1. BIRD 2007: Berlin, Germany

Microarray and Systems Biology I (Networks)

• Nicole Radde, Lars Kaderali:
  Bayesian Inference of Gene Regulatory Networks Using Gene Expression Time Series Data. 1-15
  
• Patrick Emmanuel Meyer, Kevin Kontos, Gianluca Bontempi:
  Biological Network Inference Using Redundancy Analysis. 16-27
  
• Judit Kumuthini, Lionel Jouffe, Conrad Bessant:
  A Novel Graph Optimisation Algorithm for the Extraction of Gene Regulatory Networks from Temporal Microarray Data. 28-37
  

Microarray and Systems Biology II

• Matthias Scholz:
  Analysing Periodic Phenomena by Circular PCA. 38-47
  
• Angelica Lindlöf, Marcus Bräutigam, Aakash Chawade, Björn Olsson, Olof Olsson:
  Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets. 48-65
  
• Jano I. van Hemert, Richard A. Baldock:
  Mining Spatial Gene Expression Data for Association Rules. 66-76
  

Medical, SNPs, Genomics I

• Lars Kaderali:
  Individualized Predictions of Survival Time Distributions from Gene Expression Data Using a Bayesian MCMC Approach. 77-89
  
• Arno Fritsch, Katja Ickstadt:
  Comparing Logic Regression Based Methods for Identifying SNP Interactions. 90-103
  
• Evgeny Gladilin, Sandra Götze, Jose Mateos-Langerak, Roel van Driel, Karl Rohr, Roland Eils:
  Stochastical Analysis of Finite Point Sampling of 3D Chromatin Fiber in Interphase Cell Nuclei. 104-118
  

Medical, SNPs, Genomics II

• Piyarat Nimmanpipug, Vannajan Sanghiran Lee, Jeerayut Chaijaruwanich, Sukon Prasitwattanaseree, Patrinee Traisathit:
  Structural Screening of HIV-1 Protease/Inhibitor Docking by Non-parametric Binomial Distribution Test. 119-130
  
• Rafael Navajas-Pérez, Manuel Ruiz Rejón, Manuel A. Garrido-Ramos, José Luis Aznarte, Cristina Rubio-Escudero:
  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). 131-139
  
• Jehan Zeb Shah, Naomie Salim:
  A Soft Hierarchical Algorithm for the Clustering of Multiple Bioactive Chemical Compounds. 140-153
  

Systems Biology

• Da Jiang, Shuigeng Zhou, Jihong Guan:
  A Novel Method for Flux Distribution Computation in Metabolic Networks. 154-167
  
• James Lu, Heinz W. Engl, Rainer Machné, Peter Schuster:
  Inverse Bifurcation Analysis of a Model for the Mammalian G ₁/ S Regulatory Module. 168-184
  
• Zelmina Lubovac, David Corne, Jonas Gamalielsson, Björn Olsson:
  Weighted Cohesiveness for Identification of Functional Modules and Their Interconnectivity. 185-198
  
• Elena Tsiporkova, Veselka Boeva:
  Modelling and Simulation of the Genetic Phenomena of Additivity and Dominance via Gene Networks of Parallel Aggregation Processes. 199-211
  

Sequence Analysis I (Coding)

• Qiwen Dong, Lei Lin, Xiaolong Wang:
  Protein Remote Homology Detection Based on Binary Profiles. 212-223
  
• Rabie Saidi, Mondher Maddouri, Engelbert Mephu Nguifo:
  Biological Sequences Encoding for Supervised Classification. 224-238
  
• Cinzia Pizzi, Pasi Rastas, Esko Ukkonen:
  Fast Search Algorithms for Position Specific Scoring Matrices. 239-250
  

Sequence Analysis II

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

Proteomics I

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

Proteomics II (Measurements)

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

Proteomics III (Structure)

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

Databases, Web and Text Analysis

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

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