2. BIRD 2008: Vienna, Austria

Gene Expression/Regulation and Micro Arrays

• Christian Martin, Tim W. Nattkemper:
  A Tree Index to Support Clustering Based Exploratory Data Analysis. 1-15
  
• Ben Dalziel, Hui Yang, Rahul Singh, Matthew Gormley, Susan Fisher:
  XMAS: An Experiential Approach for Visualization, Analysis, and Exploration of Time Series Microarray Data. 16-31
  
• Nguyen Phuong, Hoang Tuan:
  Clustering in a Fixed Manifold to Detect Groups of Genes with Similar Expression Patterns. 32-42
  

Sequence Analysis and Alignment I

• Fei Xia, Yong Dou, Jiaqing Xu:
  Families of FPGA-Based Accelerators for BLAST Algorithm with Multi-seeds Detection and Parallel Extension. 43-57
  
• Mihail Halachev, Nematollaah Shiri:
  Fast Structured Motif Search in DNA Sequences. 58-73
  
• Bin Liu, Lei Lin, Xiaolong Wang, Qiwen Dong, Xuan Wang:
  A Discriminative Method for Protein Remote Homology Detection Based on N-nary Profiles. 74-86
  

Sequence Analysis and Alignment II

• Chen Na Lian, Mihail Halachev, Nematollaah Shiri:
  Searching for Supermaximal Repeats in Large DNA Sequences. 87-101
  
• Mohammed Al-Shalalfa, Reda Alhajj:
  Motif Location Prediction by Divide and Conquer. 102-113
  

Protein and RNA Structure and Function I

• Ulrike Mückstein, Hakim Tafer, Stephan H. F. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker:
  Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. 114-127
  
• Xiangchao Gan, Leonidas Kapsokalivas, Andreas Alexander Albrecht, Kathleen Steinhöfel:
  A Symmetry-Free Subspace for Ab initioProtein Folding Simulations. 128-139
  

Protein and RNA Structure and Function II

• Timothy Lee, Rahul Singh:
  Comparative Analysis of Disulfide Bond Determination Using Computational-Predictive Methods and Mass Spectrometry-Based Algorithmic Approach. 140-153
  
• Natalja Kurbatova, Juris Viksna:
  Exploration of Evolutionary Relations between Protein Structures. 154-166
  
• Leonidas Kapsokalivas, Xiangchao Gan, Andreas Alexander Albrecht, Kathleen Steinhöfel:
  Two Local Search Methods for Protein Folding Simulation in the HP and the MJ Lattice Models. 167-179
  
• Alireza Hadj Khodabakhshi, Ján Manuch, Arash Rafiey, Arvind Gupta:
  A Robust Class of Stable Proteins in the 2D HPC Model. 180-192
  

Machine Learning and Data Analysis

• Veselka Boeva, Elena Tsiporkova:
  A Novel Adaptive Multiple Imputation Algorithm. 193-206
  
• Pietro Liò, Matteo Brilli, Renato Fani:
  Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies. 207-220
  
• Ramkishore Bhattacharyya, Balaram Bhattacharyya:
  Gene Expression Mining for Cohesive Pattern Discovery. 221-234
  

Databases and Data Integration I

• Luís Pedro Coelho, Robert F. Murphy:
  Identifying Subcellular Locations from Images of Unknown Resolution. 235-242
  
• Ingo H. C. Wassink, Han Rauwerda, Paul E. van der Vet, Timo M. Breit, Anton Nijholt:
  E-BioFlow: Different Perspectives on Scientific Workflows. 243-257
  
• Dominic Mainz, Ingo Paulsen, Indra Mainz, Katrin Weller, Jochen Kohl, Arndt von Haeseler:
  Knowledge Acquisition Focused Cooperative Development of Bio-ontologies - A Case Study with BIO2Me. 258-272
  

Pathways, Networks, Systems Biology I

• Kevin Kontos, Gianluca Bontempi:
  Nested q-Partial Graphs for Genetic Network Inference from "Small n, Large p" Microarray Data. 273-287
  
• Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen:
  A Computational Method for Reconstructing Gapless Metabolic Networks. 288-302
  
• Hans Zantema, Stefan Wagemans, Dragan Bosnacki:
  Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets. 303-317
  
• Clara Pizzuti, Simona E. Rombo:
  Multi-functional Protein Clustering in PPI Networks . 318-330
  

Pathways, Networks, Systems Biology II

• Valeria Fionda, Luigi Palopoli, Simona Panni, Simona E. Rombo:
  Protein-Protein Interaction Network Querying by a "Focus and Zoom" Approach. 331-346
  
• Jano I. van Hemert, Richard A. Baldock:
  Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns. 347-361
  
• Emanuel Schwarz, F. Markus Leweke, Sabine Bahn, Pietro Liò:
  Combining Molecular and Physiological Data of Complex Disorders. 362-376
  
• Richard J. B. Dobson, Patricia B. Munroe, Charles A. Mein, Mark J. Caulfield, Mansoor A. S. Saqi:
  Combining Protein-Protein Interaction (PPI) Network and Sequence Attributes for Predicting Hypertension Related Proteins. 377-391
  

Databases and Data Integration II

• Roziah Kambol, M. Faris Abtholuddin:
  Genome Structure and Characterisation of an Endogenous Retrovirus from the Zebrafish Genome Project Database. 392-403
  
• Richard C. van der Wath, Elizabeth van der Wath, Antonio Carapelli, Francesco Nardi, Francesco Frati, Luciano Milanesi, Pietro Liò:
  Bayesian Phylogeny on Grid. 404-416
  

Workshop ALBIO

• Petri Kalsi, Hannu Peltola, Jorma Tarhio:
  Comparison of Exact String Matching Algorithms for Biological Sequences. 417-426
  
• Hatem Tahri, Mourad Elloumi:
  A New Approximation Algorithm for the Minimum Fragment Removal Problem. 427-435
  
• Tomás Flouri, Costas S. Iliopoulos, Mohammad Sohel Rahman, Ladislav Vagner, Michal Vorácek:
  Indexing Factors in DNA/RNA Sequences. 436-445
  
• Pavlos Antoniou, Costas S. Iliopoulos, Inuka Jayasekera, M. Sohel Rahman:
  Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model. 446-455
  
• Maria Federico, Nadia Pisanti:
  Suffix Tree Characterization of Maximal Motifs in Biological Sequences. 456-465
  
• Mikhail A. Roytberg, Anna Gambin, Laurent Noé, Slawomir Lasota, Eugenia Furletova, Ewa Szczurek, Gregory Kucherov:
  Efficient Seeding Techniques for Protein Similarity Search. 466-478
  
• Mourad Elloumi, Ahmed Mokaddem:
  An Algorithm for Multiple and Global Alignments. 479-488
  
• Ernst Althaus, Stefan Canzar:
  LASA: A Tool for Non-heuristic Alignment of Multiple Sequences. 489-498
  
• Jose Crispin Hernandez Hernandez, Béatrice Duval, Jin-Kao Hao:
  SVM-Based Local Search for Gene Selection and Classification of Microarray Data. 499-508
  
• M. A. Lijo Anto, G. Gopakumar, Achuthsankar S. Nair, Indira Ghosh:
  GENFOCS - A Comparative Tool on Gene Finding with Sensitivity and Specificity. 509-516
  
• Roger Marshall:
  Gene Machine© - A Hardware/Software Platform for Analyzing Genome Data. 517-527
  

Workshop PETRIN

• Carlo Cattani:
  Complex Representation of DNA Sequences. 528-537
  
• Carlo Cattani, Massimo Scalia:
  Wavelet Analysis of Impulses in Axon Physiology. 538-545
  
• Elena Mocanu, Paul E. Sterian:
  Acquisition and Algorithms for Fluorescence Applications. 546-555
  
• Paul E. Sterian, Octavian Marin, Valerica Ninulescu:
  Control of the Lasers Dynamics by Pumping Modulation for Biophotonics Applications. 556-562
  
• Valerica Ninulescu, Vladua-Bogdan Nicolae, Andreea Sterian:
  Quantum Well Lasers for Medical Industry. 563-570
  
• Stefan Pusca, Theodora Toma:
  Computational Model for the Study of the Fractal Parameters Characteristic for the Surface of Titanium Dental Implants. 571-580
  
• Trandafir Moisa, Cristian Morarescu:
  VEMS-TM - A Management Infrastructure. 581-586
  
• Irina Codita, Stefan Pusca:
  PTF Model for Evaluating the Relationships between the VAC and Antimicrobial Resistance in Human Communities. 587-593