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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 11
Volume 11, Number 1, January - February 2014
- Ying Xu:
Editorial from the Editor-in-Chief. 1-4 - Frank Eisenhaber
, Wing-Kin Sung, Limsoon Wong:
Guest Editorial for the International Conference on Genome Informatics (GIW 2013). 5-6 - Liang Zhao, Steven C. H. Hoi, Zhenhua Li, Limsoon Wong, Hung T. Nguyen, Jinyan Li:
Coupling Graphs, Efficient Algorithmsand B-Cell Epitope Prediction. 7-16 - Ying Fan, Ruoshui Lu, Lusheng Wang, Massimo Andreatta, Shuai Cheng Li:
Quantifying Significance of MHC II Residues. 17-25 - Paul D. Yoo, Sami Muhaidat, Kamal Taha, Jamal Bentahar, Abdallah Shami:
Intelligent Consensus Modeling for ProlineCis-Trans Isomerization Prediction. 26-32 - Laleh Soltan Ghoraie, Forbes J. Burkowski, Shuai Cheng Li, Mu Zhu:
Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation. 33-41 - Ruiqi Liao, Ruichang Zhang, Jihong Guan, Shuigeng Zhou:
A New Unsupervised Binning Approachfor Metagenomic Sequences Based onN-grams and Automatic Feature Weighting. 42-54 - Jui-Chen Hsiao, Chih-Hsuan Wei, Hung-Yu Kao:
Gene Name Disambiguation UsingMulti-Scope Species Detection. 55-62 - Jing Guo, Ritika Jain, Peng Yang, Rui Fan, Chee Keong Kwoh, Jie Zheng:
Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo. 63-72 - Yanglan Gan, Jihong Guan, Shuigeng Zhou, Weixiong Zhang:
Identifying Cis-Regulatory Elements and Modules Using Conditional Random Fields. 73-82 - Sriganesh Srihari, Venkatesh Raman, Hon Wai Leong, Mark A. Ragan:
Evolution and Controllability of CancerNetworks: A Boolean Perspective. 83-94 - Sanghamitra Bandyopadhyay, Saurav Mallik, Anirban Mukhopadhyay:
A Survey and Comparative Study of Statistical Tests for Identifying Differential Expressionfrom Microarray Data. 95-115 - Sanghamitra Bandyopadhyay, Koushik Mallick:
A New Path Based Hybrid Measurefor Gene Ontology Similarity. 116-127 - Fahad Saeed, Jason D. Hoffert, Mark A. Knepper:
CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling. 128-141 - Biing-Feng Wang, Chien-Hsin Lin, I-Tse Yang:
Constructing a Gene Team Treein Almost $O$$(n\; {\rm lg}\; n)$ Time. 142-153 - Mitsunori Kayano, Motoki Shiga, Hiroshi Mamitsuka:
Detecting Differentially Coexpressed Genesfrom Labeled Expression Data: A Brief Review. 154-167 - Vangelis Metsis, Fillia Makedon, Dinggang Shen, Heng Huang:
DNA Copy Number Selection Using Robust Structured Sparsity-Inducing Norms. 168-181 - Sandhya Prabhakaran, Mélanie Rey, Osvaldo Zagordi, Niko Beerenwinkel, Volker Roth:
HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. 182-191 - Leyi Wei, Minghong Liao, Yue Gao, Rongrong Ji, Zengyou He, Quan Zou:
Improved and Promising Identificationof Human MicroRNAs by Incorporatinga High-Quality Negative Set. 192-201 - Mohammad Shahrokh Esfahani, Edward R. Dougherty:
Incorporation of Biological PathwayKnowledge in the Construction of Priorsfor Optimal Bayesian Classification. 202-218 - Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Otto, Sebastian Will:
Local Exact Pattern Matching for Non-FixedRNA Structures. 219-230 - Pawel Górecki, Oliver Eulenstein:
Maximizing Deep Coalescence Cost. 231-242 - Jun Sun, Vasile Palade, Xiaojun Wu, Wei Fang:
Multiple Sequence Alignment with HiddenMarkov Models Learned by Random DriftParticle Swarm Optimization. 243-257 - John Healy, Desmond Chambers:
Approximate k-Mer Matching UsingFuzzy Hash Maps. 258-264 - Guo-Xian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, Zhiwen Yu:
Erratum to "Protein Function Prediction Using Multilabel Ensemble Classification". 265
Volume 11, Number 2, March - April 2014
- ChangKug Kim, Jin-A. Kim, Ji-Weon Choi, In-Seon Jeong, Yi-Seul Moon, Dong-Suk Park, Young-Joo Seol, Yong-Kab Kim, Yong-Hwan Kim, Yeon-Ki Kim:
A Multi-Layered Screening Method to Identify Plant Regulatory Genes. 293-303 - Tom M. W. Nye:
An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace. 304-315 - Abeer Eshra, Ayman El-Sayed:
An Odd Parity Checker Prototype Using DNAzyme Finite State Machine. 316-324 - Ruth Davidson, Seth Sullivant:
Distance-Based Phylogenetic MethodsAround a Polytomy. 325-335 - Kristopher L. Patton, David J. John, James L. Norris, Daniel R. Lewis, Gloria K. Muday:
Hierarchical Probabilistic Interaction Modeling for Multiple Gene Expression Replicates. 336-346 - Pugalendhi GaneshKumar, Chellasamy Rani, Durairaj Devaraj, T. Aruldoss Albert Victoire:
Hybrid Ant Bee Algorithm for Fuzzy Expert System Based Sample Classification. 347-360 - Shunji Tanaka:
Improved Exact Enumerative Algorithmsfor the Planted ($l$, $d$)-Motif Search Problem. 361-374 - Veli Mäkinen, Niko Välimäki, Jouni Sirén:
Indexing Graphs for Path Queries with Applications in Genome Research. 375-388 - Anthony Labarre, Sicco Verwer:
Merging Partially Labelled Trees: Hardness and a DeclarativeProgramming Solution. 389-397 - Weiming Li, Bin Ma, Kaizhong Zhang:
Optimizing Spaced $k$-mer Neighbors for Efficient Filtration in Protein Similarity Search. 398-406 - Xiwei Tang, Jianxin Wang, Jiancheng Zhong, Yi Pan:
Predicting Essential Proteins Basedon Weighted Degree Centrality. 407-418 - Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Lin Chen, Jing He:
Solving the Secondary Structure MatchingProblem in Cryo-EM De Novo ModelingUsing a Constrained $K$-Shortest Path Graph Algorithm. 419-430 - Miha Moskon, Miha Mraz:
Systematic Approach to Computational Designof Gene Regulatory Networks with Information Processing Capabilities. 431-440 - Dan Tulpan, Derek H. Smith, Roberto Montemanni:
Thermodynamic Post-Processing versusGC-Content Pre-Processing for DNA CodesSatisfying the Hamming Distance andReverse-Complement Constraints. 441-452
Volume 11, Number 3, May - June 2014
- Zhipeng Cai, Oliver Eulenstein, Cynthia Gibas:
Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications. 453-454 - Falk Hüffner, Christian Komusiewicz, Adrian Liebtrau, Rolf Niedermeier:
Partitioning Biological Networks into Highly Connected Clusters with Maximum Edge Coverage. 455-467 - Xuebo Song, Lin Li, Pradip K. Srimani, Philip S. Yu, James Z. Wang:
Measure the Semantic Similarity of GO Terms Using Aggregate Information Content. 468-476 - Yu Zheng, Louxin Zhang:
Effect of Incomplete Lineage SortingOn Tree-Reconciliation-Based Inferenceof Gene Duplication. 477-485 - Bihai Zhao, Jianxin Wang, Min Li, Fang-Xiang Wu, Yi Pan:
Detecting Protein Complexes Basedon Uncertain Graph Model. 486-497 - Elena Marchiori, Alioune Ngom, Raj Acharya:
Guest Editorial: Pattern Recognition in Bioinformatics. 498-499 - Matteo Comin, Morris Antonello:
Fast Entropic Profiler: An InformationTheoretic Approach for the Discovery ofPatterns in Genomes. 500-509 - Abdollah Dehzangi, Kuldip K. Paliwal, James G. Lyons, Alok Sharma, Abdul Sattar:
A Segmentation-Based Method to Extract Structural and Evolutionary Features for Protein Fold Recognition. 510-519 - Michael F. Ochs, Jason E. Farrar, Michael Considine, Yingying Wei, Soheil Meshinchi, Robert J. Arceci:
Outlier Analysis and Top Scoring Pairfor Integrated Data Analysisand Biomarker Discovery. 520-532 - Shaurya Jauhari, Syed Afzal Murtaza Rizvi:
Mining Gene Expression Data Focusing Cancer Therapeutics: A Digest. 533-547 - Andrew K. C. Wong, En-Shiun Annie Lee:
Aligning and Clustering Patterns to Reveal the Protein Functionality of Sequences. 548-560 - Marco Mina, Pietro Hiram Guzzi:
Improving the Robustness of Local Network Alignment: Design and Extensive Assessmentof a Markov Clustering-Based Approach. 561-572 - Qingliang Shen, Hong Tian, Daoqi Tang, Wenbing Yao, Xiangdong Gao:
Ligand-K* Sequence Elimination: A NovelAlgorithm for Ensemble-Based Redesignof Receptor-Ligand Binding. 573-578 - Guo-Xian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, Zhiwen Yu:
Protein Function Prediction withIncomplete Annotations. 579-591 - Fernando Lopez-Caamal, Diego A. Oyarzún, Richard H. Middleton, Míriam R. García:
Spatial Quantification of Cytosolic Ca2+ Accumulation in Nonexcitable Cells: An Analytical Study. 592-603 - Benjamin Xueqi Guan, Bir Bhanu, Prudence Talbot, Sabrina Lin:
Bio-Driven Cell Region Detection in Human Embryonic Stem Cell Assay. 604-611
Volume 11, Number 4, July - August 2014
- Ying Xu:
Reviewer Appreciation Editorial. 613 - Shuigeng Zhou, Yi-Ping Phoebe Chen:
Guest editorial for the 12th Asia Pacific Bioinformatics Conference. 614-615 - Bin Xu, Jihong Guan:
From Function to Interaction: A New Paradigm for Accurately Predicting Protein Complexes Based on Protein-to-Protein Interaction Networks. 616-627 - Matteo Comin, Davide Verzotto:
Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison. 628-637 - Yanglan Gan, Guobing Zou, Jihong Guan, Guangwei Xu:
A Novel Wavelet-Based Approach for Predicting Nucleosome Positions Using DNAS tructural Information. 638-647 - Christine Lo, Boyko Kakaradov, Daniel Lokshtanov, Christina Boucher:
SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers. 648-656 - Hualong Yu, Jun Ni:
An Improved Ensemble Learning Methodfor Classifying High-Dimensionaland Imbalanced Biomedicine Data. 657-666 - Fei Hu, Jun Zhou, Lingxi Zhou, Jijun Tang:
Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions. 667-672 - Minta Thomas, Anneleen Daemen, Bart De Moor:
Maximum Likelihood Estimation ofGEVD: Applications in Bioinformatics. 673-680 - Kazuki Ichikawa, Shinichi Morishita:
A Simple but Powerful Heuristic Methodfor Accelerating $k$ -Means Clusteringof Large-Scale Data in Life Science. 681-692 - Yuan Gao, Rosa H. M. Chan, Tommy W. S. Chow, Liyun Zhang, Sylvia Bonilla, Chi-Pui Pang, Mingzhi Zhang, Yuk Fai Leung:
A High-Throughput Zebrafish ScreeningMethod for Visual Mutants by Light-Induced Locomotor Response. 693-701 - Chia-Hua Chuang, Chun-Liang Lin:
A Novel Synthesizing Genetic Logic Circuit: Frequency Multiplier. 702-713 - Hai Su, Fuyong Xing, Jonah D. Lee, Charlotte A. Peterson, Lin Yang:
Automatic Myonuclear Detection in IsolatedSingle Muscle Fibers Using Robust EllipseFitting and Sparse Representation. 714-726 - Zhiwen Yu, Hongsheng Chen, Jane You, Hau-San Wong, Jiming Liu, Le Li, Guoqiang Han:
Double Selection Based Semi-Supervised Clustering Ensemble for Tumor Clustering from Gene Expression Profiles. 727-740 - Rui Fa, Asoke K. Nandi:
Noise Resistant Generalized Parametric Validity Index of Clustering for Gene Expression Data. 741-752 - Beatriz García Jiménez, Tirso Pons, Araceli Sanchis, Alfonso Valencia:
Predicting Protein Relationshipsto Human Pathways througha Relational Learning ApproachBased on Simple Sequence Features. 753-765 - Ao Kong, Chinmaya Gupta, Mauro Ferrari, Marco Agostini, Chiara Bedin, Ali Bouamrani, Ennio Tasciotti, Robert Azencott:
Biomarker Signature Discovery from Mass Spectrometry Data. 766-772
Volume 11, Number 5, September - October 2014
- Gaurav Pandey, Huzefa Rangwala:
Guest Editorial for Special Section on BIOKDD2013. 773-774 - Shobeir Fakhraei, Bert Huang, Louiqa Raschid, Lise Getoor:
Network-Based Drug-Target Interaction Prediction with Probabilistic Soft Logic. 775-787 - Raed I. Seetan, Anne M. Denton, Omar Al Azzam, Ajay Kumar, Muhammad Javed Iqbal, Shahryar F. Kianian:
Reliable Radiation Hybrid Maps: An Efficient Scalable Clustering-Based Approach. 788-800 - Joana P. Gonçalves, Sara C. Madeira:
LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification. 801-813 - Cheng Zhou, Pieter Meysman, Boris Cule, Kris Laukens, Bart Goethals:
Discovery of Spatially Cohesive Itemsets in Three-Dimensional Protein Structures. 814-825 - Michael Zeller, Christophe N. Magnan, Vishal R. Patel, Paul Rigor, Leonard Sender, Pierre Baldi:
A Genomic Analysis Pipeline and Its Application to Pediatric Cancers. 826-839 - Peng Chen, Chao Wang, Xi Li, Xuehai Zhou:
Accelerating the Next Generation Long Read Mapping with the FPGA-Based System. 840-852 - Luis A. A. Meira, Vinícius R. Máximo, Álvaro Luiz Fazenda, Arlindo Flávio da Conceição:
acc-Motif: Accelerated Network Motif Detection. 853-862 - Imen Messaoudi, Afef Elloumi Oueslati, Zied Lachiri:
Building Specific Signals from Frequency Chaos Game and Revealing Periodicities Using a Smoothed Fourier Analysis. 863-877 - Timo Krotzky, Thomas Fober, Eyke Hüllermeier, Gerhard Klebe:
Extended Graph-Based Models for Enhanced Similarity Search in Cavbase. 878-890 - Jian-Sheng Wu, Sheng-Jun Huang, Zhi-Hua Zhou:
Genome-Wide Protein Function Prediction through Multi-Instance Multi-Label Learning. 891-902 - Tulaya Limpiti, Chainarong Amornbunchornvej, Apichart Intarapanich, Anunchai Assawamakin, Sissades Tongsima:
iNJclust: Iterative Neighbor-Joining Tree Clustering Framework for Inferring Population Structure. 903-914 - Xiaoqing Liu, Jun Wu, Haipeng Gong, Shengchun Deng, Zengyou He:
Mining Conditional Phosphorylation Motifs. 915-927 - Bonnie Kirkpatrick, Kristian Stevens:
Perfect Phylogeny Problems with Missing Values. 928-941 - Danilo Horta, Ricardo J. G. B. Campello:
Similarity Measures for Comparing Biclusterings. 942-954 - Yulia M. Suvorova, Maria A. Korotkova, Eugene V. Korotkov:
Study of the Paired Change Points in Bacterial Genes. 955-964 - Hao Zhang, Xing-Yuan Wang, Xiaohui Lin:
Synchronization of Boolean Networks with Different Update Schemes. 965-972 - Jing Li, Jun Hu, Matthew Newman, Kejun Liu, Huanying Ge:
RNA-Seq Analysis Pipeline Based on Oshell Environment. 973-978
Volume 11, Number 6, November - December 2014
- Yufei Huang, Yidong Chen, Xiaoning Qian:
Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012). 981-983 - Karl B. Gregory, Amin A. Momin, Kevin R. Coombes, Veerabhadran Baladandayuthapani:
Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data. 984-994 - Noah Berlow, Saad Haider, Qian Wan, Mathew Geltzeiler, Lara E. Davis, Charles Keller, Ranadip Pal:
An Integrated Approach to Anti-Cancer Drug Sensitivity Prediction. 995-1008 - Ye Tian, Sean S. Wang, Zhen Zhang, Olga C. Rodriguez, Emanuel Petricoin III, Ie-Ming Shih, Daniel Chan, Maria Avantaggiati, Guoqiang Yu, Shaozhen Ye, Robert Clarke, Chao Wang, Bai Zhang, Yue Joseph Wang, Chris Albanese:
Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses. 1009-1019 - Meng Lu, Hye-Seung Lee, David Hadley, Jianhua Z. Huang, Xiaoning Qian:
Logistic Principal Component Analysis for Rare Variants in Gene-Environment Interaction Analysis. 1020-1028 - Seyed Javad Sajjadi, Xiaoning Qian, Bo Zeng, Amin Ahmadi Adl:
Network-Based Methods to Identify Highly Discriminating Subsets of Biomarkers. 1029-1037 - Yanxun Xu, Xiaofeng Zheng, Yuan Yuan, Marcos R. Estecio, Jean-Pierre Issa, Peng Qiu, Yuan Ji, Shoudan Liang:
BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data. 1038-1044 - Peng Qiu:
Unfold High-Dimensional Clouds for Exhaustive Gating of Flow Cytometry Data. 1045-1051 - Mainá Bitar, Glória Regina Franco:
A Basic Protein Comparative Three-Dimensional Modeling Methodological Workflow Theory and Practice. 1052-1065 - Choujun Zhan, Wuchao Situ, Lam Fat Yeung, Peter Wai-Ming Tsang, Genke Yang:
A Parameter Estimation Method for Biological Systems modelled by ODE/DDE Models Using Spline Approximation and Differential Evolution Algorithm. 1066-1076 - Fumihide Shiraishi, Erika Yoshida, Eberhard O. Voit:
An Efficient and Very Accurate Method for Calculating Steady-State Sensitivities in Metabolic Reaction Systems. 1077-1086 - Anveshi Charuvaka, Huzefa Rangwala:
Classifying Protein Sequences Using Regularized Multi-Task Learning. 1087-1098 - László Dávid, Alexander Bockmayr:
Computing Elementary Flux Modes Involving a Set of Target Reactions. 1099-1107 - Ahsan Zaigam Rizvi, C. Bhattacharya:
Detection of Replication Origin Sites in Herpesvirus Genomes by Clustering and Scoring of Palindromes with Quadratic Entropy Measures. 1108-1118 - Kamal Taha:
Determining Semantically Related Significant Genes. 1119-1130 - Saima Rathore, Mutawarra Hussain, Asifullah Khan:
GECC: Gene Expression Based Ensemble Classification of Colon Samples. 1131-1145 - Bo Liao, Yan Jiang, Wei Liang, Wen Zhu, Lijun Cai, Zhi Cao:
Gene Selection Using Locality Sensitive Laplacian Score. 1146-1156 - Michiel Stock, Thomas Fober, Eyke Hüllermeier, Serghei Glinca, Gerhard Klebe, Tapio Pahikkala, Antti Airola, Bernard De Baets, Willem Waegeman:
Identification of Functionally Related Enzymes by Learning-to-Rank Methods. 1157-1169 - Anirban Mukhopadhyay, Monalisa Mandal:
Identifying Non-Redundant Gene Markers from Microarray Data: A Multiobjective Variable Length PSO-Based Approach. 1170-1183 - Yoram Zarai, Michael Margaliot, Tamir Tuller:
Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case. 1184-1195 - Umesh Kalathiya, Monikaben Padariya, Maciej Baginski:
Molecular Modeling and Evaluation of Novel Dibenzopyrrole Derivatives as Telomerase Inhibitors and Potential Drug for Cancer Therapy. 1196-1207 - Andri Mirzal:
Nonparametric Tikhonov Regularized NMF and Its Application in Cancer Clustering. 1208-1217 - Parthan Kasarapu, Maria Garcia de la Banda, Arun Siddharth Konagurthu:
On Representing Protein Folding Patterns Using Non-Linear Parametric Curves. 1218-1228 - Filippo Disanto, Noah A. Rosenberg:
On the Number of Ranked Species Trees Producing Anomalous Ranked Gene Trees. 1229-1238 - Hasin Afzal Ahmed, Priyakshi Mahanta, Dhruba Kumar Bhattacharyya, Jugal K. Kalita:
Shifting-and-Scaling Correlation Based Biclustering Algorithm. 1239-1252 - Koichi Kobayashi, Kunihiko Hiraishi:
ILP/SMT-Based Method for Design of Boolean Networks Based on Singleton Attractors. 1253-1259 - Loes Olde Loohuis, Andreas Witzel, Bud Mishra:
Improving Detection of Driver Genes: Power-Law Null Model of Copy Number Variation in Cancer. 1260-1263 - Haiying Wang, Huiru Zheng:
Organized Modularity in the Interactome: Evidence from the Analysis of Dynamic Organization in the Cell Cycle. 1264-1270
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