Table of Contents

• The effect of unhealthy β-cells in synchronized insulin secretionYang Pu, Saangho Lee, David C. Samuels, Layne T. Watson, Yang Cao. 1-4 [doi]
• Bridging encounter forms and electronic medical record databases: Annotation, mapping, and integrationYuan An, Ritu Khare, Xiaohua Hu, Il-Yeol Song. 1-4 [doi]
• PhylOnt: A domain-specific ontology for phylogeny analysisMaryam Panahiazar, Ajith Ranabahu, Vahid Taslimi, Hima Yalamanchili, Arlin Stoltzfus, Jim Leebens-Mack, Amit P. Sheth. 1-6 [doi]
• Linking and querying genomic datasets using natural languageBobby McKnight, Ismailcem Budak Arpinar. 1-4 [doi]
• Systematic drug repositioning: A new paradigm in drug discoveryVinod Kumar. 1 [doi]
• CWT-PLSR for quantitative analysis of Raman spectrumShuo Li, James O. Nyagilo, Digant P. Dave, Jean Gao. 1-6 [doi]
• Clinical Case: Enhancing medical monitoring with visualization and analyticsMichael Farnum, Victor S. Lobanov, Michael Brennan, Dimitris K. Agrafiotis, Jeremy Kolpak, Joseph Ciervo, Laurent Alquier. 1 [doi]
• Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesiaXia Bi, Hongzhan Huang, Sherri Matis-Mitchell, Peter B. McGarvey, Manabu Torii, Hagit Shatkay, Cathy H. Wu. 1-4 [doi]
• Combining gene expression and function in a spatially localized approachEvangelia I. Zacharaki, Angeliki Skoura, Desmond J. Smith, Scott Faro, Li An, Vasileios Megalooikonomou. 1-8 [doi]
• De-noise biological network from heterogeneous sources via link propagationNan Du, Jing Gao, Vishrawas Gopalakrishnan, Aidong Zhang. 1-6 [doi]
• A basin hopping algorithm for protein-protein dockingIrina Hashmi, Amarda Shehu. 1-4 [doi]
• Personalized semantic assistance for the curation of biochemical literatureFedor Bakalov, Marie-Jean Meurs, Birgitta König-Ries, Bahar Sateli, René Witte, Greg Butler, Adrian Tsang. 1-4 [doi]
• Finding genomic features from enriched regions in ChlP-Seq dataIman Rezaeian, Luis Rueda. 1-4 [doi]
• A novel dynamic graph-based computational model for predicting salivary gland branching morphogenesisNimit Dhulekar, Lauren Bange, Abiurami Baskaran, Daniel Yuan, Basak Oztan, Bülent Yener, Shayoni Ray, Melinda Larsen. 1-8 [doi]
• Comprehensive human membrane protein databaseMin Sung Kim, Gwan-Su Yi. 1-6 [doi]
• OWA-PSSM - A position specific scoring matrix based method integrated with OWA weights for HLA-DR peptide binding predictionWen-Jun Shen, Hau-San Wong. 1-4 [doi]
• An automated blood vessel extraction algorithm in fundus imagesMarwan D. Saleh, C. Eswaran. 1-5 [doi]
• An efficient algorithm for clustering of large-scale mass spectrometry dataFahad Saeed, Trairak Pisitkun, Mark A. Knepper, Jason D. Hoffert. 1-4 [doi]
• A neural network approach to the identification of b-/y-ions in MS/MS spectraJames P. Cleveland, John R. Rose. 1-5 [doi]
• ENISI Visual, an agent-based simulator for modeling gut immunityYongguo Mei, Raquel Hontecillas, Xiaoying Zhang, Keith R. Bisset, Stephen Eubank, Stefan Hoops, Madhav V. Marathe, Josep Bassaganya-Riera. 1-5 [doi]
• Discovering breast cancer prognostic biomarkers using a novel feature selection toolJie Cheng. 1 [doi]
• Manifold learning reveals nonlinear structure in metagenomic profilesXingpeng Jiang, Xiaohua Hu, Huiyu Shen, Tingting He. 1-6 [doi]
• Improving interacting residue prediction using long-distance information in hidden Markov modelsColin Kern, Alvaro J. González, Li Liao, K. Vijay-Shanker. 1-6 [doi]
• Systematic measurement of missmatch effect for designing inter-species microarrayMutsumi Fukuzaki, Masa-Aki Yoshida, Atsushi Ogura, Jun Sese. 1-4 [doi]
• Rotation crossover and K-site move mutation for evolutionary protein folding in 3D FCC HP model (preliminary version)Shih-Chieh Su, Jyh-Jong Tsay. 1-4 [doi]
• Combining homolog and motif similarity data with Gene Ontology relationships for protein function predictionHafeez Ur Rehman, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino, Prashanth Suravajhala. 1-4 [doi]
• Multi-instance learning for skin biopsy image features recognitionGang Zhang, Xiangyang Shu, Zhaohui Liang, Yunting Liang, Shuyi Chen, Jian Yin. 1-6 [doi]
• A Bayesian-based prediction model for personalized medical health careJiashu Zhao, Jimmy Xiangji Huang, Xiaohua Hu, C. Joseph Kurian, William Melek. 1-4 [doi]
• Drug-drug interaction analysis using heterogeneous biological information networkKyubum Lee, Sunwon Lee, Minji Jeon, Jaehoon Choi, Jaewoo Kang. 1-5 [doi]
• ForeTell: Facilitating doctor-patient conversation through interactive information visualization of risk prediction indexPratibha Bhaskaran, Milind Kaduskar, Preeti Saluja, Smitha Tallimani, Sandip Bhaumik, Sanghyun Yoo. 1-4 [doi]
• (3) The CellOrganizer project: An open source system to learn image-derived models of subcellular organization over time and spaceRobert F. Murphy. 1-2 [doi]
• Predicting viral infection by selecting informative biomarkers from temporal high-dimensional gene expression dataQiang Lou, Zoran Obradovic. 1-4 [doi]
• Aligning protein-protein interaction networks using random neural networksHang T. T. Phan, Michael J. E. Sternberg, Erol Gelenbe. 1-6 [doi]
• Epileptic EEG signal analysis and identification based on nonlinear featuresYuedong Song, Jon Crowcroft, Jiaxiang Zhang. 1-6 [doi]
• Immune system simulation: Modeling the mast cellCharles Cassio Da Silva, Alcione de Paiva Oliveira, Maurilio De Araujo Possi, Fabio Ribeiro Cerqueira, Andreia Patricia Gomes, Luiz Alberto Santana, Rodrigo Siqueira-Batista. 1-4 [doi]
• Uncertain interactions affect degree distribution of biological networksAndrei Todor, Alin Dobra, Tamer Kahveci. 1-5 [doi]
• Composition of bioinformatics model federations using communication aspectsKeith L. Lee, David Stotts. 1-5 [doi]
• Placement of unique restriction sites in synthetic genomes using multi-objective optimizationMahfuza Sharmin, M. Sohel Rahman. 1-4 [doi]
• iSimp: A sentence simplification system for biomedicail textYifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker. 1-6 [doi]
• A weighted hypergeometric statistic for the enrichment of gene setsRehman Qureshi, Ahmet Sacan. 1-6 [doi]
• An accurate scalable template-based alignment algorithmDavid P. Gardner, Weijia Xu, Daniel P. Miranker, Stuart Ozer, Jamie J. Cannone, Robin Ray Gutell. 1-7 [doi]
• Accurate detection of SNPs using base-specific cleavage and mass spectrometryRuimin Sun, Xiang Gao, Nanyu Han, Qiong Wu, Yuguang Mu, Kai Tang, Xin Chen. 1-4 [doi]
• A new method for computational drug repositioning using drug pairwise similarityJiao Li, Zhiyong Lu. 1-4 [doi]
• Predicting distant metastasis in breast cancer using ensemble classifier based on context-specific miRNA regulation modulesXionghui Zhou, Juan Liu, Jianghui Xiong. 1-6 [doi]
• In Silico Target Portal: An integrated Oncology target discovery web portalYing Li, Jyothi Venkatiahgari, Liping Jin, Donavan T. Cheng, James Cai. 1-8 [doi]
• Bio marker identification for diagnosis of schizophrenia with integrated analysis of fMRI and SNPsHongbao Cao, Dongdong Lin, Junbo Duan, Yu-Ping Wang, Vince D. Calhoun. 1-6 [doi]
• A random walk based approach for improving protein-protein interaction network and protein complex predictionChengwei Lei, Jianhua Ruan. 1-6 [doi]
• Keyword annotation of biomedicai documents with graph-based similarity methodsShuguang Wang, Milos Hauskrecht. 1-4 [doi]
• Prediction of novel systems components in cell cycle regulation in malaria parasite by subnetwork alignmentsHong Cai, Changjin Hong, Jianying Gu, Timothy G. Lilburn, Rui Kuang, Yufeng Wang. 1-6 [doi]
• A high-throughput analysis pipeline for large next generation DNA sequencing studiesZayed Albertyn, Jörg Hakenberg, Hongjin Bian, Huifeng Niu, James Cai. 1 [doi]
• Using similarity learning to improve network-based gene function predictionNgo Phuong Nhung, Tu Minh Phuong. 1-6 [doi]
• Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coliM. Fayez Aziz, Philemon Chan, Johan S. Osorio, Bushra F. Minhas, Vaisak Parekatt, Gustavo Caetano-Anollés. 1-5 [doi]
• A link prediction based unsupervised rank aggregation algorithm for informative gene selectionKang Li, Nan Du, Aidong Zhang. 1-6 [doi]
• Drug-target network in myocardial infarction: A structural analysisHaiying Wang, Huiru Zheng, Francisco Azuaje, Xing-Ming Zhao. 1-4 [doi]
• A Monte Carlo approach to biomedicai time series searchJonathan Woodbridge, Bobak Mortazavi, Majid Sarrafzadeh, Alex A. T. Bui. 1-6 [doi]
• Modeling semantic influence for biomedicai research topics using MeSH hierarchyDan He. 1-6 [doi]
• Significance analysis by minimizing false discovery rateYuanzhe Bei, Pengyu Hong. 1-6 [doi]
• The human imprintome vl.O: Over 120 imprinted genes in the human genome impose a major review on previous censusesSamara C. Silva-Santiago, Elton José R. Vasconcelos, Diana M. Oliveira, Ana Carolina L. Pacheco, Monica F. Silva, Teresa Cristina L. Rocha, Samyra M. V. Brasil. 1-5 [doi]
• Discovering distal regulatory elements by integrating multiple types of chromatin state mapsLi Teng, Kai Tan. 1-4 [doi]
• The e!DAL JAVA-API: Store, share and cite primary data in life sciencesDaniel Arend, Matthias Lange, Christian Colmsee, Steffen Flemming, Jinbo Chen, Uwe Scholz. 1-5 [doi]
• The role of Eigen-matrix translation in classification of biological datasetsHao Jiang, Wai-Ki Ching. 1-4 [doi]
• A multi-objective program for quantitative subtyping of clinically relevant phenotypesJiangwen Sun, Jinbo Bi, Henry R. Kranzler. 1-6 [doi]
• The effect of measurement approach and noise level on gene selection stabilityRandall Wald, Taghi M. Khoshgoftaar, Ahmad Abu Shanab. 1-5 [doi]
• Integrating protein networks for identifying cooperative miRNA activity in disease gene signaturesMohammed Al-Shalalfa, Reda Alhajj. 1-8 [doi]
• Improving health records search using multiple query expansion collectionsDongqing Zhu, Ben Carterette. 1-7 [doi]
• (2) Protein structure determination on demandMing Li. 1 [doi]
• Classification of multicolor fluorescence in-situ hybridization (M-FISH) image using structure based sparse representation modelJingyao Li, Dongdong Lin, Hongbao Cao, Yu-Ping Wang. 1-6 [doi]
• Formalization of clinical trial eligibility criteria: Evaluation of a pattern-based approachKrystyna Miliari, Anca I. D. Bucur, Annette ten Teije. 1-4 [doi]
• Aligning ligand binding cavities by optimizing superposed volumeRuobing Chen, Katya Scheinberg, Brian Y. Chen. 1-5 [doi]
• Pre-miRNA classification via combinatorial feature mining and boostingLing Zhong, Jason T. L. Wang, Dongrong Wen, Bruce A. Shapiro. 1-4 [doi]
• Parallel simulation of apoptotic receptor-clustering on GPGPU many-core architecturesClaus Braun, Markus Daub, Alexander Scholl, Guido Schneider, Hans-Joachim Wunderlich. 1-6 [doi]
• Efficient filtration for similarity search with spaced k-mer neighborsWeiming Li, Bin Ma, Kaizhong Zhang. 1-6 [doi]
• Estimating a gene's mutation burden by the number of observed synonymous base substitutionsPerry Evans, Michael Krauthammer. 1-6 [doi]
• Inferring Fuzzy Cognitive Map models for Gene Regulatory Networks from gene expression dataYe Chen, Lawrence J. Mazlack, Long J. Lu. 1-4 [doi]
• Integration of multiple annotators by aggregating experts and filtering novicesPing Zhang 0016, Zoran Obradovic. 1-6 [doi]
• Prediction of human immunodeficiency virus type 1 drug resistance: Representation of target sequence mutational patterns via an n-grams approachMajid Masso. 1-6 [doi]
• PPIExtractor: A protein-protein interaction Extractor for biomédical literatureZhihao Yang, Zhehuan Zhao, Yanpeng Li, Yuncui Hu, Hongfei Lin. 1-6 [doi]
• Reconstructing isoform graphs from RNA-Seq dataStefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova. 1-4 [doi]
• SiS: Significant subnetworks in massive number of network topologiesMd Mahmudul Hasan, Yusuf Kavurucu, Tamer Kahveci. 1-6 [doi]
• Network-based inferring drug-disease associations from chemical, genomic and phenotype dataYu-Fen Huang, Hsiang-Yuan Yeh, Von-Wun Soo. 1-6 [doi]
• MDAsim: A multiple displacement amplification simulatorZeinab Tagliavi, Sorin Draghici. 1-4 [doi]
• New approaches for better-informed decisionsAnastasia Christianson. 1 [doi]
• MultiFacTV: Finding modules from higher-order gene expression profiles with time dimensionXutao Li, Yunming Ye, Qingyao Wu, Michael K. Ng. 1-6 [doi]
• Identifying protein complexes based on local fitness methodJun Ren, Jianxin Wang, Min Li. 1-6 [doi]
• Recognizing drosha processing sites by a two-step prediction model with structure and sequence informationXingchi Hu, Yanhong Zhou, Chuang Ma. 1-4 [doi]
• Extracting BI-RADS features from Portuguese clinical textsHoussam Nassif, Filipe Cunha, Inês C. Moreira, Ricardo Cruz-Correia, Eliana Sousa, David Page, Elizabeth S. Burnside, Inês de Castro Dutra. 1-4 [doi]
• (1) Obstacles and options for big-data applications in biomedicine: The role of standards and normalizationsChristopher G. Chute. 1 [doi]
• Skeleton Timed Up and GoOkko Lohmann, Thomas Luhmann, Andreas Hein. 1-5 [doi]
• Efficient basin hopping in the protein energy surfaceBrian S. Olson, Amarda Shehu. 1-6 [doi]
• Fast sparse representation approaches for the classification of high-dimensional biological dataYifeng Li, Alioune Ngom. 1-6 [doi]
• Identifying essential proteins via integration of protein interaction and gene expression dataXiwei Tang, Jianxin Wang, Yi Pan. 1-4 [doi]
• Automated wound identification system based on image segmentation and Artificial Neural NetworksBo Song, Ahmet Sacan. 1-4 [doi]
• Identifying enterotype in human microbiome by decomposing probabilistic topics into componentsXingpeng Jiang, Jonathan Dushoff, Xin Chen, Xiaohua Hu. 1-4 [doi]
• Robust segmentation of biomedical figures for image-based document retrievalLuis D. Lopez, Jingyi Yu, Catalina O. Tudor, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu. 1-6 [doi]
• Title: Approach to information management in an externalized business environmentBob O'Hara. 1-2 [doi]
• Drug-induced QT prolongation prediction using co-regularized multi-view learningJintao Zhang, Jun Huan. 1-6 [doi]
• Incorporating semantic similarity into clustering process for identifying protein complexes from Affinity Purification/Mass Spectrometry dataBingjing Cai, Haiying Wang, Huiru Zheng, Hui Wang. 1-4 [doi]
• M-Finder: Functional association mining from protein interaction networks weighted by semantic similarityYoung-Rae Cho, Tak Chien Chiam, Yanxin Lu. 1-6 [doi]
• Modelling non-stationary gene regulatory process with hidden Markov Dynamic Bayesian NetworkShijiazhu, Yadong Wang. 1-4 [doi]
• A model to predict and analyze protein-protein interaction types using electrostatic energiesGokul Vasudev, Luis Rueda. 1-5 [doi]
• An adaptive feature selection method for microarray data analysisJie Cheng, Joel Greshock, Leming Shi, Jeffery Painter, Xiwu Lin, Kwan Lee, Shu Zheng, Richard Wooster, Lajos Pusztai, Alan Menius. 1-6 [doi]
• An efficient sequential pattern mining algorithm for motifs with gap constraintsVance Chiang-Chi Liao, Ming-Syan Chen. 1 [doi]
• A model of cellular decision making in photodynamic therapy of cancerIoannis Gkigkitzis, Xin-Hua Hu. 1-5 [doi]
• Not AU protein complexes exhibit dense structures in S. cerevisiae PPI networkBolin Chen, Jin-Hong Shi, Fang-Xiang Wu. 1-4 [doi]
• De novo co-assembly of bacterial genomes from multiple single cellsNarjes S. Movahedi, Elmirasadat Forouzmand, Hamidreza Chitsaz. 1-5 [doi]
• Identifying protein binding functionality of protein family sequences by Aligned Pattern clustersEn-Shiun Annie Lee, Andrew K. C. Wong. 1-6 [doi]
• A data mining approach for optimization of acute inflammation therapyVladan Radosavljevic, Kosta Ristovski, Zoran Obradovic. 1-6 [doi]
• Using gene sets to identify putative drugs for breast cancerTzu-Hung Hsiao, Hung-I Harry Chen, Yidong Chen, Yu-Heng Chen, Eric Y. Chuang. 1-4 [doi]
• Unsupervised kernel parameter estimation by constrained nonlinear optimization for clustering nonlinear biological dataHyokyeong Lee, Rahul Singh. 1-6 [doi]
• Extending the ball-histogram method with continuous distributions and an application to prediction of DNA-binding proteinsOndrej Kuzelka, Andrea Szabóová, Filip Zelezný. 1-4 [doi]
• CTGR-Span: Efficient mining of cross-timepoint gene regulation sequential patterns from microarray datasetsChun-Pei Cheng, Yi-Lin Tsai, Vincent S. Tseng. 1-4 [doi]
• Computation of biochemical pathway fluctuations beyond the linear noise approximation using iNAPhilipp Thomas, Hannes Matuschek, Ramon Grima. 1-5 [doi]
• Data driven knowledge acquisition method for domain knowledge enrichment in the healthcareSujan Perera, Cory A. Henson, Krishnaprasad Thirunarayan, Amit P. Sheth, Suhas Nair. 1-8 [doi]
• A Log-Linear Graphical Model for inferring genetic networks from high-throughput sequencing dataGenevera I. Allen, Zhandong Liu. 1-6 [doi]
• Identifying context-specific transcription factor targets from prior knowledge and gene expression dataElana J. Fertig, Alexander V. Favorov, Michael F. Ochs. 1-6 [doi]
• LSH-Div: Species diversity estimation using locality sensitive hashingZeehasham Rasheed, Huzefa Rangwala, Daniel Barbará. 1-6 [doi]
• Improved biomarker performance for the detection of hepatocellular carcinoma by inclusion of clinical parametersMengjun Wang, Timothy M. Block, Jorge Marrero, Adrian M. Di Bisceglie, Karthik Devarajan, Anand Mehta. 1-5 [doi]
• Novel image features for categorizing biomedical imagesJianqiang Sheng, Songhua Xu, Weicai Deng, Xiaonan Luo. 1-6 [doi]
• Labor contraction prediction via demographic and obstetrical information analysisZifang Huang, Mei-Ling Shyu, James M. Tien, David J. Birnbach, Michael M. Vigoda. 1-6 [doi]
• Maps, rates, and fuzzy mountains: Generating meaningful risk mapsTamara Jiménez, Armin R. Mikler, Marty O'Neill II, Chetan Tiwari. 1-4 [doi]
• A two-variable model for stochastic modelling of chemical events with multi-step reactionsQianqian Wu, Kate Smith-Miles, Tianhai Tian. 1-6 [doi]
• Robust RFCM algorithm for identification of co-expressed miRNAsSushmita Paul, Pradipta Maji. 1-4 [doi]
• A comparison study on protein-protein interaction network modelsMingyu Shao, Yi Yang, Jihong Guan, Shuigeng Zhou. 1-4 [doi]
• Using microenvironments to identify allosteric binding sitesChristopher E. Foley, Sana Al Azwari, Mark Dufton, John N. Wilson. 1-5 [doi]
• An advanced method for identifying protein-protein interaction by analyzing TAP/MS dataXiaoyun Sun, Pengyu Hong, Meghana Kulkarni, Young Kwon, Norbert Perrimon. 1-6 [doi]
• A discrete Bayesian network framework for discrimination of gene expression profilesNikolay Balov. 1-7 [doi]
• Automatic analysis method of protein expression images based on generalized data fieldShuliang Wang, Ying Li, Wenchen Tu, Peng Wang. 1-4 [doi]
• Similarity analysis of feature ranking techniques on imbalanced DNA microarray datasetsDavid J. Dittman, Taghi M. Khoshgoftaar, Randall Wald, Amri Napolitano. 1-5 [doi]
• A semi-supervised learning method for Names of Traditional Chinese Prescriptions and Drugs recognitionDongfeng Cai, Changlin Ding, Junjun Zuo, Yu Bai. 1-4 [doi]
• Early classification of multivariate time series using a hybrid HMM/SVM modelMohamed F. Ghalwash, Dusan Ramljak, Zoran Obradovic. 1-6 [doi]
• On the design of advanced filters for biological networks using graph theoretic propertiesKathryn Dempsey, Tzu-Yi Chen, Sanjukta Bhowmick, Hesham H. Ali. 1-5 [doi]