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

    Volume 2, Issue 4

    273 -- 288Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre. A Framework for Three-Dimensional Simulation of Morphogenesis
    289 -- 301Riccardo Boscolo, Chiara Sabatti, James C. Liao, Vwani P. Roychowdhury. A Generalized Framework for Network Component Analysis
    302 -- 315Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang. Assignment of Orthologous Genes via Genome Rearrangement
    316 -- 329Heather L. Turner, Trevor C. Bailey, Wojtek J. Krzanowski, Cheryl A. Hemingway. Biclustering Models for Structured Microarray Data
    330 -- 338José L. Sevilla Campo, Victor Segura, Adam Podhorski, Elizabeth Guruceaga, Jose M. Mato, Luis A. Martínez-Cruz, Fernando J. Corrales, Angel Rubio. Correlation between Gene Expression and GO Semantic Similarity
    339 -- 354Sungroh Yoon, Christine Nardini, Luca Benini, Giovanni De Micheli. Discovering Coherent Biclusters from Gene Expression Data Using Zero-Suppressed Binary Decision Diagrams
    355 -- 365Vincent Shin-Mu Tseng, Ching-Pin Kao. Efficiently Mining Gene Expression Data via a Novel Parameterless Clustering Method
    366 -- 379Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna. Searching Genomes for Noncoding RNA Using FastR

    Volume 2, Issue 3

    177 -- 178Charles X. Ling, William Stafford Noble, Qiang Yang. Guest Editor s Introduction to the Special Issue: Machine Learning for Bioinformatics-Part 2
    179 -- 193Alexander Schliep, Ivan G. Costa, Christine Steinhoff, Alexander Schönhuth. Analyzing Gene Expression Time-Courses
    194 -- 202Anshul Kundaje, Manuel Middendorf, Feng Gao, Chris Wiggins, Christina S. Leslie. Combining Sequence and Time Series Expression Data to Learn Transcriptional Modules
    203 -- 216Samuel Kaski, Janne Nikkilä, Janne Sinkkonen, Leo Lahti, Juha E. A. Knuuttila, Christophe Roos. Associative Clustering for Exploring Dependencies between Functional Genomics Data Sets
    217 -- 230Jingfen Zhang, Wen Gao, Jinjin Cai, Simin He, Rong Zeng, Runsheng Chen. Predicting Molecular Formulas of Fragment Ions with Isotope Patterns in Tandem Mass Spectra
    231 -- 242Ed Keedwell, Ajit Narayanan. Discovering Gene Networks with a Neural-Genetic Hybrid
    243 -- 253John Hawkins, Mikael Bodén. The Applicability of Recurrent Neural Networks for Biological Sequence Analysis
    254 -- 261Mikael Gustafsson, Michael Hornquist, Anna Lombardi. Constructing and Analyzing a Large-Scale Gene-to-Gene Regulatory Network-Lasso-Constrained Inference and Biological Validation
    262 -- 270Cigdem Demir, S. Humayun Gultekin, Bülent Yener. Learning the Topological Properties of Brain Tumors

    Volume 2, Issue 2

    81 -- 82Charles X. Ling, William Stafford Noble, Qiang Yang. Guest Editors Introduction to the Special Issue: Machine Learning for Bioinformatics - Part 1
    83 -- 101Wai-Ho Au, Keith C. C. Chan, Andrew K. C. Wong, Yang Wang. Attribute Clustering for Grouping, Selection, and Classification of Gene Expression Data
    102 -- 109Pravesh Biyani, Xiaolin Wu, Abhijit Sinha. Joint Classification and Pairing of Human Chromosomes
    110 -- 118Cesare Furlanello, Maria Serafini, Stefano Merler, Giuseppe Jurman. Semisupervised Learning for Molecular Profiling
    119 -- 130Hiroshi Mamitsuka. Essential Latent Knowledge for Protein-Protein Interactions: Analysis by an Unsupervised Learning Approach
    131 -- 142Jagath C. Rajapakse, Loi Sy Ho. Markov Encoding for Detecting Signals in Genomic Sequences
    143 -- 156Simon Rogers, Mark Girolami, Colin Campbell, Rainer Breitling. The Latent Process Decomposition of cDNA Microarray Data Sets
    157 -- 165Jinbo Xu. Fold Recognition by Predicted Alignment Accuracy
    166 -- 175Li Shen, Eng Chong Tan. Dimension Reduction-Based Penalized Logistic Regression for Cancer Classification Using Microarray Data

    Volume 2, Issue 1

    1 -- 2Junhyong Kim, Inge Jonassen. Guest Editorial: WABI Special Section Part II
    3 -- 14Julien Allali, Marie-France Sagot. A New Distance for High Level RNA Secondary Structure Comparison
    15 -- 28Denis Bertrand, Olivier Gascuel. Topological Rearrangements and Local Search Method for Tandem Duplication Trees
    29 -- 38Daniel G. Brown. Optimizing Multiple Seeds for Protein Homology Search
    39 -- 0Dan Gusfield. Editorial-State of the Transaction
    40 -- 50Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot. Bases of Motifs for Generating Repeated Patterns with Wild Cards
    51 -- 61Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg. Multiseed Lossless Filtration
    62 -- 76Ying Liu, Shamkant B. Navathe, Jorge Civera, Venu Dasigi, Ashwin Ram, Brian J. Ciliax, Ray Dingledine. Text Mining Biomedical Literature for Discovering Gene-to-Gene Relationships: A Comparative Study of Algorithms
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