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

    Volume 7, Issue 4

    577 -- 578Ion Mandou, Giri Narasimhan, Yi Pan, Yanqing Zhang. Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications
    579 -- 587Adriana Muñoz, David Sankoff. Rearrangement Phylogeny of Genomes in Contig Form
    588 -- 597Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield. Untangling Tanglegrams: Comparing Trees by Their Drawings
    598 -- 610Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi. Pure Parsimony Xor Haplotyping
    611 -- 618Yufeng Wu. Exact Computation of Coalescent Likelihood for Panmictic and Subdivided Populations under the Infinite Sites Model
    619 -- 627Sanguthevar Rajasekaran, Sahar Al Seesi, Reda A. Ammar. Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots
    628 -- 635Guillaume Blin, Florian Sikora, Stéphane Vialette. Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set
    636 -- 646Qiang Cheng. A Sparse Learning Machine for High-Dimensional Data with Application to Microarray Gene Analysis
    647 -- 653William B. Langdon, Graham J. G. Upton, Renata da Silva Camargo, Andrew P. Harrison. A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips
    654 -- 668Gang Li, Tak-Ming Chan, Kwong-Sak Leung, Kin-Hong Lee. A Cluster Refinement Algorithm for Motif Discovery
    669 -- 680Jianjun Zhou, Jörg Sander, Zhipeng Cai, Lusheng Wang, Guohui Lin. Finding the Nearest Neighbors in Biological Databases Using Less Distance Computations
    681 -- 687Liang-Tsung Huang, Lien Fu Lai, M. Michael Gromiha. Human-Readable Rule Generator for Integrating Amino Acid Sequence Information and Stability of Mutant Proteins
    688 -- 703Christophe Godin, Pascal Ferraro. Quantifying the Degree of Self-Nestedness of Trees: Application to the Structural Analysis of Plants
    704 -- 718Sagi Snir, Satish Rao. Quartets MaxCut: A Divide and Conquer Quartets Algorithm
    719 -- 726Xin Lu, Anthony Gamst, Ronghui Xu. RDCurve: A Nonparametric Method to Evaluate the Stability of Ranking Procedures
    727 -- 740Herbert H. Tsang, Kay C. Wiese. SARNA-Predict: Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-Based Simulated Annealing
    741 -- 751Liwen You, Vladimir Brusic, Marcus Gallagher, Mikael Bodén. Using Gaussian Process with Test Rejection to Detect T-Cell Epitopes in Pathogen Genomes
    752 -- 762Alberto Apostolico, Matteo Comin, Laxmi Parida. VARUN: Discovering Extensible Motifs under Saturation Constraints
    763 -- 767István Miklós, Bence Melykuti, Krister Swenson. The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths

    Volume 7, Issue 3

    385 -- 399Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia. An Overview of BioCreative II.5
    400 -- 411Artemy Kolchinsky, Alaa Abi-Haidar, Jasleen Kaur, Ahmed Abdeen Hamed, Luis Mateus Rocha. Classification of Protein-Protein Interaction Full-Text Documents Using Text and Citation Network Features
    412 -- 420Hong-Jie Dai, Po-Ting Lai, Richard Tzong-Han Tsai. Multistage Gene Normalization and SVM-Based Ranking for Protein Interactor Extraction in Full-Text Articles
    421 -- 427Man Lan, Jian Su. Empirical Investigations into Full-Text Protein Interaction Article Categorization Task (ACT) in the BioCreative II.5 Challenge
    428 -- 441Yifei Chen, Feng Liu, Bernard Manderick. BioLMiner System: Interaction Normalization Task and Interaction Pair Task in the BioCreative II.5 Challenge
    442 -- 453Rune Sætre, Kazuhiro Yoshida, Makoto Miwa, Takuya Matsuzaki, Yoshinobu Kano, Jun-ichi Tsujii. Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System
    454 -- 461Yong-gang Cao, Zuofeng Li, Feifan Liu, Shashank Agarwal, Qing Zhang, Hong Yu. An IR-Aided Machine Learning Framework for the BioCreative II.5 Challenge
    462 -- 471Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter. Exploring Species-Based Strategies for Gene Normalization
    472 -- 480Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Simon Clematide, Thérèse Vachon, Martin Romacker. OntoGene in BioCreative II.5
    481 -- 494Jörg Hakenberg, Robert Leaman, Nguyen Ha Vo, Siddhartha Jonnalagadda, Ryan Sullivan, Christopher Miller, Luis Tari, Chitta Baral, Graciela Gonzalez. Efficient Extraction of Protein-Protein Interactions from Full-Text Articles
    495 -- 510Rezaul Alam Chowdhury, Hai-son Le, Vijaya Ramachandran. Cache-Oblivious Dynamic Programming for Bioinformatics
    511 -- 523Leonardo Tininini, Paola Bertolazzi, Alessandra Godi, Giuseppe Lancia. CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony
    524 -- 536Ronald Jackups Jr., Jie Liang. Combinatorial Analysis for Sequence and Spatial Motif Discovery in Short Sequence Fragments
    537 -- 549Xiaoxu Han. Nonnegative Principal Component Analysis for Cancer Molecular Pattern Discovery
    550 -- 562Jia Zeng, Xiaoyu Zhao, Xiao-Qin Cao, Hong Yan. SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition
    563 -- 571Arthur Zimek, Fabian Buchwald, Eibe Frank, Stefan Kramer. A Study of Hierarchical and Flat Classification of Proteins
    572 -- 576Maria Luisa Bonet, Katherine St. John. On the Complexity of uSPR Distance

    Volume 7, Issue 2

    193 -- 194Marie-France Sagot. EIC Editorial
    195 -- 196Stefano Lonardi, Jake Yue Chen. Data Mining in Bioinformatics: Selected Papers from BIOKDD
    197 -- 207Aaron M. Smalter, Jun Huan, Yi Jia, Gerald H. Lushington. GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics
    208 -- 217Petko Bogdanov, Ambuj K. Singh. Molecular Function Prediction Using Neighborhood Features
    218 -- 222Luay Nakhleh. A Metric on the Space of Reduced Phylogenetic Networks
    223 -- 237Gunjan Gupta, Alexander Liu, Joydeep Ghosh. Automated Hierarchical Density Shaving: A Robust Automated Clustering and Visualization Framework for Large Biological Data Sets
    238 -- 250Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer. Automated Isolation of Translational Efficiency Bias That Resists the Confounding Effect of GC(AT)-Content
    251 -- 262Arthur Tenenhaus, Vincent Guillemot, Xavier Gidrol, Vincent Frouin. Gene Association Networks from Microarray Data Using a Regularized Estimation of Partial Correlation Based on PLS Regression
    263 -- 277Zexuan Zhu, Yew-Soon Ong, Jacek M. Zurada. Identification of Full and Partial Class Relevant Genes
    278 -- 287Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson. Model Composition for Macromolecular Regulatory Networks
    288 -- 298Shahid H. Bokhari, Daniel Janies. Reassortment Networks for Investigating the Evolution of Segmented Viruses
    299 -- 308Tracy L. Bergemann, Lue Ping Zhao. Signal Quality Measurements for cDNA Microarray Data
    309 -- 322Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet. Alignments of RNA Structures
    323 -- 332Minghui Jiang. Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots
    333 -- 341Tetsuo Shibuya. Fast Hinge Detection Algorithms for Flexible Protein Structures
    342 -- 353Sylvain Guillemot, Vincent Berry. Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem
    354 -- 364Xiaowen Liu, Jinyan Li, Lusheng Wang. Modeling Protein Interacting Groups by Quasi-Bicliques: Complexity, Algorithm, and Application
    365 -- 374Xingqin Qi, Guojun Li, Shuguang Li, Ying Xu. Sorting Genomes by Reciprocal Translocations, Insertions, and Deletions
    375 -- 381Giora Unger, Benny Chor. Linear Separability of Gene Expression Data Sets

    Volume 7, Issue 1

    2 -- 11Ester Díaz, Guillermo Ayala, Maria Diaz-Fernandez, Liang Gong, Derek Toomre. Automatic Detection of Large Dense-Core Vesicles in Secretory Cells and Statistical Analysis of Their Intracellular Distribution
    12 -- 24Carol Lushbough, Michael K. Bergman, Carolyn J. Lawrence, Douglas Jennewein, Volker Brendel. BioExtract Server - An Integrated Workflow-Enabling System to Access and Analyze Heterogeneous, Distributed Biomolecular Data
    25 -- 36Shenghuo Zhu, Dingding Wang, Kai Yu, Tao Li, Yihong Gong. Feature Selection for Gene Expression Using Model-Based Entropy
    37 -- 49Petri Pehkonen, Garry Wong, Petri Törönen. Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions
    50 -- 63Rafal Kustra, Adam Zagdanski. Data-Fusion in Clustering Microarray Data: Balancing Discovery and Interpretability
    64 -- 79Oliver Rübel, Gunther H. Weber, Min-Yu Huang, E. Wes Bethel, Mark D. Biggin, Charless C. Fowlkes, Cris L. Luengo Hendriks, Soile V. E. Keränen, Michael B. Eisen, David W. Knowles, Jitendra Malik, Hans Hagen, Bernd Hamann. Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data
    80 -- 90Ju Han, Hang Chang, Kumari L. Andarawewa, Paul Yaswen, Mary Helen Barcellos-Hoff, Bahram Parvin. Multidimensional Profiling of Cell Surface Proteins and Nuclear Markers
    91 -- 99Bogdan Done, Purvesh Khatri, Arina Done, Sorin Draghici. Predicting Novel Human Gene Ontology Annotations Using Semantic Analysis
    100 -- 107Zhenqiu Liu, Shili Lin, Ming Tan. Sparse Support Vector Machines with L_{p} Penalty for Biomarker Identification
    108 -- 117Yukyee Leung, Yeung Sam Hung. A Multiple-Filter-Multiple-Wrapper Approach to Gene Selection and Microarray Data Classification
    118 -- 125Theodore J. Perkins, Michael T. Hallett. A Trade-Off between Sample Complexity and Computational Complexity in Learning Boolean Networks from Time-Series Data
    126 -- 137Richard Pelikan, Milos Hauskrecht. Efficient Peak-Labeling Algorithms for Whole-Sample Mass Spectrometry Proteomics
    138 -- 152Pritha Mahata. Exploratory Consensus of Hierarchical Clusterings for Melanoma and Breast Cancer
    153 -- 165Sara C. Madeira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira. Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm
    166 -- 171Elchanan Mossel, Sébastien Roch. Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci
    172 -- 182Alex Alves Freitas, Daniela Wieser, Rolf Apweiler. On the Importance of Comprehensible Classification Models for Protein Function Prediction
    183 -- 187Noga Alon, Benny Chor, Fabio Pardi, Anat Rapoport. Approximate Maximum Parsimony and Ancestral Maximum Likelihood
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