Journal: IEEE/ACM Trans. Comput. Biology Bioinform.

Volume 15, Issue 6

1752 -- 1753Tianhai Tian, Jingshan Huang. Guest Editorial for Special Section on BIBM 2015
1754 -- 1764Yu-Chiao Chiu, Tzu-Hung Hsiao, Li-Ju Wang, Yidong Chen, Eric Y. Chuang. Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme
1765 -- 1773Bin Hu 0001, Yongqiang Dai, Yun Su, Philip Moore, Xiaowei Zhang 0001, Chengsheng Mao, Jing Chen 0002, Lixin Xu. Feature Selection for Optimized High-Dimensional Biomedical Data Using an Improved Shuffled Frog Leaping Algorithm
1774 -- 1782Wei Lan, Jianxin Wang, Min Li 0007, Jin Liu, Fang-Xiang Wu, Yi Pan 0001. Predicting MicroRNA-Disease Associations Based on Improved MicroRNA and Disease Similarities
1783 -- 1796Tatiana Maximova, Erion Plaku, Amarda Shehu. Structure-Guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm
1797 -- 1809Bo Xu 0009, Hongfei Lin, Yuan Lin 0001, Yunlong Ma, Liang Yang 0003, Jian Wang, Zhihao Yang. Improve Biomedical Information Retrieval Using Modified Learning to Rank Methods
1810 -- 1820Hongbo Zhang, Lin Zhu 0008, De-Shuang Huang. DiscMLA: An Efficient Discriminative Motif Learning Algorithm over High-Throughput Datasets
1821 -- 0Sun Kim. Editorial for Selected Papers of a Joint Conferences, Genome Informatics Workshop/International Conference on Bioinformatics (GIW/InCoB) 2015
1822 -- 1831Osamu Hirose, Shotaro Kawaguchi, Terumasa Tokunaga, Yu Toyoshima, Takayuki Teramoto, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida. SPF-CellTracker: Tracking Multiple Cells with Strongly-Correlated Moves Using a Spatial Particle Filter
1832 -- 1843Zhanzhan Cheng, Shuigeng Zhou, Yang Wang, Hui Liu, Jihong Guan, Yi-Ping Phoebe Chen. Effectively Identifying Compound-Protein Interactions by Learning from Positive and Unlabeled Examples
1844 -- 1852Hamid D. Ismail, Hiroto Saigo, K. C. Dukka B.. RF-NR: Random Forest Based Approach for Improved Classification of Nuclear Receptors
1853 -- 1862Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu. Computing Minimum Reaction Modifications in a Boolean Metabolic Network
1863 -- 1864Ying Tan 0002, Yuhui Shi. Special Section on Swarm-Based Algorithms and Applications in Computational Biology and Bioinformatics
1865 -- 1876Ben Niu 0002, Jing Liu, Teresa Wu, Xianghua Chu, Zhengxu Wang, Yanmin Liu. Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimization
1877 -- 1890Biao Xu, Yong Zhang 0016, Dunwei Gong, Yi-Nan Guo, Miao Rong. Environment Sensitivity-Based Cooperative Co-Evolutionary Algorithms for Dynamic Multi-Objective Optimization
1891 -- 1903Yi-Nan Guo, Jian Cheng 0004, Sha Luo, Dunwei Gong, Yu Xue. Robust Dynamic Multi-Objective Vehicle Routing Optimization Method
1904 -- 1915Weian Guo, Chengyong Si, Yu Xue, Yanfen Mao, Lei Wang, Qidi Wu. A Grouping Particle Swarm Optimizer with Personal-Best-Position Guidance for Large Scale Optimization
1916 -- 1928Chao Gao, Mingxin Liang, Xianghua Li, Zili Zhang, Zhen Wang, Zhili Zhou. Network Community Detection Based on the Physarum-Inspired Computational Framework
1929 -- 1942Andrés Iglesias 0001, Akemi Gálvez, Andreina Avila. Immunological Approach for Full NURBS Reconstruction of Outline Curves from Noisy Data Points in Medical Imaging
1943 -- 1950Qirong Tang, Lu Ding, Fangchao Yu, Yuan Zhang, Yinghao Li, Haibo Tu. Swarm Robots Search for Multiple Targets Based on an Improved Grouping Strategy
1951 -- 1952Xin Gao 0001, Jake Y. Chen, Mohammed J. Zaki. Multiscale and Multimodal Analysis for Computational Biology
1953 -- 1959Miguel Monteiro, Ana Catarina Fonseca, Ana Teresa Freitas, Teresa Pinho e Melo, Alexandre P. Francisco, Jose M. Ferro, Arlindo L. Oliveira. Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients
1960 -- 1967Annie Wang, Hansaim Lim, Shu-Yuan Cheng, Lei Xie. ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy
1968 -- 1978Haishuai Wang, Zhicheng Cui, Yixin Chen, Michael Avidan, Arbi Ben Abdallah, Alexander Kronzer. Predicting Hospital Readmission via Cost-Sensitive Deep Learning
1979 -- 1990Ahmed Halioui, Petko Valtchev, Abdoulaye Baniré Diallo. Bioinformatic Workflow Extraction from Scientific Texts based on Word Sense Disambiguation
1991 -- 1998Zongliang Yue, Michael T. Neylon, Thanh Nguyen 0005, Timothy Ratliff, Jake Y. Chen. "Super Gene Set" Causal Relationship Discovery from Functional Genomics Data
1999 -- 2008Meshari Alazmi, Ahmed Abbas, Xianrong Guo, Ming Fan, Lihua Li, Xin Gao 0001. 13C-detected NMR Spin System Forming and Resonance Assignment Method
2009 -- 2016Kavitha Mukund, Samuel R. Ward, Richard L. Lieber, Shankar Subramaniam. Co-Expression Network Approach to Studying the Effects of Botulinum Neurotoxin-A
2017 -- 2027Daniel P. Martins, Michael Taynnan Barros, Massimiliano Pierobon, Meenakshisundaram Kandhavelu, Pietro Lio', Sasitharan Balasubramaniam. Computational Models for Trapping Ebola Virus Using Engineered Bacteria
2028 -- 2038Juntao Li, Wenpeng Dong, Deyuan Meng. Grouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Based on Conditional Mutual Information
2039 -- 2052Ho-Chun Wu, Xi-Guang Wei, Shing-Chow Chan. Novel Consensus Gene Selection Criteria for Distributed GPU Partial Least Squares-Based Gene Microarray Analysis in Diffused Large B Cell Lymphoma (DLBCL) and Related Findings
2053 -- 2059Surama Biswas, Sriyankar Acharyya. A Bi-Objective RNN Model to Reconstruct Gene Regulatory Network: A Modified Multi-Objective Simulated Annealing Approach
2060 -- 2066Warith Eddine Djeddi, Sadok Ben Yahia, Engelbert Mephu Nguifo. A Novel Computational Approach for Global Alignment for Multiple Biological Networks
2067 -- 2073Martin C. Frith, Anish Man Singh Shrestha. A Simplified Description of Child Tables for Sequence Similarity Search
2074 -- 2078Xizhe Zhang. Altering Indispensable Proteins in Controlling Directed Human Protein Interaction Network
2079 -- 2085Ting Xu, Le Ou-Yang, Xiaohua Hu, Xiao-fei Zhang. Identifying Gene Network Rewiring by Integrating Gene Expression and Gene Network Data
2086 -- 2093Hongmei Jiao, Liping Zhang, Qikun Shen, Junwu Zhu, Peng Shi. Robust Gene Circuit Control Design for Time-Delayed Genetic Regulatory Networks Without SUM Regulatory Logic
2094 -- 2100Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler. Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

Volume 15, Issue 5

1403 -- 1404Erman Ayday, Xiaoqian Jiang, Bradley Malin. GenoPri'16: International Workshop on Genome Privacy and Security
1405 -- 1412Michael Backes 0001, Pascal Berrang, Mathias Humbert, Xiaoyu Shen, Verena Wolf. Simulating the Large-Scale Erosion of Genomic Privacy Over Time
1413 -- 1426Jean Louis Raisaro, Gwangbae Choi, Sylvain Pradervand, Raphael Colsenet, Nathalie Jacquemont, Nicolas Rosat, Vincent Mooser, Jean-Pierre Hubaux. Protecting Privacy and Security of Genomic Data in i2b2 with Homomorphic Encryption and Differential Privacy
1427 -- 1432Dan Bogdanov, Liina Kamm, Sven Laur, Ville Sokk. Implementation and Evaluation of an Algorithm for Cryptographically Private Principal Component Analysis on Genomic Data
1433 -- 1435De-Shuang Huang, Vitoantonio Bevilacqua, M. Michael Gromiha. Guest Editorial for Special Section on the 12th International Conference on Intelligent Computing (ICIC)
1436 -- 1444A. Kulandaisamy, Ambuj Srivastava, Pradeep Kumar, R. Nagarajan, S. Binny Priya, M. Michael Gromiha. Identification and Analysis of Key Residues in Protein-RNA Complexes
1445 -- 1452Hongjie Wu, Chengyuan Cao, Xiaoyan Xia, Qiang Lv. Unified Deep Learning Architecture for Modeling Biology Sequence
1453 -- 1460Wenzheng Bao, Chang-an Yuan, Youhua Zhang, Kyungsook Han, Asoke K. Nandi, Barry Honig, De-Shuang Huang. Mutli-Features Prediction of Protein Translational Modification Sites
1461 -- 1469Wook Lee, Byungkyu Park, Kyungsook Han. Sequence-Based Prediction of Putative Transcription Factor Binding Sites in DNA Sequences of Any Length
1470 -- 1479Xiaoli Lin, Xiaolong Zhang. Prediction of Hot Regions in PPIs Based on Improved Local Community Structure Detecting
1480 -- 1491Su-Ping Deng, Wenxing Hu, Vince D. Calhoun, Yu-Ping Wang. Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizophrenia Disease
1492 -- 1499Giulia Russo, Marzio Pennisi, Roberta Boscarino, Francesco Pappalardo 0001. Continuous Petri Nets and microRNA Analysis in Melanoma
1500 -- 1512Jian Liu, Yuhu Cheng, Xuesong Wang, Xiaoluo Cui, Yi Kong, Junping Du. Low Rank Subspace Clustering via Discrete Constraint and Hypergraph Regularization for Tumor Molecular Pattern Discovery
1513 -- 1514Lusheng Wang, Shuai Cheng Li, Yi-Ping Phoebe Chen. Guest Editorial for the 15th Asia Pacific Bioinformatics Conference
1515 -- 1524Jaroslaw Paszek, Pawel Górecki. Efficient Algorithms for Genomic Duplication Models
1525 -- 1537Andrzej Mizera, Jun Pang, Qixia Yuan. Reviving the Two-State Markov Chain Approach
1538 -- 1548Shuai An, Jun Wang 0023, Jinmao Wei. Local-Nearest-Neighbors-Based Feature Weighting for Gene Selection
1549 -- 1559Nan Jiang, Wenge Rong, Yifan Nie, Yikang Shen, Zhang Xiong. Biological Event Trigger Identification with Noise Contrastive Estimation
1560 -- 1570Manuel Lafond, Cédric Chauve, Nadia El-Mabrouk, Aïda Ouangraoua. Gene Tree Construction and Correction Using SuperTree and Reconciliation
1571 -- 1578Agnieszka Mykowiecka, Pawel Szczesny, Pawel Górecki. Inferring Gene-Species Assignments in the Presence of Horizontal Gene Transfer
1579 -- 1584Yue Zhang, Chunfang Zheng, David Sankoff. Evolutionary Model for the Statistical Divergence of Paralogous and Orthologous Gene Pairs Generated by Whole Genome Duplication and Speciation
1585 -- 1593Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf, Matthias Bernt. Genome Rearrangement with ILP
1594 -- 1604Nafiseh Sedaghat, Mahmood Fathy, Mohammad Hossein Modarressi, Ali Shojaie. Combining Supervised and Unsupervised Learning for Improved miRNA Target Prediction
1605 -- 1610Safwat Hamad, Ahmed Elhadad, Amal Khalifa. DNA Watermarking Using Codon Postfix Technique
1611 -- 1624Jorge E. Duarte-Sanchez, Jaime Velasco-Medina, Pedro A. Moreno. Hardware Accelerator for the Multifractal Analysis of DNA Sequences
1625 -- 1635Nha Nguyen, An P. N. Vo, Haibin Sun, Heng Huang. Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram for Detecting DNA Copy Number Aberrations
1636 -- 1648Xiaoke Ma, Penggang Sun, Guimin Qin. Identifying Condition-Specific Modules by Clustering Multiple Networks
1649 -- 1659Jin Liu, Jianxin Wang, Zhenjun Tang, Bin Hu 0001, Fang-Xiang Wu, Yi Pan 0001. Improving Alzheimer's Disease Classification by Combining Multiple Measures
1660 -- 1668Shuai Ren, Yan Shi 0003, Maolin Cai, Weiqing Xu. Influence of Airway Secretion on Airflow Dynamics of Mechanical Ventilated Respiratory System
1669 -- 1682Vipin Vijayan, Tijana Milenkovic. Multiple Network Alignment via MultiMAGNA++
1683 -- 1691Chunjiang Yu, Wentao Wu 0004, Jing Wang, Yuxin Lin, Yang Yang, Jiajia Chen, Fei Zhu, Bairong Shen. NGS-FC: A Next-Generation Sequencing Data Format Converter
1692 -- 1705Hasan M. Jamil. Optimizing Phylogenetic Queries for Performance
1706 -- 1717Min Liu, Yue He, Weili Qian, Yangliu Wei, Xiaoyan Liu. Cell Population Tracking in a Honeycomb Structure Using an IMM Filter Based 3D Local Graph Matching Model
1718 -- 1722Shifu Chen, Ming Liu, Xiaoni Zhang, Renwen Long, Yixing Wang, Yue Han, Shiwei Zhang, Mingyan Xu, Jia Gu. A Study of Cell-Free DNA Fragmentation Pattern and Its Application in DNA Sample Type Classification
1723 -- 1727Pawel Górecki, Oliver Eulenstein. Bijective Diameters of Gene Tree Parsimony Costs
1728 -- 1731Youyuan Li, Yingping Zhuang. fmpRPMF: A Web Implementation for Protein Identification by Robust Peptide Mass Fingerprinting
1732 -- 1737Jorge González-Domínguez, María J. Martín. MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks on Multicore Clusters
1738 -- 1747Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab. Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?

Volume 15, Issue 4

1036 -- 0T. M. Murali. Guest Editorial
1037 -- 1051Asish Ghoshal, Jinyi Zhang, Michael A. Roth, Kevin Muyuan Xia, Ananth Y. Grama, Somali Chaterji. A Distributed Classifier for MicroRNA Target Prediction with Validation Through TCGA Expression Data
1052 -- 1065Shi Qiao, Mehmet Koyutürk, Z. Meral Özsoyoglu. Querying of Disparate Association and Interaction Data in Biomedical Applications
1066 -- 1078Alexej Gossmann, Shaolong Cao, Damian Brzyski, Lan-Juan Zhao, Hong-Wen Deng, Yu-Ping Wang. A Sparse Regression Method for Group-Wise Feature Selection with False Discovery Rate Control
1079 -- 1091Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My T. Thai, Tamer Kahveci. Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks
1092 -- 0Xiaodan Fan, Xinglai Ji, Rui Jiang. Guest Editorial for Special Section on the Sixth National Conference on Bioinformatics and System Biology of China
1093 -- 1106Mahdi Zamanighomi, Mostafa Zamanian, Michael Kimber, Zhengdao Wang. Gene Regulatory Network Inference from Perturbed Time-Series Expression Data via Ordered Dynamical Expansion of Non-Steady State Actors
1107 -- 1110Ke Liu, Sha Hou, Junbiao Dai, Zhirong Sun. PyMut: A Web Tool for Overlapping Gene Loss-of-Function Mutation Design
1111 -- 1121Xiangfei Cheng, Yue Hou, Yumin Nie, Yiru Zhang, Huan Huang, Hongde Liu, Xiao Sun. Nucleosome Positioning of Intronless Genes in the Human Genome
1122 -- 1123Ezio Bartocci, Pietro Liò, Nicola Paoletti. Guest Editors' Introduction to the Special Section on the 14th International Conference on Computational Methods in Systems Biology (CMSB 2016)
1124 -- 1137Jérôme Feret, Kim Quyen Ly. Local Traces: An Over-Approximation of the Behavior of the Proteins in Rule-Based Models
1138 -- 1151François Fages, Thierry Martinez, David A. Rosenblueth, Sylvain Soliman. Influence Networks Compared with Reaction Networks: Semantics, Expressivity and Attractors
1152 -- 1166Chunyan Mu, Peter Dittrich, David Parker 0001, Jonathan E. Rowe. Organisation-Oriented Coarse Graining and Refinement of Stochastic Reaction Networks
1167 -- 1179Loïc Paulevé. Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis
1180 -- 1192Michael Backenköhler, Luca Bortolussi, Verena Wolf. Moment-Based Parameter Estimation for Stochastic Reaction Networks in Equilibrium
1193 -- 1202Alejandro Fernández Villaverde, Kolja Becker, Julio R. Banga. PREMER: A Tool to Infer Biological Networks
1203 -- 1216Andrzej Mizera, Jun Pang, Cui Su, Qixia Yuan. ASSA-PBN: A Toolbox for Probabilistic Boolean Networks
1217 -- 1228Eugen Czeizler, Wu Kai Chiu, Cristian Gratie, Krishna Kanhaiya, Ion Petre. Structural Target Controllability of Linear Networks
1229 -- 1230Tijana Milenkovic, Sarath Chandra Janga. Great Lakes Bioinformatics Conference (GLBIO) 2015 Special Section Editorial
1231 -- 1238James B. Pease, Benjamin K. Rosenzweig. Encoding Data Using Biological Principles: The Multisample Variant Format for Phylogenomics and Population Genomics
1239 -- 1246Adam Roth, Sandeep Subramanian, Madhavi K. Ganapathiraju. Towards Extracting Supporting Information About Predicted Protein-Protein Interactions
1247 -- 1258Satwica Yerneni, Ishita K. Khan, Qing Wei, Daisuke Kihara. IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks
1259 -- 1269Seyedsasan Hashemikhabir, Ran Xia, Yang Xiang, Sarath Chandra Janga. A Framework for Identifying Genotypic Information from Clinical Records: Exploiting Integrated Ontology Structures to Transfer Annotations between ICD Codes and Gene Ontologies
1270 -- 1283Pranjal Patra, Tatsuo Izawa, Lourdes Peña Castillo. REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data
1284 -- 1289Rodrigo F. Ramalho, Sujun Li, Predrag Radivojac, Matthew W. Hahn. Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse
1290 -- 1300Rami Al-ouran, Robert Schmidt, Ashwini Naik, Jeffrey Jones, Frank Drews, David W. Juedes, Laura Elnitski, Lonnie R. Welch. Discovering Gene Regulatory Elements Using Coverage-Based Heuristics
1301 -- 1314Liliana Ironi, Ettore Lanzarone. A Model-Based Tool for the Analysis and Design of Gene Regulatory Networks
1315 -- 1324Chun-Qiu Xia, Ke Han, Yong Qi, Yang Zhang, Dong-jun Yu. A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data
1325 -- 1332Xinyu He, Lishuang Li, Yang Liu, Xiaoming Yu, Jun Meng. A Two-Stage Biomedical Event Trigger Detection Method Integrating Feature Selection and Word Embeddings
1333 -- 1343Iman Deznabi, Mohammad Mobayen, Nazanin Jafari, Oznur Tastan, Erman Ayday. An Inference Attack on Genomic Data Using Kinship, Complex Correlations, and Phenotype Information
1344 -- 1350Qian Xie, Xiaoyan He, Fangji Yang, Xuling Liu, Ying Li, Yujing Liu, ZhengMeng Yang, Jianhai Yu, Bao Zhang, Wei Zhao. Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of the Envelope Protein of Middle East Respiratory Syndrome-Coronavirus
1351 -- 1364Yoram Zarai, Michael Margaliot, Eduardo D. Sontag, Tamir Tuller. Controllability Analysis and Control Synthesis for the Ribosome Flow Model
1365 -- 1378Shangce Gao, Shuangbao Song, Jiujun Cheng, Yuki Todo, MengChu Zhou. Incorporation of Solvent Effect into Multi-Objective Evolutionary Algorithm for Improved Protein Structure Prediction
1379 -- 1389Karlene Nicole Meyer, Michelle R. Lacey. Modeling Methylation Patterns with Long Read Sequencing Data
1390 -- 1402Guoxian Yu, Guangyuan Fu, Jun Wang 0035, Yingwen Zhao. NewGOA: Predicting New GO Annotations of Proteins by Bi-Random Walks on a Hybrid Graph

Volume 15, Issue 3

688 -- 689Julia Handl, Amarda Shehu, José Santos Reyes. Advances in the Application and Development of Non-Linear Global Optimization Techniques in Computational Structural Biology
690 -- 704Leonardo de Lima Correa, Bruno Borguesan, Camilo Farfán, Mario Inostroza-Ponta, Márcio Dorn. A Memetic Algorithm for 3D Protein Structure Prediction Problem
705 -- 718Jiaxiang Huang, Maoguo Gong, Lijia Ma. A Global Network Alignment Method Using Discrete Particle Swarm Optimization
719 -- 731Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu. From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes
732 -- 739Jakub Rydzewski, Rafal Jakubowski, Giuseppe Nicosia, Wieslaw Nowak. Conformational Sampling of a Biomolecular Rugged Energy Landscape
740 -- 752Matthias Leinweber, Thomas Fober, Bernd Freisleben. GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites
753 -- 759Jie Zhou, Yuan-Yuan Shi. A Bipartite Network and Resource Transfer-Based Approach to Infer lncRNA-Environmental Factor Associations
760 -- 773Maiju Pesonen, Jaakko Nevalainen, Steven Potter, Somnath Datta, Susmita Datta. A Combined PLS and Negative Binomial Regression Model for Inferring Association Networks from Next-Generation Sequencing Count Data
774 -- 787Xiangtao Li, Ka Chun Wong. A Comparative Study for Identifying the Chromosome-Wide Spatial Clusters from High-Throughput Chromatin Conformation Capture Data
788 -- 801Xin Peng, Yang Tang, Wangli He, Wenli Du, Feng Qian. A Just-in-Time Learning Based Monitoring and Classification Method for Hyper/Hypocalcemia Diagnosis
802 -- 812Xichuan Zhou, Fan Yang, Yujie Feng, Qin Li, Fang Tang, Shengdong Hu, Zhi Lin, Lei Zhang. A Spatial-Temporal Method to Detect Global Influenza Epidemics Using Heterogeneous Data Collected from the Internet
813 -- 827Neslihan Avcu, Nihal Pekergin, Ferhan Pekergin, Cüneyt Güzelis. Aggregation for Computing Multi-Modal Stationary Distributions in 1-D Gene Regulatory Networks
828 -- 838Wei Shao, Mingxia Liu, Ying-Ying Xu, Hong-bin Shen, Daoqiang Zhang. An Organelle Correlation-Guided Feature Selection Approach for Classifying Multi-Label Subcellular Bio-Images
839 -- 849Pritha Dutta, Subhadip Basu, Mahantapas Kundu. Assessment of Semantic Similarity between Proteins Using Information Content and Topological Properties of the Gene Ontology Graph
850 -- 860Aurélie Pirayre, Camille Couprie, Laurent Duval, Jean-Christophe Pesquet. BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement
861 -- 868Somaya Hashem, Gamal Esmat, Wafaa Elakel, Shahira Habashy, Safaa Abdel Raouf, Mohamed Elhefnawi, Mohamed Eladawy, Mahmoud ElHefnawi. Comparison of Machine Learning Approaches for Prediction of Advanced Liver Fibrosis in Chronic Hepatitis C Patients
869 -- 877Sumanta Ray, Ujjwal Maulik. Discovering Perturbation of Modular Structure in HIV Progression by Integrating Multiple Data Sources Through Non-Negative Matrix Factorization
878 -- 891Aseel Awdeh, Hilary Phenix, Mads Kærn, Theodore J. Perkins. Dynamics in Epistasis Analysis
892 -- 904Tiantian He, Keith C. C. Chan. Evolutionary Graph Clustering for Protein Complex Identification
905 -- 912Najmul Ikram Qazi, Muhammad Abdul Qadir, Muhammad Tanvir Afzal. Investigating Correlation between Protein Sequence Similarity and Semantic Similarity Using Gene Ontology Annotations
913 -- 925Lin Zhu 0008, Hong-Bo Zhang, De-Shuang Huang. LMMO: A Large Margin Approach for Refining Regulatory Motifs
926 -- 933Pedro Alves, Shuang Liu, Daifeng Wang, Mark Gerstein. Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology
934 -- 943Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris. NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithm for Flexible Protein Structure Alignment
944 -- 953Wenwen Min, Juan Liu, Shihua Zhang. Network-Regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery
954 -- 965Davide Chicco, Fernando Palluzzi, Marco Masseroli. Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations
966 -- 973Zoya Khalid, Osman Ugur Sezerman. Prediction of HIV Drug Resistance by Combining Sequence and Structural Properties
974 -- 987Jin-Xing Liu, Dong Wang, Ying-Lian Gao, Chun-Hou Zheng, Yong Xu 0001, Jiguo Yu. Regularized Non-Negative Matrix Factorization for Identifying Differentially Expressed Genes and Clustering Samples: A Survey
988 -- 998Junhua Zhang, Shihua Zhang. The Discovery of Mutated Driver Pathways in Cancer: Models and Algorithms
999 -- 1002Bin Wang, Xuedong Zheng, Shihua Zhou, Changjun Zhou, Xiaopeng Wei, Qiang Zhang 0008, Ziqi Wei. Constructing DNA Barcode Sets Based on Particle Swarm Optimization
1003 -- 1009Carl Poirier, Benoit Gosselin, Paul Fortier. DNA Assembly with De Bruijn Graphs Using an FPGA Platform
1010 -- 1015Ruth Davidson, MaLyn Lawhorn, Joseph Rusinko, Noah Weber. Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods
1016 -- 1021Xianpeng Liang, Lin Zhu 0008, De-Shuang Huang. Optimization of Gene Set Annotations Using Robust Trace-Norm Multitask Learning
1022 -- 1027Chengyu Liu, Rainer Lehtonen, Sampsa Hautaniemi. PerPAS: Topology-Based Single Sample Pathway Analysis Method
1028 -- 1034Abolfazl Doostparast Torshizi, Linda Petzold. Sparse Pathway-Induced Dynamic Network Biomarker Discovery for Early Warning Signal Detection in Complex Diseases
1035 -- 0Wei Zhang 0079, Jia Xu 0002, Yuanyuan Li, Xiufen Zou. Correction to "Detecting Essential Proteins Based on Network Topology, Gene Expression Data, and Gene Ontology Information"

Volume 15, Issue 2

350 -- 351Adrian Horia Dediu, Carlos Martín-Vide. Selected Papers of the First International Conference on Algorithms for Computational Biology (AlCoB 2014)
352 -- 363Thiago da Silva Arruda, Ulisses Dias, Zanoni Dias. A GRASP-Based Heuristic for the Sorting by Length-Weighted Inversions Problem
364 -- 376Ivo Hedtke, Ioana M. Lemnian, Ivo Grosse, Matthias Müller-Hannemann. Optimal Block-Based Trimming for Next Generation Sequencing
377 -- 386Congping Lin, Laurent Lemarchand, Reinhardt Euler, Imogen Sparkes. Modeling the Geometry and Dynamics of the Endoplasmic Reticulum Network
387 -- 395Amina Noor, Aitzaz Ahmad, Erchin Serpedin. SparseNCA: Sparse Network Component Analysis for Recovering Transcription Factor Activities with Incomplete Prior Information
396 -- 397Jijun Tang, Lu Tian, Yi-Ping Phoebe Chen. th Asia Pacific Bioinformatics Conference
398 -- 410Daniel H. Huson, Simone Linz. Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees
411 -- 421W. Ma, D. Smirnov, J. Forman, A. Schweickart, C. Slocum, S. Srinivasan, R. Libeskind-Hadas. DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations
422 -- 431Zhi-Zhong Chen, Qilong Feng, Chao Shen, Jianxin Wang, Lusheng Wang. Algorithms for Pedigree Comparison
432 -- 440Moonshik Shin, Donjin Jang, Hojung Nam, Kwang Hyung Lee, Doheon Lee. Predicting the Absorption Potential of Chemical Compounds Through a Deep Learning Approach
441 -- 451Seunghyun Park, Hyun Soo Choi, Byunghan Lee, Jongsik Chun, Joong-Ho Won, Sungroh Yoon. hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Units Based on Homopolymer Compaction
452 -- 459Dimitris P. Papamichail, Hongmei Liu, Vitor Machado, Nathan Gould, J. Robert Coleman, Georgios Papamichail. Codon Context Optimization in Synthetic Gene Design
460 -- 468Jiangeng Li, Wei Zhang, Xiaodan Li. 3D Genome Reconstruction with ShRec3D+ and Hi-C Data
469 -- 481Rahul Singh, Rachel Beasley, Thavy Long, Conor R. Caffrey. Algorithmic Mapping and Characterization of the Drug-Induced Phenotypic-Response Space of Parasites Causing Schistosomiasis
482 -- 483Bijoy K. Ghosh, Aniruddha Datta, Ranadip Pal. Deep Sequencing Data Analysis
484 -- 493Jason M. Knight, Ivan Ivanov, Karen Triff, Robert S. Chapkin, Edward R. Dougherty. Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification
494 -- 505Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha Datta, Charles D. Johnson. Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline
506 -- 515Mansuck Kim, Huan Zhang, Charles Woloshuk, Won Bo Shim, Byung-Jun Yoon. Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides
516 -- 525Arghavan Bahadorinejad, Ulisses Braga-Neto. Optimal Fault Detection and Diagnosis in Transcriptional Circuits Using Next-Generation Sequencing
526 -- 534Xiaodong Cui, Lin Zhang 0015, Jia Meng, Manjeet K. Rao, Yidong Chen, Yufei Huang. MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data
535 -- 536Jing Zhang 0010, Tianming Liu, Gopikrishna Deshpande. Probabilistic Methods in Computational Neuroscience
537 -- 550Yize Zhao, Jian Kang, Qi Long. Bayesian Multiresolution Variable Selection for Ultra-High Dimensional Neuroimaging Data
551 -- 561Lin Yuan, Fanglin Chen, Ling-Li Zeng, Lubin Wang, Dewen Hu. Gender Identification of Human Brain Image with A Novel 3D Descriptor
562 -- 569Meng Hu, Wu Li, Hualou Liang. A Copula-Based Granger Causality Measure for the Analysis of Neural Spike Train Data
570 -- 580Lijun Zhang, Ming Wang, Nicholas W. Sterling, Eun-Young Lee, Paul J. Eslinger, Daymond Wagner, Guangwei Du, Mechelle Lewis, Young Truong, F. DuBois Bowman, Xuemei Huang 0004. Cortical Thinning and Cognitive Impairment in Parkinson's Disease without Dementia
581 -- 587João Ricardo Sato, Maciel Calebe Vidal, Suzana de Siqueira Santos, Katlin Brauer Massirer, André Fujita. Complex Network Measures in Autism Spectrum Disorders
588 -- 598Biing-Feng Wang. A New Efficient Algorithm for the Frequent Gene Team Problem
599 -- 612Suneetha Uppu, Aneesh Krishna, Raj P. Gopalan. A Review on Methods for Detecting SNP Interactions in High-Dimensional Genomic Data
613 -- 623Mahdi Barat Zadeh Joveini, Javad Sadri. Application of Fractal Theory on Motifs Counting in Biological Networks
624 -- 632Jin Liu, Min Li 0007, Wei Lan, Fang-Xiang Wu, Yi Pan 0001, Jianxin Wang. Classification of Alzheimer's Disease Using Whole Brain Hierarchical Network
633 -- 646Jinghui Li, Hiroshi Nagamochi, Tatsuya Akutsu. Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs
647 -- 658Xiaoke Ma, Wanxin Tang, Peizhuo Wang, Xingli Guo, Lin Gao. Extracting Stage-Specific and Dynamic Modules Through Analyzing Multiple Networks Associated with Cancer Progression
659 -- 672Jayanta Kumar Pal, Shubhra Sankar Ray, Sung-Bae Cho, Sankar K. Pal. Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection for miRNA Ranking in Cancer
673 -- 687Sanghamitra Bandyopadhyay, Saurav Mallik. Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis

Volume 15, Issue 1

1 -- 14Yanbo Wang, Weikang Qian, Bo Yuan. A Graphical Model of Smoking-Induced Global Instability in Lung Cancer
15 -- 26Jesper Jansson, Ramesh Rajaby, Chuanqi Shen, Wing-Kin Sung. Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree
27 -- 37Renu Vyas, Sanket Bapat, Purva Goel, Muthukumarasamy Karthikeyan, Sanjeev S. Tambe, Bhaskar D. Kulkarni. Application of Genetic Programming (GP) Formalism for Building Disease Predictive Models from Protein-Protein Interactions (PPI) Data
38 -- 45Bin Hu 0001, Xiaowei Li 0005, Shuting Sun, Martyn Ratcliffe. Attention Recognition in EEG-Based Affective Learning Research Using CFS+KNN Algorithm
46 -- 59Anton Ushakov, Xenia Klimentova, Igor Vasilyev. Bi-level and Bi-objective p-Median Type Problems for Integrative Clustering: Application to Analysis of Cancer Gene-Expression and Drug-Response Data
60 -- 67Narayanan C. Viswanath. Calculating the Expected Time to Eradicate HIV-1 Using a Markov Chain
68 -- 82Alireza Karbalayghareh, Ulisses M. Braga-Neto, Jianping Hua, Edward Russell Dougherty. Classification of State Trajectories in Gene Regulatory Networks
83 -- 95Tom Hartmann, An-Chiang Chu, Martin Middendorf, Matthias Bernt. Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes
96 -- 108Ademir Hujdurovic, Ursa Kacar, Martin Milanic, Bernard Ries, Alexandru I. Tomescu. Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples
109 -- 116Wei Zhang, Jia Xu, Yuanyuan Li, Xiufen Zou. Detecting Essential Proteins Based on Network Topology, Gene Expression Data, and Gene Ontology Information
117 -- 128Cinzia Pizzi, Mattia Ornamenti, Simone Spangaro, Simona E. Rombo, Laxmi Parida. Efficient Algorithms for Sequence Analysis with Entropic Profiles
129 -- 146Hyunjin Kim, Sang-Min Choi, Sanghyun Park. GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity
147 -- 156Jian Zhang, Haiting Chai, Bo Gao, Guifu Yang, Zhiqiang Ma. HEMEsPred: Structure-Based Ligand-Specific Heme Binding Residues Prediction by Using Fast-Adaptive Ensemble Learning Scheme
157 -- 167Kamal Taha. Inferring the Functions of Proteins from the Interrelationships between Functional Categories
168 -- 180Guillermo Leale, Ariel E. Bayá, Diego H. Milone, Pablo M. Granitto, Georgina Stegmayer. Inferring Unknown Biological Function by Integration of GO Annotations and Gene Expression Data
181 -- 190Nikolaos-Kosmas Chlis, Ekaterini S. Bei, Michalis Zervakis. Introducing a Stable Bootstrap Validation Framework for Reliable Genomic Signature Extraction
191 -- 204Eddie Y. T. Ma, Sujeevan Ratnasingham, Stefan C. Kremer. Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding
205 -- 217Laura Jetten, Leo van Iersel. Nonbinary Tree-Based Phylogenetic Networks
218 -- 230Daniel N. Mohsenizadeh, Roozbeh Dehghannasiri, Edward R. Dougherty. Optimal Objective-Based Experimental Design for Uncertain Dynamical Gene Networks with Experimental Error
231 -- 243Behnam Behinaein, Karen Rudie, Waheed Sangrar. Petri Net Siphon Analysis and Graph Theoretic Measures for Identifying Combination Therapies in Cancer
244 -- 250Shujaat Khan, Imran Naseem, Roberto Togneri, Mohammed Bennamoun. RAFP-Pred: Robust Prediction of Antifreeze Proteins Using Localized Analysis of n-Peptide Compositions
251 -- 256Roman Czapla. Random Sets of Stadiums in Square and Collective Behavior of Bacteria
257 -- 270Vinicius R. P. Borges, Maria Cristina Ferreira de Oliveira, Thaís Garcia Silva, Armando Augusto Henriques Vieira, Bernd Hamann. Region Growing for Segmenting Green Microalgae Images
271 -- 285M. Syed Ali 0001, N. Gunasekaran, Choon Ki Ahn, Peng Shi 0001. Sampled-Data Stabilization for Fuzzy Genetic Regulatory Networks with Leakage Delays
286 -- 299Chendra Hadi Suryanto, Hiroto Saigo, Kazuhiro Fukui. Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images
300 -- 308Gerd Anders, Ulrich Hassiepen, Stephan Theisgen, Stephan Heymann, Lionel Muller, Tania Panigada, Daniel Huster, Sergey A. Samsonov. The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from a Combined Bioinformatical and Experimental Approach
309 -- 315Jiawei Luo 0001, Wei Huang, Buwen Cao. A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Modules in Cancer
316 -- 322Feng Bao 0002, Yue Deng 0001, Qionghai Dai. ACID: Association Correction for Imbalanced Data in GWAS
323 -- 329Hongmei Jiao, Michael Shi, Qikun Shen, Junwu Zhu, Peng Shi 0001. Filter Design with Adaptation to Time-Delay Parameters for Genetic Regulatory Networks
330 -- 336Ahed Elmsallati, Abdulghani Msalati, Jugal Kalita. Index-Based Network Aligner of Protein-Protein Interaction Networks
337 -- 342Elizabeth S. Allman, James H. Degnan, John A. Rhodes. Species Tree Inference from Gene Splits by Unrooted STAR Methods
343 -- 349Frederick A. Matsen IV, Sara C. Billey, Arnold Kas, Matjaz Konvalinka. Tanglegrams: A Reduction Tool for Mathematical Phylogenetics