Bioinformatics Research and Development

1. Front Matter

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2. Session 1: Microarray and Systems Biology I (Networks)

   1. Bayesian Inference of Gene Regulatory Networks Using Gene Expression Time Series Data

      • Nicole Radde, Lars Kaderali

      Pages 1-15

   2. Biological Network Inference Using Redundancy Analysis

      • Patrick E. Meyer, Kevin Kontos, Gianluca Bontempi

      Pages 16-27

   3. A Novel Graph Optimisation Algorithm for the Extraction of Gene Regulatory Networks from Temporal Microarray Data

      • Judit Kumuthini, Lionel Jouffe, Conrad Bessant

      Pages 28-37

3. Session 2: Microarray and Systems Biology II

   1. Analysing Periodic Phenomena by Circular PCA

      • Matthias Scholz

      Pages 38-47

   2. Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets

      • Angelica Lindlöf, Marcus Bräutigam, Aakash Chawade, Björn Olsson, Olof Olsson

      Pages 48-65

   3. Mining Spatial Gene Expression Data for Association Rules

      • Jano van Hemert, Richard Baldock

      Pages 66-76

4. Session 3: Medical, SNPs, Genomics I

   1. Individualized Predictions of Survival Time Distributions from Gene Expression Data Using a Bayesian MCMC Approach

      • Lars Kaderali

      Pages 77-89

   2. Comparing Logic Regression Based Methods for Identifying SNP Interactions

      • Arno Fritsch, Katja Ickstadt

      Pages 90-103

   3. Stochastical Analysis of Finite Point Sampling of 3D Chromatin Fiber in Interphase Cell Nuclei

      • E. Gladilin, S. Goetze, J. Mateos-Langerak, R. van Driel, K. Rohr, R. Eils

      Pages 104-118

5. Session 4: Medical, SNPs, Genomics II

   1. Structural Screening of HIV-1 Protease/Inhibitor Docking by Non-parametric Binomial Distribution Test

      • Piyarat Nimmanpipug, Vannajan Sanghiran Lee, Jeerayut Chaijaruwanich, Sukon Prasitwattanaseree, Patrinee Traisathit

      Pages 119-130

   2. satDNA Analyzer 1.2 as a Valuable Computing Tool for Evolutionary Analysis of Satellite-DNA Families: Revisiting Y-Linked Satellite-DNA Sequences of Rumex (Polygonaceae)

      • Rafael Navajas-Pérez, Manuel Ruiz Rejón, Manuel Garrido-Ramos, José Luis Aznarte, Cristina Rubio-Escudero

      Pages 131-139

   3. A Soft Hierarchical Algorithm for the Clustering of Multiple Bioactive Chemical Compounds

      • Jehan Zeb Shah, Naomie bt Salim

      Pages 140-153

6. Session 5: Systems Biology

   1. A Novel Method for Flux Distribution Computation in Metabolic Networks

      • Da Jiang, Shuigeng Zhou, Jihong Guan

      Pages 154-167

   2. Inverse Bifurcation Analysis of a Model for the Mammalian G ₁/S Regulatory Module

      • James Lu, Heinz W. Engl, Rainer Machné, Peter Schuster

      Pages 168-184

   3. Weighted Cohesiveness for Identification of Functional Modules and Their Interconnectivity

      • Zelmina Lubovac, David Corne, Jonas Gamalielsson, Björn Olsson

      Pages 185-198

   4. Modelling and Simulation of the Genetic Phenomena of Additivity and Dominance via Gene Networks of Parallel Aggregation Processes

      • Elena Tsiporkova, Veselka Boeva

      Pages 199-211

7. Session 6: Sequence Analysis I (Coding)

   1. Protein Remote Homology Detection Based on Binary Profiles

      • Qiwen Dong, Lei Lin, Xiaolong Wang

      Pages 212-223

   2. Biological Sequences Encoding for Supervised Classification

      • Rabie Saidi, Mondher Maddouri, Engelbert Mephu Nguifo

      Pages 224-238

   3. Fast Search Algorithms for Position Specific Scoring Matrices

      • Cinzia Pizzi, Pasi Rastas, Esko Ukkonen

      Pages 239-250

This volume contains the papers which were selected for oral presentation at the first Bioinformatics Research and Development (BIRD) conference held in Berlin, Germany during March 12-14, 2007. BIRD covers a wide range of topics related to bioinformatics like microarray data, genomics, single nucleotide polymorphism, sequence analysis, systems biology, medical applications, proteomics, information systems. The conference was very competitive. From about 140 submissions only 36 were selected by the Program Committee for oral presentation at BIRD and for publication in these proceedings. The acceptance rate was 1/4. The decisions of the Program Committee were guided by the recommendations of several reviewers for each paper. It should be mentioned that these proceedings have companion proceedings published by the Austrian Computer Society where selected poster presentations of the BIRD conference are included. The invited talk titled "From Flies to Human Disease" by Josef Penninger, one of the leading researcher in genetic experiments for investigating disease pathogenesis, was very inspiring and gave new insights into future bioinformatics challenges.

• Microarray
• bioinformatics
• biology
• database
• databases
• genome
• sequence analysis

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