2. BIRD 2008: Vienna, Austria

Mourad Elloumi, Josef Küng, Michal Linial, Robert F. Murphy, Kristan Schneider, Cristian Toma (Eds.): Bioinformatics Research and Development, Second International Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008, Proceedings. Communications in Computer and Information Science 13 Springer 2008, ISBN 978-3-540-70598-7

Gene Expression/Regulation and Micro Arrays

Christian W. 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

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

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

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

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

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

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

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

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

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

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

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

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