1st International Student Symposium in
Computational Biology



The ISCB Student Council is organizing an International Symposium to be held on Wednesday, September 28, immediately preceding ECCB 2005 in Madrid. This symposium is targeted to young computational biology researchers who are keen to develop their research communication skills, want to meet like minded colleagues, network with accomplished scientists and learn about career opportunities available in Europe and globally.


Register for ECCB 2005 at http://www.eccb05.org/registration.html and sign up for the symposium at the same time. If you have already registered with ECCB, but did not sign up with the symposium, you can still attend the symposium if you register at: http://www.iscbsc.org/marketing/symposium_reg.htm. The symposium is free of charge for all participants of ECCB.


Oral presentations on the symposium day will all be eligible for the best student presentation competition if the main contributor is a student. The process for selection of the best presentation will be based on the quality of the research presented, the clarity and style of the ideas and on originality. All in attendance at the symposium will be asked to submit a paper ballot to select the winner. The Student Council is grateful to the on line journal BMC Bioinformatics for kindly sponsoring our ‘Best Student Presentation Award’. 


September 28, 2005
Room 7 (2nd Floor)

Keynote Talk:
SS-1: How old is your fold?
Charlotte M. Deane

Abstracts selected for Presentation:

SS-2: Statistical alignment with a sequence evolution model allowing heterogeneous evolution behaviors along the sequence
Ana Arribas Gil
SS-3: Hybrid approach based on a combination of methods for operon prediction
C. Hubans1,2, D. Hot2, Y. Lemoine2,4, E. Mephu-Nguifo3
SS-4: An Alternative Method for Detecting Conserved Elements in Multiple Sequence Alignments
Pavol Hanus1, Janis Dingel1, Joachim Hagenauer1 and Jakob C. Mueller2

SS-5: Save a thousand words: Advanced visualisations for Pfam and iPfam
Benjamin Schuster-Böckler, Robert D. Finn, Alex Bateman
SS-6: High-throughput computational proteomics - challenges and solutions in the creation of the Genome Annotating Proteome Pipeline (GAPP)
Ian Shadforth

Gene Expression
SS-7: Highly Expressed Proteins Contain Increased Frequency of Alanine in the Second Amino Acid Position
Age Tats, Maido Remm, Tanel Tenson

Genes and Genomes
SS-8: discoveryBASE. Virtual screening for disease associated proteins
Ronald Rapberger, Martin Haiduk, Paul Perco, Arno Lukas, Christian Siehs and Bernd Mayer

SS-9: Long branch attraction and topology testing using weighted least-squares
Borys Wrobel

Protein Folding and Function
SS-10: False occurrences of functional motifs on protein sequences highlight evolutionary constraints
Allegra Via 1, Federico Gherardini, Enrico Ferraro, Gianpaolo Scalia Tomba, Gabriele Ausiello and Manuela Helmer-Citterich
SS-11: Visualization and clustering of Protein Local Conformational Space using Geometric Invariant Theory
Ashish V. Tendulkar, Pramod P. Wangikar
SS-12: Structural Bioinformatics of Protein-Bound
Water Christopher Bottoms, Tommi White, John J. Tanner
SS-13: Simple fold composition and modular architecture of the nuclear pore complex
Damien Devos, Svetlana Dokudovskaya, Rosemary Williams, Frank Alber, Narayanan Eswar, Brian T. Chait, Michael P. Rout, and Andrej Sali
SS-14: REPPER repeats and their periodicities in fibrous proteins
Markus Gruber,Johannes Soding and Andrei N. Lupas 
SS-15: A novel pair-to-pair substitution matrix improves contact prediction in protein cores
Milana Frenkel-Morgenstern, Eran Eya, Vladimir Sobolev, Shmuel Pietrokovski
SS-16: Molecular Recognition and Partner Prediction for Transient Protein Complexes: CDK-Cyclin Homologue Interactions
Xueping Quan, Peter Doerner, and Dietlind L.Gerloff

Systems Biology
SS-17: Discovering regulatory modules from heterogeneous information sources
Karen Lemmens T. De Bie, P. Monsieurs, K. Engelen, B. De Moor, N. Cristianini, and K. Marchal
SS-18: A semi-automated method to study the intersection of metabolic network and interactome
Joan Planas Iglesias
SS-19: Is there a relationship between protein connectivity and evolutionary rate?
Ramazan Saeed
SS-20: BioQSpace: An interactive visualisation tool for clustering MEDLINE abstracts
Anna Divoli, Rasmus Winter, Steve Pettifer& Terri Attwood

Abstracts selected for Posters:

SS-21: Rigid Body Protein-Protein Docking Using Biochemical Data
Domantas Motiejunas, Razif Gabdoulline, Rebecca Wade
SS-22: Guide structure calculation: a critical step for the accuracy of progressive multiple sequence alignment algorithms
Laure Vescovo Jean-Christophe Aude, Geraldine Polaillon

SS-23: IGD: A Resssource for Human intronless genes
Amel Louhichi
SS-24: Developing a knowledge base for PID-expert system
Crina Samarghitean, Jouni Vliaho, Mauno Vihinen
SS-25: Codon usage analysis based on web services
Denis Shestakov, Tapio Salakoski, Mauno Vihinen.
SS-26: VITAMIN: An Ontology-Driven Information System for Mutant Annotation
Óscar D. Sánchez, Ana Conesa, José Alberto Maldonado, Montserrat Robles, Manuel Talón
SS-27: MicrobialTREE: A user friendly tool for bacterial taxonomy navigation
Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Raquel Tobes y Eduardo Pareja

Genes and Genomes
SS-28: Bioinformatic sequence identification from sequence family databases
Anne-Muriel Arigon, Guy Perriere and Manolo Gouy
SS-29: In silico markovian prediction of variable and constant regions of lentivirus genomes
Aurélia Boissin-Quillon, Didier Piau, Caroline Leroux
SS-30: Aligning intron-exon structures of alternatively spliced genes
Michael Sammeth, Eduardo Eyras and Roderic Guigo
SS-31: Addressing Drosophila Gene Duplications: Protein Sequence Redundancy and Genome Evolution
Carlos Quijano
SS-32: ELEANALYZER: an automated method for analysis of retrotransposons in genomes and prediction of their insertion sites
Kamal Rawal, Alok Bhattacharya Sudha Bhattacharya and Ram Ramaswamy
SS-33: BlastXtract: a web-based tool for managing and visualizing results from large translated BLAST and FastA searches
Marcus Claesson
SS-34: Measuring Selection in RNA molecules
Naila Mimouni, Rune lyngsoe and Jotun Hein.
SS-35: Prediction of Heat-Induced Replication Sites in Replication Origins from Escherichia Coli and Other Plasmidic Replicons
González-Soltero, R., Botello, E., and Jiménez-Sánchez, A.
SS-36: In silico modelling of the PCR process for detection of bacteria from clinical samples
Triinu Kõressaar, Maido Remm
SS-37: Understanding Promoter Logic
Utz J. Pape

SS-38: Accounting for Probe-level Noise in Principal Component Analysis of Microarray Data
Guido Sanguinetti
SS-39: Data-adaptive test statistics for microarray data
Sach Mukherjee
SS-40: GALGO: Software for building statistical models from microarray data
Victor Trevino and Francesco Falciani

SS-41: Exploring the evolution and the diversity of bacterial genes
Zara Ghazoui
SS-42: Biological/Chemical/ and Physical behavioral analyses for Protein Classifications
Rauf Ahmed Shams Malick, Dr. Kamran Azim
SS-43: More than 140 genes have been acquired through horizontal gene transfer from Bacteria to rumen ciliates
Guanola Ricarda, Neil R. McEwanb, Johannes H.P. Hacksteinc and Martijn A. Huynena.
SS-44: Bioinformatics tools to encode and integrate microscopy time-lapse sequences for drug discovery: Lineage analysis the basis for novel cell-based assays
Imtiaz A. Khan, Lee Campbell, Paul J Smith and Rachel J Errington

Protein Structure and Function
SS-45: The ANNOTATOR sequence analysis suite
Georg Schneider, Michael Wildpaner, Florian Leitner, Birgit Eisenhaber, Miklos Kozlovsky, Werner Kubina, Sebastian Maurer-Stroh, Maria Novatchkova, Alexander Schleiffer, Sun Tian and Frank Eisenhaber
SS-46: Sequence and Structural Analysis of Extracellular Matrix and Cell Adhesion Molecules
Hosil Park, Terri Attwood, Lydia Tabernero, and Jordi Bella
SS-47: FILTREST3D: program for discrimination of protein structure models that match the restraints from experimental data
Michal J. Gajda, Marta Kaczor, Anastasia Bakulina, Janusz M. Bujnicki
SS-48: Computational approach for understanding substrate specificity of nonribosomal peptide synthetases
Mohd. Zeeshan Ansari, Rajesh S. Gokhale and Debasisa Mohanty
SS-49: Discovery of Protein Substructures in EM Maps
Keren Lasker, Oranit Dror, Ruth Nussinov, Haim J.Wolfson
SS-50: Amino Acid Dependent Weighting Factors for FFT-based Unbound Protein Docking
Philipp Heuser, Dietmar Schomburg
SS-51: Molecular Modelling and Dynamics of Membrane Proteins
Shiva Amiri
SS-52: B7 and CD28 family immunoglobulins structure-function analysis
Xiaoxia Ge
SS-53: Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling

SS-54: Prediction of the insurgence of human genetic diseases due to single point protein mutation
Calabrese Remo, Capriotti Emidio, Fariselli Piero and Casadio Rita

Systems Biology
SS-55: How system biology can improve the production of L-carnitine using Escherichia coli?
Angel Sevilla Camins

Text Mining
SS-56: Natural Language Processing and Information Retrieval Techniques Applied to the Reproductive Biology Literature
R. Farhan, J. D. Aplin, T. K. Attwood, M. McGee Wood and C. P. Sibley
University of Manchester, UK



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