Judith Ramey. Scenarios, personas and user stories: User-centered evidence-based design representations of communicable disease investigations
585 -- 593Rong Xu, QuanQiu Wang. A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine
594 -- 601Zhiyi Mao, Wensheng Cai, Xueguang Shao. Selecting significant genes by randomization test for cancer classification using gene expression data
602 -- 614Vivekanand Sharma, Indra Neil Sarkar. Leveraging concept-based approaches to identify potential phyto-therapies
615 -- 625Kate Button, Robert W. van Deursen, Larisa N. Soldatova, Irena Spasic. TRAK ontology: Defining standard care for the rehabilitation of knee conditions
626 -- 641Martin Schmettow, Wendy Vos, Jan Maarten Schraagen. With how many users should you test a medical infusion pump? Sampling strategies for usability tests on high-risk systems
642 -- 652Chunhua Weng, Yu Li, Solomon Berhe, Mary Regina Boland, Junfeng Gao, Gregory William Hruby, Richard C. Steinman, Carlos Lopez-Jimenez, Linda Busacca, George Hripcsak, Suzanne Bakken, J. Thomas Bigger. An Integrated Model for Patient Care and Clinical Trials (IMPACT) to support clinical research visit scheduling workflow for future learning health systems
653 -- 664Óscar Jesús Rubio Martí, Alvaro Alesanco, José García. Secure information embedding into 1D biomedical signals based on SPIHT
665 -- 675Todd R. Johnson, Eliz Markowitz, Elmer V. Bernstam, Jorge R. Herskovic, Harold Thimbleby. SYFSA: A framework for Systematic Yet Flexible Systems Analysis
676 -- 689Mar Marcos, José Alberto Maldonado, Begoña Martínez-Salvador, Diego Boscá, Montserrat Robles. Interoperability of clinical decision-support systems and electronic health records using archetypes: A case study in clinical trial eligibility
690 -- 696Qian Zhu, Robert R. Freimuth, Jyotishman Pathak, Matthew J. Durski, Christopher G. Chute. Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL
697 -- 709Arief Gusnanto, Alexander Ploner, Farag Shuweihdi, Yudi Pawitan. Partial least squares and logistic regression random-effects estimates for gene selection in supervised classification of gene expression data
710 -- 720Pablo Gay, Beatriz López, Albert Pla, Jordi Saperas, Carles Pous. Enabling the use of hereditary information from pedigree tools in medical knowledge-based systems
721 -- 733Joseph Cooley, Sean Smith. Privacy-preserving screen capture: Towards closing the loop for health IT usability
734 -- 743Mike Conway, John N. Dowling, Wendy Webber Chapman. Using chief complaints for syndromic surveillance: A review of chief complaint based classifiers in North America
744 -- 763Mor Peleg. Computer-interpretable clinical guidelines: A methodological review

Volume 46, Issue 3

379 -- 387David Riaño 0001, John A. Bohada, Antoni Collado, Joan Albert López-Vallverdú. MPM: A knowledge-based functional model of medical practice
388 -- 400José Luis Iglesias Allones, Maria Taboada, D. Martinez, R. Lozano, María Jesús Sobrido. SNOMED CT module-driven clinical archetype management
401 -- 409Jörn Kretschmer, Christoph Schranz, Christian Knöbel, J. Wingender, E. Koch, Knut Möller. Efficient computation of interacting model systems
410 -- 424Andrew R. Post, Tahsin M. Kurç, Sharath R. Cholleti, Jingjing Gao, Xia Lin, William Bornstein, Dedra Cantrell, David Levine, Sam Hohmann, Joel H. Saltz. The Analytic Information Warehouse (AIW): A platform for analytics using electronic health record data
425 -- 435Andrea Esuli, Diego Marcheggiani, Fabrizio Sebastiani 0001. An enhanced CRFs-based system for information extraction from radiology reports
436 -- 443Samah Jamal Fodeh, Cynthia Brandt, Thaibinh Luong, Ali Haddad, Martin H. Schultz, Terrence Murphy, Michael Krauthammer. Complementary ensemble clustering of biomedical data
444 -- 457Ricardo Villamarín-Salomón, Gregory F. Cooper, Michael M. Wagner, Fu-Chiang Tsui, Jeremy U. Espino. A method for estimating from thermometer sales the incidence of diseases that are symptomatically similar to influenza
458 -- 469Maarten van der Heijden, Peter J. F. Lucas, Bas Lijnse, Yvonne F. Heijdra, Tjard R. J. Schermer. An autonomous mobile system for the management of COPD
470 -- 479Frank Weichert, C. Mertens, Lars Walczak, Gabriele Kern-Isberner, Mathias Wagner. A novel approach for connecting temporal-ontologies with blood flow simulations
480 -- 496Shuang Wang, Xiaoqian Jiang, Yuan Wu, Lijuan Cui, Samuel Cheng, Lucila Ohno-Machado. EXpectation Propagation LOgistic REgRession (EXPLORER): Distributed privacy-preserving online model learning
497 -- 505Lingyun Luo, José L. V. Mejino Jr., Guo-Qiang Zhang. An analysis of FMA using structural self-bisimilarity
506 -- 515Md. Faisal Mahbub Chowdhury, Pierre Zweigenbaum. A controlled greedy supervised approach for co-reference resolution on clinical text
516 -- 529Nelia Lasierra, Alvaro Alesanco, S. Guillén, J. García. A three stage ontology-driven solution to provide personalized care to chronic patients at home
530 -- 540Kornel Skalkowski, Krzysztof Zielinski. Applying formalized rules for treatment procedures to data delivered by personal medical devices
541 -- 562José Luis Fernández Alemán, Inmaculada Carrión Señor, Pedro Ángel Oliver Lozoya, Ambrosio Toval. Security and privacy in electronic health records: A systematic literature review
563 -- 573Dimitris Kleftogiannis, Aigli Korfiati, Konstantinos A. Theofilatos, Spiros Likothanassis, Athanasios K. Tsakalidis, Seferina Mavroudi. Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

Volume 46, Issue 2

200 -- 211Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen. Biomedical text mining and its applications in cancer research
212 -- 227Thomas Lippincott, Laura Rimell, Karin Verspoor, Anna Korhonen. Approaches to verb subcategorization for biomedicine
228 -- 237Laura Rimell, Thomas Lippincott, Karin Verspoor, Helen L. Johnson, Anna Korhonen. Acquisition and evaluation of verb subcategorization resources for biomedicine
238 -- 251Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit P. Sheth, Thomas C. Rindflesch. A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications
252 -- 258Xin Sun, Yanheng Liu, Da Wei, Mantao Xu, Hui-Ling Chen, Jiawei Han. Selection of interdependent genes via dynamic relevance analysis for cancer diagnosis
259 -- 265Jihad S. Obeid, Catherine A. McGraw, Brenda L. Minor, Jose G. Conde, Robert Pawluk, Michael Lin, Janey Wang, Sean R. Banks, Sheree A. Hemphill, Robert Taylor, Paul A. Harris. Procurement of shared data instruments for Research Electronic Data Capture (REDCap)
266 -- 274Yuanxi Li, Stephen Swift, Allan Tucker. Modelling and analysing the dynamics of disease progression from cross-sectional studies
275 -- 285Xiaodan Zhu, Colin Cherry, Svetlana Kiritchenko, Joel D. Martin, Berry de Bruijn. Detecting concept relations in clinical text: Insights from a state-of-the-art model
286 -- 293Qian Zhu, Robert R. Freimuth, Zonghui Lian, Scott Bauer, Jyotishman Pathak, Cui Tao, Matthew J. Durski, Christopher G. Chute. Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study
294 -- 303Sergio Martínez, David Sánchez 0001, Aïda Valls. A semantic framework to protect the privacy of electronic health records with non-numerical attributes
304 -- 317Marcos Menárguez Tortosa, Jesualdo Tomás Fernández-Breis. OWL-based reasoning methods for validating archetypes
318 -- 327Sylvie M. N. Ngouongo, Matthias Löbe, Jürgen Stausberg. The ISO/IEC 11179 norm for metadata registries: Does it cover healthcare standards in empirical research?
328 -- 340Ilhan Ilhan, Gülay Tezel. A genetic algorithm-support vector machine method with parameter optimization for selecting the tag SNPs
341 -- 353Szymon Wilk, Wojtek Michalowski, Martin Michalowski, Ken Farion, Marisela Mainegra Hing, Subhra Mohapatra. Mitigation of adverse interactions in pairs of clinical practice guidelines using constraint logic programming
354 -- 362Meliha Yetisgen-Yildiz, Martin L. Gunn, Fei Xia, Thomas H. Payne. A text processing pipeline to extract recommendations from radiology reports
363 -- 376Luca Anselma, Alessio Bottrighi, Stefania Montani, Paolo Terenziani. Managing proposals and evaluations of updates to medical knowledge: Theory and applications

Volume 46, Issue 1

1 -- 4Tudor Groza, Tania Tudorache, Michel Dumontier. State of the art and open challenges in community-driven knowledge curation
5 -- 14James Malone, Robert Stevens. Measuring the level of activity in community built bio-ontologies
15 -- 32Michael Hartung, Anika Groß, Erhard Rahm. COnto-Diff: generation of complex evolution mappings for life science ontologies
33 -- 39Zhihui Luo, Riccardo Miotto, Chunhua Weng. A human-computer collaborative approach to identifying common data elements in clinical trial eligibility criteria
40 -- 46Radhakrishnan Nagarajan, Alex T. Kalinka, William R. Hogan. Evidence of community structure in Biomedical Research Grant Collaborations
47 -- 55Milos Hauskrecht, Iyad Batal, Michal Valko, Shyam Visweswaran, Gregory F. Cooper, Gilles Clermont. Outlier detection for patient monitoring and alerting
56 -- 67Jean-Baptiste Lamy, Lina Fatima Soualmia, Gaétan Kerdelhué, Alain Venot, Catherine Duclos. Validating the semantics of a medical iconic language using ontological reasoning
68 -- 74Cosmin Adrian Bejan, Lucy Vanderwende, Fei Xia, Meliha Yetisgen-Yildiz. Assertion modeling and its role in clinical phenotype identification
75 -- 86Tânia F. G. G. Cova, Jorge Luis G. C. Pereira, Alberto A. C. C. Pais. Is standard multivariate analysis sufficient in clinical and epidemiological studies?
87 -- 96Dennis Lee, Ronald Cornet, Francis Y. Lau, Nicolette de Keizer. A survey of SNOMED CT implementations
97 -- 110James Geller, Zhe He 0001, Yehoshua Perl, C. Paul Morrey, Julia Xu. Rule-based support system for multiple UMLS semantic type assignments
111 -- 127Zhengxing Huang, Xudong Lu, Huilong Duan, Wu Fan. Summarizing clinical pathways from event logs
128 -- 138Cui Tao, Jyotishman Pathak, Harold R. Solbrig, Wei-Qi Wei, Christopher G. Chute. Terminology representation guidelines for biomedical ontologies in the semantic web notations
139 -- 141David K. Vawdrey, George Hripcsak. Publication bias in clinical trials of electronic health records
142 -- 151Óscar Jesús Rubio Martí, Alvaro Alesanco, José García. A robust and simple security extension for the medical standard SCP-ECG
152 -- 159Stefan Franke, Jürgen Meixensberger, Thomas Neumuth. Intervention time prediction from surgical low-level tasks
160 -- 173Tien Tuan Dao, Tuan Nha Hoang, Xuan Hien Ta, Marie Christine Ho Ba Tho. Knowledge-based personalized search engine for the Web-based Human Musculoskeletal System Resources (HMSR) in biomechanics
174 -- 180Lorenzo Beretta, Alessandro Santaniello. Extension of the survival dimensionality reduction algorithm to detect epistasis in competing risks models (SDR-CR)
181 -- 195Jan Maarten Schraagen, Fenne Verhoeven. Methods for studying medical device technology and practitioner cognition: The case of user-interface issues with infusion pumps