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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 13
Volume 13, Number 1, January - February 2016
- De-Shuang Huang, Vitoantonio Bevilacqua
, M. Michael Gromiha:
Guest Editorial for Special Section on the 10th International Conference on Intelligent Computing (ICIC). 1-3 - Kyungsook Han, Jeonghoon Lee:
GeneNetFinder2: Improved Inference of Dynamic Gene Regulatory Relations with Multiple Regulators. 4-11 - Edmundo 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. 12-26 - Suping Deng, Lin Zhu, De-Shuang Huang:
Predicting Hub Genes Associated with Cervical Cancer through Gene Co-Expression Networks. 27-35 - Xumi Qu, Dong Wang, Yuehui Chen, Shanping Qiao, Qing Zhao:
Predicting the Subcellular Localization of Proteins with Multiple Sites Based on Multiple Features Fusion. 36-42 - Sun-Yuan Hsieh, Yu-Chun Chou:
A Faster cDNA Microarray Gene Expression Data Classifier for Diagnosing Diseases. 43-54 - Lin 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. 55-63 - Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Müller, Christoph Flamm, Ivo L. Hofacker, Philipp Kügler:
Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks. 64-75 - Yi Fang, Mengtian Sun, Guoxian Dai, Karthik Ramani:
The Intrinsic Geometric Structure of Protein-Protein Interaction Networks for Protein Interaction Prediction. 76-85 - Yu-Huei Cheng:
A Novel Teaching-Learning-Based Optimization for Improved Mutagenic Primer Design in Mismatch PCR-RFLP SNP Genotyping. 86-98 - Indranil Roy, Srinivas Aluru:
Discovering Motifs in Biological Sequences Using the Micron Automata Processor. 99-111 - Samia Bahlouli, Allel Mokaddem, Fatima Hamdache, Houaria Riane, Mostefa Kameche:
Fractal Behavior of the Pancreatic β-Cell Near the Percolation Threshold: Effect of the KATP Channel On the Electrical Response. 112-121 - Ehsan Ullah, Shuchin Aeron, Soha Hassoun:
gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal. 122-134 - Xian Zhang, Ligang Wu, Jiahua Zou:
Globally Asymptotic Stability Analysis for Genetic Regulatory Networks with Mixed Delays: An M-Matrix-Based Approach. 135-147 - Preethi Ranganarayanan, Narmadha Thanigesan, R. P. Vivek-Ananth, Valadi K. Jayaraman, Vigneshwar Ramakrishnan:
Identification of Glucose-Binding Pockets in Human Serum Albumin Using Support Vector Machine and Molecular Dynamics Simulations. 148-157 - Oscar Miguel Rivera-Borroto, José Manuel García de la Vega, Yovani Marrero-Ponce, Ricardo Grau:
Relational Agreement Measures for Similarity Searching of Cheminformatic Data Sets. 158-167
Volume 13, Number 2, March - April 2016
- Pietro Hiram Guzzi, Marco Mina:
Guest Editorial for Special Section on Semantic-Based Approaches for Analysis of Biological Data. 196 - Giuseppe Agapito, Marianna Milano, Pietro Hiram Guzzi, Mario Cannataro:
Extracting Cross-Ontology Weighted Association Rules from Gene Ontology Annotations. 197-208 - Marco Masseroli, Arif Canakoglu, Stefano Ceri:
Integration and Querying of Genomic and Proteomic Semantic Annotations for Biomedical Knowledge Extraction. 209-219 - Guo-Xian Yu, Guangyuan Fu, Jun Wang, Hailong Zhu:
Predicting Protein Function via Semantic Integration of Multiple Networks. 220-232 - Javier D. Fernández, Maurizio Lenzerini, Marco Masseroli, Francesco Venco, Stefano Ceri:
Ontology-Based Search of Genomic Metadata. 233-247 - Davide Chicco, Marco Masseroli:
Ontology-Based Prediction and Prioritization of Gene Functional Annotations. 248-260 - Ka-Chun Wong, Yue Li, Chengbin Peng, Hau-San Wong:
A Comparison Study for DNA Motif Modeling on Protein Binding Microarray. 261-271 - An Nguyen, Adam Prügel-Bennett, Srinandan Dasmahapatra:
A Low Dimensional Approximation For Competence In Bacillus Subtilis. 272-280 - Xumin 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. 281-290 - Yuanqi Hu, Pantelis Georgiou:
A Real-Time de novo DNA Sequencing Assembly Platform Based on an FPGA Implementation. 291-300 - Nitin K. Singh, Mathukumalli Vidyasagar:
bLARS: An Algorithm to Infer Gene Regulatory Networks. 301-314 - Daniel Taliun, Johann Gamper, Ulf Leser, Cristian Pattaro:
Fast Sampling-Based Whole-Genome Haplotype Block Recognition. 315-325 - Madhu 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. 326-340 - Tyler A. Land, Perry Fizzano, Robin B. Kodner:
Measuring Cluster Stability in a Large Scale Phylogenetic Analysis of Functional Genes in Metagenomes Using pplacer. 341-349 - Nimit 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. 350-364 - Narayan 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. 365-379 - Xudong Tu, Yuanliang Wang, Maolan Zhang, Jinchuan Wu:
Using Formal Concept Analysis to Identify Negative Correlations in Gene Expression Data. 380-391 - Jin-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. 392-398
Volume 13, Number 3, May - June 2016
- Mehran 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. 399-400 - Övünç Kocabas, Tolga Soyata, Mehmet K. Aktas:
Emerging Security Mechanisms for Medical Cyber Physical Systems. 401-416 - Cheng Chen, Fengchao Zhang, Jamie Barras, Kaspar Althoefer, Swarup Bhunia, Soumyajit Mandal:
Authentication of Medicines Using Nuclear Quadrupole Resonance Spectroscopy. 417-430 - Yanmin Gong, Yuguang Fang, Yuanxiong Guo:
Private Data Analytics on Biomedical Sensing Data via Distributed Computation. 431-444 - Sk Subidh Ali, Mohamed Ibrahim, Ozgur Sinanoglu, Krishnendu Chakrabarty, Ramesh Karri:
Security Assessment of Cyberphysical Digital Microfluidic Biochips. 445-458 - David A. Knox, Robin D. Dowell:
A Modeling Framework for Generation of Positional and Temporal Simulations of Transcriptional Regulation. 459-471 - Xu Gu:
A Multi-State Optimization Framework for Parameter Estimation in Biological Systems. 472-482 - Jiang (Linda) Xie, Chaojuan Xiang, Jin Ma, Jun Tan, Tieqiao Wen, Jinzhi Lei, Qing Nie:
An Adaptive Hybrid Algorithm for Global Network Alignment. 483-493 - Rami Al-Dalky, Kamal Taha, Dirar Mohammad Al Homouz, Murad Qasaimeh:
Applying Monte Carlo Simulation to Biomedical Literature to Approximate Genetic Network. 494-504 - Antonín Pavelka, Eva Sebestova, Barbora Kozlíková, Jan Brezovsky, Jirí Sochor, Jirí Damborský:
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. 505-517 - Zrinka Puljiz, Haris Vikalo:
Decoding Genetic Variations: Communications-Inspired Haplotype Assembly. 518-530 - Cong Li, Can Yang, Greg Hather, Ray Liu, Hongyu Zhao:
Efficient Drug-Pathway Association Analysis via Integrative Penalized Matrix Decomposition. 531-540 - Isaac 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. 541-548 - Cheng Liang, Yue Li, Jiawei Luo:
A Novel Method to Detect Functional microRNA Regulatory Modules by Bicliques Merging. 549-556 - Ben Teng, Can Yang, Jiming Liu, Zhipeng Cai, Xiang Wan:
Exploring the Genetic Patterns of Complex Diseases via the Integrative Genome-Wide Approach. 557-564 - Sajad Mirzaei, Yufeng Wu:
Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. 565-570 - Hai-Peng Ren, Xiao-Na Huang, Jia-Xuan Hao:
Finding Robust Adaptation Gene Regulatory Networks Using Multi-Objective Genetic Algorithm. 571-577 - Dan He, Irina Rish, David Haws, Laxmi Parida:
MINT: Mutual Information Based Transductive Feature Selection for Genetic Trait Prediction. 578-583 - Catherine Stamoulis, Rebecca A. Betensky:
Optimization of Signal Decomposition Matched Filtering (SDMF) for Improved Detection of Copy-Number Variations. 584-591 - Yongchao Liu, Thomas Hankeln, Bertil Schmidt:
Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data. 592-598
Volume 13, Number 4, July - August 2016
- Biing-Feng Wang:
A New Efficient Algorithm for the All Sorting Reversals Problem with No Bad Components. 599-609 - Junzhong Ji, Jia Wei Lv, Cuicui Yang, Aidong Zhang:
Detecting Functional Modules Based on a Multiple-Grain Model in Large-Scale Protein-Protein Interaction Networks. 610-622 - Ngoc Hieu Tran, Xin Chen:
AMAS: Optimizing the Partition and Filtration of Adaptive Seeds to Speed up Read Mapping. 623-633 - Zhenchao Jiang, Lishuang Li, Degen Huang:
An Unsupervised Graph Based Continuous Word Representation Method for Biomedical Text Mining. 634-642 - Daniele 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. 643-655 - Jianing Xi, Ao Li:
Discovering Recurrent Copy Number Aberrations in Complex Patterns via Non-Negative Sparse Singular Value Decomposition. 656-668 - Lishuang Li, Shanshan Liu, Meiyue Qin, Yiwen Wang, Degen Huang:
Extracting Biomedical Event with Dual Decomposition Integrating Word Embeddings. 669-677 - Benjamin Xueqi Guan, Bir Bhanu, Prue Talbot, Nikki Jo-Hao Weng:
Extraction of Blebs in Human Embryonic Stem Cell Videos. 678-688 - Ahed Elmsallati, Connor Clark, Jugal Kalita:
Global Alignment of Protein-Protein Interaction Networks: A Survey. 689-705 - Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung:
Mem-mEN: Predicting Multi-Functional Types of Membrane Proteins by Interpretable Elastic Nets. 706-718 - Lori A. Dalton:
Optimal ROC-Based Classification and Performance Analysis under Bayesian Uncertainty Models. 719-729 - Shun-ichi Azuma, Katsuya Owaki, Nobuhiro Shinohara, Toshiharu Sugie:
Performance Analysis of Chemotaxis Controllers: Which has Better Chemotaxis Controller, Escherichia coli or Paramecium caudatum? 730-741 - Sajid A. Marhon, Stefan C. Kremer:
Prediction of Protein Coding Regions Using a Wide-Range Wavelet Window Method. 742-753 - Yun-Bo Zhao, J. Krishnan:
Probabilistic Boolean Network Modelling and Analysis Framework for mRNA Translation. 754-766 - Young Hwan Chang, Roel Dobbe, Palak Bhushan, Joe W. Gray, Claire J. Tomlin:
Reconstruction of Gene Regulatory Networks Based on Repairing Sparse Low-Rank Matrices. 767-777 - Yang Tang, Huijun Gao, Wei Du, Jianquan Lu, Athanasios V. Vasilakos, Jürgen Kurths:
Robust Multiobjective Controllability of Complex Neuronal Networks. 778-791 - Yifeng Li, Haifen Chen, Jie Zheng, Alioune Ngom:
The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations. 792-803 - Ling Jian, Zhonghang Xia, Xinnan Niu, Xijun Liang, Parimal Samir, Andrew J. Link:
ℓ2 Multiple Kernel Fuzzy SVM-Based Data Fusion for Improving Peptide Identification. 804-809
Volume 13, Number 5, September - October 2016
- Chao Wang, Hong Yu, Aili Wang, Kai Xia:
Guest Editorial for Special Section on Big Data Computing and Processing in Computational Biology and Bioinformatics. 810-811 - Erin J. Moore, Thirimachos Bourlai:
Expectation Maximization of Frequent Patterns, a Specific, Local, Pattern-Based Biclustering Algorithm for Biological Datasets. 812-824 - Ya Zhang, Ao Li, Chen Peng, Minghui Wang:
Improve Glioblastoma Multiforme Prognosis Prediction by Using Feature Selection and Multiple Kernel Learning. 825-835 - Xiaoyi Xu, Minghui Wang:
Inferring Disease Associated Phosphorylation Sites via Random Walk on Multi-Layer Heterogeneous Network. 836-844 - Cheng Ling, Tsuyoshi Hamada, Jing-Yang Gao, Guoguang Zhao, Donghong Sun, Weifeng Shi:
MrBayes tgMC3++: A High Performance and Resource-Efficient GPU-Oriented Phylogenetic Analysis Method. 845-854 - Jingsong Zhang, Yinglin Wang, Chao Zhang, Yongyong Shi:
Mining Contiguous Sequential Generators in Biological Sequences. 855-867 - Keru Hua, Qin Yu, Ruiming Zhang:
A Guaranteed Similarity Metric Learning Framework for Biological Sequence Comparison. 868-877 - Steinar Thorvaldsen:
A Mutation Model from First Principles of the Genetic Code. 878-886 - Xiao-hu Hao, Gui-jun Zhang, Xiaogen Zhou, Xufeng Yu:
A Novel Method Using Abstract Convex Underestimation in Ab-Initio Protein Structure Prediction for Guiding Search in Conformational Feature Space. 887-900 - Peng 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. 901-912 - Filippo Disanto, Noah A. Rosenberg:
Asymptotic Properties of the Number of Matching Coalescent Histories for Caterpillar-Like Families of Species Trees. 913-925 - David Nogueira, Pedro Tomás, Nuno Roma:
BowMapCL: Burrows-Wheeler Mapping on Multiple Heterogeneous Accelerators. 926-938 - Yan Shi, Jinglong Niu, Zhixin Cao, Maolin Cai, Jian Zhu, Weiqing Xu:
Online Estimation Method for Respiratory Parameters Based on a Pneumatic Model. 939-946 - Liqi 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. 947-953 - Apostolos Axenopoulos, Dimitrios Rafailidis, Georgios Th. Papadopoulos, Elias N. Houstis, Petros Daras:
Similarity Search of Flexible 3D Molecules Combining Local and Global Shape Descriptors. 954-970 - Jun Chin Ang, Andri Mirzal, Habibollah Haron, Haza Nuzly Abdull Hamed:
Supervised, Unsupervised, and Semi-Supervised Feature Selection: A Review on Gene Selection. 971-989 - Yuanning Liu, Qi Zhao, Hao Zhang, Rui Xu, Yang Li, Liyan Wei:
A New Method to Predict RNA Secondary Structure Based on RNA Folding Simulation. 990-995 - Yung-Keun Kwon, Junil Kim, Kwang-Hyun Cho:
Dynamical Robustness against Multiple Mutations in Signaling Networks. 996-1002
Volume 13, Number 6, November - December 2016
- Xing-Ming Zhao:
Data Mining in Systems Biology. 1003 - Jian Tang, Shuigeng Zhou:
A New Approach for Feature Selection from Microarray Data Based on Mutual Information. 1004-1015 - Xi Yin, Ying-Ying Xu, Hong-Bin Shen:
Enhancing the Prediction of Transmembrane β-Barrel Segments with Chain Learning and Feature Sparse Representation. 1016-1026 - Gui-Min Qin, Rui-Yi Li, Xing-Ming Zhao:
Identifying Disease Associated miRNAs Based on Protein Domains. 1027-1035 - Hao Wu, Lin Gao, Nikola K. Kasabov:
Network-Based Method for Inferring Cancer Progression at the Pathway Level from Cross-Sectional Mutation Data. 1036-1044 - Fabio Fabris, Alex Alves Freitas, Jennifer M. A. Tullet:
An Extensive Empirical Comparison of Probabilistic Hierarchical Classifiers in Datasets of Ageing-Related Genes. 1045-1058 - Dong Wang, Jin-Xing Liu, Ying-Lian Gao, Chun-Hou Zheng, Yong Xu:
Characteristic Gene Selection Based on Robust Graph Regularized Non-Negative Matrix Factorization. 1059-1067 - Adriano N. Raposo, Abel João Padrão Gomes:
Computational 3D Assembling Methods for DNA: A Survey. 1068-1085 - Sumanta Ray, Sanghamitra Bandyopadhyay:
Discovering Condition Specific Topological Pattern Changes in Coexpression Network: An Application to HIV-1 Progression. 1086-1099 - Natalia Vilor-Tejedor, Juan R. González, Malu Luz Calle:
Efficient and Powerful Method for Combining P-Values in Genome-Wide Association Studies. 1100-1106 - Xiaoqing Cheng, Tomoya Mori, Yushan Qiu, Wai-Ki Ching, Tatsuya Akutsu:
Exact Identification of the Structure of a Probabilistic Boolean Network from Samples. 1107-1116 - Maoguo Gong, Zhenglin Peng, Lijia Ma, Jiaxiang Huang:
Global Biological Network Alignment by Using Efficient Memetic Algorithm. 1117-1129 - Meredith Ray, Jian Kang, Hongmei Zhang:
Identifying Activation Centers with Spatial Cox Point Processes Using fMRI Data. 1130-1141 - Hong Wang, Xicheng Wang, Zheng Li, Keqiu Li:
Kriging-Based Parameter Estimation Algorithm for Metabolic Networks Combined with Single-Dimensional Optimization and Dynamic Coordinate Perturbation. 1142-1154 - Guanyun Wei, Sheng Qin, Wenjuan Li, Liming Chen, Fei Ma:
MDTE DB: A Database for MicroRNAs Derived from Transposable Element. 1155-1160 - Shuang Cheng, Maozu Guo, Chunyu Wang, Xiaoyan Liu, Yang Liu, Xuejian Wu:
MiRTDL: A Deep Learning Approach for miRNA Target Prediction. 1161-1169 - Yi Qi, Jiawei Luo:
Prediction of Essential Proteins Based on Local Interaction Density. 1170-1182 - Sergiy Ancherbak, Ercan E. Kuruoglu, Martin Vingron:
Time-Dependent Gene Network Modelling by Sequential Monte Carlo. 1183-1193 - Yang Liu, Bowen Li, Jungang Lou:
Disturbance Decoupling of Singular Boolean Control Networks. 1194-1200
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