Accepted Posters ISMB-98

 

Please notify Christoph Sensen at sensencw@niji.imb.nrc.ca if your poster is not correctly marked as a student poster.

[P01] Thread Synchronization: Determining Global Structure From Local Threadings of Crystallographic Data {student poster}

Alan Ableson

[P02] Structural Classification Of Proteins SCOP

Bartlett G Ailey, Steven E Brenner, Tim JP, Hubbard, Alexey G Murzin and Cyrus Chothia.

[P03] Exploring Neural Network Input Representations to Increase Consensus Accuracy in DNA Fragment Assemblies {student poster}

Carolyn F. Allex (1,2), Jude W. Shavlik (1), Frederick R. Blattner (2,3)

[P04] Canonical Structures and Variability of the Antigen Binding Site of TCRs: Towards an automated key residue assignment. {student poster}

Bissan Al-Lazikani*, Olga Ignatovich, Arthur M.Lesk, Cyrus Chothia

[P05] Automatic extraction of biological information about protein families from scientific text

Miguel A. Andrade* and Alfonso Valencia

[P06] Genomewide Analysis of Tc1-like Repetitive Elements in Caenorhabditis elegans {student poster}

Zhirong Bao* and Sean R. Eddy

[P07] Protein Structure Determination - Improving Segmentation and Analysis of Electron Density Maps {student poster}

Kim Baxter

[P08] Bielefeld University Bioinformatics Server

Ole Bents, Dirk Evers, Folker Meyer, Chris Schleiermacher, Alexander Sczyrba and Robert Giegerich

[P09] Micado : a functional analysis database for microbial genomes

V. Biaudet, F. Samson, S.D. Ehrlich and Ph. Bessières

[P10] GeneWise and SyWise: gene identification tools

Ewan Birney and Richard Durbin

[P11] Measuring Confidence in Sequence Fragment Assembly

Blackwell, Thomas W. and David J. States

[P12] Mouse Genome Informatics: Integrating Mouse Genetic and Genomic Information.

J.A. Blake, M.T.Davisson, J.T.Eppig, J.A. Kadin, J.E. Richardson, M. Ringwald, and the Mouse Genome Informatics Staff

[P13] Gene order breakpoint evidence in animal mitochondrial phylogeny

Mathieu Blanchette (1) and Takashi Kunisawa (2) and David Sankoff (3)

[P14] Evaluation of Gapped Blast and PSI-Blast with Reliable Structurally Determined Evolutionary Relationships

Steven E. Brenner and Michael Levitt

[P15] Optimization of Clone/Reaction-Type Selection in Genome Sequencing

Nicolas Brossard, Pierre Rioux and Gertraud Burger

[P16] ACEDB for Microsoft Windows: Standalone, Client/Server and Web Server Versions

Richard Bruskiewich [1] (*), Richard Durbin [2], Jean Thierry-Mieg [3] and Stephen Wood [1]

[P17] Agreement subtrees using triples and fans

David Bryant

[P18] Developing an Automated System for High Throughput Reading Frame Assignment on Expressed Sequence Tags {student poster}

Yue Chen, Elizabeth Shoop, Ed H Chi, Sheila St. Cyr, Sopheak Sim, Juan Munoz, John Riedl, Ernest Retzel, and John Carlis

[P19] Bioperl: Standard Perl Modules for Bioinformatics

S. A. Chervitz(a), G. Fuellen(b), C. Dagdigian(c). and S. E. Brenner(d)

[P20] Detection of hidden signals in mRNA

Mark E. Dalphin, Peter A. Stockwell, Warren P. Tate, Chris M. Brown

[P21] CGD : A program for multiple sequence alignment analysis into Excel© worksheets.

Christian Delamarche, Alexandrine Froger, Stéphane Deschamps, Jean Gouranton, Jean- François Hubert, Valérie Lagrée, Isabelle Pellerin, Daniel Thomas

[P22] Three Optimizations to the BLASTP Algorithm

Shawn Delaney, Greg Butler, Clement Lam, and Larry Thiel

[P23] A Bayesian Statistical Algorithm for RNA Secondary Structure Prediction

Ye Ding, Charles E. Lawrence

[P24] Prediction of stabilization centers in different secondary classes. {student poster}

Zsuzsanna Dosztanyi and Istvan Simon

[P25] HMMER2 : Hidden Markov Model Profiles for Sequence Analysis

Sean R. Eddy

[P26] Protein Model Determination from Crystallographic Data

Kenneth Edgecombe (1), Alan Ableson(1), Kim Baxter(1), Antony Chiverton(1), Janice Glasgow(1) and Suzanne Fortier(2)

[P27] Genome Halving

Nadia El-Mabrouk (1) and Joseph H. Nadeau (2) and David Sankoff (3)

[P28] Comparing Arc-Annotated Sequences

Patricia A. Evans

[P29] AutoBlast: a web-based server to keep you aware of relevant new sequences from a variety of databases

Youyi Fang

[P30] NEURAL NETWORKS FOR PREDICTING THE CONTACT MAPS OF PROTEINS

Piero Fariselli1 and Rita Casadio1,2

[P31] Correlation between GC bias in genes and amino acid composition of their encoded proteins

Peter G. Foster*, Donal A. Hickey

[P32] Study on automatic knowledge extraction: How to extract knowledge on protein interaction from original papers {student poster}

K. Fukuda, T. Okazaki, M. Yoshida, T. Takagi

[P33] Comparison of methods for identification of remote homologues in Proteins

V Geetha(1), Valentina Di Francesco(2), Jean Garnier(1,3), Peter J Munson(1)

[P34] Identification of disulfide bridges in protein models from crystallographic data {student poster}

Jean Gerster (1), Janice Glasgow (1), Suzanne Fortier (2)

[P35] Searching the TOPS protein topology database http://tops.ebi.ac.uk/tops

David Gilbert (1), David Westhead (2) and Janet Thornton (3)

[P36] Basecalling Algorithms for Ultra-High Throughput Sequencing Devices

Jim Golden, Mike Kliegl and Kevin O’Brien

[P37] DBsolve WWW software for metabolic simulations after genome sequencing.

Igor Goryanin*1,2,4, Charles Hodgman2, Andrew Lyall2, Evgeni Selkov1,3

[P38] Whole Cell Modeling with the E-CELL Simulation System

Kenta Hashimoto, Tom S. Shimizu, Yuri Matsuzaki, Fumihiko Miyoshi, Kanako Saito, Sakura Tanida, Hisako Nakano and Masaru Tomita

[P39] SPTR - A comprehensive, non-redundant and up-to-date view on the protein sequence world

Henning Hermjakob, Rolf Apweiler

[P40] Periodicity of TF distributions in the promoter area.

Ilya Ioshikhes, Edward N. Trifonov, Michael Q. Zhang

[P41] A Workbench for Comparative Genomic Sequence Analysis

Niclas Jareborg, Richard Durbin

[P42] Subtle sequence motifs and structure prediction for the membrane fusion proteins and outer membrane proteins of Gram-negative efflux pumps

Jason M. Johnson and George M. Church

[P43] Local and Global Transcriptional Asymmetry in Complete Genomes*

Steen Knudsen, Lars Boe (1), Soren Brunak

[P44] The Organelle Genome Database Project (GOBASE)

Maria Korab-Laskowska(1), Pierre Rioux(1), Timothy G. Littlejohn(2), Michael W. Gray(3), B. Franz Lang(1) and Gertraud Burger(1)

[P45] HUMAN GENOME ANALYSIS AT THE G.S.C.

Korf I, Yandell M, Pepin K, Speith J, Hillier L, Gish W

[P46] Automated Evaluation of Protein Models {student poster}

Max Kotlyar, Janice Glasgow, Evan Steeg, Ken Edgecombe, David Verbrugge, Suzanne Fortier

[P47] Predicting Genetic Interaction for Drosophila Leg Formation Using Computer Simulation

Koji Kyoda(1) and Hiroaki Kitano (2)

[P48] A Multi-Level Nearest-Neighbour Algorithm for Predicting Protein Secondary Structure

Authors: Iustin Lazar*, Greg Butler*, Peter Montgomery**, and Wendy Findlay

[P49] Modeling 3-D structures of cyclic RNA using a constraint-based approach {student poster}

Sebastien Lemieux, Dwight Anderson* and Francois Major

[P50] Eukaryotic promoter prediction using a data compression approach.

Samuel Levy and Gary D. Stormo

[P51] RAPID AND ACCURATE PREDICTION OF PROTEIN FUNCTION AT THE GENOME SCALE: WHAT SHOULD BE

EXPECTED FROM AN INTELLIGENT SYSTEM IN MOLECULAR BIOLOGY.

Maurice Leysens and Arcady Mushegian, PhD

[P52] A Visual Interface for the Data Mining of Molecular Biology Databases {student poster}

Simon Meng Lin

[P53] Computational identification of novel small nucleolar RNA genes {student poster}

Todd M. Lowe, Sean R. Eddy

[P54] EST/STS Guided Identification of Genes in Human Genomic DNA. {student poster}

Niels Mache

[P55] DNA-Binding Site Matrices for 55 Proteins Applied to the Complete Escherichia coli K12 Genome {student poster}

Abigail Manson McGuire, Keith Robison, George M. Church

[P56] Removing redundancy in the SWISS-PROT and TREMBL protein databases

Maria-Jesus Martin, Alain Gateau*, Claire O'Donovan and Rolf Apweiler

[P57] EDITtoTREMBL: A Distributed Approach to High-Quality Automated Protein Sequence Annotation {student poster}

Steffen Moeller, Wolfgang Fleischmann, Rolf Apweiler

[P58] Highly sensitive methods for homology search on a parallel computer: DNA sequence comparison on the amino acid level

K. Nagai, N. Kasahara, R. Irie, S. Hiraoka

[P59] Description of optimal translation initiation patterns in E. coli using a symbolic-numeric approach.

Jacques Nicolas1, Christian Delamarche2, Pascale Guerdoux-Jamet1, Robin Gras1

[P60] Title: Optimising ribosomal RNA profile alignment.

Emmet A. O'Brien, Cedric Notredame and Desmond G. Higgins

[P61] Towards a Virtual Department of BioComputing

R. J. Parsons (a), G. Fuellen (b), and R. Giegerich (b)

[P62] SEGMENTATION OF CHROMOSOME SIZE DNA SEQUENCES INTO COMPOSITIONALLY HOMOGENEOUS DOMAINS USING HIDDEN MARKOV MODELS

Leonid Peshkin(1), PhD candidate and Mikhail Gelfand(2)

[P63] "Automated filtering of sequence analysis results using decision support technology"

Pouliot, Y., Bernstein, J. & Plevin, R.

[P64] Integration of Sequence Data Banks: EMBL, TREMBL and SWISS-PROT

Nicole Redaschi, Sergio Contrino, and Phil McNeil

[P65] A dynamic programming algorithm for RNA pseudoknots.

Elena Rivas and Sean R. Eddy

[P66] Development of a Mediator to Integrate Access to Databases in Molecular Biology

Chris J. Robertson [1,2], Graham J.L. Kemp [1], Peter M.D. Gray [1], John E. Fothergill [2]

[P67] Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis {student poster}

Eric C. Rouchka and David J. States

[P68] Detection of protein three-dimensional side-chain patterns: New examples of convergent evolution

Robert Bruce Russell

[P69] On Negative Selection Against ATG Triplets Near Start Codons in Eucaryotic and Procaryotic Genomes

Rintaro Saito 1,2, Masaru Tomita 1,3

[P70] Protein Analyst - a distributed object environment for protein sequence and structure analysis

M. Saqi(1) . D. Wild(1,2) . M. Hartshorn(1)

[P71] Model of a Relational Apoptosis Database: ApoBase

Christian Schoenbach

[P72] Getting to grips with a duplicated genome {student poster}

Cathal Seoighe and Kenneth H. Wolfe

[P73] AppLab: A generated CORBA/Java based interface to the distributed applications

Martin Senger

[P74] Sequence Alignment with Convex Gap Penalties. {student poster}

Guy St. C. Slater. 1, Mansoor A. S. Saqi. 2

[P75] Study of Water-mediated Interactions between DNA and the C-terminal Zinc Finger of Fpg, a DNA Reapair Enzyme. {student poster}

Serge Smirnov, Teri Klein*, Arthur Grollman, Carlos de los Santos, Moshe Eisenberg

[P76] Title: Testing a neural net approach to classify protein sequences

Juerg R. Straubhaar, Jack E. Tabaska, Gary D. Stormo

[P77] Software Architecture and Modeling Theory of the E-CELL Simulation System

Kouichi Takahashi, Tom Shimizu, Katsuyuki Yugi and Masaru Tomita

[P78] MIAH: A server for the automatic alignment of eukaryotic ssu rRNAs.

Thebault P., Monestie P., McGrath A., O'Brian E, Higgins DG.

[P79] HMM priors derived from protein threading

Paul D. Thomas

[P80] INVESTIGATING THE DETERMINANTS OF PROTEIN THERMAL STABILITY VIA COMPARATIVE PROTEOME ANALYSIS

M. J. Thompson* and D. S. Eisenberg

[P81] A Prolog Database Unifying Taxonomic and Structural Information

Marcel Turcotte(1), S. H. Muggleton(2) and Michael J. E. Sternberg(1)

[P82] Statistical geometry of four-residue clusters in protein structures

Iosif I. Vaisman*, Alexander Tropsha, and Weifan Zheng

[P83] Analysis of completed genomes suggests that hairpin formation is not a universal mechanism for procaryotic transcription termination

Takanori Washio[1], Junji Sasayama[2] and Masaru Tomita[2]

[P84] Identification of regulatory modules directing context-specific gene expression.

Wyeth W. WASSERMAN and James W. FICKETT

[P85] A Bayesian Network Approach to Protein Fold Recognition

D. Wild (1,2) and Z. Ghahramani

[P86] A structural view of gaps in sequence analysis

Jian (John)Yao, Michael Levitt, Christopher Lee

[P87] Regularisation of the protein secondary structure predictions.

Karel Zimmermann, Jean-François Gibrat

[P88] Computational Detection of Selectively Expressed Genes and Proteins

Larry D. Greller and Frank L. Tobin

[P89] Using Evolutionary Computation Techniques to Model Emerging Virus Diseases

Donald S. Burke, Kenneth A. De Jong, John J. Grefenstette, Connie Loggia Ramsey, Annie S. Wu

[P90] Knowing your way in the inter-net of databases: SRS and its `Databank of Databanks'. {student poster}

D.P. Kreil, T. Etzold

[P91] Improving the detection of very weak sequence homologies

Astrid Reinhardt, Tim Hubbard

[P92] Evolution of Metabolisms

Christian V. Forst, Klaus Schulten

[P93] Shotgun: Another way to shoot distant family members. {student poster}

Scott C-H Pegg and Patricia C Babbitt

[P94] European Drosophila Sequencing Consortium: sequencing the X chromosome of the fly

M. Ashburner, B. Barrell, P. Benos, V. Bolshakov, A. Bucheton, S. Cox, P. Deak, J. Demaille, C. Ferraz, F. Galibert, D. Glover, D. Harris, H. Jaeckle, F. Kafatos, C. Louis, E. Madueno, J. Modolell, I. Mougenot, L. Murphy, G. Papagiannakis, J. Rogers, C. Salles, R. Saunders, C. Savakis, U. Schaefer, I. Siden-Kiamos, L. Spanos, Y. Zhang

[P95] Dynamic programming for hidden Markov models

Richard Hughey