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    Journal: IEEE/ACM Trans. Comput. Biology Bioinform.

    Volume 11, Issue 6

    981 -- 983Yufei Huang, Yidong Chen, Xiaoning Qian. Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012)
    984 -- 994Karl B. Gregory, Amin A. Momin, Kevin R. Coombes, Veerabhadran Baladandayuthapani. Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data
    995 -- 1008Noah Berlow, Saad Haider, Qian Wan, Mathew Geltzeiler, Lara E. Davis, Charles Keller, Ranadip Pal. An Integrated Approach to Anti-Cancer Drug Sensitivity Prediction
    1009 -- 1019Ye 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 Wang, Chris Albanese. Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses
    1020 -- 1028Meng Lu, Hye-Seung Lee, David Hadley, Jianhua Z. Huang, Xiaoning Qian. Logistic Principal Component Analysis for Rare Variants in Gene-Environment Interaction Analysis
    1029 -- 1037Seyed Javad Sajjadi, Xiaoning Qian, Bo Zeng, Amin Ahmadi-Adl. Network-Based Methods to Identify Highly Discriminating Subsets of Biomarkers
    1038 -- 1044Yanxun 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
    1045 -- 1051Peng Qiu. Unfold High-Dimensional Clouds for Exhaustive Gating of Flow Cytometry Data
    1052 -- 1065Maina Bitar, Glória Regina Franco. A Basic Protein Comparative Three-Dimensional Modeling Methodological Workflow Theory and Practice
    1066 -- 1076Choujun 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
    1077 -- 1086Fumihide Shiraishi, Erika Yoshida, Eberhard O. Voit. An Efficient and Very Accurate Method for Calculating Steady-State Sensitivities in Metabolic Reaction Systems
    1087 -- 1098Anveshi Charuvaka, Huzefa Rangwala. Classifying Protein Sequences Using Regularized Multi-Task Learning
    1099 -- 1107László Dávid, Alexander Bockmayr. Computing Elementary Flux Modes Involving a Set of Target Reactions
    1108 -- 1118Ahsan Zaigam Rizvi, C. Bhattacharya. Detection of Replication Origin Sites in Herpesvirus Genomes by Clustering and Scoring of Palindromes with Quadratic Entropy Measures
    1119 -- 1130Kamal Taha. Determining Semantically Related Significant Genes
    1131 -- 1145Saima Rathore, Mutawarra Hussain, Asifullah Khan. GECC: Gene Expression Based Ensemble Classification of Colon Samples
    1146 -- 1156Bo Liao, Yan Jiang, Wei Liang, Wen Zhu, Lijun Cai, Zhi Cao. Gene Selection Using Locality Sensitive Laplacian Score
    1157 -- 1169Michiel 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
    1170 -- 1183Anirban Mukhopadhyay 0001, Monalisa Mandal. Identifying Non-Redundant Gene Markers from Microarray Data: A Multiobjective Variable Length PSO-Based Approach
    1184 -- 1195Yoram Zarai, Michael Margaliot, Tamir Tuller. Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case
    1196 -- 1207Umesh Kalathiya, Monikaben Padariya, Maciej Baginski. Molecular Modeling and Evaluation of Novel Dibenzopyrrole Derivatives as Telomerase Inhibitors and Potential Drug for Cancer Therapy
    1208 -- 1217Andri Mirzal. Nonparametric Tikhonov Regularized NMF and Its Application in Cancer Clustering
    1218 -- 1228Parthan Kasarapu, Maria Garcia de la Banda, Arun Siddharth Konagurthu. On Representing Protein Folding Patterns Using Non-Linear Parametric Curves
    1229 -- 1238Filippo Disanto, Noah A. Rosenberg. On the Number of Ranked Species Trees Producing Anomalous Ranked Gene Trees
    1239 -- 1252Hasin Afzal Ahmed, Priyakshi Mahanta, Dhruba Kumar Bhattacharyya, Jugal K. Kalita. Shifting-and-Scaling Correlation Based Biclustering Algorithm
    1253 -- 1259Koichi Kobayashi, Kunihiko Hiraishi. ILP/SMT-Based Method for Design of Boolean Networks Based on Singleton Attractors
    1260 -- 1263Loes Olde Loohuis, Andreas Witzel, Bud Mishra. Improving Detection of Driver Genes: Power-Law Null Model of Copy Number Variation in Cancer
    1264 -- 1270Haiying Wang, Huiru Zheng. Organized Modularity in the Interactome: Evidence from the Analysis of Dynamic Organization in the Cell Cycle

    Volume 11, Issue 5

    773 -- 774Gaurav Pandey, Huzefa Rangwala. Guest Editorial for Special Section on BIOKDD2013
    775 -- 787Shobeir Fakhraei, Bert Huang, Louiqa Raschid, Lise Getoor. Network-Based Drug-Target Interaction Prediction with Probabilistic Soft Logic
    788 -- 800Raed 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
    801 -- 813Joana P. Gonçalves, Sara C. Madeira. LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification
    814 -- 825Cheng Zhou, Pieter Meysman, Boris Cule, Kris Laukens, Bart Goethals. Discovery of Spatially Cohesive Itemsets in Three-Dimensional Protein Structures
    826 -- 839Michael Zeller, Christophe N. Magnan, Vishal R. Patel, Paul Rigor, Leonard Sender, Pierre Baldi. A Genomic Analysis Pipeline and Its Application to Pediatric Cancers
    840 -- 852Peng Chen 0004, Chao Wang, Xi Li, Xuehai Zhou. Accelerating the Next Generation Long Read Mapping with the FPGA-Based System
    853 -- 862Luis A. A. Meira, Vinicius R. Máximo, Álvaro L. Fazenda, Arlindo Flávio da Conceição. acc-Motif: Accelerated Network Motif Detection
    863 -- 877Imen Messaoudi, Afef Elloumi Oueslati, Zied Lachiri. Building Specific Signals from Frequency Chaos Game and Revealing Periodicities Using a Smoothed Fourier Analysis
    878 -- 890Timo Krotzky, Thomas Fober, Eyke Hüllermeier, Gerhard Klebe. Extended Graph-Based Models for Enhanced Similarity Search in Cavbase
    891 -- 902Jian-Sheng Wu, Sheng-Jun Huang, Zhi-Hua Zhou. Genome-Wide Protein Function Prediction through Multi-Instance Multi-Label Learning
    903 -- 914Tulaya Limpiti, Chainarong Amornbunchornvej, Apichart Intarapanich, Anunchai Assawamakin, Sissades Tongsima. iNJclust: Iterative Neighbor-Joining Tree Clustering Framework for Inferring Population Structure
    915 -- 927Xiaoqing Liu, Jun Wu, Haipeng Gong, Shengchun Deng, Zengyou He. Mining Conditional Phosphorylation Motifs
    928 -- 941Bonnie Kirkpatrick, Kristian Stevens. Perfect Phylogeny Problems with Missing Values
    942 -- 954Danilo Horta, Ricardo J. G. B. Campello. Similarity Measures for Comparing Biclusterings
    955 -- 964Yulia Suvorova, Maria A. Korotkova, Eugene V. Korotkov. Study of the Paired Change Points in Bacterial Genes
    965 -- 972Hao Zhang, Xing-Yuan Wang, Xiao-Hui Lin. Synchronization of Boolean Networks with Different Update Schemes
    973 -- 978Jing Li, Jun Hu, Matthew Newman, Kejun Liu, Huanying Ge. RNA-Seq Analysis Pipeline Based on Oshell Environment

    Volume 11, Issue 4

    613 -- 0Ying Xu. Reviewer Appreciation Editorial
    614 -- 615Shuigeng Zhou, Yi-Ping Phoebe Chen. Guest editorial for the 12th Asia Pacific Bioinformatics Conference
    616 -- 627Bin Xu, Jihong Guan. From Function to Interaction: A New Paradigm for Accurately Predicting Protein Complexes Based on Protein-to-Protein Interaction Networks
    628 -- 637Matteo Comin, Davide Verzotto. Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison
    638 -- 647Yanglan Gan, Guobing Zou, Jihong Guan, Guangwei Xu. A Novel Wavelet-Based Approach for Predicting Nucleosome Positions Using DNAS tructural Information
    648 -- 656Christine Lo, Boyko Kakaradov, Daniel Lokshtanov, Christina Boucher. SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers
    657 -- 666Hualong Yu, Jun Ni. An Improved Ensemble Learning Methodfor Classifying High-Dimensionaland Imbalanced Biomedicine Data
    667 -- 672Fei Hu, Jun Zhou, Lingxi Zhou, Jijun Tang. Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions
    673 -- 680Minta Thomas, Anneleen Daemen, Bart De Moor. Maximum Likelihood Estimation ofGEVD: Applications in Bioinformatics
    681 -- 692Kazuki Ichikawa, Shinichi Morishita. A Simple but Powerful Heuristic Methodfor Accelerating $k$ -Means Clusteringof Large-Scale Data in Life Science
    693 -- 701Yuan 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
    702 -- 713Chia-Hua Chuang, Chun-Liang Lin. A Novel Synthesizing Genetic Logic Circuit: Frequency Multiplier
    714 -- 726Hai Su, Fuyong Xing, Jonah D. Lee, Charlotte A. Peterson, Lin Yang. Automatic Myonuclear Detection in IsolatedSingle Muscle Fibers Using Robust EllipseFitting and Sparse Representation
    727 -- 740Zhiwen 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
    741 -- 752Rui Fa, Asoke K. Nandi. Noise Resistant Generalized Parametric Validity Index of Clustering for Gene Expression Data
    753 -- 765Beatriz García Jiménez, Tirso Pons, Araceli Sanchis, Alfonso Valencia. Predicting Protein Relationshipsto Human Pathways througha Relational Learning ApproachBased on Simple Sequence Features
    766 -- 772Ao Kong, Chinmaya Gupta, Mauro Ferrari, Marco Agostini, Chiara Bedin, Ali Bouamrani, Ennio Tasciotti, Robert Azencott. Biomarker Signature Discovery from Mass Spectrometry Data

    Volume 11, Issue 3

    453 -- 454Zhipeng Cai, Oliver Eulenstein, Cynthia Gibas. Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications
    455 -- 467Falk Hüffner, Christian Komusiewicz, Adrian Liebtrau, Rolf Niedermeier. Partitioning Biological Networks into Highly Connected Clusters with Maximum Edge Coverage
    468 -- 476Xuebo Song, Lin Li, Pradip K. Srimani, Philip S. Yu, James Z. Wang. Measure the Semantic Similarity of GO Terms Using Aggregate Information Content
    477 -- 485Yu Zheng, Louxin Zhang. Effect of Incomplete Lineage SortingOn Tree-Reconciliation-Based Inferenceof Gene Duplication
    486 -- 497Bihai Zhao, Jianxin Wang, Min Li, Fang-Xiang Wu, Yi Pan. Detecting Protein Complexes Basedon Uncertain Graph Model
    498 -- 499Elena Marchiori, Alioune Ngom, Raj Acharya. Guest Editorial: Pattern Recognition in Bioinformatics
    500 -- 509Matteo Comin, Morris Antonello. Fast Entropic Profiler: An InformationTheoretic Approach for the Discovery ofPatterns in Genomes
    510 -- 519Abdollah 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
    520 -- 532Michael 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
    533 -- 547Shaurya Jauhari, S. A. M. Rizvi. Mining Gene Expression Data Focusing Cancer Therapeutics: A Digest
    548 -- 560Andrew K. C. Wong, En-Shiun Annie Lee. Aligning and Clustering Patterns to Reveal the Protein Functionality of Sequences
    561 -- 572Marco Mina, Pietro Hiram Guzzi. Improving the Robustness of Local Network Alignment: Design and Extensive Assessmentof a Markov Clustering-Based Approach
    573 -- 578Qingliang Shen, Hong Tian, Daoqi Tang, Wenbing Yao, Xiangdong Gao. * Sequence Elimination: A NovelAlgorithm for Ensemble-Based Redesignof Receptor-Ligand Binding
    579 -- 591Guo-Xian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, Zhiwen Yu. Protein Function Prediction withIncomplete Annotations
    592 -- 603Fernando Lopez-Caamal, Diego A. Oyarzún, Richard H. Middleton, Miriam R. Garcia. 2+ Accumulation in Nonexcitable Cells: An Analytical Study
    604 -- 611Benjamin Xueqi Guan, Bir Bhanu, Prudence Talbot, Sabrina Lin. Bio-Driven Cell Region Detection in Human Embryonic Stem Cell Assay

    Volume 11, Issue 2

    293 -- 303ChangKug 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
    304 -- 315Tom M. W. Nye. An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace
    316 -- 324Abeer Eshra, Ayman El-Sayed. An Odd Parity Checker Prototype Using DNAzyme Finite State Machine
    325 -- 335Ruth Davidson, Seth Sullivant. Distance-Based Phylogenetic MethodsAround a Polytomy
    336 -- 346Kristopher L. Patton, David J. John, James L. Norris, Daniel R. Lewis, Gloria K. Muday. Hierarchical Probabilistic Interaction Modeling for Multiple Gene Expression Replicates
    347 -- 360Pugalendhi GaneshKumar, Chellasamy Rani, Durairaj Devaraj, T. Aruldoss Albert Victoire. Hybrid Ant Bee Algorithm for Fuzzy Expert System Based Sample Classification
    361 -- 374Shunji Tanaka. Improved Exact Enumerative Algorithmsfor the Planted ($l$, $d$)-Motif Search Problem
    375 -- 388Veli Mäkinen, Niko Välimäki, Jouni Sirén. Indexing Graphs for Path Queries with Applications in Genome Research
    389 -- 397Anthony Labarre, Sicco Verwer. Merging Partially Labelled Trees: Hardness and a DeclarativeProgramming Solution
    398 -- 406Weiming Li, Bin Ma, Kaizhong Zhang. Optimizing Spaced $k$-mer Neighbors for Efficient Filtration in Protein Similarity Search
    407 -- 418Xiwei Tang, Jianxin Wang, Jiancheng Zhong, Yi Pan. Predicting Essential Proteins Basedon Weighted Degree Centrality
    419 -- 430Kamal 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
    431 -- 440Miha Moskon, Miha Mraz. Systematic Approach to Computational Designof Gene Regulatory Networks with Information Processing Capabilities
    441 -- 452Dan Tulpan, Derek H. Smith, Roberto Montemanni. Thermodynamic Post-Processing versusGC-Content Pre-Processing for DNA CodesSatisfying the Hamming Distance andReverse-Complement Constraints

    Volume 11, Issue 1

    1 -- 4Ying Xu. Editorial from the Editor-in-Chief
    5 -- 6Frank Eisenhaber, Wing-Kin Sung, Limsoon Wong. Guest Editorial for the International Conference on Genome Informatics (GIW 2013)
    7 -- 16Liang Zhao, Steven C. H. Hoi, Zhenhua Li, Limsoon Wong, Hung Nguyen, Jinyan Li. Coupling Graphs, Efficient Algorithmsand B-Cell Epitope Prediction
    17 -- 25Ying Fan, Ruoshui Lu, Lusheng Wang, Massimo Andreatta, Shuai Cheng Li. Quantifying Significance of MHC II Residues
    26 -- 32Paul D. Yoo, Sami Muhaidat, Kamal Taha, Jamal Bentahar, Abdallah Shami. Intelligent Consensus Modeling for ProlineCis-Trans Isomerization Prediction
    33 -- 41Laleh Soltan Ghoraie, Forbes Burkowski, Shuai Cheng Li, Mu Zhu. Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation
    42 -- 54Ruiqi Liao, Ruichang Zhang, Jihong Guan, Shuigeng Zhou. A New Unsupervised Binning Approachfor Metagenomic Sequences Based onN-grams and Automatic Feature Weighting
    55 -- 62Jui-Chen Hsiao, Chih-Hsuan Wei, Hung-Yu Kao. Gene Name Disambiguation UsingMulti-Scope Species Detection
    63 -- 72Jing 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
    73 -- 82Yanglan Gan, Jihong Guan, Shuigeng Zhou, Weixiong Zhang. Identifying Cis-Regulatory Elements and Modules Using Conditional Random Fields
    83 -- 94Sriganesh Srihari, Venkatesh Raman, Hon Wai Leong, Mark A. Ragan. Evolution and Controllability of CancerNetworks: A Boolean Perspective
    95 -- 115Sanghamitra Bandyopadhyay, Saurav Mallik, Anirban Mukhopadhyay 0001. A Survey and Comparative Study of Statistical Tests for Identifying Differential Expressionfrom Microarray Data
    116 -- 127Sanghamitra Bandyopadhyay, Koushik Mallick. A New Path Based Hybrid Measurefor Gene Ontology Similarity
    128 -- 141Fahad 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
    142 -- 153Biing-Feng Wang, Chien-Hsin Lin, I.-Tse Yang. Constructing a Gene Team Treein Almost $O$$(n\; {\rm lg}\; n)$ Time
    154 -- 167Mitsunori Kayano, Motoki Shiga, Hiroshi Mamitsuka. Detecting Differentially Coexpressed Genesfrom Labeled Expression Data: A Brief Review
    168 -- 181Vangelis Metsis, Fillia Makedon, Dinggang Shen, Heng Huang. DNA Copy Number Selection Using Robust Structured Sparsity-Inducing Norms
    182 -- 191Sandhya Prabhakaran, Mélanie Rey, Osvaldo Zagordi, Niko Beerenwinkel, Volker Roth. HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model
    192 -- 201Leyi Wei, Minghong Liao, Yue Gao, Rongrong Ji, Zengyou He, Quan Zou. Improved and Promising Identificationof Human MicroRNAs by Incorporatinga High-Quality Negative Set
    202 -- 218Mohammad Shahrokh Esfahani, Edward R. Dougherty. Incorporation of Biological PathwayKnowledge in the Construction of Priorsfor Optimal Bayesian Classification
    219 -- 230Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Otto, Sebastian Will. Local Exact Pattern Matching for Non-FixedRNA Structures
    231 -- 242Pawel Górecki, Oliver Eulenstein. Maximizing Deep Coalescence Cost
    243 -- 257Jun Sun 0008, Vasile Palade, Xiaojun Wu, Wei Fang. Multiple Sequence Alignment with HiddenMarkov Models Learned by Random DriftParticle Swarm Optimization
    258 -- 264John Healy, Desmond Chambers. Approximate k-Mer Matching UsingFuzzy Hash Maps
    265 -- 0Guo-Xian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, Zhiwen Yu. Erratum to "Protein Function Prediction Using Multilabel Ensemble Classification"
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