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IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 14

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> Home > Journals > IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volume 14, Number 1, January - February 2017

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Ying Tan, Yuhui Shi:
Editorial: Special Section on Bio-Inspired Swarm Computing and Engineering. 1-3
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Ben Niu, Huali Huang, Lijing Tan, Qiqi Duan:
Symbiosis-Based Alternative Learning Multi-Swarm Particle Swarm Optimization. 4-14
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Hongwei Mo, Lili Liu, Jiao Zhao:
A New Magnetotactic Bacteria Optimization Algorithm Based on Moment Migration. 15-26
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Shaoqiu Zheng, Junzhi Li, Andreas Janecek, Ying Tan:
A Cooperative Framework for Fireworks Algorithm. 27-41
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Bei Zhang, Yujun Zheng, Min-Xia Zhang, Shengyong Chen:
Fireworks Algorithm with Enhanced Fireworks Interaction. 42-55
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Shan Cheng, Long-Long Zhao, Xiaoyu Jiang:
An Effective Application of Bacteria Quorum Sensing and Circular Elimination in MOPSO. 56-63
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Yong Zhang, Dun-Wei Gong, Jian Cheng:
Multi-Objective Particle Swarm Optimization Approach for Cost-Based Feature Selection in Classification. 64-75
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Qingjian Ni, Qianqian Pan, Huimin Du, Cen Cao, Yuqing Zhai:
A Novel Cluster Head Selection Algorithm Based on Fuzzy Clustering and Particle Swarm Optimization. 76-84
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Fei Han, Chun Yang, Ya-Qi Wu, Jiansheng Zhu, Qing-Hua Ling, Yuqing Song, De-Shuang Huang:
A Gene Selection Method for Microarray Data Based on Binary PSO Encoding Gene-to-Class Sensitivity Information. 85-96
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Bo Zhang, Haibin Duan:
Three-Dimensional Path Planning for Uninhabited Combat Aerial Vehicle Based on Predator-Prey Pigeon-Inspired Optimization in Dynamic Environment. 97-107
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Yuxin Liu, Chao Gao, Zili Zhang, Yuxiao Lu, Shi Chen, Mingxin Liang, Li Tao:
Solving NP-Hard Problems with Physarum-Based Ant Colony System. 108-120
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Elena Czeizler, Tommi Hirvola, Kalle Karhu:
A Graph-Theoretical Approach for Motif Discovery in Protein Sequences. 121-130
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Hasan M. Jamil:
A Visual Interface for Querying Heterogeneous Phylogenetic Databases. 131-144
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Lin Zhang, Hui Liu, Yufei Huang, Xuesong Wang, Yidong Chen, Jia Meng:
Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. 145-154
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Lun Hu, Keith C. C. Chan:
Extracting Coevolutionary Features from Protein Sequences for Predicting Protein-Protein Interactions. 155-166
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Mehrdad J. Gangeh, Hadi Zarkoob, Ali Ghodsi:
Fast and Scalable Feature Selection for Gene Expression Data Using Hilbert-Schmidt Independence Criterion. 167-181
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Hailong Hu, Zhong Li, Hongwei Dong, Tianhe Zhou:
Graphical Representation and Similarity Analysis of Protein Sequences Based on Fractal Interpolation. 182-192
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Vincenzo Bonnici, Rosalba Giugno:
On the Variable Ordering in Subgraph Isomorphism Algorithms. 193-203
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Arvind Kumar Sinha, Pradeep Singh, Anand Prakash, Dharm Pal, Anuradha Dube, Awanish Kumar:
Putative Drug and Vaccine Target Identification in Leishmania donovani Membrane Proteins Using Naïve Bayes Probabilistic Classifier. 204-211
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Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung:
Transductive Learning for Multi-Label Protein Subchloroplast Localization Prediction. 212-224
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Kuize Zhang, Lijun Zhang, Shaoshuai Mou:
An Application of Invertibility of Boolean Control Networks to the Control of the Mammalian Cell Cycle. 225-229

Volume 14, Number 2, March - April 2017

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Aidong Zhang:
Editorial from the New Editor-in-Chief. 251
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Illhoi Yoo, Amarda Shehu:
Guest Editorial for Special Section on BIBM 2014. 252-253
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En-Shiun Annie Lee, Ho-Yin Antonio Sze-To, Man Hon Wong, Kwong-Sak Leung, Terrence Chi-Kong Lau, Andrew K. C. Wong:
Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering. 254-263
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Yong Zhang, Xiaohua Hu, Xingpeng Jiang:
Multi-View Clustering of Microbiome Samples by Robust Similarity Network Fusion and Spectral Clustering. 264-271
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Ilona Kifer, Rui M. Branca, Amir Ben-Dor, Linhui Zhai, Ping Xu, Janne Lehtiö, Zohar Yakhini:
Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics. 272-281
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Huiru Zheng, Chaoyang Wang, Haiying Wang:
Analysis of Organization of the Interactome Using Dominating Sets: A Case Study on Cell Cycle Interaction Networks. 282-289
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Matthias Becker, Nadia Magnenat-Thalmann:
Muscle Tissue Labeling of Human Lower Limb in Multi-Channel mDixon MR Imaging: Concepts and Applications. 290-299
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Daniel Veltri, Uday Kamath, Amarda Shehu:
Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming. 300-313
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Mitra Basu, Yi Pan, Jianxin Wang:
Guest Editors Introduction to the Special Section on ISBRA 2014. 314-315
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Fa Zhang, Yu Chen, Fei Ren, Xuan Wang, Zhiyong Liu, Xiaohua Wan:
A Two-Phase Improved Correlation Method for Automatic Particle Selection in Cryo-EM. 316-325
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Yi Liu, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie:
An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra. 326-336
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Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu:
NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra. 337-344
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Lin Zhu, Suping Deng, Zhu-Hong You, De-Shuang Huang:
Identifying Spurious Interactions in the Protein-Protein Interaction Networks Using Local Similarity Preserving Embedding. 345-352
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Xingpeng Jiang, Xiaohua Hu, Weiwei Xu:
Microbiome Data Representation by Joint Nonnegative Matrix Factorization with Laplacian Regularization. 353-359
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Wei Peng, Min Li, Lu Chen, Lusheng Wang:
Predicting Protein Functions by Using Unbalanced Random Walk Algorithm on Three Biological Networks. 360-369
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Min Li, Yu Lu, Zhibei Niu, Fang-Xiang Wu:
United Complex Centrality for Identification of Essential Proteins from PPI Networks. 370-380
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Behrang Mahjani, Salman Zubair Toor, Carl Nettelblad, Sverker Holmgren:
A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits. 381-392
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Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, K. Robert Lai, Tzong-Yi Lee:
A New Scheme to Characterize and Identify Protein Ubiquitination Sites. 393-403
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Julia Matsieva, Steven Kelk, Céline Scornavacca, Chris Whidden, Dan Gusfield:
A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. 404-417
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Ashok Rajaraman, João Paulo Pereira Zanetti, Ján Manuch, Cédric Chauve:
Algorithms and Complexity Results for Genome Mapping Problems. 418-430
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Kieran Alden, Jon Timmis, Paul S. Andrews, Henrique Veiga-Fernandes, Mark Coles:
Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models. 431-442
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Oscar Días, Daniel Gomes, Paulo Vilaça, João Cardoso, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
Genome-Wide Semi-Automated Annotation of Transporter Systems. 443-456
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Katya Mkrtchyan, Anirban Chakraborty, Amit K. Roy-Chowdhury:
Optimal Landmark Selection for Registration of 4D Confocal Image Stacks in Arabidopsis. 457-467
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Momoko Hayamizu, Hiroshi Endo, Kenji Fukumizu:
A Characterization of Minimum Spanning Tree-Like Metric Spaces. 468-471
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Olivier Boes, Mareike Fischer, Steven Kelk:
A Linear Bound on the Number of States in Optimal Convex Characters for Maximum Parsimony Distance. 472-477
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Thao Thi Phuong Nguyen, Le Sy Vinh, Hai Bich Ho, Si Quang Le:
Building Ancestral Recombination Graphs for Whole Genomes. 478-483
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Emmanouil Athanasiadis, Marilena M. Bourdakou, George M. Spyrou:
D-Map: Random Walking on Gene Network Inference Maps Towards differential Avenue Discovery. 484-490
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Stéphane Mottelet, Gil Gaullier, Georges Sadaka:
Metabolic Flux Analysis in Isotope Labeling Experiments Using the Adjoint Approach. 491-497
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Scott Goldweber, Jamal Theodore, John Torcivia-Rodriguez, Vahan Simonyan, Raja Mazumder:
Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices. 498-500

Volume 14, Number 3, May - June 2017

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Fei Wang, Xiaoli Li, Jason T. L. Wang, See-Kiong Ng:
Guest Editorial: Special Section on Biological Data Mining and Its Applications in Healthcare. 501-502
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Hua Wang, Lin Yan, Heng Huang, Chris H. Q. Ding:
From Protein Sequence to Protein Function via Multi-Label Linear Discriminant Analysis. 503-513
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Jianqiang Li, Fei Wang:
Towards Unsupervised Gene Selection: A Matrix Factorization Framework. 514-521
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Chelsea J.-T. Ju, Zhuangtian Zhao, Wei Wang:
Efficient Approach to Correct Read Alignment for Pseudogene Abundance Estimates. 522-533
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Peter B. Walker, Jacob N. Norris, Anna E. Tschiffely, Melissa L. Mehalick, Craig A. Cunningham, Ian N. Davidson:
Applications of Transductive Spectral Clustering Methods in a Military Medical Concussion Database. 534-544
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Jelena Stojanovic, Djordje Gligorijevic, Vladan Radosavljevic, Nemanja Djuric, Mihajlo Grbovic, Zoran Obradovic:
Modeling Healthcare Quality via Compact Representations of Electronic Health Records. 545-554
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Robert Moskovitch, Hyunmi Choi, George Hripcsak, Nicholas P. Tatonetti:
Prognosis of Clinical Outcomes with Temporal Patterns and Experiences with One Class Feature Selection. 555-563
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Xin Wang, Jinbo Bi:
Bi-convex Optimization to Learn Classifiers from Multiple Biomedical Annotations. 564-575
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Robert W. Harrison, Ion I. Mandoiu, Alexander Zelikovsky:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 576-577
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Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al-Nasr, Jing He:
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images. 578-586
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Misagh Kordi, Mukul S. Bansal:
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. 587-599
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Xuan Guo, Jing Zhang, Zhipeng Cai, Ding-Zhu Du, Yi Pan:
Searching Genome-Wide Multi-Locus Associations for Multiple Diseases Based on Bayesian Inference. 600-610
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Hao Ji, Yaohang Li, Seth H. Weinberg:
Calcium Ion Fluctuations Alter Channel Gating in a Stochastic Luminal Calcium Release Site Model. 611-619
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Gustavo Rodrigues Galvão, Christian Baudet, Zanoni Dias:
Sorting Circular Permutations by Super Short Reversals. 620-633
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Weihua Zheng, Kenli Li, Keqin Li, Hing-Cheung So:
A Modified Multiple Alignment Fast Fourier Transform with Higher Efficiency. 634-645
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Ali Ezzat, Peilin Zhao, Min Wu, Xiaoli Li, Chee Keong Kwoh:
Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization. 646-656
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Vo Hong Thanh, Roberto Zunino, Corrado Priami:
Efficient Constant-Time Complexity Algorithm for Stochastic Simulation of Large Reaction Networks. 657-667
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James Arram, Thomas Kaplan, Wayne Luk, Peiyong Jiang:
Leveraging FPGAs for Accelerating Short Read Alignment. 668-677
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Feng He, Guanghui Zhu, Yin-Ying Wang, Xing-Ming Zhao, De-Shuang Huang:
PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-Scale Data. 678-686
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Xiangxiang Zeng, Yuanlu Liao, Yuansheng Liu, Quan Zou:
Prediction and Validation of Disease Genes Using HeteSim Scores. 687-695
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Boris Shabash, Kay C. Wiese:
RNA Visualization: Relevance and the Current State-of-the-Art Focusing on Pseudoknots. 696-712
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Chen Peng, Ao Li:
A Heterogeneous Network Based Method for Identifying GBM-Related Genes by Integrating Multi-Dimensional Data. 713-720
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Anastasiia Vasylchenkova, Miha Mraz, Nikolaj Zimic, Miha Moskon:
Classical Mechanics Approach Applied to Analysis of Genetic Oscillators. 721-727
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Poly H. da Silva, Raphael Machado, Simone Dantas, Marília D. V. Braga:
Genomic Distance with High Indel Costs. 728-732
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Min Wu, Le Ou-Yang, Xiaoli Li:
Protein Complex Detection via Effective Integration of Base Clustering Solutions and Co-Complex Affinity Scores. 733-739
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Fangfei Li, Yang Tang:
Robust Reachability of Boolean Control Networks. 740-745
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Zhangming Yan, Ke Liu, Shunian Xiang, Zhirong Sun:
txCoords: A Novel Web Application for Transcriptomic Peak Re-Mapping. 746-748

Volume 14, Number 4, July - August 2017

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Manjari Jha, Raunaq Malhotra, Raj Acharya:
A Generalized Lattice Based Probabilistic Approach for Metagenomic Clustering. 749-761
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Sanghamitra Bandyopadhyay, Koushik Mallick:
A New Feature Vector Based on Gene Ontology Terms for Protein-Protein Interaction Prediction. 762-770
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Heewon Park, Yuichi Shiraishi, Seiya Imoto, Satoru Miyano:
A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity. 771-782
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Chao Wang, Dong Dai, Xi Li, Aili Wang, Xuehai Zhou:
SuperMIC: Analyzing Large Biological Datasets in Bioinformatics with Maximal Information Coefficient. 783-795
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Rao Muhammad Adeel Nawab, Mark Stevenson, Paul D. Clough:
An IR-Based Approach Utilizing Query Expansion for Plagiarism Detection in MEDLINE. 796-804
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Sugeerth Murugesan, Kristopher E. Bouchard, Jesse A. Brown, Bernd Hamann, William W. Seeley, Andrew Trujillo, Gunther H. Weber:
Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity. 805-818
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Sandra Barragan, Cristina Rueda, Miguel A. Fernández:
Circular Order Aggregation and Its Application to Cell-Cycle Genes Expressions. 819-829
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Jing Zhang, Hao Wang, Wu-chun Feng:
cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU. 830-843
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Lu Xie, Gregory R. Smith, Russell Schwartz:
Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data. 844-855
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Yue Zhang, Yiu-ming Cheung, Bo Xu, Weifeng Su:
Detection Copy Number Variants from NGS with Sparse and Smooth Constraints. 856-867
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Xiaofei Fan, Xian Zhang, Ligang Wu, Michael Shi:
Finite-Time Stability Analysis of Reaction-Diffusion Genetic Regulatory Networks with Time-Varying Delays. 868-879
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Maziyar Baran Pouyan, Mehrdad Nourani:
Identifying Cell Populations in Flow Cytometry Data Using Phenotypic Signatures. 880-891
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  - journals/tcbb/KellerALBBBBM17
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Anne Florence Keller, Nicolas Ambert, Arnaud Legendre, Mathieu Bedez, Jean-Marie Bouteiller, Serge Bischoff, Michel Baudry, Saliha Moussaoui:
Impact of Synaptic Localization and Subunit Composition of Ionotropic Glutamate Receptors on Synaptic Function: Modeling and Simulation Studies. 892-904
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Yuansheng Liu, Xiangxiang Zeng, Zengyou He, Quan Zou:
Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources. 905-915
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Min Li, Zhongxiang Liao, Yiming He, Jianxin Wang, Junwei Luo, Yi Pan:
ISEA: Iterative Seed-Extension Algorithm for De Novo Assembly Using Paired-End Information and Insert Size Distribution. 916-925
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Tianle Ma, Aidong Zhang:
Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems. 926-946
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Jianhua Zhang, Zhong Yin, Rubin Wang:
Pattern Classification of Instantaneous Cognitive Task-load Through GMM Clustering, Laplacian Eigenmap, and Ensemble SVMs. 947-965
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Liang Yu, Ruidan Su, Bingbo Wang, Long Zhang, Yapeng Zou, Jing Zhang, Lin Gao:
Prediction of Novel Drugs for Hepatocellular Carcinoma Based on Multi-Source Random Walk. 966-977
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Egils Stalidzans, Ivars Mozga, Jurijs Sulins, Peteris Zikmanis:
Search for a Minimal Set of Parameters by Assessing the Total Optimization Potential for a Dynamic Model of a Biochemical Network. 978-985
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Imren Dinç, Semih Dinç, Madhav Sigdel, Madhu S. Sigdel, Marc L. Pusey, Ramazan Savas Aygün:
Super-Thresholding: Supervised Thresholding of Protein Crystal Images. 986-998

Volume 14, Number 5, September - October 2017

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Ümit V. Çatalyürek:
Guest Editor's Introduction: Selected Papers from ACM-BCB 2014. 1000-1001
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Pawel Górecki, Jaroslaw Paszek, Oliver Eulenstein:
Unconstrained Diameters for Deep Coalescence. 1002-1012
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Zhiyong Wang, Benika Hall, Jinbo Xu, Xinghua Shi:
A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants. 1013-1027
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Dan F. DeBlasio, John D. Kececioglu:
Learning Parameter-Advising Sets for Multiple Sequence Alignment. 1028-1041
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Anna M. Ritz, Brendan Avent, T. M. Murali:
Pathway Analysis with Signaling Hypergraphs. 1042-1055
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Boyoung Yoo, Fazle Elahi Faisal, Huili Chen, Tijana Milenkovic:
Improving Identification of Key Players in Aging via Network De-Noising and Core Inference. 1056-1069
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Joseph Azofeifa, Mary A. Allen, Manuel E. Lladser, Robin D. Dowell:
An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq. 1070-1081
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Norman Goodacre, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy H. Wu:
Predicting nsSNPs that Disrupt Protein-Protein Interactions Using Docking. 1082-1093
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Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin:
IPED2: Inheritance Path Based Pedigree Reconstruction Algorithm for Complicated Pedigrees. 1094-1103
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De-Shuang Huang, Vitoantonio Bevilacqua, M. Michael Gromiha:
Guest Editorial for Special Section on the 11th International Conference on Intelligent Computing (ICIC). 1104-1105
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Hongjie Wu, Kun Wang, Liyao Lu, Yu Xue, Qiang Lyu, Min Jiang:
Deep Conditional Random Field Approach to Transmembrane Topology Prediction and Application to GPCR Three-Dimensional Structure Modeling. 1106-1114
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Shu-Guang Ge, Junfeng Xia, Wen Sha, Chun-Hou Zheng:
Cancer Subtype Discovery Based on Integrative Model of Multigenomic Data. 1115-1121
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Wenzheng Bao, Dong Wang, Yuehui Chen:
Classification of Protein Structure Classes on Flexible Neutral Tree. 1122-1133
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Qingfeng Chen, Chaowang Lan, Baoshan Chen, Lusheng Wang, Jinyan Li, Chengqi Zhang:
Exploring Consensus RNA Substructural Patterns Using Subgraph Mining. 1134-1146
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Su-Ping Deng, Shaolong Cao, De-Shuang Huang, Yu-Ping Wang:
Identifying Stages of Kidney Renal Cell Carcinoma by Combining Gene Expression and DNA Methylation Data. 1147-1153
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Lin Yuan, Lin Zhu, Wei-Li Guo, Xiaobo Zhou, Youhua Zhang, Zhenhua Huang, De-Shuang Huang:
Nonconvex Penalty Based Low-Rank Representation and Sparse Regression for eQTL Mapping. 1154-1164
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Jian-Qiang Li, Zhu-Hong You, Xiao Li, Zhong Ming, Xing Chen:
PSPEL: In Silico Prediction of Self-Interacting Proteins from Amino Acids Sequences Using Ensemble Learning. 1165-1172
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Pu Wang, Ruiquan Ge, Xuan Xiao, Manli Zhou, Fengfeng Zhou:
hMuLab: A Biomedical Hybrid MUlti-LABel Classifier Based on Multiple Linear Regression. 1173-1180
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Tuomo Mäki-Marttunen:
An Algorithm for Motif-Based Network Design. 1181-1186
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Lichun Ma, Debby Dan Wang, Bin Zou, Hong Yan:
An Eigen-Binding Site Based Method for the Analysis of Anti-EGFR Drug Resistance in Lung Cancer Treatment. 1187-1194
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Antonio d'Acierno:
IsAProteinDB: An Indexed Database of Trypsinized Proteins for Fast Peptide Mass Fingerprinting. 1195-1201

Volume 14, Number 6, November - December 2017

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Ahmad Al Kawam, Sunil Khatri, Aniruddha Datta:
A Survey of Software and Hardware Approaches to Performing Read Alignment in Next Generation Sequencing. 1202-1213
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Utku Sirin, Faruk Polat, Reda Alhajj:
Batch Mode TD(λ) for Controlling Partially Observable Gene Regulatory Networks. 1214-1227
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Biji C. L., Achuthsankar S. Nair:
Benchmark Dataset for Whole Genome Sequence Compression. 1228-1236
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Francisco do Nascimento, Katia S. Guimarães:
Copy Number Variations Detection: Unravelling the Problem in Tangible Aspects. 1237-1250
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