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Elloumi, Mourad

Bioinformatics Research and Development

Elloumi, Mourad - Bioinformatics Research and Development, ebook

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ISBN: 9783540706007
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Table of contents

1. A Tree Index to Support Clustering Based Exploratory Data Analysis
Christian Martin, Tim W. Nattkemper

2. XMAS: An Experiential Approach for Visualization, Analysis, and Exploration of Time Series Microarray Data
Ben Dalziel, Hui Yang, Rahul Singh, Matthew Gormley, Susan Fisher

3. Clustering in a Fixed Manifold to Detect Groups of Genes with Similar Expression Patterns
N. M. Phuong, H. D. Tuan

4. Families of FPGA-Based Accelerators for BLAST Algorithm with Multi-seeds Detection and Parallel Extension
Fei Xia, Yong Dou, Jiaqing Xu

5. Fast Structured Motif Search in DNA Sequences
Mihail Halachev, Nematollaah Shiri

6. A Discriminative Method for Protein Remote Homology Detection Based on N-nary Profiles
Bin Liu, Lei Lin, Xiaolong Wang, Qiwen Dong, Xuan Wang

7. Searching for Supermaximal Repeats in Large DNA Sequences
Chen Na Lian, Mihail Halachev, Nematollaah Shiri

8. Motif Location Prediction by Divide and Conquer
Mohammed Alshalalfa, Reda Alhajj

9. Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics
Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker

10. A Symmetry-Free Subspace for Ab initio Protein Folding Simulations
Xiangchao Gan, Leonidas Kapsokalivas, Andreas A. Albrecht, Kathleen Steinhöfel

11. Comparative Analysis of Disulfide Bond Determination Using Computational-Predictive Methods and Mass Spectrometry-Based Algorithmic Approach
Timothy Lee, Rahul Singh

12. Exploration of Evolutionary Relations between Protein Structures
Natalja Kurbatova, Juris Viksna

13. Two Local Search Methods for Protein Folding Simulation in the HP and the MJ Lattice Models
L. Kapsokalivas, X. Gan, A. Albrecht, K. Steinhöfel

14. A Robust Class of Stable Proteins in the 2D HPC Model
Alireza Hadj Khodabakhshi, Ján Ma?uch, Arash Rafiey, Arvind Gupta

15. A Novel Adaptive Multiple Imputation Algorithm
Veselka Boeva, Elena Tsiporkova

16. Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies
Pietro Lió, Matteo Brilli, Renato Fani

17. Gene Expression Mining for Cohesive Pattern Discovery
Ramkishore Bhattacharyya, Balaram Bhattacharyya

18. Identifying Subcellular Locations from Images of Unknown Resolution
Luís Pedro Coelho, Robert F. Murphy

19. E-BioFlow: Different Perspectives on Scientific Workflows
Ingo Wassink, Han Rauwerda, Paul Vet, Timo Breit, Anton Nijholt

20. Knowledge Acquisition Focused Cooperative Development of Bio-ontologies – A Case Study with BIO2Me
Dominic Mainz, Ingo Paulsen, Indra Mainz, Katrin Weller, Jochen Kohl, Arndt Haeseler

21. Nested q-Partial Graphs for Genetic Network Inference from ”Small n, Large p” Microarray Data
Kevin Kontos, Gianluca Bontempi

22. A Computational Method for Reconstructing Gapless Metabolic Networks
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen

23. Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets
Hans Zantema, Stefan Wagemans, Dragan Bošna?ki

24. Multi-functional Protein Clustering in PPI Networks
Clara Pizzuti, Simona E. Rombo

25. Protein-Protein Interaction Network Querying by a “Focus and Zoom” Approach
Valeria Fionda, Luigi Palopoli, Simona Panni, Simona E. Rombo

26. Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns
Jano Hemert, Richard Baldock

27. Combining Molecular and Physiological Data of Complex Disorders
Emanuel Schwarz, F. Markus Leweke, Sabine Bahn, Pietro Liò

28. Combining Protein-Protein Interaction (PPI) Network and Sequence Attributes for Predicting Hypertension Related Proteins
Richard J. B. Dobson, Patricia B. Munroe, Charles A. Mein, Mark J. Caulfield, Mansoor A. S. Saqi

29. Genome Structure and Characterisation of an Endogenous Retrovirus from the Zebrafish Genome Project Database
Roziah Kambol, M. Faris Abtholuddin

30. Bayesian Phylogeny on Grid
Richard C. Wath, Elizabeth Wath, Antonio Carapelli, Francesco Nardi, Francesco Frati, Luciano Milanesi, Pietro Lió

31. Comparison of Exact String Matching Algorithms for Biological Sequences
Petri Kalsi, Hannu Peltola, Jorma Tarhio

32. A New Approximation Algorithm for the Minimum Fragment Removal Problem
Hatem Tahri, Mourad Elloumi

33. Indexing Factors in DNA/RNA Sequences
Tomáš Flouri, Costas Iliopoulos, M. Sohel Rahman, Ladislav Vagner, Michal Vorá?ek

34. Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model
Pavlos Antoniou, Costas S. Iliopoulos, Inuka Jayasekera, M. Sohel Rahman

35. Suffix Tree Characterization of Maximal Motifs in Biological Sequences
Maria Federico, Nadia Pisanti

36. Efficient Seeding Techniques for Protein Similarity Search
Mikhail Roytberg, Anna Gambin, Laurent Noé, S?awomir Lasota, Eugenia Furletova, Ewa Szczurek, Gregory Kucherov

37. An Algorithm for Multiple and Global Alignments
Mourad Elloumi, Ahmed Mokaddem

38. LASA: A Tool for Non-heuristic Alignment of Multiple Sequences
Ernst Althaus, Stefan Canzar

39. SVM-Based Local Search for Gene Selection and Classification of Microarray Data
Jose Crispin Hernandez Hernandez, Béatrice Duval, Jin-Kao Hao

40. GENFOCS – A Comparative Tool on Gene Finding with Sensitivity and Specificity
M. A. Lijo Anto, G. Gopakumar, Achuthsankar S. Nair, Indira Ghosh

41. Gene Machine© – A Hardware/Software Platform for Analyzing Genome Data
Roger Marshall

42. Complex Representation of DNA Sequences
Carlo Cattani

43. Wavelet Analysis of Impulses in Axon Physiology
Carlo Cattani, Massimo Scalia

44. Acquisition and Algorithms for Fluorescence Applications
Elena Mocanu, Paul Sterian

45. Control of the Lasers Dynamics by Pumping Modulation for Biophotonics Applications
Paul Sterian, Octavian Marin, Valeric? Ninulescu

46. Quantum Well Lasers for Medical Industry
Valeric? Ninulescu, Vl?du?-Bogdan Nicolae, Andreea Sterian

47. Computational Model for the Study of the Fractal Parameters Characteristic for the Surface of Titanium Dental Implants
Stefan Pusca, Theodora Toma

48. VEMS-TM – A Management Infrastructure
Trandafir Moisa, Cristian Morarescu

49. PTF Model for Evaluating the Relationships between the VAC and Antimicrobial Resistance in Human Communities
Irina Codita, Stefan Pusca

Keywords: Computer Science, Computational Biology/Bioinformatics, Bioinformatics

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