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

Volume 13, Issue 6

1003 -- 0Xing-Ming Zhao. Data Mining in Systems Biology
1004 -- 1015Jian Tang, Shuigeng Zhou. A New Approach for Feature Selection from Microarray Data Based on Mutual Information
1016 -- 1026Xi-yin, Ying-Ying Xu, Hong-bin Shen. Enhancing the Prediction of Transmembrane β-Barrel Segments with Chain Learning and Feature Sparse Representation
1027 -- 1035Gui-Min Qin, Rui-Yi Li, Xing-Ming Zhao. Identifying Disease Associated miRNAs Based on Protein Domains
1036 -- 1044Hao Wu, Lin Gao, Nikola K. Kasabov. Network-Based Method for Inferring Cancer Progression at the Pathway Level from Cross-Sectional Mutation Data
1045 -- 1058Fábio Fabris, Alex Alves Freitas, Jennifer M. A. Tullet. An Extensive Empirical Comparison of Probabilistic Hierarchical Classifiers in Datasets of Ageing-Related Genes
1059 -- 1067Dong Wang, Jin-Xing Liu, Ying-Lian Gao, Chun-Hou Zheng, Yong Xu. Characteristic Gene Selection Based on Robust Graph Regularized Non-Negative Matrix Factorization
1068 -- 1085Adriano N. Raposo, Abel J. P. Gomes. Computational 3D Assembling Methods for DNA: A Survey
1086 -- 1099Sumanta Ray, Sanghamitra Bandyopadhyay. Discovering Condition Specific Topological Pattern Changes in Coexpression Network: An Application to HIV-1 Progression
1100 -- 1106Natalia Vilor-Tejedor, Juan R. Gonzalez, Malu Luz Calle. Efficient and Powerful Method for Combining P-Values in Genome-Wide Association Studies
1107 -- 1116Xiaoqing Cheng, Tomoya Mori, Yushan Qiu, Wai-Ki Ching, Tatsuya Akutsu. Exact Identification of the Structure of a Probabilistic Boolean Network from Samples
1117 -- 1129Maoguo Gong, Zhenglin Peng, Lijia Ma, Jiaxiang Huang. Global Biological Network Alignment by Using Efficient Memetic Algorithm
1130 -- 1141Meredith Ray, Jian Kang, Hongmei Zhang. Identifying Activation Centers with Spatial Cox Point Processes Using fMRI Data
1142 -- 1154Hong Wang, Xicheng Wang, Zheng Li, Keqiu Li. Kriging-Based Parameter Estimation Algorithm for Metabolic Networks Combined with Single-Dimensional Optimization and Dynamic Coordinate Perturbation
1155 -- 1160Guanyun Wei, Sheng Qin, Wenjuan Li, Liming Chen, Fei Ma. MDTE DB: A Database for MicroRNAs Derived from Transposable Element
1161 -- 1169Shuang Cheng, Maozu Guo, Chunyu Wang, Xiaoyan Liu, Yang Liu, Xuejian Wu. MiRTDL: A Deep Learning Approach for miRNA Target Prediction
1170 -- 1182Yi Qi, Jiawei Luo. Prediction of Essential Proteins Based on Local Interaction Density
1183 -- 1193Sergiy Ancherbak, Ercan E. Kuruoglu, Martin Vingron. Time-Dependent Gene Network Modelling by Sequential Monte Carlo
1194 -- 1200Yang Liu, Bowen Li, Jungang Lou. Disturbance Decoupling of Singular Boolean Control Networks

Volume 13, Issue 5

810 -- 811Chao Wang, Hong Yu, Aili Wang, Kai Xia. Guest Editorial for Special Section on Big Data Computing and Processing in Computational Biology and Bioinformatics
812 -- 824Erin J. Moore, Thirimachos Bourlai. Expectation Maximization of Frequent Patterns, a Specific, Local, Pattern-Based Biclustering Algorithm for Biological Datasets
825 -- 835Ya Zhang, Ao Li, Chen Peng, Minghui Wang. Improve Glioblastoma Multiforme Prognosis Prediction by Using Feature Selection and Multiple Kernel Learning
836 -- 844Xiaoyi Xu, Minghui Wang. Inferring Disease Associated Phosphorylation Sites via Random Walk on Multi-Layer Heterogeneous Network
845 -- 854Cheng Ling, Tsuyoshi Hamada, Jing-Yang Gao, Guoguang Zhao, Donghong Sun, Weifeng Shi. 3++: A High Performance and Resource-Efficient GPU-Oriented Phylogenetic Analysis Method
855 -- 867Jingsong Zhang, Yinglin Wang, Chao Zhang, Yongyong Shi. Mining Contiguous Sequential Generators in Biological Sequences
868 -- 877Keru Hua, Qin Yu, Ruiming Zhang. A Guaranteed Similarity Metric Learning Framework for Biological Sequence Comparison
878 -- 886Steinar Thorvaldsen. A Mutation Model from First Principles of the Genetic Code
887 -- 900Xiao-hu Hao, Gui-jun Zhang, Xiao-gen Zhou, Xufeng Yu. A Novel Method Using Abstract Convex Underestimation in Ab-Initio Protein Structure Prediction for Guiding Search in Conformational Feature Space
901 -- 912Peng Chen, Shanshan Hu, Jun Zhang, Xin Gao, Jinyan Li, Junfeng Xia, Bing Wang. A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction
913 -- 925Filippo Disanto, Noah A. Rosenberg. Asymptotic Properties of the Number of Matching Coalescent Histories for Caterpillar-Like Families of Species Trees
926 -- 938David Nogueira, Pedro Tomás, Nuno Roma. BowMapCL: Burrows-Wheeler Mapping on Multiple Heterogeneous Accelerators
939 -- 946Yan Shi, Jinglong Niu, Zhixin Cao, Maolin Cai, Jian Zhu, Weiqing Xu. Online Estimation Method for Respiratory Parameters Based on a Pneumatic Model
947 -- 953Liqi Li, Jinhui Li, Weidong Xiao, Yongsheng Li, Yufang Qin, Shiwen Zhou, Hua Yang. Prediction the Substrate Specificities of Membrane Transport Proteins Based on Support Vector Machine and Hybrid Features
954 -- 970Apostolos Axenopoulos, Dimitrios Rafailidis, Georgios Th. Papadopoulos, Elias N. Houstis, Petros Daras. Similarity Search of Flexible 3D Molecules Combining Local and Global Shape Descriptors
971 -- 989Jun Chin Ang, Andri Mirzal, Habibollah Haron, Haza Nuzly Abdull Hamed. Supervised, Unsupervised, and Semi-Supervised Feature Selection: A Review on Gene Selection
990 -- 995Yuanning Liu, Qi Zhao, Hao Zhang, Rui Xu, Yang Li, Liyan Wei. A New Method to Predict RNA Secondary Structure Based on RNA Folding Simulation
996 -- 1002Yung-Keun Kwon, Junil Kim, Kwang-Hyun Cho. Dynamical Robustness against Multiple Mutations in Signaling Networks

Volume 13, Issue 4

599 -- 609Biing-Feng Wang. A New Efficient Algorithm for the All Sorting Reversals Problem with No Bad Components
610 -- 622Junzhong Ji, Jia Wei Lv, Cuicui Yang, Aidong Zhang. Detecting Functional Modules Based on a Multiple-Grain Model in Large-Scale Protein-Protein Interaction Networks
623 -- 633Ngoc Hieu Tran, Xin Chen. AMAS: Optimizing the Partition and Filtration of Adaptive Seeds to Speed up Read Mapping
634 -- 642Zhenchao Jiang, Lishuang Li, Degen Huang. An Unsupervised Graph Based Continuous Word Representation Method for Biomedical Text Mining
643 -- 655Daniele Catanzaro, Stanley E. Shackney, Alejandro A. Schäffer, Russell Schwartz. Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study
656 -- 668Jianing Xi, Ao Li. Discovering Recurrent Copy Number Aberrations in Complex Patterns via Non-Negative Sparse Singular Value Decomposition
669 -- 677Lishuang Li, Shanshan Liu, Meiyue Qin, Yiwen Wang, Degen Huang. Extracting Biomedical Event with Dual Decomposition Integrating Word Embeddings
678 -- 688Benjamin Xueqi Guan, Bir Bhanu, Prue Talbot, Nikki Jo-Hao Weng. Extraction of Blebs in Human Embryonic Stem Cell Videos
689 -- 705Ahed Elmsallati, Connor Clark, Jugal Kalita. Global Alignment of Protein-Protein Interaction Networks: A Survey
706 -- 718Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung. Mem-mEN: Predicting Multi-Functional Types of Membrane Proteins by Interpretable Elastic Nets
719 -- 729Lori A. Dalton. Optimal ROC-Based Classification and Performance Analysis under Bayesian Uncertainty Models
730 -- 741Shun-ichi Azuma, Katsuya Owaki, Nobuhiro Shinohara, Toshiharu Sugie. Performance Analysis of Chemotaxis Controllers: Which has Better Chemotaxis Controller, Escherichia coli or Paramecium caudatum?
742 -- 753Sajid A. Marhon, Stefan C. Kremer. Prediction of Protein Coding Regions Using a Wide-Range Wavelet Window Method
754 -- 766Yun-Bo Zhao, J. Krishnan. Probabilistic Boolean Network Modelling and Analysis Framework for mRNA Translation
767 -- 777Young-Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire J. Tomlin. Reconstruction of Gene Regulatory Networks Based on Repairing Sparse Low-Rank Matrices
778 -- 791Yang Tang, Huijun Gao, Wei Du, Jianquan Lu, Athanasios V. Vasilakos, Jürgen Kurths. Robust Multiobjective Controllability of Complex Neuronal Networks
792 -- 803Yifeng Li, Haifen Chen, Jie Zheng, Alioune Ngom. The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations
804 -- 809Ling Jian, Zhonghang Xia, Xinnan Niu, Xijun Liang, Parimal Samir, Andrew J. Link. 2 Multiple Kernel Fuzzy SVM-Based Data Fusion for Improving Peptide Identification

Volume 13, Issue 3

399 -- 400Mehran Mozaffari Kermani, Reza Azarderakhsh, Kui Ren, Jean-Luc Beuchat. Guest Editorial: Introduction to the Special Section on Emerging Security Trends for Biomedical Computations, Devices, and Infrastructures
401 -- 416Övünç Kocabas, Tolga Soyata, Mehmet K. Aktas. Emerging Security Mechanisms for Medical Cyber Physical Systems
417 -- 430Cheng Chen, Fengchao Zhang, Jamie Barras, Kaspar Althoefer, Swarup Bhunia, Soumyajit Mandal. Authentication of Medicines Using Nuclear Quadrupole Resonance Spectroscopy
431 -- 444Yanmin Gong, Yuguang Fang, Yuanxiong Guo. Private Data Analytics on Biomedical Sensing Data via Distributed Computation
445 -- 458Sk Subidh Ali, Mohamed Ibrahim, Ozgur Sinanoglu, Krishnendu Chakrabarty, Ramesh Karri. Security Assessment of Cyberphysical Digital Microfluidic Biochips
459 -- 471David A. Knox, Robin D. Dowell. A Modeling Framework for Generation of Positional and Temporal Simulations of Transcriptional Regulation
472 -- 482Xu Gu. A Multi-State Optimization Framework for Parameter Estimation in Biological Systems
483 -- 493Jiang (Linda) Xie, Chaojuan Xiang, Jin Ma, Jun Tan, Tieqiao Wen, Jinzhi Lei, Qing Nie. An Adaptive Hybrid Algorithm for Global Network Alignment
494 -- 504Rami Al-Dalky, Kamal Taha, Dirar Mohammad Al Homouz, Murad Qasaimeh. Applying Monte Carlo Simulation to Biomedical Literature to Approximate Genetic Network
505 -- 517Antonin Pavelka, Eva Sebestova, Barbora Kozlíková, Jan Brezovsky, Jirí Sochor, Jirí Damborský. CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules
518 -- 530Zrinka Puljiz, Haris Vikalo. Decoding Genetic Variations: Communications-Inspired Haplotype Assembly
531 -- 540Cong Li, Can Yang, Greg Hather, Ray Liu, Hongyu Zhao. Efficient Drug-Pathway Association Analysis via Integrative Penalized Matrix Decomposition
541 -- 548Isaac G. Macwan, Zihe Zhao, Omar T. Sobh, Ishita Mukerji, Bhushan Dharmadhikari, Prabir K. Patra. Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin
549 -- 556Cheng Liang, Yue Li, Jiawei Luo. A Novel Method to Detect Functional microRNA Regulatory Modules by Bicliques Merging
557 -- 564Ben-teng, Can Yang, Jiming Liu, Zhipeng Cai, Xiang Wan. Exploring the Genetic Patterns of Complex Diseases via the Integrative Genome-Wide Approach
565 -- 570Sajad Mirzaei, Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees
571 -- 577Hai Peng Ren, Xiao-Na Huang, Jia-Xuan Hao. Finding Robust Adaptation Gene Regulatory Networks Using Multi-Objective Genetic Algorithm
578 -- 583Dan He, Irina Rish, David Haws, Laxmi Parida. MINT: Mutual Information Based Transductive Feature Selection for Genetic Trait Prediction
584 -- 591Catherine Stamoulis, Rebecca A. Betensky. Optimization of Signal Decomposition Matched Filtering (SDMF) for Improved Detection of Copy-Number Variations
592 -- 598Yongchao Liu, Thomas Hankeln, Bertil Schmidt. Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data

Volume 13, Issue 2

196 -- 0Pietro Hiram Guzzi, Marco Mina. Guest Editorial for Special Section on Semantic-Based Approaches for Analysis of Biological Data
197 -- 208Giuseppe Agapito, Marianna Milano, Pietro Hiram Guzzi, Mario Cannataro. Extracting Cross-Ontology Weighted Association Rules from Gene Ontology Annotations
209 -- 219Marco Masseroli, Arif Canakoglu, Stefano Ceri. Integration and Querying of Genomic and Proteomic Semantic Annotations for Biomedical Knowledge Extraction
220 -- 232Guo-Xian Yu, Guangyuan Fu, Jun Wang, Hailong Zhu. Predicting Protein Function via Semantic Integration of Multiple Networks
233 -- 247Javier D. Fernandez, Maurizio Lenzerini, Marco Masseroli, Francesco Venco, Stefano Ceri. Ontology-Based Search of Genomic Metadata
248 -- 260Davide Chicco, Marco Masseroli. Ontology-Based Prediction and Prioritization of Gene Functional Annotations
261 -- 271Ka Chun Wong, Yue Li, Chengbin Peng, Hau-San Wong. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray
272 -- 280An Nguyen, Adam Prügel-Bennett, Srinandan Dasmahapatra. A Low Dimensional Approximation For Competence In Bacillus Subtilis
281 -- 290Xumin Ni, Wei Guo, Kai Yuan, Xiong Yang, Zhiming Ma, Shuhua Xu, Shihua Zhang. A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration
291 -- 300Yuanqi Hu, Pantelis Georgiou. A Real-Time de novo DNA Sequencing Assembly Platform Based on an FPGA Implementation
301 -- 314Nitin K. Singh, Mathukumalli Vidyasagar. bLARS: An Algorithm to Infer Gene Regulatory Networks
315 -- 325Daniel Taliun, Johann Gamper, Ulf Leser, Cristian Pattaro. Fast Sampling-Based Whole-Genome Haplotype Block Recognition
326 -- 340Madhu S. Sigdel, Madhav Sigdel, Semih Dinç, Imren Dinç, Marc L. Pusey, Ramazan Savas Aygün. FocusALL: Focal Stacking of Microscopic Images Using Modified Harris Corner Response Measure
341 -- 349Tyler A. Land, Perry Fizzano, Robin B. Kodner. Measuring Cluster Stability in a Large Scale Phylogenetic Analysis of Functional Genes in Metagenomes Using pplacer
350 -- 364Nimit Dhulekar, Shayoni Ray, Daniel Yuan, Abhirami Baskaran, Basak Oztan, Melinda Larsen, Bülent Yener. Prediction of Growth Factor-Dependent Cleft Formation During Branching Morphogenesis Using A Dynamic Graph-Based Growth Model
365 -- 379Narayan Ganesan, Jie Li, Vishakha Sharma, Hanyu Jiang, Adriana B. Compagnoni. Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms
380 -- 391Xudong Tu, Yuanliang Wang, Maolan Zhang, Jinchuan Wu. Using Formal Concept Analysis to Identify Negative Correlations in Gene Expression Data
392 -- 398Jin-Xing Liu, Yong Xu, Ying-Lian Gao, Chun-Hou Zheng, Dong Wang, Qi Zhu. A Class-Information-Based Sparse Component Analysis Method to Identify Differentially Expressed Genes on RNA-Seq Data

Volume 13, Issue 1

1 -- 3De-Shuang Huang, Vitoantonio Bevilacqua, M. Michael Gromiha. Guest Editorial for Special Section on the 10th International Conference on Intelligent Computing (ICIC)
4 -- 11Kyungsook Han, Jeonghoon Lee. GeneNetFinder2: Improved Inference of Dynamic Gene Regulatory Relations with Multiple Regulators
12 -- 26Edmundo Bonilla Huerta, Alberto Luis Hernández-Montiel, Roberto Morales-Caporal, Marco A. Arjona López. Hybrid Framework Using Multiple-Filters and an Embedded Approach for an Efficient Selection and Classification of Microarray Data
27 -- 35Suping Deng, Lin Zhu, De-Shuang Huang. Predicting Hub Genes Associated with Cervical Cancer through Gene Co-Expression Networks
36 -- 42Xumi Qu, Dong Wang, Yuehui Chen, Shanping Qiao, Qing Zhao. Predicting the Subcellular Localization of Proteins with Multiple Sites Based on Multiple Features Fusion
43 -- 54Sun-Yuan Hsieh, Yu-Chun Chou. A Faster cDNA Microarray Gene Expression Data Classifier for Diagnosing Diseases
55 -- 63Lin Zhu, Wei-Li Guo, Suping Deng, De-Shuang Huang. ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition
64 -- 75Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Müller 0009, Christoph Flamm, Ivo L. Hofacker, Philipp Kügler. Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks
76 -- 85Yi Fang, Mengtian Sun, Guoxian Dai, Karthik Ramain. The Intrinsic Geometric Structure of Protein-Protein Interaction Networks for Protein Interaction Prediction
86 -- 98Yu-Huei Cheng. A Novel Teaching-Learning-Based Optimization for Improved Mutagenic Primer Design in Mismatch PCR-RFLP SNP Genotyping
99 -- 111Indranil Roy, Srinivas Aluru. Discovering Motifs in Biological Sequences Using the Micron Automata Processor
112 -- 121S. Bahlouli, A. Mokaddem, F. Hamdache, H. Riane, M. Kameche. ATP Channel On the Electrical Response
122 -- 134Ehsan Ullah, Shuchin Aeron, Soha Hassoun. gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal
135 -- 147Xian Zhang, Ligang Wu, Jiahua Zou. Globally Asymptotic Stability Analysis for Genetic Regulatory Networks with Mixed Delays: An M-Matrix-Based Approach
148 -- 157Preethi Ranganarayanan, Narmadha Thanigesan, Vivek Ananth, Valadi K. Jayaraman, Vigneshwar Ramakrishnan. Identification of Glucose-Binding Pockets in Human Serum Albumin Using Support Vector Machine and Molecular Dynamics Simulations
158 -- 167Oscar Miguel Rivera-Borroto, José Manuel García de la Vega, Yovani Marrero-Ponce, Ricardo Grau. Relational Agreement Measures for Similarity Searching of Cheminformatic Data Sets