Data
and Knowledge Bases (DKB)
Gene Expression (GE) Gene
Finding and Motifs (GFM) Genetic
Networks (GN)
Metabolism
and Systems Biology (MSB) Phylogeny,
Rearrangements, Evolution (PER)
Protein-Protein
Interactions and proteomics (PPI) Protein
Structure (PS) Protein
Sequence Analysis (PSA)
Transcripts
Detection, RNA et DNA Motifs and Structure (RDNA)
Regulatory
Motifs and Modules (RM)
General
Sequence Analysis and Annotation (SQA) Others
(Oth)
|
Data
and Knowledge Bases (DKB)  |
| DKB_1 |
LIFE-DB:
A database for storing the results of functional experiments, recombining
data from various data sources, and serving as a sample tracking system
Detlev Bannasch, Alexander Mehrle, Karl-Heinz Glatting,
Rainer Pepperkok, Annemarie Poustka, Stefan Wiemann |
| DKB_2 |
ISYMOD:
a Knowledge Base for Integrated System Modeling
Julie Chabalier, Yves Quentin, Cecile Capponi,
Gwennaele Fichant |
| DKB_3 |
An
example of an Integrated Bioinformatic System to support detection/quantification
of GMOs
Domenica D'Elia, Pietro Leo, Gaetano Scioscia,
Pietro Lopriore, Gianfranco Delle Foglie, Flavio Licciulli, Michel Millot,
Florian Weighardt, Laura Bonfini, Ruth Lorberth, Petra Heinze, Guy Van den
Eede, Marcella Attimonelli, Hans-Jorg Buhk |
| DKB_4 |
A
Generic Solution for Automated Collecting and Integration of Biological
Data from Web Sources
Marie-Dominique Devignes, Yvan Norsa, Malika Smaïl,
Philippe Collet, Lionel Domenjoud, Michel Dauça |
| DKB_5 |
Ontologies
for description, discovery and integration of genomic data sources: state
of the art and propositions
M-D Devignes, N. Boudjlida, M. Smail |
| DKB_6 |
A
human-machine platform for 3D visualization and management of genomic databases
Pierre-Emmanuel Gros, Joan Herisson, Rachid Gherbi
|
| DKB_7 |
Deployment
of heterogeneous resources of genomic, biological and medical knowledge
on the liver to build a datawarehouse
Émilie GUERIN, Gwenaëlle MARQUET, Fouzia MOUSSOUNI,
Anita BURGUN, Fleur MOUGIN, Olivier LOREAL |
| DKB_8 |
Data
Scheme Derivation Based on Regular Expression
Vasudev Kumanduri, Matthias Lange, Roland Schnee,
Thomas Münch, Uwe Scholz, Patrick Schweizer |
| DKB_9 |
A
metabase of biological datasources for biologists and grid systems
David Laurent |
| DKB_10 |
Use
of metadata for biomedical heterogeneous data sources integration
Fleur Mougin, Gwenaëlle Marquet, Anita Burgun,
Emilie Guérin, Fouzia Moussouni and Olivier Loréal |
| DKB_11 |
BioDesk:
A platform for the Plant Data WareHouse at the Bioinformatics Center Gatersleben-Halle
Andreas Stephanik, Ivo Grosse |
| DKB_12 |
A
mediation framework for a transparent access to biological data sources
The MEDIAGRID project |
| DKB_13 |
Tropgene:
Quick Implementation of New Web Interfaces for ACEDB Databases
Mathieu Rouard, Manuel Ruiz |
| DKB_14 |
cliX
– Centralised Linking and Querying of Biological Databases
Jacob Köhler, Alexander Rüegg, Ralf Hofestädt
|
| DKB_15 |
A
First Experiment on the STANISLAS Cohort Using Closed Frequent Pattern Search
Sandy Maumus, Amedeo Napoli, Sophie Visvikis
|
| DKB_16 |
Mining
corpora of texts on genes involved in thyroid cancers: a bioinformatic text
mining and clustering process
Jean Royauté, Claire François, Alain Zasadzinski,
Dominique Besagni, Philippe Dessen, Sylvaine Le Minor and Marie-Thérèse
Maunoury |
| DKB_17 |
Reconstruction
of intercellular communication networks
Andre Skusa, Klaus Prank, Jacob Köhler |
| DKB_18 |
Classifying
Genes into Gene Ontology Categories Using Text-Based Supervised Learning
Methods
Frederic Tingaud, Tomonori Izumitani, Hirotoshi
Taira, Eisaku Maeda |
| DKB_19 |
Automatic
peculiarities detection in PhenoScreen information system
Samuel Wieczorek, Gilles Bisson, Laurence Lafanechère,
Laurent Trilling, Eric Maréchal, Sylvaine Roy |
| DKB_20 |
A
Data Warehouse for Analyzing Protein Families
Markus Fischer, Rolf D. Schmid, Jürgen Pleiss
|
| DKB_21 |
Integrated
Relational Enzyme Database (IntEnz)
Astrid Fleischmann, Kirill Degtyarenko, Michael
Darsow, Wolfgang Fleischmann, Rolf Apweiler |
| DKB_22 |
ChEBI:
Chemical Compounds of Biological Interest
Paula de Matos, Kirill Degtayarenko, Michael Darsow
|
| DKB_23 |
ANTIMIC:
A Database of Antimicrobial Peptides
Manisha Brahmachary, Judice L.Y.Koh, S.P.T.Krishnan,
Mohammad Asif Khan, Seah Seng Hong , Tin Wee Tan, Vladimir Bajic
|
| DKB_24 |
New
developments in RTKdb
Julien Grassot, Guy Perrière, Guy Mouchiroud
|
| DKB_25 |
Third
party annotation data in EMBL-Bank
Guy Cochrane, Carola Kanz, Vincent Lombard, Renato
Mancuso, Michelle McHale, Maria Pilar Garcia Pastor, Guenther Strosser,
Mary Ann Tuli |
| DKB_26 |
Swiss-Prot:
more than a PROTEIN SEQUENCE DATABASE
Xavier Martin, Brigitte Boeckmann, Elisabeth Gasteiger,
Amos Bairoch |
| DKB_27 |
Standardization
of format and content in the Swiss-Prot protein knowledgebase
Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch
|
| DKB_28 |
SYSTERS
Protein Family Database: Taxonomy Web Interface and Taxon-related Cluster
Frequencies
Thomas Meinel, Antje Krause, Martin Vingron
|
| DKB_29 |
DBOra:
An Integrated Database for Context Based Search and Browsing in Protein
Data
Matthias Lange, Vasudev Kumanduri, Thomas Münch,
Roland Schnee, Uwe Scholz, Patrick Schweizer |
| DKB_30 |
IMGT/StructuralQuery
: a tool for structural data analysis of immunoglobulin and T cell receptor
variable domains (http://imgt.cines.fr).
Quentin Kaas, Marie-Paule Lefranc |
| DKB_31 |
The
IMGT Strategy For The Automatic Annotation of IG And TR cDNA Sequences:
IMGT/Automat
Véronique Giudicelli, Céline Protat, Marie-Paule
Lefranc |
| DKB_32 |
E-MSD:
The European Bioinformatics Institute Macromolecular Database
H.Boutselakis, D.Dimitropoulos,J.Fillon,A.Golovin,K.Henrick,A.Hussain,
J.Ionides,M.John,P.A.Keller,E.Krissinel,P.McNeil,A.Naim,R.Newman, T.Oldfield,J.Pineda,A.Rachedi,J.Copeland,A.Sitnov,S.Sobhany,
A.Suarez-Uruena,J.Swaminathan,M.Tagari,J.Tate,S.Tromm, S.Velankar and W.Vranken
|
| DKB_33 |
The
KNOTTIN website and database: A new information system dedicated to the
knottin scaffold
Jean-Christophe Gelly, Jerôme Gracy, Dung Le-Nguyen,
Annie Heitz, Laurent Chiche |
| DKB_34 |
Columba
- A Database of Annotations of Protein Structure
Kristian Rother, Silke Trissl, Heiko Müller, Patrick
May, Rene Heek, Robert Preissner, Thomas Steinke, Ina Koch, Ulf Leser, Cornelius
Frömmel |
| DKB_35 |
Celsius:
A Database of Temperature Adapted Protein Structures
Steinar Thorvaldsen, Erik Hjerde, Nils P. Willassen,
Chis Fenton, Tor Fla |
| DKB_36 |
GIN-db:
a relational scheme for the integration of multi-species gene
Claude Sabatier, Azzeddine Kadi, Catherine Verheecke-Mauzé,
Karine Souquet, David Martin, Magali Lescot, Pierre Mouren, Aitor González,
Anaïs Baudot, Christine Brun, Claudine Chaouiya, Bernard Jacq, Denis Thieffry
|
| DKB_37 |
Hoppsigen:
a database dedicated to comparative analysis of vertebrate processed pseudogenes
Adel Khelifi, Dominique Mouchiroud |
| DKB_38 |
Toward
an integrated tool for high throughput functional analysis of plant genomes
Sébastien Aubourg, Véronique Brunaud, Franck
Samson, Séverine Gagnot, Sylvain Duchêne, Yannick De Oliveira, Marion Blanchet,
Cyril Pommier, Michel Caboche, Alain Lecharny |
| DKB_39 |
MolliGen
: a database dedicated to the comparative genomics of Mollicutes
Aurélien Barré, Pascal Sirand-Pugnet, Xavier Foissac,
Eduardo P. C. Rocha, Antoine de Daruvar, Alain Blanchard |
| DKB_40 |
Examining
Mitochondrial Genomes Using OGRe
Daniel Jameson, Andrew P. Gibson, Cendrine Hudelot,
Paul G. Higgs |
| DKB_41 |
GeMCore
: a mammalian comparative mapping database
Navratil V., Spataro B., Bronner G., Faraut T.,
Mouchiroud D., Gautier C. |
| DKB_42 |
Databases
of Homologous Gene Families:New Developments and Web Interfaces.
Simon Penel, Julien Grassot, Laurent Duret, Manolo
Gouy, Guy Perriere |
| DKB_43 |
Databases
on Eukaryotic Gene Regulation: TRANSFAC®, TRANSCompel®, and TRANSPATH®.
Annotation, Information Processing, and Application for Analysis of Gene
Expression Data.
Olga Kel-Margoulis, Volker Matys, Claudia Choi,
Ingmar Reuter, Ellen Goessling, Nico Voss, Mathias Krull, Susanne Pistor,
Susanne Thiele, Ellen Fricke, Sigrid Land, Anatolij Potapov, Dmitri Tchekmenev,
Birgit Lewicki-Potapov, Alexander Kel, and Edgar Wingender. |
| DKB_44 |
Biological
and medical ontology-based annotation of genes in the context of transcriptome
analysis
Gwenaëlle Marquet, Emilie Guérin, Anita Burgun,
Fouzia Moussouni , Fleur Mougin and Olivier Loréal |
| DKB_45 |
SubScript:
an Integrated Framework for Transcriptome Data Storage and Analysis
Sandrine Moreira, Laetitia Marisa, Gaëlle Lacourrège,
Céline Frily, Jean-Yves Coppée, Antoine Danchin, and Ivan Moszer
|
| DKB_46 |
CleanEx
: a Gene Expression Reference Database
Viviane Praz, Philipp Bucher |
| DKB_47 |
GCDB:
A Gene Expression Database for immune cells trancriptomes GCDB: A Gene Expression
Database for immune cells trancriptomes
Andrea Splendiani, Caterina Vizzardelli, Norman
Pavelka, Mattia Pelizzola, Monica Capozzoli, Ottavio Beretta, Francesca
Granucci and Paola Ricciardi-Castagnoli. |
| DKB_48 |
TRAIT:
A KNOWLEDGEBASE TO RETRIEVE ANNOTATED AND DIFFERENTIALLY EXPRESSED TRANSCRIPTS
FOUND IN HUMAN SKELETAL MUSCLE
Stefano Toppo, Nicola Cannata, Chiara Romualdi,Paolo
Laveder, Gerolamo Lanfranchi, Giorgio Valle |
| DKB_49 |
Mouse
Phenotype Ontology Development and Application
E. C. J. Green, G. V. Gkoutos, A.M. Mallon, S.
Greenaway, A. Blake, M. Simon, J.M. Hancock & D. Davidson |
| DKB_50 |
Knowledge
Representation Model for Prokaryote Transcription Regulation
Sébastien J. Provencher |
| DKB_51 |
Modelisation
and representation of expression data in Ascidians: The virtual ascidian
embryo project
Olivier Tassy, Patrick Lemaire |
| DKB_52 |
EasyKEGG:
A data filtering and standardization system for the KEGG database
R. A. Ferreira, J. Schmith, C. K. Barcellos, N.
Lemke, A. N. dos Reis, J. C. M. Mombach |
| DKB_53 |
MetaboDB:
a database for metabolic reconstruction
Guillaume Meurice, Corinne Maufrais, Katja Schuerer
|
| DKB_54 |
Design
methodology for a bioinformatic application: the case of aMAZE
Christian Lemer, Jean Richelle, Shoshana J. Wodak
|
| DKB_55 |
An
Object-Oriented Data Model for Signal Transduction
Yves Deville, David Gilbert, Christian Lemer, Jacques
van Helden, Shoshana J. Wodak |
| DKB_56 |
The
aMAZE Light Bench : a WEB interface a relational database of biochemical
pathways and cellular processes
Christian Lemer, Erick Antezana, Fabian Couche,
Frédéric Fays, Xavier, Santolaria, Jean Richelle, Shoshana J. Wodak
|
| Gene
Expression (GE) |
| GE_1 |
New
design of oligonucleotides for microarray
Sebastien Rimour, Pierre Peyret, David Hill
|
| GE_2 |
A
novel design of whole-genome microarray probes for Saccharomyces cerevisiae
which minimizes cross-hybridization
Emmanuel Talla, Fredj Tekaia, Laurent Brino, and
Bernard Dujon |
| GE_3 |
A
prototype based gene selection approach for microarray data classification
Blaise Hanczar, Raffaella Cancello, Claire Carette,
Mélanie Courtine, Arriel Benis, Véronique Pelloux, Karine Clément, Jean-Daniel
Zucker |
| GE_4 |
Development
of a System for Monitoring Human Cytokine Genes Expression through a 50mer
Oligonucleotide Arrays from Probe Design to Data Analysis.
Cinzia Castagnini, Dario Greco, MarcoCassone ,Marco
Rinaldo Oggioni , Francesco Iannelli , Anna Cuppone, Franco Laghi Pasini,
Gianni Pozzi |
| GE_5 |
AnovArray:
a Set of SAS Macros for the Analysis of Variance of Gene Expression Data
Karine Piot, Christelle Hennequet-Antier, Helene
Chiapello, Francois Rodolphe, Severine Degrelle, Isabelle Hue, Jean-Paul
Renard, Stephane Robin |
| GE_6 |
Mixture
Model on the Variance for the differential analysis of gene expression data
Paul Delmar, Stephane Robin, Jean Jacques Daudin,
Diana Leroux |
| GE_7 |
Comparison
of different methodologies to identify differentially expressed genes in
two-sample cDNA microarrays
Kristof Engelen, Kathleen Marchal, Jos De Brabanter,
Torik Ayoubi, Paul Van Hummelen , Bart De Moor |
| GE_8 |
Comparison
of two Analysis Methods for Microarray Data
Änne Glass, Thomas Scheel |
| GE_9 |
Incidence
of missing values in hierarchical clustering of microarrays data
Alexandre G. de Brevern, Serge Hazout, Alain Malpertuy
|
| GE_10 |
Spotting
effect in cDNA experiments
Tristan Mary-Huard, Jean-Jacques Daudin, Stéphane
Robin |
| GE_11 |
Mining
microarray data by making statistical aggregates of gene expression levels
Catherine Cerutti, Catherine Thiéblemont, Ramzi
El-Feghali, Rémi Houlgatte, Marie-Paule Gustin, Christian Paultre, Jacques
Randon, Bertrand Coiffier and Giampiero Bricca |
| GE_12 |
Testing
the significance of clusters found in gene expression data
Ulrich Moeller, Doerte Radke, Frank Thies
|
| GE_13 |
Model-Driven
Clustering of Time-Course Gene Expression Data
Anne Badel-Chagnon, Gaelle Lelandais, Serge Hazout,
Pierre Vincens |
| GE_14 |
Stability
Analysis of Time Series Gene Expression Data
Jutta Gebert, Martin Lätsch, Stefan Pickl Gerhard
Weber, Röbbe Wünschiers |
| GE_15 |
Gene
Expression meets Clinical Practice
Arriel Benis, Raffaella Cancello, Claire Carette,
Mélanie Courtine, Blaise Hanczar, Véronique Pelloux, Karine Clément, Jean-Daniel
Zucker |
| GE_16 |
Design
of a clinical microarray chip
Jochen Jäger, Rainer Spang |
| GE_17 |
Computational
analysis strategies of oligo-microarray data: identification of genes expressed
in human fetal heart and of genes involved in atrioventricular septal defects
Dario Greco, Floriana Fabbrini, Paola D’Agostino,
Rosa Negri , Rita Genesio, Anna Conti, Stella Zannini and Lucio Nitsch
|
| GE_18 |
Screenig
for gain and loss of co-regulation in cancer specific expression profiles
Dennis Kostka, Rainer Spang |
| GE_19 |
Classification
of cancers by gene expression profiles from peripheral blood
Andrey Loboda, Michael Nebozhyn, Steven Johnson,
Peter O’Dwyer, Calen Nichols, Linda Alila, Louise Showe, and Michael Showe
|
| GE_20 |
Navigating
towards Biologically Resolved Diagnoses through Structured Analysis of Microarrays
Claudio Lottaz, Julie Floch, Renate Kirschner,
Christian Hagemeier, Rainer Spang |
| GE_21 |
An
Architecture for Standardization and Management of Gene Expression Data
in a Global Organization
Isabelle Crignon |
| GE_22 |
Facilitating
the interpretation of high-throughput experiments
Felix Kokocinski, Gunnar Wrobel, Grischa Toedt,
Peter Lichter |
| GE_23 |
MADTOOLS:
management tools for the mining of microarray data.
Nolwenn Le Meur, Audrey Bihouée, Raluca Teusan,
Gérard Ramstein , Jean J. Léger |
| GE_24 |
MADCAP:
MicroArray Data Characterization And Profiling.A tool for profiling lists
of genes with different expression patterns.
Jean Lozach, Roman Sasik, Sumito Ogawa, Christopher
K. Glass |
| GE_25 |
Specific-GST
design and database structure for the Complete Arabidopsis Transcriptome
Microarray (CATMA) project
Carine Serizet, Vincent Thareau, Thomas Schiex,
Sébastien Aubourg, Mark L. Crowe, Eric Bonnet, Pierre Hilson, Yves Van de
Peer, Pierre Rouzé |
| GE_26 |
Gen0m
- Software
Sven Bansemer, Thomas Scheel, Aenne Glass, Thomas
Karopka |
| GE_27 |
Drosophila
transcriptome analysis using DNA arrays. Development of an automatical tool
for the interpretation of the results.
T.P. Vu Manh, M. Mokrane, J Flavigny, L. Carrier,
M. Semeriva, M. Piovant, L. Röder |
| GE_28 |
EST
based method to identify differentially expressed gene clusters along chromosmes.
Karine Mégy, Stéphane Audic, Francois Enault and
Jean-Michel Claverie |
| GE_29 |
Bellerophon:
Graph analysis for improved EST clustering
Jérémy Just, Emmanuel Barillot, Fabrice Legeai,
Aymeric Duclert |
| GE_30 |
ADEL
: Analysis of the Distribution of ESTs in cDNA Libraries
Jean-Baptiste Veyrieras, Sophie Créno, Fabrice
Legeai, Emmanuel Barillot, Aymeric Duclert |
| Gene
Finding and Motifs (GFM)
|
| GFM_1 |
Compositional
analysis of non-coding regions in eukaryotic genomes
Emanuele Bultrini, Paolo Del Giudice, Elisabetta
Pizzi |
| GFM_2 |
Unsupervised
search for coding regions using the EM algorithm
Frédérique Galisson, Richard Greset, Emmanuelle
Becker |
| GFM_3 |
Stochastic
Indicator of Regions and Application to Protein Coding Region Prediction
Kouichi Kimura, Tetsuo Nishikawa, Keiichi Nagai,
Sumio Sugano, Nobuo Nomura, Takao Isogai |
| GFM_4 |
A
markovian approach to the analysis of the structure of genes
Christelle Melodelima, Laurent Guéguen, Christian
Gautier, Didier Piau |
| GFM_5 |
Exogean
: an Expert on Eukaryotic Gene Annotation
Sarah Djebali, Franck delaplace, Hugues Roest Crollius
|
| GFM_6 |
Modeling
of Tho Dependent Transcription Termination Sites in the Bacterium Helicobacter
pylori
List Petersen, Anders Krogh |
| GFM_7 |
A
New Method to Predict Translation Initiation Sites
Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong
|
| GFM_8 |
The
Importance of Window Length in Splice Site Prediction
Leila Taher, Burkhard Morgenstern, Peter Meinicke
|
| GFM_9 |
Genome
wide prediction of tissue and tumor specific alternative splicing based
on EST data
Shobhit Gupta, Martin Vingron, Stefan Haas
|
| GFM_10 |
Conception
and implementation of a MySQL based analysis environment for tissue specific
alternative splicing
Ralf H. Bortfeldt, Heike Pospisil, Alexander Herrmann,
Jens Reich |
| Genetic
Networks (GN) |
| GN_1 |
Using
Bayesian Networks for Estimating Gene Networks from Microarrays and Biological
Knowledge
Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke
Tashiro, Satoru Kuhara, Satoru Miyano |
| GN_2 |
Dynamic
Bayesian Network and Nonparametric Regression Model for Inferring Gene Networks
from Time Series Microarray Data
SunYong Kim, Seiya Imoto, Satoru Miyano
|
| GN_3 |
Estimating
Gene Networks from Gene Expression Data by Combining Bayesian Network Model
with Promoter Element Detection
Yoshinori Tamada, SunYong Kim, Hideo Bannai, Seiya
Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano |
| GN_4 |
Constructing
Gene Relation Networks by using Natural Language Processing
Thomas Karopka, Sven Bansemer |
| GN_5 |
SMBioNet
: a Tool for Modeling Biological Regulatory Networks Driven by Temporal
Behavior
Jean-Paul Comet, Adrien Richard |
| GN_6 |
Modelling
and simulating the regulatory network specifying the Notch boundary between
the dorsal and the ventral compartments of the wing imaginal disc
Aitor Gonzalez Gonzalez, Claudine Chaouiya, Lucas
Sanchez, Denis Thieffry |
| GN_7 |
Modeling
of genetic network regulating mammalian hematopoiesis
Anastassia Iartseva, Adrien Richard, Gilles Bernot,
François Képès |
| GN_8 |
Embedding
properties of Biological Regulatory Networks
Christophe Auberger, Fariza Tahi, Gilles Bernot
|
| GN_9 |
GINML:
Towards a GXL Based Format for Logical Regulatory Graphs and Dynamical Graphs
Claudine Chaouiya, Aitor González González, Denis
Thieffry |
| GN_10 |
GIN-sim:
a Software for a Qualitative Simulation and Analysis of Logical Regulatory
Graphs
Claudine Chaouiya, Aitor González González, Denis
Thieffry |
| GN_11 |
Graph
Theory Based Methodology for Comparing Interaction Networks between Genes
across Organisms
Gaëlle Lelandais, Pierre Vincens, Claude Jacq,
Stéphane Vialette |
| GN_12 |
Combining
logical formalisation and constraint programming to model wild-type and
perturbed genetic networks.
Vincent Devloo, Denis Thieffry |
| GN_13 |
Comparison
of known biological regulatory networks with gene regulatory networks generated
by computational analysis of disrupted gene expression profile data
Emiko Furuichi, Sachiyo Aburatani, Kosuke Tashiro,
Christopher J. Savoie, Shigeru Muta, Hisahi Nakashima, Yukihiro Eguchi,
Satoru Kuhara |
| GN_14 |
Integrated
solutions for analyzing gene regulation networks
Céline Lefebvre, Jean-Christophe Aude, Christian
Néri |
| GN_15 |
GeNetDB:
a Software for the Study of Genetic Regulatory Networks
Aurelien Mazurie, Julien Lambert |
| GN_16 |
Theoretical
study of mutations and evolution of gene networks
Alexander Ratushny, Vitaly Likhoshvai, Irina Borisova,
Nikolay Zagoruiko, Yuri Matushkin, and Nikolay Kolchanov |
| Metabolism
and Systems Biology (MSB) |
| MSB_1 |
Analysing
transcriptome in the metabolome context to understand cell regulations
Philippe Marc, John Aach, George M.Church
|
| MSB_2 |
Finding
combinatorial causal relationships in metabolite concentration data using
decision tree heuristics
André Floeter, Joachim Kopka, Torsten Schaub, Jacques
Nicolas, Joachim Selbig |
| MSB_3 |
Computation
of Extreme Pathways with Hierarchical Decompositions of Metabolic Network
Julien, Gagneur, Georg Casari |
| MSB_4 |
Metabolites
containing “Flags” and “Cargo” - a More Detailed Model of the Human Lipoprotein
Network in Blood Plasma
Katrin Hafez, Jens-Georg Reich |
| MSB_5 |
Essentiality
and Damage in Metabolic Networks
N. Lemke, C. K. Barcellos, F. Her\'edia, J. C.
M. Mombach |
| MSB_6 |
Recreating
Biopathways towards Modeling and Simulation
Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
|
| MSB_7 |
A
method for classifying metabolites in pathway analysis based on minimization
of pathway number
Stefan Schuster, Ferdinand Moldenhauer, Sascha
Bulik, Helge Bertram, Thomas Dandekar |
| MSB_8 |
Observing
and Interpreting Correlations in Metabolomic Networks
R.Steuer, J.Kurths, W.Weckwerth, O.Fiehn
|
| MSB_9 |
Modeling
the Ethylene-Response Pathway with UML-Statecharts
Claudia Täubner |
| MSB_10 |
The
Biochemical Abstract Machine BIOCHAM
Nathalie Chabrier, Francois Fages |
| MSB_11 |
Effects
of randomly placed obstacles on intracellular signal transduction
Garrit Jentsch, Reiner Kree |
| MSB_12 |
A
thermodynamic theory of cell cycle
A Kummer, R Ocone |
| MSB_13 |
4DiCes:
From Random Walk to Rate Walk:
Mark Möller, Björn E. Oleson, Klaus Prank
|
| MSB_14 |
4DiCeS:
Four-Dimensional Cell Simulation and Visualization
Björn E. Oleson, Mark Möller, Klaus Prank
|
| MSB_15 |
Analyzing
intercellular communication networks
Andre Skusa, Klaus Prank |
| MSB_16 |
Modeling
the p53 signaling network by using the Abstract Cell Model
yasuhiro suzuki, sohich ogishima, hiroshi tanaka
|
| MSB_17 |
Scaling
models from individual and/or population cellular levels issues in network
engineering
Laurent Gaubert, Magali Roux-Rouquié |
| Others
(Oth)
|
| OTH_1 |
Towards
Faster Profile HMM Evaluation
Thomas Plötz, Gernot A. Fink |
| OTH_2 |
Recognition
of the sequential motion (hand shape-change) by the GRBF network
Miwako Hirakawa, Masahiro Okamoto |
| OTH_3 |
A
set of low fidelity visualizations of bioinformatics algorithms for teaching
purposes
Miguel DeArce, Teresa Logan-Phelan |
| OTH_4 |
Structural
and Functional Annotation of the Drosophila Melanogaster Genome using
GENATLAS. A case study for the "kinase" annotation.
Sunil Patel, Mikhail Velikanov
|
| OTH_5 |
Global
Numerical Models of Circulatory and Respiratory Systems of Human Body including
their Interaction and Matter Transports
A.S.Kholodov, A.V.Evdokimov, Y.A.Kholodov |
| OTH_6 |
PROTIC:
A Database and Web-based Application to Manage, Analyse and Web-publish
Plant Proteom Expression Data
Gwenn Houel, Hélèné Ferry-Dumazet, Luc Moreau, Pierre
Montalent, Christophe Plomion, Antoine de Daruvar, Michel Zivy, Johann
Joets
|
| OTH_7 |
The
ChipYard Framework For Microarray Data Analysis
Grischa Tödt, Gunnar Wrobel, Felix Kokocinski and Peter Lichter |
| Phylogeny,
Rearrangements, Evolution (PER) |
| PER_1 |
Study
of chromosome number in Brucella and Bartonella sp.
Maxime Huvet, Siv G.E. Andersson |
| PER_2 |
On
maximal instances for the original syntenic distance
Cedric Chauve. Guillaume Fertin |
| PER_3 |
Back
to the ""pre-genomic"" era
Etienne Danchin, Pierre Pontarotti |
| PER_4 |
Importance
of Synteny in Comparative Annotation of Bacterial Genomes
Laurent Labarre, David Vallenet, Valérie Barbe,
Jérôme Lesaux, Anne Morgat, Claudine Médigue |
| PER_5 |
Synteny
among grass genomes inferred from large sequence comparisons
Bérangère Virlon, Johann Joets |
| PER_6 |
GENOFRAG:
a software to design primers optimized for whole genome scanning by long-range
PCR amplification.
Nouri Ben Zakour, Michel Gautier, Rumen Andonov,
Dominique Lavenier, Philippe Veber , Alexeï Sorokin and Yves Le Loir
|
| PER_7 |
The
consistent signal in genome trees revealed by reducing the impact of noise
Bas E. Dutilh, Martijn A. Huynen, William J. Bruno,
and Berend Snel |
| PER_8 |
Bacterial
comparative genomics: gene/operon duplications
Dirk Gevers, Cedric Simillion, Yves Van de Peer
|
| PER_9 |
Simulating
genes families
Roberto Marangoni |
| PER_10 |
Detecting
horizontal gene transfer in rumen ciliates cDNA data
Guenola Ricard, Martijn Huynen |
| PER_11 |
An
in silico approach to find out the core of the (proteo)bacterial life
Quentin Sculo, Olivier Lespinet and Bernard Labedan
|
| PER_12 |
A
gamma-Proteobacterial phylogeny based on the order in the genome of a subset
of non-horizontal-transferred genes
Francisco J. Silva |
| PER_13 |
Longest
Common Circular Chains of Maximal Unique Matches between Bacterial Genomes
Frédéric Guyon, Serge Hazout, Alain Guénoche
|
| PER_14 |
Incremental
algorithm for the management of families of similar sequences
Jean-François Dufayard, Guy Perrière, Manolo Gouy
|
| PER_15 |
Exploration
of phylogenetic relationships using DNA style
Charles Chapus, Christine Dufraigne, Alain Giron,
Scott Edwards, Bernard Fertil, Patrick Deschavanne |
| PER_16 |
Applications
of Clustering and Visualization to Phylogeny
Ruchi Kalra, Katherine St. John, Luay Nahkleh,
Tandy Warnow |
| PER_17 |
Visualizing
Restricted Landscapes of Phylogenetic Trees
Ingrid Montealegre, Katherine St. John |
| PER_18 |
ITS
phylogeny of Cylindrocarpon spp. causal agent of Black Foot Disease of grapevine,
compared with morphology
Elsa PETIT, W. Douglas GUBLER |
| PER_19 |
Homoplasy
matrices: a tool for choosing between alternative topologies?
Leonid Rusin |
| PER_20 |
Phylojava
: a Generic Client-Server Tool for Phylogenetic Tree Reconstruction - Application
to Grid Computing
Timothée SILVESTRE, Estelle Nugues, Guy Perrière,
Manolo Gouy, Laurent Duret |
| PER_21 |
RAxML:
A Parallel Program for Phylogenetic Tree Inference
Alexandros Stamatakis, Harald Meier, Thomas Ludwig
|
| PER_22 |
Genome
composition of endosymbiotic bacteria
Jörg Schaber, Claude Rispe, François Delmotte,
Francisco Silva, Andrés Moya |
| PER_23 |
Human
Endogenous Retroviruses and Evolutionary Analysis of Their Long Terminal
Repeats
Irena Artamonova |
| PER_24 |
Evolution
of HCV: Molecular Clock in the E1/E2 Region and Patterns of Change During
the Disease Progression
Borys Wróbel, Manuela Torres-Puente, Nuria Jiménez,
Mª Alma Bracho,Inmaculada García-Robles, Andrés Moya and Fernando González-Candelas
|
| PER_25 |
Conflicting
Results in Association Analyses of Complex Genotype-Phenotype Relationships:
Problems and Conclusions
Karla Köpke, Uwe Malzahn, Werner Terhalle, Christian
Meisel, Ivar Roots |
| PER_26 |
Y-chromosome
population genetics by surnames and Self Organizing Maps
Pascal Croiseau, Franz Manni |
| PER_27 |
The
Mutation-Selection Balance in an Infinite Asexual Population with Stratified
Genome of a Fixed Size
Anna Fukshansky |
| PER_28 |
Geographic
patterns of data variation:how barriers can be detected by Monmonier’s algorithm
Franz Manni, Etienne Guérard |
| PER_29 |
ActionMap:
a web-software that automate genetic mapping computation
Guillaume Albini, Matthieu Falque, Johann Joets
|
| PER_30 |
An
environment for genetic/physical map storage, visualization and comparative
analysis
Guillaume Albini, Farid Chetouani, Stéphane Rouillé,
Emmanuelle Karsenty, Bruce Thomas, Fabrice Legeai, Delphine Samson, Laurent
Pereira, Anne Arcade, Johann Joets, Denis Scala, Eric Viara, Emmanuel Barillot,
Aymeric Duclert |
| PER_31 |
BioMercator:
a Java software for genetic maps display and QTL meta-analysis
Anne Arcade, Matthieu Falque, Alain Charcosset,
Johann Joets |
| Protein-Protein
Interactions and proteomics (PPI) |
| PPI_1 |
Improving
the quality of mass spectrometry with simple and chemical-based rules
David Elguero-Claramunt, J.-M. Carazo |
| PPI_2 |
Evolution
of the Function of Duplicated Genes from an Interaction Network Point of
View
Anaïs Baudot, Alain Guénoche, Bernard Jacq, Christine
Brun |
| PPI_3 |
Mining
partners of integrated biological systems
Tristan Colombo, Gwennaele Fichant, Yves Quentin
|
| PPI_4 |
Protein
World: Connecting the proteomes of model organisms
Tim Hulsen, Peter Groenen, Martijn Huynen
|
| PPI_5 |
Computational
Investigation of the robustness of the protein network of Helicobacter pylori
J. Schmith, Jose C. M. Mombach, N. Lemke, and C.
K. Barcellos |
| PPI_6 |
A
novel pooling design for protein-protein interaction mapping
Nicolas Thierry-Mieg, Laurent Trilling, Jean-Louis
Roch |
| PPI_7 |
ProViz:
Protein Interaction Visualization and Exploration Tool
David Auber, Florian Iragne, Bertrand Mathieu,
Macha Nikolski, David Sherman |
| PPI_8 |
PARIS:
a system for 2-DE based proteomic data management
Juhui Wang, Christophe Caron, Michel-Yves Mistou,
Christophe Gitton, Alain Trubuil |
| Protein
Structure (PS)
|
| PS_1 |
"Sequence
- Structure Relation in Proteins through a ""Hybrid Protein Model"""
Cristina Benros, Alexandre G. de Brevern, Serge
Hazout |
| PS_2 |
Identification
of localized sequence structural determinants for cold adapted enzymes
Tor Flo, Oyvind Bjorkas, Steinar Thorvaldsen
|
| PS_3 |
Data
Mining the Protein Data Bank - Automatic Detection and Assignment of Carbohydrate
Structures
Thomas Lütteke, Martin Frank, Claus-W. von der
Lieth |
| PS_4 |
Detecting
Local Structure Motifs in Proteins by Analyzing Motif SequenceSignatures
Szymon Nowakowski, Andriy Kryshtafovych, Krzysztof
Fidelis, Jerzy Tiuryn |
| PS_5 |
Incorporating
Sequence and Biochemical Information in TOPS models - for Biologically Significant
Pattern Matching and Pattern Discovery in Protein Structures
Mallika Veeramalai, David Gilbert, David Westhead
|
| PS_6 |
Protein
secondary structure prediction based on
Jacek Blazewicz, Peter L. Hammer, Piotr Lukasiak
|
| PS_7 |
Structural
similarity search in databases: YAKUSA
Mathilde Carpentier, Sophie Brouillet, Joël Pothier
|
| PS_8 |
Structure
and metabolism of cytochrome P450 3A isozymes : approach by homology modeling
and molecular dynamics simulations
Magali Cottevieille, Nicolas Loiseau, Joël Pothier,
Thierry Cresteil, Marcel Delaforge, François André |
| PS_9 |
A
Highly Reliable Approach to Transmembrane Topology Prediction
Masami Ikeda, Jun-Xiong Xia, Toshikatsu Okuno,
Toshio Shimizu |
| PS_10 |
First
Step Toward 3D Protein Structure Prediction with a de novo Approach
Juliette Martin, Pierre Nicolas, Jean-François
Gibrat |
| PS_11 |
Protein
Folding in CLP(FD) with Empirical Contact Energies
Alessandro Dal Palu', Agostino Dovier, Federico
Fogolari |
| PS_12 |
An
automatic procedure for the search and identification of new unbound docking
examples
Frank Steinacker, Oliver Martin, Philipp Heuser,
Dietmar Schomburg |
| PS_13 |
Modeling
and Predicting All-alpha Transmembrane Proteins
Jerome Waldispuhl, Jean-Marc Steyaert |
| PS_14 |
Discretization
of 3D protein conformations by learning fragments library and their short
range dependence using a Hidden Markov Model
Anne-Claude Camproux, Romain Gautier, Pierre Tufféry
|
| PS_15 |
Generalized
backbone-dependence of side chain conformations, and its impact on side
chain conformational entropy
Romain Gautier, Anne-Claude Camproux, Pierre Tufféry
|
| PS_16 |
Efficient
Methods for Filtering and Ranking Fragments for Loop Prediction in Proteins
Philipp Heuser, Gerd Wohlfahrt, Dietmar Schomburg
|
| PS_17 |
PTGL
- Protein Topology Graph Library
Patrick May, Ina Koch |
| PS_18 |
Geometric
Invariant Theory applied to Protein Structure Classification
Pramod P. Wangikar, Ashish V. Tendulkar, Milind
A. Sohoni |
| PS_19 |
A
Strategy for Detection of Structural Conserved Regions and Contacts in Protein
Superfamilies: Application to the PLP-Dependent Enzymes
Alessandro Paiardini, Leonardo Di Vincenzo, Francesco
Bossa, Stefano Pascarella |
| PS_20 |
Classification
of Fourier spectra of short protein sequences compared to their corresponding
structural classification
Manoj TYAGI, Henri RALAMBONDRAINY, Frédéric CADET,
Philippe CHARTON, Bernard OFFMANN |
| PS_21 |
Study
of Macromolecular Recognition Mechanisms using Reduced Representations of
Macromolecules in terms of Critical Points of Electron Density
Andy Becue |
| PS_22 |
A
New 3D Statistical Potential to Predict Protein-Ligand Interactions Based
on Atomic Interaction Patterns in PDB
Ernesto Moreno, Luis A. Diago |
| PS_23 |
On
the calculation of protein-ligand binding constants
Anatoly Ruvinsky |
| PS_24 |
Comprehensive
Mutagenesis of HIV-1 Protease: A Statistical Geometry Approach
Majid Masso, Iosif Vaisman |
| PS_25 |
Extracting
Functional Clues from Structural Similarity using a Methodology based on
Alpha-Shapes
Natalia Jiménez-Lozano, Mónica Chagoyen, Pedro
Antonio de Alarcón, Jose Mª Carazo |
| PS_26 |
Design
of a Selective Inhibitor of Tyrosine Kinase 2
Kristin Tøndel, Endre Anderssen, Finn Drabløs
|
| PS_27 |
A
Method for Fold Recognition and Docking with Spin Images and a Bayesian
Probability Framework
Velázquez-Muriel J.A, Niels Volkmann , José María
Carazo |
| PS_28 |
IPHEx:
A System For Evaluating Protein Docking Hypothesis Using User Feedback
Franck Zoellner, Steffen Neumann, Kerstin Koch,
Franz Kummert, Gerhard Sagerer |
| PS_29 |
Statistical
analysis on transient protein-protein interfaces
Sam Ansari, Volkhard Helms |
| PS_30 |
RELATIONSHIP
BETWEEN CHROMOPHORE STRUCTURE AND SPECTRAL PROPERTIES IN BACTERIORHODOPSIN
ANALOGS SERIES.
Andrey A. Khodonov, Sergey V. Shevyakov, Vitaly
I. Shvets, Olga V. Demina. |
| PS_31 |
Low
Frequency Normal Modes of Methylamine Dehydrogenase. Can They Promote H-Tunneling?
Juliana Palma, Cecilia M. Ridruejo, Sebastián Fernández-Alberti
and Julián Echave |
| PS_32 |
IMGT
standardization and analysis of V-LIKE-, C-LIKE- and G-LIKE-DOMAINs
Elodie Duprat, Marie-Paule Lefranc |
| PS_33 |
Functionally
induced structural changes in immunoglobulin G domains registered by liquid
crystal ligand binding ? a computer simulation
Marcin Krol, Irena Roterman, Barbara Piekarska,
Barbara Stopa, Joanna Rybarska, Leszek Konieczny |
| PS_34 |
Common
dynamic behavior in members of the same fold family
Sandra Maguid, Leticia Ferrelli, Sebastian Fernandez-Alberti
and Julian Echave |
| PS_35 |
BRAGI
– An Updated Protein Modelling Package supporting Windows®, Unix® and Linux
Joachim Reichelt, Guido Dieterich, and Dirk Heinz
|
| Protein
Sequence Analysis (PSA) |
| PSA_1 |
TIGERSearch
attacks Proteins
Jasmin Saric, Uwe Reyle |
| PSA_2 |
Automated
extraction of mutation data from the literature
Florence Horn, Lawrence C..Lee, Fred E.Cohen
|
| PSA_3 |
Protein
Function Prediction: Application of a Propositional Rules Learning System
to a set of Human Protein Sequences
Gomez, Alfonso Valencia |
| PSA_4 |
A
rule-based approach for generating phylogentic relationships between bacterial
protein functional classes from taxonomical and sequence information
Ali Al-Shahib, Aik Choon Tan, David Gilbert
|
| PSA_5 |
Bayesian
analysis of the evolution of protein families
Catherine Bru, Thomas Schiex, Daniel Kahn
|
| PSA_6 |
Learning
sets of positive rules of amino acid properties to classify protein functional
classes
Aik Choon TAN, Ali AL-SHAHIB, David GILBERT and
Yves DEVILLE |
| PSA_7 |
Fourier
Spectral Analysis of Protein Functional Families
Salma Locate, Bénédicte Beylot, Emmanuelle Huitelec,
Claude Rouch, Bernard Offmann |
| PSA_8 |
Grammatical
inference for disulfide bonds prediction within proteins
Ingrid Jacquemin, Jacques Nicolas |
| PSA_9 |
MutScan,
A Fourier Based Method For the Identification of Key Amino Acids in Protein
Sequences
HUITELEC Emmanuelle, CHARTON Philippe, BEYLOT Bénédicte,
LOCATE Salma, ROUCH Claude, OFFMANN Bernard |
| PSA_10 |
Inferring
Site-Specific Evolutionary Rates: Bayesian Methods are Superior
Itay Mayrose, Dan Graur, Tal Pupko |
| PSA_11 |
Gamma
Carbonic anhydrases in plants
Gustavo Parisi, Mariano Perales, María Silvina
Fornasari, Alejandro Colaneri, Nahuel Gonzalez-Schain, Diego Gomez, Axel
Brennicke, Alejandro Araya, Julian Echave, James Ferry, Eduardo Zabaleta
|
| PSA_12 |
IMGT
standardized criteria for statistical analysis of immunoglobulin V-REGION
amino acid properties
Christelle Pommié, Séverine Levadoux, Robert Sabatier,
Gérard Lefranc, Marie-Paule Lefranc |
| PSA_13 |
Genome
wide survey of drosophila G-protein-coupled receptors
Raghu Prasad Rao Metpally and R. Sowdhamini
|
| PSA_14 |
Noise
decomposition and search of the latent periodicity in protein active sites
Eugene Korotkov, Andrei A.Laskin, Nikolai A.Kudryashov
|
| PSA_15 |
Cryptically
Simple Proteins Sequences in Eukaryotic Proteomes
M.Mar Alba, Michelle Simon, John M. Hancock
|
| PSA_16 |
Sequence
based prediction of endoplasmic reticulum resident proteins
Michelle Scott, Michael Hallet and David Thomas |
| PSA_17 |
Discrimination
of the subcellular locations of the yeast proteins by their biological sequences
H. Richard, M.H. mucchielli, B. Prum, F. Kepes
|
| Transcripts
Detection, RNA et DNA Motifs and Structure (RDNA) |
| RDNA_1 |
Transcripts
under selection compose nearly half of the human genome
Marie Sémon, Laurent Duret |
| RDNA_2 |
Overlapping
antisense transcription in the human genome
Marie Fahey, Tom Moore, Des Higgins |
| RDNA_3 |
Searching
for ncRNAs in protist genomes.
Lesley J. Collins, Thomas J. Macke and David Penny.
|
| RDNA_4 |
Detection
of DNA encoding structural RNAs in genomes
Fabien Cornille, Christine Dufraigne, Alain Giron,
Bernard Fertil, Patrick Deschavanne |
| RDNA_5 |
Computational
Detection of MicroRNAs in Animal Genomes
Matthieu Legendre and Daniel Gautheret |
| RDNA_6 |
Relevance
of the secondary structure of messenger RNA: a statistical study
Fabrice Thalmann and Herve Isambert |
| RDNA_7 |
PatSearch:
a Program for the Detection of Patterns and Structural Motifs in Nucleotide
Sequences
Giorgio Grillo, Flavio Licciulli, Sabino Liuni,
Elisabetta Sbisà and Graziano Pesole |
| RDNA_8 |
P-DCFold:
an algorithm for RNA secondary structure prediction including all kinds
of pseudoknots
Fariza Tahi, Stéfan Engelen, Mireille Régnier
|
| RDNA_9 |
SCANNING
THE GENOME FOR TRIPLEX-FORMING SEQUENCES
J.Ramon Goñi, Xavier de la Cruz, Modesto Orozco
|
| RDNA_10 |
Topologically
Probing Molecular Reactions
Dorothy Buck |
| RDNA_11 |
Reparametrizing
loop entropy weights: effect on DNA melting
Ralf Blossey, Enrico Carlon |
| Regulatory
Motifs and Modules (RM)
|
| RM_1 |
The
Singal Search Analysis Server
Giovanna Ambrosini, Viviane Praz, Vidhya Jagannathan,
Philipp Bucher |
| RM_2 |
Prediction
of Transcription factors and DNA-binding sites
Shandar Ahmad, M. Michael Gromiha and Akinori Sarai
|
| RM_3 |
Transcriptional
regulation of Plasmodium falciparum genes
Charlotte Boschet, Sylvie Briquet, Catherine Vaquero
|
| RM_4 |
Computational
identification of transcription factor binding sites by functional analysis
of set of genes sharing overrepresented upstream motifs in yeast S.cerevisiae
D. Cora', P. Provero, M. Pellegrino, F. Di Cunto,
M. Caselle |
| RM_5 |
A
Fast Algorithm for Analysing Regulation Regions of Related Genes
Matthieu Defrance, Hélène Touzet, Stéphane Janot
|
| RM_6 |
HMM,
an efficient way to detect transcriptional promoters in bacterial genomes?
Sébastien Hergalant, Bertrand Aigle, Bernard Decaris,
Jean-François Mari, Pierre Leblond |
| RM_7 |
In Silico prediction of regulatory signals on plant promoter sequences
Magali Lescot, Mireille Régnier |
| RM_8 |
Genome-wide
identification of transcription factor
David Martin, Magali Lescot, Florence Maschat,
Nicolas Negre, Giacomo Cavalli, Denis Thieffry, Bernard Jacq |
| RM_9 |
In
silico identification and experimental validation of novel PmrAB targets
in Salmonella typhimurium by regulatory motif detection
Kathleen Marchal, Pieter Monsieurs, Karen Lemmens,
Nadja van Boxel, Sigrid de Keersmaecker, Gert Thijs, Jos Vanderleyden, Bart
De Moor |
| RM_10 |
Transcription
Factor Binding Site Detection by One-Dimensional Signal Analysis with Complex
Number Coding and Ambiguity Padding
Krzysztof M. Rajkowski |
| RM_11 |
Automatic
Procedures for Compilation of Promoter sequences and their Evaluation based
on Signal Content and Positional Distributions
Christoph D. Schmid, Viviane Praz, Mauro Delorenzi,
Rouaida Perier, Philipp Bucher |
| RM_12 |
Efficiently
Finding Regulatory Elements using Correlation with Gene Expression
Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara,
Masayuki Takeda, Satoru Miyano |
| RM_13 |
Associative
clustering to find dependencies between expression profiles and transcription
factor binding
Janne Nikkilä, Christophe Roos, Janne Sinkkonen,
Samuel Kaski |
| RM_14 |
Monocyte-Derived-Macrophage
Gene Expression During HIV-1 Infection
Christopher H. Woelk, Florence Ottones, Christy
D. Royer, Christine R. Plotkin, Steffney E. Rought, Jean Lozach, Roman Sasik,
and Jacques Corbeil. |
| RM_15 |
Phylogenetic
Footprinting of Co-expressed Genes by Tree-Gibbs Sampling
Stefan Van Yper, Olivier Thas, Jean-Pierre Ottoy
and Wim Van Criekinge |
| RM_16 |
Identification
of human transcription factors binding sites by comparative genomics.
Michele Caselle, Davide Cora', Carl Herrmann, Christoph
Dieterich, Ferdinando Di Cunto, Paolo Provero |
| RM_17 |
Surveys
of Phylogenetic Footprints in Large Gene Clusters
Claudia Fried, Sonja J. Prohaska, Christoph Flamm,
G¨nter P. Wagner, Peter F. Stadler |
| RM_18 |
Identification
of the PhoPQ-regulon by in silico motif detection
Pieter Monsieurs, Kathleen Marchal, Gert Thijs,
Sigrid De Keersmaecker, Jos Vanderleyden, Bart De Moor |
| RM_19 |
Identification
of Transcription Factor Binding Sites in Streptomyces coelicolor A3(2) by
Phylogenetic Comparison
Fabrice Touzain, Patricia Lavigne, Isabelle Debled-Rennesson,
Bertrand Aigle, Pierre Leblond and Gregory Kucherov |
| RM_20 |
Applicating
of the metropolis algorithm to reveal composite modules in promoters of
eucaryotic genes
Tatyana Konovalova, Evgeny Cheremushkin, Evgeny
Beschastnov, Alexander Kel |
| RM_21 |
Identification
of transcriptional modules in budding yeast
Thomas Manke, Ricardo Bringas, Martin Vingron
|
| RM_22 |
Constructing
a promoter model for antibacterial response of lung epithelial cells
Ekaterina Shelest, Alexander Kel, Edgar Wingender
|
| General
Sequence Analysis and Annotation (SQA) |
| SQA_1 |
Automatic
annotation tools
Coral del Val, Mechthild Falkenhahn, Karl-Heinz
Glatting, Agnes Hotz-Wagenblatt, Barbara Pardon, Sandor Suhai |
| SQA_2 |
Improving
the Automated Annotation Process on Protein Data from TrEMBL by Introducing
Exclusion Rules
Daniela Wieser, Ernst Kretschmann, Astrid Rakow,
Andre Hackmann, John O'Rourke, Rolf Apweiler |
| SQA_3 |
ContigBrowser:
a pipeline for Propionibacterium genome analysis
Daniel Jacob, Guillaume Meurice, Catherine Deborde,
Diliana Dimova |
| SQA_4 |
The
Genome Sequence of Bifidobacterium breve
S. Leahy, G.F. Fitzgerald, J.A. Moreno Munoz, D.
McAdam O'Connell, M. Claesson, D. Higgins, and D. van Sinderen |
| SQA_5 |
Gene
Classes in Bacterial Genomes
Stéphane CRUVEILLER, Stéphanie BOCS, Aurélie LAJUS,
Agnès ILTIS, Alain Viari, Claudine MEDIGUE |
| SQA_6 |
Identification
and characterization of GPCR Family C Odorant receptors in Zebrafish
Tyler Alioto, Percy Luu, John Ngai |
| SQA_7 |
In
silico charaterization of Na+/H+ antiporter gene family in rice (Oryza sativa)
and comparison with other cereals
Mouna Choura, Ahmed Rebai |
| SQA_8 |
Analysis
of the Del(13)Svea36H Region on Mouse Chromosome 13
J. Weekes , A. Mallon, L. Wilming, J. Ashurst,
P. Denny, J. Hancock, MRM. Botcherby, L. Mathews, S. Gregory, J. Rogers,
RD.Campbell and SDM. Brown |
| SQA_9 |
Non-random
distribution of Alu elements in genes of various functional categories:
insight from analysis of human chromosomes 21 and 22.
Deepak Grover, Partha P. Majumder, Chandrika B.
Rao, Samir K. Brahmachari, Mitali Mukerji |
| SQA_10 |
Tabu
search method for DNA sequencing by hybridization with isothermic libraries
Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak,
Wojciech T. Markiewicz, Aleksandra Swiercz |
| SQA_11 |
Positional
sequencing by hybridization with errors
Aurélia Rabia, Frédéric Guinand, Laurent Mouchard
|
| SQA_12 |
W-metric
for protein sequence comparison in SCOP database
Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S.
Almeida |
| SQA_13 |
Evaluation
of anchoring schemes for fast DNA sequence alignments
Stephane Guyetant, Dominique Lavenier |
| SQA_14 |
Methods
for automatic pairwise alignments of protein sequences from biased and non-biased
genomes: generalized model for substitution matrices and theoretical significance
of Z-value statistics
Olivier Bastien, Jean-Christophe Aude, Karine Métayer,
Sylvaine Roy, Jean-Jacques Codani, Eric Maréchal |
| SQA_15 |
Multiple
alignments of sequences and structures using T-Coffee
Orla J. O'Sullivan, Desmond G. Higgins and Cedric
Notredame |
| SQA_16 |
A
method for segmenting DNA
Gilles Didier, Ivan Laprevotte |
| SQA_17 |
How
Predictable Are Biological Sequences?
Izydor Apostol, Philippe Jacquet, Wojciech Szpankowski
|
| SQA_18 |
DNA
sequences share a common syntax
Sylvain Lespinats, Patrick Deschavanne, Alain Giron,
Bernard Fertil |
| SQA_19 |
Information
decomposition of symbolical sequences
Eugene Korotkov, Maria A.Korotkova, Nikolai A.
Kudryashov |
| SQA_20 |
Statistical
significance of the sequence repeats
Narjiss Touyar, Dominique Cellier, Sophie Schbath,
Hélène Dauchel |
| SQA_21 |
Computing
the Repetitions in a Weighted Sequence using Weighted Suffix Trees
Costas Iliopoulos, Christos Makris, Ioannis Panagis,
Katerina Perdikuri, Evangelos Theodoridis, Athanasios Tsakalidis
|
| SQA_22 |
The
suffix sequoia
Ela Hunt |
| SQA_23 |
Amino-acid
substitution matrices tuned for hemiascomycetous yeasts
Emmanuelle Beyne, Pascal Durrens, David Sherman
|
SQA_24
|
EvDTree
: structure-dependent substitution matrices based on decision tree classification
of 3D environments
Jean-Christophe Gelly, Jérôme Gracy, Laurent Chiche
|
|
|
You're
welcome to ECCB'2003, see you soon in Paris!
Catherine
Christophe |