Table of Contents

• Using MapReduce for Large-Scale Medical Image AnalysisDimitrios Markonis, Roger Schaer, Ivan Eggel, Henning Müller, Adrien Depeursinge. 1 [doi]
• Preparing Electronic Health Records Data for Comparative Effectiveness StudiesMichael G. Kahn, Lisa M. Schilling, Bethany M. Kwan, Aidan Bunting, Chris Uhrich, Colleen Singleton. 2 [doi]
• Dynamic Task Optimization in Remote Diabetes Monitoring SystemsMyung-kyung Suh, Jonathan Woodbridge, Tannaz Moin, Mars Lan, Nabil Alshurafa, Lauren Samy, Bobak Mortazavi, Hassan Ghasemzadeh, Alex A. T. Bui, Sheila Ahmadi, Majid Sarrafzadeh. 3-11 [doi]
• Clinical Decision Support for Colonoscopy Surveillance Using Natural Language ProcessingKavishwar Wagholikar, Sunghwan Sohn, Stephen Tze-Inn Wu, Vinod Kaggal, Sheila Buehler, Robert A. Greenes, Tsung-Teh Wu, David Larson, Hongfang Liu, Rajeev Chaudhry, Lisa Boardman. 12-21 [doi]
• Knowledge-Based Biomedical Word Sense Disambiguation: An Evaluation and Application to Clinical Document ClassificationVijay Garla, Cynthia Brandt. 22 [doi]
• Aggregated Indexing of Biomedical Time Series DataJonathan Woodbridge, Bobak Mortazavi, Majid Sarrafzadeh, Alex A. T. Bui. 23-30 [doi]
• Predicting Complications of Percutaneous Coronary Intervention Using a Novel Support Vector MethodGyemin Lee, Hitinder S. Gurm, Zeeshan Syed. 31 [doi]
• Using Natural Language Processing and the Electronic Health Record for Appendicitis Risk StratificationLouise Deléger, Holly Brodzinski, Haijun Zhai, Qi Li, Todd Lingren, Eric Kirkendall, Evaline Alessandrini, Imre Solti. 32 [doi]
• SPOT the Drug! An Unsupervised Pattern Matching Method to Extract Drug Names from Very Large Clinical CorporaAnni Coden, Daniel Gruhl, Neal Lewis, Michael A. Tanenblatt, Joe Terdiman. 33-39 [doi]
• Demographics Identification: Variable Extraction Resource (DIVER)Alexander Hsieh, Son Doan, Michael Conway, Ko-Wei Lin, Hyeoneui Kim. 40-49 [doi]
• An Interactive Image Retrieval Framework for Biomedical Articles Based on Visual Region-of- Interest (ROI) Identification and ClassificationMd. Mahmudur Rahman, Daekeun You, Matthew S. Simpson, Sameer Antani, Dina Demner-Fushman, George R. Thoma. 50 [doi]
• Ontological Approach for the Management of Informed Consent PermissionsMaría Adela Grando, Aziz A. Boxwala, Richard Schwab, Neda Alipanah. 51-60 [doi]
• A Robust Feature Selection Method for Novel Pre-microRNA Identification Using a Combination of Nucleotide-Structure TripletsPetra Stepanowsky, Jihoon Kim, Lucila Ohno-Machado. 61 [doi]
• Enhancing Twitter Data Analysis with Simple Semantic Filtering: Example in Tracking Influenza-Like IllnessesSon Doan, Lucila Ohno-Machado, Nigel Collier. 62-71 [doi]
• Automatically Extracting Sentences from Medline Citations to Support Clinicians' Information NeedsSiddhartha Jonnalagadda, Guilherme Del Fiol, Richard Medlin, Charlene R. Weir, Marcelo Fiszman, Javed Mostafa, Hongfang Liu. 72 [doi]
• A Comparison of Computational Approaches in the Molecular Identification of Pathogenic OrganismsDhundy Bastola, Scott McGrath, Sanjukta Bhowmick, Ishwor Thapa. 73 [doi]
• Designing Clinical Data Presentation in Electronic Dental Records Using Cognitive Task Analysis MethodsThankam Thyvalikakath, Michael P. Dziabiak, Raymond Johnson, Miguel H. Torres-Urquidy, Jonathan Yabes, Titus Schleyer. 74 [doi]
• Automated Human Embryonic Stem Cell DetectionBenjamin Xueqi Guan, Bir Bhanu, Prudence Talbot, Sabrina Lin. 75-82 [doi]
• A Network Approach for Computational Drug RepositioningJiao Li, Zhiyong Lu. 83 [doi]
• Linking Medications and Their Attributes in Clinical Notes and Clinical Trial Announcements for Information Extraction: A Sequence Labeling ApproachQi Li, Haijun Zhai, Louise Deléger, Todd Lingren, Megan Kaiser, Laura Stoutenborough, Imre Solti. 84 [doi]
• Azathioprine-Induced Comorbidity Network Reveals Patterns and Predictors of Nephrotoxicity and NeutrophiliaVishal N. Patel, David C. Kaelber. 85 [doi]
• FSCoMS: Feature Selection of Medical Images Based on Compactness Measure from ScatterplotsGabriel Humpire-Mamani, Agma Juci Machado Traina, Caetano Traina Jr.. 86-95 [doi]
• An Approach for Incorporating Context in Building Probabilistic Predictive ModelsJuan Anna Wu, William Hsu, Alex A. T. Bui. 96-105 [doi]
• Cheap, Fast, and Good Enough for the Non-biomedical Domain but is It Usable for Clinical Natural Language Processing? Evaluating Crowdsourcing for Clinical Trial Announcement Named Entity AnnotationsHaijun Zhai, Todd Lingren, Louise Deléger, Qi Li, Megan Kaiser, Laura Stoutenborough, Imre Solti. 106 [doi]
• Ontology-Guided Approach to Retrieving Disease Manifestation Images for Health Image Base ConstructionYang Chen, Xiaofeng Ren, Guoqiang Zhang, Rong Xu. 107 [doi]
• Pre-annotating Clinical Notes and Clinical Trial Announcements for Gold Standard Corpus Development: Evaluating the Impact on Annotation Speed and Potential BiasTodd Lingren, Louise Deléger, Katalin Molnár, Haijun Zhai, Jareen Meinzen-Derr, Megan Kaiser, Laura Stoutenborough, Qi Li, Imre Solti. 108 [doi]
• Small RNA Sequencing in microRNA ResearchHsei-Wei Wang. 109 [doi]
• OntoVIP: An Ontology for the Annotation of Object Models Used for Medical Image SimulationBernard Gibaud, Germain Forestier, Hugues Benoit-Cattin, Frederic Cervenansky, Patrick Clarysse, Denis Friboulet, Alban Gaignard, Patrick Hugonnard, Carole Lartizien, Hervé Liebgott, Johan Montagnat, Joachim Tabary, Tristan Glatard. 110 [doi]
• Building an Ontology of Phenotypes for Existing GWAS StudiesNeda Alipanah, Hyeoneui Kim, Lucila Ohno-Machado. 111 [doi]
• Text Mining for Personal Health Information on TwitterMarina Sokolova, Yasser Jafer, David Schramm. 112 [doi]
• AltAnalyze - An Optimized Platform for RNA-Seq Splicing and Domain-Level AnalysesNathan Salomonis. 113 [doi]
• LineageProfiler: Automated Classification and Visualization of Cell Type Identity for Mammalian TranscriptomesNathan Salomonis. 114 [doi]
• Automatic Detection of Coronary Vessels Using Mutli-scale Texture DictionariesAli Zifan, Brian E. Chapman. 115 [doi]
• Simultaneous Segmentation of Cell and Nucleus in Schizosaccharomyces pombe Images with Focus GradientJyh-Ying Peng, Yen-Jen Chen, Marc D. Green, Susan L. Forsburg, Chun-Nan Hsu. 116 [doi]
• Cohort Selection through Content-Based Image Retrieval: vfM A Case StudyMayank Agarwal, Javed Mostafa. 117 [doi]
• Systematic Analysis of Cross-Institutional Medication Description Patterns in Clinical NotesSunghwan Sohn, Sean P. Murphy, Siddhartha Jonnalagadda, Kavishwar Wagholikar, Stephen Tze-Inn Wu, Christopher G. Chute, Hongfang Liu, Scott Halgrim. 118 [doi]
• Integrating Transcriptome and Proteome Information for the Analysis of Alternative SplicingJose Eduardo Kroll, Jorge Estefano de Souza, Beatriz Stransky, Gustavo A. de Souza, Sandro J. de Souza. 119 [doi]
• MAAMD: A Workflow to Standardize Meta-Analyses of Affymetrix Microarray DataZhuohui Gan, Jianwu Wang, Nathan Salomonis, Ilkay Altintas, Andrew D. McCulloch, Alexander C. Zambon. 120 [doi]
• Pulmonary Blood Vessels and Nodules Segmentation via Vessel Energy Function and Radius-Variable Sphere ModelQingxiang Zhu, Hongkai Xiong, Xiaoqian Jiang. 121 [doi]
• InSilico-ChIP: A Coregulation and Evolutionary Conservation Based Transcription Factor and Target Gene PredictorMatthew Munoz, Alexander C. Zambon. 122 [doi]
• Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP)Ko-Wei Lin, Melissa Tharp, Michael Conway, Mindy Ross, Alexander Hsieh, Hyeoneui Kim. 123 [doi]
• Early Prediction of Potentially Preventable Events in Ambulatory Care Sensitive Admissions from Clinical DataPrasanna Kumar Desikan, Nisheeth Srivastava, Tamara Winden, Tammie Lindquist, Heather Britt, Jaideep Srivastava. 124 [doi]
• Comparison of Association Rule Mining and Crowdsourcing for Automated Generation of a Problem-Medication Knowledge BaseAllison B. McCoy, Dean F. Sittig, Adam Wright. 125 [doi]
• A Study on Studies: Exploring the Metadata Associated with dbGaP StudiesKaren Truong, Mike Conway. 126 [doi]
• Identifying Provider Counseling Practices Using Natural Language Processing: Gout ExampleOlga Patterson, Gail S. Kerr, J. Steuart Richards, Carl A. Nunziato, David D. Maron, Richard L. Amdur, Scott L. DuVall. 127 [doi]
• Privacy-Preserving Biometric System for Secure Fingerprint AuthenticationShuang Wang, Xiaoqian Jiang, Lucila Ohno-Machado, Lijuan Cui, Samuel Cheng, Hongkai Xiong. 128 [doi]
• Doubly Penalized LASSO for Reconstruction of Biological NetworksBehrang Asadi, Daniel M. Tartakovsky, Mano Ram Maurya, Shankar Subramaniam. 129 [doi]
• SecUre Privacy-presERving Medical Image CompRessiOn (SUPERMICRO)Shuang Wang, Xiaoqian Jiang, Lucila Ohno-Machado, Lijuan Cui, Samuel Cheng. 130 [doi]
• Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests DataMei Liu, Michael E. Matheny, Yonghui Wu, Eugenia R. McPeek Hinz, Joshua C. Denny, Jonathan S. Schildcrout, Randolph A. Miller, Hua Xu. 131 [doi]
• Temporal Relation Extraction from Medical Discharge SummariesEmily Silgard, Melissa Tharp, Rutu Mulkar-Mehta. 132 [doi]
• A Semantic-Web Oriented Representation of Clinical Element Model for Secondary Use of Electronic Healthcare DataCui Tao, Guoqian Jiang, Thomas A. Oniki, Robert R. Freimuth, Jyotishman Pathak, Qian Zhu, Deepak K. Sharma, Stanley M. Huff, Christopher G. Chute. 133 [doi]
• Removing Mixture Noise from Medical Images Using Block Matching Filtering and Low-Rank Matrix CompletionNafise Barzigar, Aminmohammad Roozgard, Pramode K. Verma, Samuel Cheng. 134 [doi]
• The Frequency of ConText Lexical Items in Diverse Medical TextsBrian E. Chapman, Wei Wei, Wendy Webber Chapman. 135 [doi]
• Does Domain Knowledge Matter for Assertion Annotation in Clinical Texts?Danielle Mowery, Pamela W. Jordan, Janyce Wiebe, Wendy Webber Chapman, Lin Liu. 136 [doi]
• Modelling the Effects of Genetic Changes in Tumour ProgressionVanderson Silva, Fabiana S. Santana, Beatriz Stransky, Sandro J. de Souza. 137 [doi]
• A Randomized Response Model for Privacy-Preserving Data DisseminationXiaoqian Jiang, Shuang Wang, Zhanglong Ji, Lucila Ohno-Machado, Li Xiong. 138 [doi]
• Evaluation of Segmentation Algorithms in CT ScanningSeemeen Karimi, Xiaoqian Jiang, Pamela Cosman, Harry Martz. 139 [doi]
• Temporal Analysis of Physicians' EHR Workflow during Outpatient VisitsAlan Calvitti, Neal Farber, Yunan Chen, Danielle Zuest, Lin Liu, Kristin Bell, Barbara Gray, Zia Agha. 140 [doi]
• Intra-relation Reconstruction from Inter-relation: miRNA to Gene ExpressionDo Kyoon Kim, Hyunjung Shin, Je-Gun Joung, Su-Yeon Lee, Ju Han Kim. 141 [doi]
• Cloud Computing Considerations for Biomedical ApplicationsRichard Rauscher. 142 [doi]
• Privacy Protection in Sharing Personal Genome Sequencing DataXiaofeng Wang, Haixu Tang. 143 [doi]
• A Task-Based Approach for Large-Scale Evaluation of the Gene OntologySalvatore Loguercio, Erik L. Clarke, Benjamin M. Good, Andrew I. Su. 144 [doi]
• genegames.org: High-Throughput Access to Biological Knowledge and Reasoning through Online GamesBenjamin M. Good, Salvatore Loguercio, Max Nanis, Andrew I. Su. 145 [doi]
• University of California Research eXchange (UCReX): A Federated Cohort Discovery SystemAaron Mandel, Michael Kamerick, Douglas Berman, Lisa Dahm. 146 [doi]
• Annio: A Web-Based Tool for Annotating Medical Images with OntologiesBrian E. Chapman, Mona Wong, Claudiu Farcas, Patrick Reynolds. 147 [doi]
• Improving Online Access to Drug-Related InformationJiao Li, Ritu Khare, Zhiyong Lu. 148 [doi]
• A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language ProcessingEugenia R. McPeek Hinz, Lisa Bastarache, Joshua C. Denny. 149 [doi]
• Mining Adverse Drug Side-Effects from Online Medical ForumsHariprasad Sampathkumar, Bo Luo, Xue-wen Chen. 150 [doi]