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IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 14
Volume 14, Number 1, January - February 2017
- Ying Tan
, Yuhui Shi:
Editorial: Special Section on Bio-Inspired Swarm Computing and Engineering. 1-3 - Ben Niu, Huali Huang, Lijing Tan, Qiqi Duan:
Symbiosis-Based Alternative Learning Multi-Swarm Particle Swarm Optimization. 4-14 - Hongwei Mo, Lili Liu, Jiao Zhao:
A New Magnetotactic Bacteria Optimization Algorithm Based on Moment Migration. 15-26 - Shaoqiu Zheng, Junzhi Li, Andreas Janecek, Ying Tan
A Cooperative Framework for Fireworks Algorithm. 27-41 - Bei Zhang, Yujun Zheng
Fireworks Algorithm with Enhanced Fireworks Interaction. 42-55 - Shan Cheng, Long-Long Zhao, Xiaoyu Jiang:
An Effective Application of Bacteria Quorum Sensing and Circular Elimination in MOPSO. 56-63 - Yong Zhang
Multi-Objective Particle Swarm Optimization Approach for Cost-Based Feature Selection in Classification. 64-75 - 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 - 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 - 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 - 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 - Elena Czeizler
A Graph-Theoretical Approach for Motif Discovery in Protein Sequences. 121-130 - Hasan M. Jamil
A Visual Interface for Querying Heterogeneous Phylogenetic Databases. 131-144 - Lin Zhang, Hui Liu, Yufei Huang, Xuesong Wang
Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. 145-154 - Lun Hu
Extracting Coevolutionary Features from Protein Sequences for Predicting Protein-Protein Interactions. 155-166 - Mehrdad J. Gangeh, Hadi Zarkoob, Ali Ghodsi:
Fast and Scalable Feature Selection for Gene Expression Data Using Hilbert-Schmidt Independence Criterion. 167-181 - Hailong Hu, Zhong Li, Hongwei Dong, Tianhe Zhou:
Graphical Representation and Similarity Analysis of Protein Sequences Based on Fractal Interpolation. 182-192 - Vincenzo Bonnici
On the Variable Ordering in Subgraph Isomorphism Algorithms. 193-203 - Arvind Kumar Sinha
Putative Drug and Vaccine Target Identification in Leishmania donovani Membrane Proteins Using Naïve Bayes Probabilistic Classifier. 204-211 - Shibiao Wan
Transductive Learning for Multi-Label Protein Subchloroplast Localization Prediction. 212-224 - Kuize Zhang
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
- Aidong Zhang:
Editorial from the New Editor-in-Chief. 251 - Illhoi Yoo, Amarda Shehu:
Guest Editorial for Special Section on BIBM 2014. 252-253 - En-Shiun Annie Lee, Ho-Yin Antonio Sze-To, Man Hon Wong, Kwong-Sak Leung, Terrence Chi-Kong Lau
Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering. 254-263 - Yong Zhang, Xiaohua Hu, Xingpeng Jiang:
Multi-View Clustering of Microbiome Samples by Robust Similarity Network Fusion and Spectral Clustering. 264-271 - Ilona Kifer, Rui Mamede Branca
Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics. 272-281 - Huiru Zheng
Analysis of Organization of the Interactome Using Dominating Sets: A Case Study on Cell Cycle Interaction Networks. 282-289 - Matthias Becker
Muscle Tissue Labeling of Human Lower Limb in Multi-Channel mDixon MR Imaging: Concepts and Applications. 290-299 - Daniel Veltri
Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming. 300-313 - Mitra Basu, Yi Pan
Guest Editors Introduction to the Special Section on ISBRA 2014. 314-315 - 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 - Yi Liu, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie
An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra. 326-336 - Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra. 337-344 - Lin Zhu
Identifying Spurious Interactions in the Protein-Protein Interaction Networks Using Local Similarity Preserving Embedding. 345-352 - Xingpeng Jiang, Xiaohua Hu, Weiwei Xu:
Microbiome Data Representation by Joint Nonnegative Matrix Factorization with Laplacian Regularization. 353-359 - Wei Peng, Min Li, Lu Chen, Lusheng Wang:
Predicting Protein Functions by Using Unbalanced Random Walk Algorithm on Three Biological Networks. 360-369 - Min Li, Yu Lu, Zhibei Niu, Fang-Xiang Wu
United Complex Centrality for Identification of Essential Proteins from PPI Networks. 370-380 - Behrang Mahjani
A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits. 381-392 - 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 - Julia Matsieva, Steven Kelk, Céline Scornavacca, Chris Whidden
A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. 404-417 - Ashok Rajaraman, João Paulo Pereira Zanetti, Ján Manuch, Cédric Chauve
Algorithms and Complexity Results for Genome Mapping Problems. 418-430 - Kieran Alden
Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models. 431-442 - Oscar Días
Genome-Wide Semi-Automated Annotation of Transporter Systems. 443-456 - Katya Mkrtchyan, Anirban Chakraborty, Amit K. Roy-Chowdhury:
Optimal Landmark Selection for Registration of 4D Confocal Image Stacks in Arabidopsis. 457-467 - Momoko Hayamizu, Hiroshi Endo, Kenji Fukumizu
A Characterization of Minimum Spanning Tree-Like Metric Spaces. 468-471 - Olivier Boes, Mareike Fischer
A Linear Bound on the Number of States in Optimal Convex Characters for Maximum Parsimony Distance. 472-477 - Thao Thi Phuong Nguyen, Le Sy Vinh, Hai Bich Ho, Si Quang Le:
Building Ancestral Recombination Graphs for Whole Genomes. 478-483 - Emmanouil Athanasiadis
D-Map: Random Walking on Gene Network Inference Maps Towards differential Avenue Discovery. 484-490 - Stéphane Mottelet, Gil Gaullier, Georges Sadaka:
Metabolic Flux Analysis in Isotope Labeling Experiments Using the Adjoint Approach. 491-497 - Scott Goldweber, Jamal Theodore, John Torcivia-Rodriguez
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
- Fei Wang, Xiaoli Li
Guest Editorial: Special Section on Biological Data Mining and Its Applications in Healthcare. 501-502 - Hua Wang, Lin Yan
From Protein Sequence to Protein Function via Multi-Label Linear Discriminant Analysis. 503-513 - Jianqiang Li, Fei Wang:
Towards Unsupervised Gene Selection: A Matrix Factorization Framework. 514-521 - Chelsea J.-T. Ju
Efficient Approach to Correct Read Alignment for Pseudogene Abundance Estimates. 522-533 - 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 - Jelena Stojanovic
Modeling Healthcare Quality via Compact Representations of Electronic Health Records. 545-554 - 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 - Xin Wang
Bi-convex Optimization to Learn Classifiers from Multiple Biomedical Annotations. 564-575 - Robert W. Harrison
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 576-577 - Abhishek Biswas
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images. 578-586 - Misagh Kordi, Mukul S. Bansal
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. 587-599 - Xuan Guo, Jing Zhang, Zhipeng Cai
Searching Genome-Wide Multi-Locus Associations for Multiple Diseases Based on Bayesian Inference. 600-610 - Hao Ji
Calcium Ion Fluctuations Alter Channel Gating in a Stochastic Luminal Calcium Release Site Model. 611-619 - Gustavo Rodrigues Galvão
Sorting Circular Permutations by Super Short Reversals. 620-633 - Weihua Zheng, Kenli Li, Keqin Li, Hing-Cheung So:
A Modified Multiple Alignment Fast Fourier Transform with Higher Efficiency. 634-645 - Ali Ezzat
Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization. 646-656 - Vo Hong Thanh
Efficient Constant-Time Complexity Algorithm for Stochastic Simulation of Large Reaction Networks. 657-667 - James Arram, Thomas Kaplan, Wayne Luk, Peiyong Jiang
Leveraging FPGAs for Accelerating Short Read Alignment. 668-677 - Feng He
PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-Scale Data. 678-686 - Xiangxiang Zeng
Prediction and Validation of Disease Genes Using HeteSim Scores. 687-695 - Boris Shabash
RNA Visualization: Relevance and the Current State-of-the-Art Focusing on Pseudoknots. 696-712 - Chen Peng, Ao Li
A Heterogeneous Network Based Method for Identifying GBM-Related Genes by Integrating Multi-Dimensional Data. 713-720 - Anastasiia Vasylchenkova, Miha Mraz, Nikolaj Zimic, Miha Moskon
Classical Mechanics Approach Applied to Analysis of Genetic Oscillators. 721-727 - Poly H. da Silva, Raphael Machado
Genomic Distance with High Indel Costs. 728-732 - Min Wu
Protein Complex Detection via Effective Integration of Base Clustering Solutions and Co-Complex Affinity Scores. 733-739 - Fangfei Li
Robust Reachability of Boolean Control Networks. 740-745 - Zhangming Yan
txCoords: A Novel Web Application for Transcriptomic Peak Re-Mapping. 746-748
Volume 14, Number 4, July - August 2017
- Manjari Jha
A Generalized Lattice Based Probabilistic Approach for Metagenomic Clustering. 749-761 - Sanghamitra Bandyopadhyay, Koushik Mallick
A New Feature Vector Based on Gene Ontology Terms for Protein-Protein Interaction Prediction. 762-770 - 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 - Chao Wang, Dong Dai, Xi Li, Aili Wang, Xuehai Zhou:
SuperMIC: Analyzing Large Biological Datasets in Bioinformatics with Maximal Information Coefficient. 783-795 - Rao Muhammad Adeel Nawab, Mark Stevenson, Paul D. Clough:
An IR-Based Approach Utilizing Query Expansion for Plagiarism Detection in MEDLINE. 796-804 - Sugeerth Murugesan
Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity. 805-818 - Sandra Barragan, Cristina Rueda, Miguel Alejandro Fernández
Circular Order Aggregation and Its Application to Cell-Cycle Genes Expressions. 819-829 - Jing Zhang, Hao Wang, Wu-chun Feng:
cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU. 830-843 - Lu Xie, Gregory R. Smith
Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data. 844-855 - Yue Zhang, Yiu-ming Cheung
Detection Copy Number Variants from NGS with Sparse and Smooth Constraints. 856-867 - Xiaofei Fan, Xian Zhang
Finite-Time Stability Analysis of Reaction-Diffusion Genetic Regulatory Networks with Time-Varying Delays. 868-879 - Maziyar Baran Pouyan, Mehrdad Nourani:
Identifying Cell Populations in Flow Cytometry Data Using Phenotypic Signatures. 880-891 - Anne Florence Keller
Impact of Synaptic Localization and Subunit Composition of Ionotropic Glutamate Receptors on Synaptic Function: Modeling and Simulation Studies. 892-904 - Yuansheng Liu
Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources. 905-915 - Min Li
ISEA: Iterative Seed-Extension Algorithm for De Novo Assembly Using Paired-End Information and Insert Size Distribution. 916-925 - Tianle Ma
Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems. 926-946 - Jianhua Zhang
Pattern Classification of Instantaneous Cognitive Task-load Through GMM Clustering, Laplacian Eigenmap, and Ensemble SVMs. 947-965 - Liang Yu
Prediction of Novel Drugs for Hepatocellular Carcinoma Based on Multi-Source Random Walk. 966-977 - Egils Stalidzans
Search for a Minimal Set of Parameters by Assessing the Total Optimization Potential for a Dynamic Model of a Biochemical Network. 978-985 - 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
- Ümit V. Çatalyürek:
Guest Editor's Introduction: Selected Papers from ACM-BCB 2014. 1000-1001 - Pawel Górecki
Unconstrained Diameters for Deep Coalescence. 1002-1012 - Zhiyong Wang, Benika Hall, Jinbo Xu, Xinghua Shi:
A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants. 1013-1027 - Dan F. DeBlasio
Learning Parameter-Advising Sets for Multiple Sequence Alignment. 1028-1041 - Anna M. Ritz
Pathway Analysis with Signaling Hypergraphs. 1042-1055 - 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 - Joseph Azofeifa, Mary A. Allen
An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq. 1070-1081 - Norman Goodacre
Predicting nsSNPs that Disrupt Protein-Protein Interactions Using Docking. 1082-1093 - Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin:
IPED2: Inheritance Path Based Pedigree Reconstruction Algorithm for Complicated Pedigrees. 1094-1103 - De-Shuang Huang, Vitoantonio Bevilacqua
Guest Editorial for Special Section on the 11th International Conference on Intelligent Computing (ICIC). 1104-1105 - 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 - Shu-Guang Ge, Junfeng Xia
Cancer Subtype Discovery Based on Integrative Model of Multigenomic Data. 1115-1121 - Wenzheng Bao
Classification of Protein Structure Classes on Flexible Neutral Tree. 1122-1133 - Qingfeng Chen, Chaowang Lan, Baoshan Chen, Lusheng Wang, Jinyan Li, Chengqi Zhang
Exploring Consensus RNA Substructural Patterns Using Subgraph Mining. 1134-1146 - 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 - Lin Yuan
Nonconvex Penalty Based Low-Rank Representation and Sparse Regression for eQTL Mapping. 1154-1164 - Jian-Qiang Li, Zhu-Hong You
PSPEL: In Silico Prediction of Self-Interacting Proteins from Amino Acids Sequences Using Ensemble Learning. 1165-1172 - Pu Wang, Ruiquan Ge
hMuLab: A Biomedical Hybrid MUlti-LABel Classifier Based on Multiple Linear Regression. 1173-1180 - Tuomo Mäki-Marttunen
An Algorithm for Motif-Based Network Design. 1181-1186 - Lichun Ma
An Eigen-Binding Site Based Method for the Analysis of Anti-EGFR Drug Resistance in Lung Cancer Treatment. 1187-1194 - Antonio d'Acierno
IsAProteinDB: An Indexed Database of Trypsinized Proteins for Fast Peptide Mass Fingerprinting. 1195-1201
Volume 14, Number 6, November - December 2017
- Ahmad Al Kawam
A Survey of Software and Hardware Approaches to Performing Read Alignment in Next Generation Sequencing. 1202-1213 - Utku Sirin
Batch Mode TD(λ) for Controlling Partially Observable Gene Regulatory Networks. 1214-1227 - Biji C. L.
Benchmark Dataset for Whole Genome Sequence Compression. 1228-1236 - Francisco do Nascimento, Katia S. Guimarães:
Copy Number Variations Detection: Unravelling the Problem in Tangible Aspects. 1237-1250 - Stefano Ceri, Abdulrahman Kaitoua, Marco Masseroli
Data Management for Heterogeneous Genomic Datasets. 1251-1264 - Amin Ahmadi Adl
Detecting Pairwise Interactive Effects of Continuous Random Variables for Biomarker Identification with Small Sample Size. 1265-1275 - Nivit Grewal
Effect of Aggregation Operators on Network-Based Disease Gene Prioritization: A Case Study on Blood Disorders. 1276-1287 - Gui-Jun Zhang
Enhancing Protein Conformational Space Sampling Using Distance Profile-Guided Differential Evolution. 1288-1301 - David Oliveira Aparício
Extending the Applicability of Graphlets to Directed Networks. 1302-1315 - Georgina Stegmayer
High Class-Imbalance in pre-miRNA Prediction: A Novel Approach Based on deepSOM. 1316-1326 - Abbas Akkasi
Improving Biochemical Named Entity Recognition Using PSO Classifier Selection and Bayesian Combination Methods. 1327-1338 - Arne T. Bittig
ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology. 1339-1349 - Mingon Kang, Juyoung Park, Dong-Chul Kim, Ashis Kumer Biswas
Multi-Block Bipartite Graph for Integrative Genomic Analysis. 1350-1358 - Grady Weyenberg
Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace. 1359-1365 - Yuchun Ding, Marie Christine Pardon
Novel Methods for Microglia Segmentation, Feature Extraction, and Classification. 1366-1377 - Daniel M. Savel
Pluribus - Exploring the Limits of Error Correction Using a Suffix Tree. 1378-1388 - Jun Hu, Yang Li, Ming Zhang, Xibei Yang, Hong-Bin Shen, Dong-Jun Yu
Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs. 1389-1398 - Jiancheng Zhong, Jianxin Wang
Protein Inference from the Integration of Tandem MS Data and Interactome Networks. 1399-1409 - Deqing Gu, Xingxing Jian, Cheng Zhang
Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data. 1410-1418 - Pradipta Maji
Significance and Functional Similarity for Identification of Disease Genes. 1419-1433 - Zhen Qi
Strategies for Comparing Metabolic Profiles: Implications for the Inference of Biochemical Mechanisms from Metabolomics Data. 1434-1445 - Shahin Mohammadi
Triangular Alignment (TAME): A Tensor-Based Approach for Higher-Order Network Alignment. 1446-1458 - Yun Liu
Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method. 1459-1467 - Jiawei Luo
Collective Prediction of Disease-Associated miRNAs Based on Transduction Learning. 1468-1475 - Maxime Dureau, Angelo Alessandri, Patrizia Bagnerini
Modeling and Identification of Amnioserosa Cell Mechanical Behavior by Using Mass-Spring Lattices. 1476-1481 - Pietro Lovato
Soft Ngram Representation and Modeling for Protein Remote Homology Detection. 1482-1488
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