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Bioinformatics (BioInfo)

Group Members
  Group leader
    DENISE Alain

    AMAR Patrick
    DENISE Alain
    FROIDEVAUX Christine
    JAY Flora
    PIERROT Adeline
    POUYET Fanny

  Non-permanent research staff
    MAHOUT Maxime
    PETIT Ferdinand
    SUN Qibo

Research activities
  System Biology
  Structural biology

Software & patents
  GenRGenS: Generation of Random Genomic Sequences and Structures
  VARNA: Visualisation Applet for RNA
  HSIM: Hyperstructure Simulator
  BioGuide: Guiding scientists through biological sources
  GenoQuery: Querying genomic data warehouse
  NestedAlign: Pairwise RNA secondary structure comparison
  Rna3Dmotif: Software for extracting RNA tertiary motifs
  GeneValorization: Gene List significance at-a-glance
  Cartaj: Classification Of RNA threeway Junctions
  SPFlow: Rewriting a non SP workflow into an SP workflow while preserving provenance
  Pint: Static analyzer for dynamics of Automata Networks
  ConQuR-Bio: ConQuR-Bio
  Causalex: Causality Graph Explorer
  LiCoRNA: aLignment of Complex RNAs
  GARN: Game Algorithms for RNa 3D sampling
  CaRNAval: Database of RNA Recurrent Interaction Networks
  Silicell Maker: Silicell Maker: computer aided synthetic bionetwork design system
  Orphea: Pseudo-knot RNA sequence finder
  DNADNA: Deep Neural Architectures for DNA

  Swiss Institute of Bioinformatics (Geneva)

Recent Ph.D. dissertations & faculty habilitations
  Passage à l'échelle, propriétés et qualité des algorithmes de classements consensuels pour les données biologiques massives
  Analyse des voies métabolique au cours du cycle cellulaire : application au métabolisme du cancer
  Metabolic pathway analysis : from constraint-based modelling to dynamical analysis

Datamining in Epi- and Phylogenetics
Thomas Haschka
15 March 2022 11h00

Répétition soutenance de thèse - Reconstructing our past: deep learning for population genetics
Théophile Sanchez
10 March 2022 14h00

Pierre Andrieu - Agrégation de classements pour les données biologiques : évaluer la qualité des classements consensuels obtenus.

21 October 2021 00h00

Demographic reconstruction from paleogenomes of the origins of Western first farmers
Nina Marchi
25 February 2021 14h00

A Graph-based Similarity Approach to Classify Recurrent Complex Motifs from their Context in RNA Structures
Coline Gianfrotta
18 February 2021 14h00

"Answer Set Programming for computing constraints-based elementary flux modes: application to Escherichia coli core metabolism"
Maxime Mahout
4 February 2021 14h00

"Pandæsim: An Epidemic Spreading Stochastic Simulator"
Patrick Amar
14 January 2021 14h00

Ancient genomic analysis of Neolithization in the Aegean
Dilek Koptekin
19 October 2020 00h00

Disentangling the role of selection on the evolution of genomes.
Fanny Pouyet
2 October 2020 17h30

Langage d'icônes et visualisation d'ensembles : méthodes et applications biomédicales
Jean-Baptiste Lamy
14 November 2019 14h30

Algorithms for Cell Reprogramming Strategies in Boolean Networks
Hugues Mandon
7 November 2019 00h00

Langage d'icônes et visualisation d'ensembles : méthodes et applications biomédicales
Jean-Baptiste Lamy
24 October 2019 14h30

Conservation of structural long-range modules in RNAs
Vladimir Reinharz
17 October 2019 14h30

New models to disentangle patterns of adaptation in complex population histories
Fernando Racimo
3 October 2019 14h30

Predicting the structure of RNA-binding protein recognition elements
François Major
23 May 2019 00h00

Asymptotic behaviour of the 3-state cyclic cellular automaton
Benjamin Hellouin de Menibus
11 April 2019 13h30

Deep learning for phenotype prediction based on gene expression data
Blaize Hanczar
28 March 2019 14h30

Deep learning for phenotype prediction based on gene expression data
Blaize Hanczar
28 March 2019 14h30

Non-redundant sampling in RNA Bioinformatics
Juraj Michalik
21 March 2019 14h30

Non-redundant sampling in RNA Bioinformatics
Juraj Michalik
21 March 2019 14h30

Programmation mathématique multi-objectif pour la prédiction de structures secondaires d'ARN et de complexes d'ARN
Audrey Legendre
13 December 2018 14h30

Scalable and exhaustive screening of metabolic functions in microbiotas.
Clémence Frioux
28 November 2018 11h00

Studying the three-dimensional structure of DNA from Hi-C data
Nelle Varoquaux
22 November 2018 15h00

On the Median and Small Parsimony problems in some genome rearrangement models.
Cédric Chauve
22 November 2018 14h00

Integrating Phosphoproteomic Time Series Data into Prior Knowledge Networks to build Cell Line Specific Boolean Networks
Misbah Razzaq
8 November 2018 14h30

Deep learning in evolutionary genomics: are we there (yet)?
Matteo Fumagalli
29 October 2018 11h00

Techniques de réduction d’espace pour le problème de la médiane de permutations
Sylvie Hamel
18 October 2018 14h30

Identification des motifs de voisinage conservés
Alexandra Zaharia
20 September 2018 14h30

Réduction de dimension pour la paléogénomique
Séverine Liegeois
29 August 2018 14h30

Qualité des données médicales. Données observationnelles et dirty data
Bastien Rance
3 May 2018 14h30

Approximate Bayesian Computation and Random Forests to investigate population genetics and population linguistics
Valentin Thouzeau
29 March 2018 14h30

Finite state machine computation with bio-inspired neural networks
Jérémie Cabessa
8 March 2018 14h30

Variational Bayesian Compressed Sensing
Bradley Worley
22 February 2018 14h30

Linear-Time Tree Containment in Phylogenetic Networks
Mathias Weller
11 February 2018 14h30

How mathematics can help us elucidate lipid metabolismbl
Stefan Schuster
7 December 2017 14h30

SBGNlog: a logical framework based on SBGN to reason on molecular networks
Adrien Rougny
30 November 2017 14h30

Parsimony meets our understanding of recent human evolution: from phylogenetic trees to admixture galore
Luca Pagani
23 November 2017 14h30

Perfect sampling of closed queueing networks and random generation of combinatorial objects
Christelle Rovetta
9 November 2017 14h30

RNALands: Understanding Cellular Mechanisms through Simulation of RNA Folding Kinetics"
Andrea Tanzer
26 October 2017 14h30

Evolutionary genomics of integrons and conjugative elements
Jean Cury
19 October 2017 00h00

Finding the rank median of three genomes
Leonid Chindelevitch
29 September 2017 14h30

Modélisation énergétique qualitative de l'organisme humain assimilé à un système dynamique
Marc Irigoin-Guichandut
21 September 2017 14h30

Know Thy Ancestors to Know Thyself: Improving Our Understanding of the Human Genome Using Computational Paleogenomics
Mathieu Blanchette
9 June 2017 16h00

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction
Martin Weigt
18 May 2017 16h00

Bioinformatics and experimental exploration of the infection process of Candida glabrata
Fabrice Jossinet
27 April 2017 14h30

Over a decade applying robotics-inspired algorithms to the study of biomolecules
Juan Cortes
20 April 2017 14h30

Data analyses in functional genomics: two different stories based on deep sequencing technologies in micro-organisms
Gaelle Lelandais
23 March 2017 14h30

Causal Network Inference for Biology Workshop - Amphi Dig. Shannon
H. Isambert, O Goudet, L. Paulevé
27 February 2017 09h45

Comprehensive and Formal Modelling Platform for Biological Processes
David Safranek
2 February 2017 14h30

Protein coevolution and the viral world
Alessandra Carbone
26 January 2017 14h30

Finding a gene tree in a phylogenetic network
Philippe Gambette
19 January 2017 16h00

Inférence de réseaux à partir de données RNA-seq
Mélina Gallopin
15 December 2016 14h30

Dynamic metabolic model of yeast for lipid production
Jorgelindo da Veiga Moreira
17 November 2016 14h30

Streaming k-mismatch and applications
6 October 2016 14h30

Assessing the robustness of predictions algorithms for ancestral adjacencies
Yann Ponty
11 February 2016 14h30

Counting, generating and sampling tree alignments
Julien Courtiel
14 January 2016 11h00

Biological Network inference by quantitative and nonparametric modeling
Florence d’Alché-Buc
19 November 2015 00h00

Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Nicolas Le Novère
28 October 2015 00h00

Formal Modeling, Data Integration and Quantitative Verification of large-scale cell-based models.
Louis Fippo Fitime
8 October 2015 00h00

Navigating in a Sea of Repeats in RNA-seq Without Drowning
Blerina Sinaimeri
23 April 2015 14h30

Derivation of dynamical qualitative models from biochemical networks
Wassim Abou-Jaoudé
9 April 2015 14h30

Handling large logical models: the role of model reduction
Aurélien Naldi
19 March 2015 14h30

Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information
Anne Lopes
12 March 2015 14h30

Programmer et compiler les fonctions de biologie de synthèse
Franck Deleplace
12 February 2015 14h30

Metabolic graph for the research of conserved pathways of chemical transformations
Maria Sorokina
18 December 2014 14h30

From a biological question to a mathematical model: an example of patterns of genetic alterations in bladder tumorigenesis
Laurence Calzone
4 December 2014 14h30

Logical modelling of cell fate decisions
Denis Thieffry
20 November 2014 14h00

Multiple network alignment via data fusion
Noël Malod-Dognin
13 November 2014 15h00

Stringology, Data Compression and Biology
Jan Holub
25 September 2014 14h00

La coopération symbiotique métabolique des cellules au sein des cancers
Philippe Icard
26 June 2014 14h00

Minimal conditions for proto-cell stationary growth
Erwan Bigan
19 June 2014 14h00

Modéliser et intégrer des informations hétérogènes sur la réponse d un système biologique
Anne Siegel
12 June 2014 14h00

Combining machine learning approaches for functional annotation and classification of remote homologous proteins, and for the analysis of microarray data
Juliana Bernardes
17 April 2014 14h00

Apport de la modélisation pour le traitement du cancer métastatique, résultats cliniques
Laurent Schwartz
10 April 2014 14h00

Constraint-based analysis of metabolic networks
Alexander Bockmayr
6 March 2014 14h00

Mathematical modeling of miRNA-mediated mechanisms of translation regulation
Andrei Zinovyev
5 December 2013 14h30

Recent and future work on discrete reaction networks, RNA dynamics, spatial simulation, and qualitative networks
Loïc Paulevé
3 October 2013 14h00

Translating the SBGN-AF language into logic to analyze signalling networks
Adrien Rougny
26 September 2013 15h00

Ranking biological data: Designing and combining ranking algorithms
Bryan Brancotte
20 June 2013 14h00

SV-Bay algorithm
Daria Iakovishina
13 June 2013 14h00

Scientific workflows: Applications and optimization
Ulf Leser
4 April 2013 14h30

From protein structure prediction to non-coding RNA identification
Van Du TRAN Thong
28 March 2013 14h30

Inférence de réseaux biologiques par noyaux à valeur opérateur
Florence d'Alché-Buc
14 March 2013 14h00

Modèle multi-échelle et multi-physique pour la simulation et la modélisation moléculaire interactive.
Nicolas Ferey
21 February 2013 14h00

Application of Expressive Statistical Model Checking to the analysis of biological stochastic models
P. Ballarini
14 February 2013 14h30

Gene Family Assignment-Free Comparative Genomics
Annelyse Thévenin
29 November 2012 14h30

RNA folding with pseudoknots: Intractable, honestly?
Yann Ponty
25 October 2012 14h00

Modeling RNA by hierarchical natural moves
Adelene Sim
18 October 2012 15h00

Protein-protein interactions: co-evolution, prediction and design
Jessica Andreani-Feuillet
18 October 2012 14h00

Adjustable Chain Trees for Proteins
Rasmus Fonseca
20 September 2012 14h00

Integrating chemical footprinting data into RNA secondary structure prediction
Peter Clote
14 June 2012 14h30

Ensemble Predictions of beta-sheet Protein Structures
Jérôme Waldispuhl
24 May 2012 14h00

Enjoy Dynamic Programming in Bellman's GAP
Robert Giegerich
16 May 2012 14h00

Sequence-based identification of RNA 3D structural modules
José Cruz Almeida
10 May 2012 14h30

Protein folding, unfolding, and ligand docking by computer simulations
29 March 2012 14h00

Characterizing the Morphology of Protein Binding Patches
Noël Malod-Dognin
8 March 2012 14h30

Predicting copy number changes and structural variants in cancer genomes using next-generation sequencing data
Valentina Boeva
2 February 2012 14h30

From sequence to structure: Detecting RNA structural modules on sequences
José Almeida Cruz
12 January 2012 14h30

Computational Structural Biology: Its Birth and Future
Michael Levitt
28 November 2011 14h30

Graphite-MicroMégas, a tool for DNA modeling
Samuel Hornus
10 November 2011 14h30

Prédire des noeuds dans les ARN avec des hypergraphes...
Yann Ponty
15 September 2011 14h00

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure
Yann Ponty
13 July 2011 14h00

Recent results on RNAomics
Peter Clote
13 July 2011 11h00

Systematic analysis of large-scale networks Investigating biological functions to link genotype and phenotype
Magali Michaut
7 July 2011 14h00

UniProtKB and the processes of protein biocuration.
Lionel Breuza
16 June 2011 14h00

Génomique comparée et Fouille de données enzymatiques.
Olivier Lespinet
9 June 2011 14h00

Study of positions of genes to better understand driver mutations
Annelyse Thévenin
26 May 2011 14h00

The microRNA Mastermind for Cancer
Stefan Vagner
31 March 2011 14h00

TBA (Sujet: Data mining and computational Biology)
Tu Bao Ho
28 March 2011 11h00

Discovering Patterns of Data Anomalies: A New Perspective for Quantitative Data Cleaning
Laure Berti-Equille
24 March 2011 14h00

Determinants of protein affinity and promiscuity for in-silico engineering of biological circuits and devices
Pablo Carbonell
17 March 2011 14h00

MicroScope: a platform for microbial genome annotation and comparative genomics
Claudine Médigue
3 March 2011 14h00

The complete genome of Propionibacterium freudenreichii CIRM 1, a hardy actinobacterium with food and probiotic applications
Hélène Falentin
10 February 2011 14h00

Consensus and Energy-based Structure Prediction of Transmembrane Beta-Barrel Proteins
Saad Sheikh
27 January 2011 13h30

Optimisation of stochastic processes as an extension of stochastic verification.
Sylvain Pradalier
2 December 2010 14h00

Colloquium LIX
Colloquium LIX
8 November 2010 09h00

Investigating conformational changes of biological macromolecules using multi-resolution Markov State Models
Xuhui Huang
7 October 2010 15h00

Sur la médiane de m permutations
Sylvie Hamel
30 September 2010 14h00

Modeling macromolecular structure and dynamics with RNABuilder
Samuel Flores
6 September 2010 14h00

Towards Reproducible Science with Scientific Workflows and Provenance
Bertram Ludäscher
26 July 2010 10h00

Peter Clote
1 July 2010 14h00

Scalable Inference and Matching of Object Annotations
Ambuj Singh
10 June 2010 14h00

Knowledge Management in Bioinformatics @ Humboldt
Ulf Leser
27 May 2010 14h00

The Discretizable Molecular Distance Geometry Problem
Antonio Mucherino
29 April 2010 15h30

Eléments transposables et Bioinformatique
Sébastien Tempel
29 April 2010 14h00

BioPsi: a formal description of biological processes based on elementary bricks of actions
Sabine Pérès
22 April 2010 14h00

Prédiction de nouveaux microARN dans les génomes
Anthony Mathelier
1 April 2010 14h00

Transcriptome of the Human Polymerase III.
Galina Boldina
11 March 2010 14h00

Thermodynamics of RNA structures by Wang-Landau sampling
Feng LOU
11 February 2010 14h00

Evolution des récepteurs couplés aux protéines G de classe A
Marie Chabbert
28 January 2010 14h00

Prédiction à gros-grain de la structure tridimensionnelle de l'ARN
Alexis Lamiable
21 January 2010 15h00

Apprentissage d'automates pour la modélisation de familles de protéines
Francois Coste
14 January 2010 14h00

New concepts and approaches in RNA Structural Bioinformatics
N. Leontis
8 December 2009 14h00

Caractérisation de sites de recodage par une approche de génomique comparative
Thomas Moncion
26 November 2009 14h00

Structural classification of alpha-helical membrane proteins
Sindy Neuman
19 November 2009 14h00

Aspects algorithmiques des réarrangements génomiques : duplications et ordres partiels.
Annelyse Thévenin
3 November 2009 10h30

Modélisation 3D d'interactions entre protéines et ARN structuré ou non structuré: méthodes et applications
Fabrice Leclerc
29 October 2009 14h00

Profil transcriptionel de l'hétérochromatine : impact des éléments transposables
Matthias Zytnicki
24 September 2009 14h00

Geometry for the structural modelling of biomolecules: the protein, complex and RNA structure examples
Julie Bernauer
10 September 2009 14h00

Sampling of RNA Secondary Structure to Predict the Density of States
Feng LOU
3 July 2009 14h00

Comparaison de génomes partiellement ordonné
Annelyse Thévenin
2 July 2009 14h00

An adaptive combination of matchers: application to the mapping of biological ontologies for genome annotation
Bastien Rance
25 June 2009 15h30

Enumération de structures d'ARN avec pseudo-noeuds
Cédric Saule
25 June 2009 14h00

Comparaison de voies métaboliques entre espèces : similarité sémantique des annotations GO associées
Olivier Dameron
16 April 2009 14h00

Métagénomique des microorganismes non cultivés du plancton océanique profond
Puri Lopez
10 April 2009 10h00

Two case studies: Prediction and Classification of biological molecular structures
Guillaume Santini
9 April 2009 15h30

Méthodes formelles et modélisation
Fabien Tarissan
9 April 2009 14h00

Une nouvelle approche du Docking protéine-protéine
Thomas Bourquard
27 March 2009 14h00

Robustesse environnementale des réseaux de régulation : théorie et application.
Sylvain Séné
20 March 2009 14h00

Le projet BRASERO
Alain Denise
13 March 2009 14h30

Classification de structures ARN avec pseudonoeuds
Cédric Saule
5 February 2009 14h00

Application des banques de données de familles de gènes à l'étude des transferts horizontaux chez les procaryotes
Guy Perrière
8 December 2008 14h45

Intégration, Interrogation et Analyse de données de génomique comparative
Frédéric Lemoine
4 December 2008 14h00

PlasmoDraft: prédictions d'annotations fonctionnelles des gènes de Plasmodium falciparum à partir de données post-génomiques
Laurent Bréhélin
27 November 2008 14h30

Phylo-MCOA : Visualiser la concordance entre arbres de gènes en phylogénomique.
Damien de Vienne
20 November 2008 14h00

Identification des gènes du groupe d'orthologie le plus conservé au sein de la famille des gènes WOX de plantes : un exemple où l'analyse de séquences guide la paillasse
Claire Toffano-Nioche
13 November 2008 14h00

Recherche de patterns fermés fréquents dans des DAGs : application à la découverte de réseaux d'interactions gènes.
Alexandre Termier
5 June 2008 14h00

Algorithms for exploring the mutation landscape of RNA molecules
Jérôme Waldispuhl
29 May 2008 14h00

Réduction de dimension et classification de données issues de puces à ADN.
3 April 2008 14h00

Algorithmique pour la comparaison de structures biologiques arborescentes
Aïda Ouangraoua
27 March 2008 14h00

A method for automated discovering of RNA tertiary motifs
Mahassine Djeloul
20 March 2008 14h00

Analyse et optimisation des techniques d'échantillonage statistique pour la structure d'ARN
Yann Ponty
19 March 2008 14h00

Queries on Biological Graphs
Ulf Leser
15 February 2008 14h00

Résultats majeurs
A new dichotomic algorithm for the uniform random generation of words in regular languages
16 August 2012
Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Theoretical Computer Science (2012), DOI 10.1016/j.tcs.2012.07.025

A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency
25 March 2008
By Patrick Amar et Al. BMC Systems Biology 2008, 2:27

Automated motif extraction and classification in RNA tertiary structures
29 November 2008
Mahassine Djelloul and Alain Denise. RNA December 2008 14:2489-2497.

Automated prediction of three-way junction topological families in RNA secondary structures
11 February 2012
Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, Éric Westhof. Computational Biology and Chemistry 37 (2012) 1–5

Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm
1 June 2010
Claire Herrbach, Alain Denise and Serge Dulucq. Theoretical Computer Science 411 (2010) 2423-2432.

Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis
9 February 2016
D. Ellison, A. Mugler, M.D. Brennan, S.H. Lee, R.J. Huebner, E.R. Shamir, L.A. Woo, J. Kim, P. Amar, I. Nemenman, A.J. Ewald and A. Levchenko

Chromosome Replication in Escherichia coli: Life on the Scales. Vic NORRIS and Patrick AMAR
29 October 2012
Life 2012, 2(4), 286-312; doi:10.3390/life2040286

Computer‐aided biochemical programming of synthetic microreactors as diagnostic devices
27 April 2018
Alexis Courbet, Patrick Amar, Francois Fages, Eric Renard, Franck Molina Mol Syst Biol. (2018) 14: e7845 DOI 10.15252/msb.20177845

Computing with Synthetic Protocells
13 May 2015
Alexis Courbet, Franck Molina and Patrick Amar

Coverage-biased random explo-ration of large models and application to testing
27 March 2011
A. Denise, M.-C. Gaudel, S.-D. Gouraud, R. Lassaigne, J. Oudinet S. Peyronnet, STTT: Int. Jal on SOFTWARE TOOLS FOR TECHNOLOGY TRANSFER, DOI: 10.1007/s10009-011-0190-1

GenoQuery: a new querying module for functional annotation in a genomic warehouse
1 July 2008

Novel insights regarding the sigmoidal pattern of resistance to neomycin conferred by the aphII gene in Streptomyces lividans.
2 May 2013
Nicolas Seghezzi, Marie-Joelle Virolle and Patrick Amar

Sensor potency of the moonlighting enzyme-decorated cytoskeleton: the cytoskeleton as a metabolic sensor
26 February 2013
Vic Norris, Patrick Amar, Guillaume Legent, Camille Ripoll, Michel Thellier and Judit Ovádi

The Average Complexity of Tree Alignment
28 January 2008
We have proved that the average complexity of the pairwise ordered tree alignment algorithm of Jiang, Wang and Zhang is in O(nm), where n and m stand for the sizes of the two trees, respectively.

The Mimic Chain Reaction. V. Norris, A. Thierry, P. Amar, B. Holland, F. Molina
5 December 2012
J Mol Microbiol Biotechnol 2012;22:335-343 (doi: 10.1159/000345328)

Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots
7 August 2012
Philippe Rinaudo, Yann Ponty, Dominique Barth, and Alain Denise. WABI 2012.

Uniform trace sampling in very large models
6 November 2007
A new algorithm makes it possible to draw traces uniformly at random in very large models of concurrent systems.

VARNA software distinguished
15 July 2011
VARNA distinguished in the 2010 CNRS scientific report.

Software & patents