IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 2

Volume 2, Number 1, January 2005

• Junhyong Kim, Inge Jonassen:
  Guest Editorial: WABI Special Section Part II. 1-2
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• Julien Allali, Marie-France Sagot:
  A New Distance for High Level RNA Secondary Structure Comparison. 3-14
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• Denis Bertrand, Olivier Gascuel:
  Topological Rearrangements and Local Search Method for Tandem Duplication Trees. 15-28
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• Daniel G. Brown:
  Optimizing Multiple Seeds for Protein Homology Search. 29-38
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• Dan Gusfield:
  Editorial-State of the Transaction. 39
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• Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot:
  Bases of Motifs for Generating Repeated Patterns with Wild Cards. 40-50
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• Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg:
  Multiseed Lossless Filtration. 51-61
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• Ying 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. 62-76
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Volume 2, Number 2, April 2005

• Charles X. Ling, William Stafford Noble, Qiang Yang:
  Guest Editors' Introduction to the Special Issue: Machine Learning for Bioinformatics - Part 1. 81-82
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• Wai-Ho Au, Keith C. C. Chan, Andrew K. C. Wong, Yang Wang:
  Attribute Clustering for Grouping, Selection, and Classification of Gene Expression Data. 83-101
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• Pravesh Biyani, Xiaolin Wu, Abhijit Sinha:
  Joint Classification and Pairing of Human Chromosomes. 102-109
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• Cesare Furlanello, Maria Serafini, Stefano Merler, Giuseppe Jurman:
  Semisupervised Learning for Molecular Profiling. 110-118
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• Hiroshi Mamitsuka:
  Essential Latent Knowledge for Protein-Protein Interactions: Analysis by an Unsupervised Learning Approach. 119-130
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• Jagath C. Rajapakse, Loi Sy Ho:
  Markov Encoding for Detecting Signals in Genomic Sequences. 131-142
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• Simon Rogers, Mark Girolami, Colin Campbell, Rainer Breitling:
  The Latent Process Decomposition of cDNA Microarray Data Sets. 143-156
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• Jinbo Xu:
  Fold Recognition by Predicted Alignment Accuracy. 157-165
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• Li Shen, Eng Chong Tan:
  Dimension Reduction-Based Penalized Logistic Regression for Cancer Classification Using Microarray Data. 166-175
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Volume 2, Number 3, July 2005

• Charles X. Ling, William Stafford Noble, Qiang Yang:
  Guest Editor's Introduction to the Special Issue: Machine Learning for Bioinformatics-Part 2. 177-178
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• Alexander Schliep, Ivan G. Costa, Christine Steinhoff, Alexander Schönhuth:
  Analyzing Gene Expression Time-Courses. 179-193
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• Anshul Kundaje, Manuel Middendorf, Feng Gao, Chris Wiggins, Christina S. Leslie:
  Combining Sequence and Time Series Expression Data to Learn Transcriptional Modules. 194-202
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• Samuel Kaski, Janne Nikkilä, Janne Sinkkonen, Leo Lahti, Juha E. A. Knuuttila, Christophe Roos:
  Associative Clustering for Exploring Dependencies between Functional Genomics Data Sets. 203-216
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• Jingfen Zhang, Wen Gao, Jinjin Cai, Simin He, Rong Zeng, Runsheng Chen:
  Predicting Molecular Formulas of Fragment Ions with Isotope Patterns in Tandem Mass Spectra. 217-230
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• Ed Keedwell, Ajit Narayanan:
  Discovering Gene Networks with a Neural-Genetic Hybrid. 231-242
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• John Hawkins, Mikael Bodén:
  The Applicability of Recurrent Neural Networks for Biological Sequence Analysis. 243-253
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• Mikael Gustafsson, Michael Hornquist, Anna Lombardi:
  Constructing and Analyzing a Large-Scale Gene-to-Gene Regulatory Network-Lasso-Constrained Inference and Biological Validation. 254-261
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• Cigdem Demir, S. Humayun Gultekin, Bülent Yener:
  Learning the Topological Properties of Brain Tumors. 262-270
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Volume 2, Number 4, October 2005

• Trevor 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. 273-288
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• Riccardo Boscolo, Chiara Sabatti, James C. Liao, Vwani P. Roychowdhury:
  A Generalized Framework for Network Component Analysis. 289-301
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• Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang:
  Assignment of Orthologous Genes via Genome Rearrangement. 302-315
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• Heather L. Turner, Trevor C. Bailey, Wojtek J. Krzanowski, Cheryl A. Hemingway:
  Biclustering Models for Structured Microarray Data. 316-329
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• José 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. 330-338
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• Sungroh Yoon, Christine Nardini, Luca Benini, Giovanni De Micheli:
  Discovering Coherent Biclusters from Gene Expression Data Using Zero-Suppressed Binary Decision Diagrams. 339-354
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• Vincent Shin-Mu Tseng, Ching-Pin Kao:
  Efficiently Mining Gene Expression Data via a Novel Parameterless Clustering Method. 355-365
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• Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna:
  Searching Genomes for Noncoding RNA Using FastR. 366-379
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