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Bioinformatics Research and Development

First International Conference, BIRD 2007, Berlin, Germany, March 12-14, 2007. Proceedings

  • Editors
  • Sepp Hochreiter
  • Roland Wagner
Conference proceedings BIRD 2007

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4414)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 4414)

Table of contents

  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 G1/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

  8. Session 7: Sequence Analysis II

    1. A Markovian Approach for the Segmentation of Chimpanzee Genome
      Christelle Melodelima, Christian Gautier
      Pages 251-262
    2. Synthetic Protein Sequence Oversampling Method for Classification and Remote Homology Detection in Imbalanced Protein Data
      Majid M. Beigi, Andreas Zell
      Pages 263-277
    3. Stem Kernels for RNA Sequence Analyses
      Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato
      Pages 278-291
    4. Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models
      Piero Fariselli, Daniele Molinini, Rita Casadio, Anders Krogh
      Pages 292-302

  9. Session 8: Proteomics I

    1. Patch Prediction of Protein Interaction Sites: Validation of a Scoring Function for an Online Server
      Susan Jones, Yoichi Mukarami
      Pages 303-313
    2. Statistical Inference on Distinct RNA Stem-Loops in Genomic Sequences
      Shu-Yun Le, Jih-H. Chen
      Pages 314-327
    3. Interpretation of Protein Subcellular Location Patterns in 3D Images Across Cell Types and Resolutions
      Xiang Chen, Robert F. Murphy
      Pages 328-342

  10. Session 9: Proteomics II (Measurements)

    1. Bayesian Inference for 2D Gel Electrophoresis Image Analysis
      Ji Won Yoon, Simon J. Godsill, ChulHun Kang, Tae-Seong Kim
      Pages 343-356
    2. SimShiftDB: Chemical-Shift-Based Homology Modeling
      Simon W. Ginzinger, Thomas Gräupl, Volker Heun
      Pages 357-370
    3. Annotation of LC/ESI-MS Mass Signals
      Ralf Tautenhahn, Christoph Böttcher, Steffen Neumann
      Pages 371-380

  11. Session 10: Proteomics III (Structure)

    1. Stochastic Protein Folding Simulation in the d-Dimensional HP-Model
      K. Steinhöfel, A. Skaliotis, A. A. Albrecht
      Pages 381-394
    2. Enhancing Protein Disorder Detection by Refined Secondary Structure Prediction
      Chung-Tsai Su, Tong-Ming Hsu, Chien-Yu Chen, Yu-Yen Ou, Yen-Jen Oyang
      Pages 395-409
    3. Joining Softassign and Dynamic Programming for the Contact Map Overlap Problem
      Brijnesh J. Jain, Michael Lappe
      Pages 410-423

  12. Session 11: Databases, Web and Text Analysis

    1. An Evaluation of Text Retrieval Methods for Similarity Search of Multi-dimensional NMR-Spectra
      Alexander Hinneburg, Andrea Porzel, Karina Wolfram
      Pages 424-438
    2. Ontology-Based MEDLINE Document Classification
      Fabrice Camous, Stephen Blott, Alan F. Smeaton
      Pages 439-452
    3. Integrating Mutations Data of the TP53 Human Gene in the Bioinformatics Network Environment
      Domenico Marra, Paolo Romano
      Pages 453-463
    4. Efficient and Scalable Indexing Techniques for Biological Sequence Data
      Mihail Halachev, Nematollaah Shiri, Anand Thamildurai
      Pages 464-479
  13. Back Matter
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About these proceedings

Introduction

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.

Keywords

Microarray bioinformatics biology database databases genome sequence analysis

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-540-71233-6
  • Copyright Information Springer-Verlag Berlin Heidelberg 2007
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science Computer Science (R0)
  • Print ISBN 978-3-540-71232-9
  • Online ISBN 978-3-540-71233-6
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site
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