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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 15
Volume 15, Number 1, January - February 2018
- Yanbo Wang
, Weikang Qian, Bo Yuan:
A Graphical Model of Smoking-Induced Global Instability in Lung Cancer. 1-14
- Jesper Jansson, Ramesh Rajaby, Chuanqi Shen, Wing-Kin Sung:
Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree. 15-26 - Renu 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. 27-37 - Bin Hu, Xiaowei Li, Shuting Sun, Martyn Ratcliffe:
Attention Recognition in EEG-Based Affective Learning Research Using CFS+KNN Algorithm. 38-45 - Anton V. 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. 46-59 - Viswanath C. Narayanan:
Calculating the Expected Time to Eradicate HIV-1 Using a Markov Chain. 60-67 - Alireza Karbalayghareh, Ulisses M. Braga-Neto, Jianping Hua, Edward Russell Dougherty:
Classification of State Trajectories in Gene Regulatory Networks. 68-82 - Tom Hartmann, An-Chiang Chu, Martin Middendorf, Matthias Bernt:
Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes. 83-95 - Ademir Hujdurovic, Ursa Kacar, Martin Milanic, Bernard Ries, Alexandru I. Tomescu:
Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples. 96-108 - Wei Zhang, Jia Xu, Yuanyuan Li, Xiufen Zou:
Detecting Essential Proteins Based on Network Topology, Gene Expression Data, and Gene Ontology Information. 109-116 - Cinzia Pizzi, Mattia Ornamenti, Simone Spangaro, Simona E. Rombo, Laxmi Parida:
Efficient Algorithms for Sequence Analysis with Entropic Profiles. 117-128 - Hyunjin Kim, Sang-Min Choi, Sanghyun Park:
GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity. 129-146 - Jian 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. 147-156 - Kamal Taha:
Inferring the Functions of Proteins from the Interrelationships between Functional Categories. 157-167 - Guillermo 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. 168-180 - Nikolaos-Kosmas Chlis, Ekaterini S. Bei, Michalis E. Zervakis:
Introducing a Stable Bootstrap Validation Framework for Reliable Genomic Signature Extraction. 181-190 - Eddie Y. T. Ma, Sujeevan Ratnasingham, Stefan C. Kremer:
Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding. 191-204 - Laura Jetten, Leo van Iersel:
Nonbinary Tree-Based Phylogenetic Networks. 205-217 - Daniel N. Mohsenizadeh, Roozbeh Dehghannasiri, Edward R. Dougherty:
Optimal Objective-Based Experimental Design for Uncertain Dynamical Gene Networks with Experimental Error. 218-230 - Behnam Behinaein, Karen Rudie, Waheed Sangrar:
Petri Net Siphon Analysis and Graph Theoretic Measures for Identifying Combination Therapies in Cancer. 231-243 - Shujaat Khan, Imran Naseem, Roberto Togneri, Mohammed Bennamoun:
RAFP-Pred: Robust Prediction of Antifreeze Proteins Using Localized Analysis of n-Peptide Compositions. 244-250 - Roman Czapla:
Random Sets of Stadiums in Square and Collective Behavior of Bacteria. 251-256 - Vinicius R. P. Borges, Maria Cristina Ferreira de Oliveira, Thaís Garcia Silva, Armando Augusto Henriques Vieira, Bernd Hamann:
Region Growing for Segmenting Green Microalgae Images. 257-270 - M. Syed Ali, N. Gunasekaran, Choon Ki Ahn, Peng Shi:
Sampled-Data Stabilization for Fuzzy Genetic Regulatory Networks with Leakage Delays. 271-285 - Chendra Hadi Suryanto, Hiroto Saigo, Kazuhiro Fukui:
Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images. 286-299 - Gerd 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. 300-308 - Jiawei Luo, Wei Huang, Buwen Cao:
A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Modules in Cancer. 309-315 - Feng Bao, Yue Deng, Qionghai Dai:
ACID: Association Correction for Imbalanced Data in GWAS. 316-322 - Hongmei Jiao, Michael Shi, Qikun Shen, Junwu Zhu, Peng Shi:
Filter Design with Adaptation to Time-Delay Parameters for Genetic Regulatory Networks. 323-329 - Ahed Elmsallati, Abdulghani Msalati, Jugal Kalita:
Index-Based Network Aligner of Protein-Protein Interaction Networks. 330-336 - Elizabeth S. Allman, James H. Degnan, John A. Rhodes:
Species Tree Inference from Gene Splits by Unrooted STAR Methods. 337-342 - Frederick A. Matsen IV, Sara C. Billey, Arnold Kas, Matjaz Konvalinka:
Tanglegrams: A Reduction Tool for Mathematical Phylogenetics. 343-349
Volume 15, Number 2, March - April 2018
- Adrian-Horia Dediu, Carlos Martín-Vide:
Selected Papers of the First International Conference on Algorithms for Computational Biology (AlCoB 2014). 350-351 - Thiago da Silva Arruda, Ulisses Dias, Zanoni Dias:
A GRASP-Based Heuristic for the Sorting by Length-Weighted Inversions Problem. 352-363 - Ivo Hedtke, Ioana M. Lemnian, Ivo Grosse, Matthias Müller-Hannemann:
Optimal Block-Based Trimming for Next Generation Sequencing. 364-376 - Congping Lin, Laurent Lemarchand, Reinhardt Euler, Imogen Sparkes:
Modeling the Geometry and Dynamics of the Endoplasmic Reticulum Network. 377-386 - Amina Noor, Aitzaz Ahmad, Erchin Serpedin:
SparseNCA: Sparse Network Component Analysis for Recovering Transcription Factor Activities with Incomplete Prior Information. 387-395 - Jijun Tang, Lu Tian, Yi-Ping Phoebe Chen:
Guest Editorial for the 14th Asia Pacific Bioinformatics Conference. 396-397 - Daniel H. Huson, Simone Linz:
Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. 398-410 - Weiyun Ma, Dmitriy Smirnov, Juliet Forman, A. Schweickart, C. Slocum, S. Srinivasan, Ran Libeskind-Hadas:
DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations. 411-421 - Zhi-Zhong Chen, Qilong Feng, Chao Shen, Jianxin Wang, Lusheng Wang:
Algorithms for Pedigree Comparison. 422-431 - Moonshik Shin, Donjin Jang, Hojung Nam, Kwang Hyung Lee, Doheon Lee:
Predicting the Absorption Potential of Chemical Compounds Through a Deep Learning Approach. 432-440 - Seunghyun 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. 441-451 - Dimitris P. Papamichail, Hongmei Liu, Vitor Machado, Nathan Gould, J. Robert Coleman, Georgios Papamichail:
Codon Context Optimization in Synthetic Gene Design. 452-459 - Jiangeng Li, Wei Zhang, Xiaodan Li:
3D Genome Reconstruction with ShRec3D+ and Hi-C Data. 460-468 - Rahul Singh, Rachel Beasley, Thavy Long, Conor R. Caffrey:
Algorithmic Mapping and Characterization of the Drug-Induced Phenotypic-Response Space of Parasites Causing Schistosomiasis. 469-481 - Bijoy K. Ghosh, Aniruddha Datta, Ranadip Pal:
Deep Sequencing Data Analysis. 482-483 - Jason M. Knight, Ivan Ivanov, Karen Triff, Robert S. Chapkin, Edward R. Dougherty:
Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification. 484-493 - Noushin 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. 494-505 - Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon:
Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides. 506-515 - Arghavan Bahadorinejad, Ulisses M. Braga-Neto:
Optimal Fault Detection and Diagnosis in Transcriptional Circuits Using Next-Generation Sequencing. 516-525 - Xiaodong Cui, Lin Zhang, Jia Meng, Manjeet K. Rao, Yidong Chen, Yufei Huang:
MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data. 526-534 - Jing Zhang, Tianming Liu, Gopikrishna Deshpande:
Probabilistic Methods in Computational Neuroscience. 535-536 - Yize Zhao, Jian Kang, Qi Long:
Bayesian Multiresolution Variable Selection for Ultra-High Dimensional Neuroimaging Data. 537-550 - Lin Yuan, Fanglin Chen, Ling-Li Zeng, Lubin Wang, Dewen Hu:
Gender Identification of Human Brain Image with A Novel 3D Descriptor. 551-561 - Meng Hu, Wu Li, Hualou Liang:
A Copula-Based Granger Causality Measure for the Analysis of Neural Spike Train Data. 562-569 - Lijun 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:
Cortical Thinning and Cognitive Impairment in Parkinson's Disease without Dementia. 570-580 - João Ricardo Sato, Maciel Calebe Vidal, Suzana de Siqueira Santos, Katlin Brauer Massirer, André Fujita:
Complex Network Measures in Autism Spectrum Disorders. 581-587 - Biing-Feng Wang:
A New Efficient Algorithm for the Frequent Gene Team Problem. 588-598 - Suneetha Uppu, Aneesh Krishna, Raj P. Gopalan:
A Review on Methods for Detecting SNP Interactions in High-Dimensional Genomic Data. 599-612 - Mahdi Barat Zadeh Joveini, Javad Sadri:
Application of Fractal Theory on Motifs Counting in Biological Networks. 613-623 - Jin Liu, Min Li, Wei Lan, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
Classification of Alzheimer's Disease Using Whole Brain Hierarchical Network. 624-632 - Jinghui Li, Hiroshi Nagamochi, Tatsuya Akutsu:
Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs. 633-646 - Xiaoke Ma, Wanxin Tang, Peizhuo Wang, Xingli Guo, Lin Gao:
Extracting Stage-Specific and Dynamic Modules Through Analyzing Multiple Networks Associated with Cancer Progression. 647-658 - Jayanta 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. 659-672 - Sanghamitra Bandyopadhyay, Saurav Mallik:
Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis. 673-687
Volume 15, Number 3, May - June 2018
- Julia Handl, Amarda Shehu, José Santos Reyes:
Advances in the Application and Development of Non-Linear Global Optimization Techniques in Computational Structural Biology. 688-689 - Leonardo de Lima Correa, Bruno Borguesan, Camilo Farfán, Mario Inostroza-Ponta, Márcio Dorn:
A Memetic Algorithm for 3D Protein Structure Prediction Problem. 690-704 - Jiaxiang Huang, Maoguo Gong, Lijia Ma:
A Global Network Alignment Method Using Discrete Particle Swarm Optimization. 705-718 - Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu:
From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes. 719-731 - Jakub Rydzewski, Rafal Jakubowski, Giuseppe Nicosia, Wieslaw Nowak:
Conformational Sampling of a Biomolecular Rugged Energy Landscape. 732-739 - Matthias Leinweber, Thomas Fober, Bernd Freisleben:
GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites. 740-752 - Jie Zhou, Yuan-Yuan Shi:
A Bipartite Network and Resource Transfer-Based Approach to Infer lncRNA-Environmental Factor Associations. 753-759 - Maiju 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. 760-773 - Xiangtao Li, Ka-Chun Wong:
A Comparative Study for Identifying the Chromosome-Wide Spatial Clusters from High-Throughput Chromatin Conformation Capture Data. 774-787 - Xin Peng, Yang Tang, Wangli He, Wenli Du, Feng Qian:
A Just-in-Time Learning Based Monitoring and Classification Method for Hyper/Hypocalcemia Diagnosis. 788-801 - Xichuan 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. 802-812 - Neslihan Avcu, Nihal Pekergin, Ferhan Pekergin, Cüneyt Güzelis:
Aggregation for Computing Multi-Modal Stationary Distributions in 1-D Gene Regulatory Networks. 813-827 - Wei 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. 828-838 - Pritha Dutta, Subhadip Basu, Mahantapas Kundu:
Assessment of Semantic Similarity between Proteins Using Information Content and Topological Properties of the Gene Ontology Graph. 839-849 - Aurélie Pirayre, Camille Couprie, Laurent Duval, Jean-Christophe Pesquet:
BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement. 850-860 - Somaya Hashem, Gamal Esmat, Wafaa Elakel, Shahira M. 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. 861-868 - Sumanta Ray, Ujjwal Maulik:
Discovering Perturbation of Modular Structure in HIV Progression by Integrating Multiple Data Sources Through Non-Negative Matrix Factorization. 869-877 - Aseel Awdeh, Hilary Phenix, Mads Kærn, Theodore J. Perkins:
Dynamics in Epistasis Analysis. 878-891 - Tiantian He, Keith C. C. Chan:
Evolutionary Graph Clustering for Protein Complex Identification. 892-904 - Najmul Ikram Qazi, Muhammad Abdul Qadir, Muhammad Tanvir Afzal:
Investigating Correlation between Protein Sequence Similarity and Semantic Similarity Using Gene Ontology Annotations. 905-912 - Lin Zhu, Hong-Bo Zhang, De-Shuang Huang:
LMMO: A Large Margin Approach for Refining Regulatory Motifs. 913-925 - Pedro 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. 926-933 - Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris:
NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithm for Flexible Protein Structure Alignment. 934-943 - Wenwen Min, Juan Liu, Shihua Zhang:
Network-Regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery. 944-953 - Davide Chicco, Fernando Palluzzi, Marco Masseroli:
Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations. 954-965 - Zoya Khalid, Osman Ugur Sezerman:
Prediction of HIV Drug Resistance by Combining Sequence and Structural Properties. 966-973 - Jin-Xing Liu, Dong Wang, Ying-Lian Gao, Chun-Hou Zheng, Yong Xu, Jiguo Yu:
Regularized Non-Negative Matrix Factorization for Identifying Differentially Expressed Genes and Clustering Samples: A Survey. 974-987 - Junhua Zhang, Shihua Zhang:
The Discovery of Mutated Driver Pathways in Cancer: Models and Algorithms. 988-998 - Bin Wang, Xuedong Zheng, Shihua Zhou, Changjun Zhou, Xiaopeng Wei, Qiang Zhang, Ziqi Wei:
Constructing DNA Barcode Sets Based on Particle Swarm Optimization. 999-1002 - Carl Poirier, Benoit Gosselin, Paul Fortier:
DNA Assembly with De Bruijn Graphs Using an FPGA Platform. 1003-1009 - Ruth Davidson, MaLyn Lawhorn, Joseph Rusinko, Noah Weber:
Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods. 1010-1015 - Xianpeng Liang, Lin Zhu, De-Shuang Huang:
Optimization of Gene Set Annotations Using Robust Trace-Norm Multitask Learning. 1016-1021 - Chengyu Liu, Rainer Lehtonen, Sampsa Hautaniemi:
PerPAS: Topology-Based Single Sample Pathway Analysis Method. 1022-1027 - Abolfazl Doostparast Torshizi, Linda R. Petzold:
Sparse Pathway-Induced Dynamic Network Biomarker Discovery for Early Warning Signal Detection in Complex Diseases. 1028-1034 - Wei Zhang, Jia Xu, Yuanyuan Li, Xiufen Zou:
Correction to "Detecting Essential Proteins Based on Network Topology, Gene Expression Data, and Gene Ontology Information". 1035
Volume 15, Number 4, July - August 2018
- T. M. Murali:
Guest Editorial. 1036 - Asish 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. 1037-1051 - Shi Qiao, Mehmet Koyutürk, Z. Meral Özsoyoglu:
Querying of Disparate Association and Interaction Data in Biomedical Applications. 1052-1065 - Alexej 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. 1066-1078 - Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My T. Thai, Tamer Kahveci:
Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks. 1079-1091 - Xiaodan Fan, Xinglai Ji, Rui Jiang:
Guest Editorial for Special Section on the Sixth National Conference on Bioinformatics and System Biology of China. 1092