CSTB team: Complex Systems and Translational Bioinformatics

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Team activities in 2022 | Previous years

Scientific highlights

01/07 : Participation of J.-S. Sereni in the PhD jury of Hoang La, LIRMM, Université de Montpellier
06/07 : Presentation at International Conference on Graph Theory: Spanning trees in regular graphs (J.-S. Sereni)

03/06 : Meeting with Google Cloud to present the OrthoInspector project, and use of IA for intégration of 3D structures in the analysis of genetic variants (Olivier Poch, Kirsley Chennen, Arnaud Kress, Julie Thompson)
10/06 : Participation of J.-S. Sereni in the PhD jury of Yitting Jiang, IRIF, Université de Paris
15/06 : Presentation at the doctoral school day of the UHA in Mulhouse : "Intelligence Artificielle : de la technique aux enjeux sociaux" (Anne Jeannin-Girardon)
16-17/06 : Kickoff meeting of the project Atelier de la Donnée, Unistra ADELE Helpdesk (J. Thompson)

17/05 : Seminar by Kirsley Chennen : Printemps de la donnée, les données dans la thèse, organisé par l'Université de Strasbourg et l'Université de Haute-Alsace
20/05 : Team seminar 'une éthique pour le 21è siècle', Pierre Collet

04-08/04 : Online colloque "Directed Minors & Digraphs Structure Theory", organised by J.-S. Sereni, R. Steiner & S. Wiederrecht in the context of the network « A Sparse (Graphs) Coalition
05/04 : Meeting with SDC team (N. Lachiche, G. Frey) : graph-based analysis of biological networks
20/04 : RMeeting Institut Francais de Bioinformatique, GT Bioinfo Santé (K. Chennen, J. Thompson)
22/04 : Poster presentations at Doctoral School days for Sciences de la Vie et de la Santé (C. Rutz, C. Meyer)
25/04 : First meeting of GT RDA (Research Data Alliance) Strasbourg (J. Thompson)
29/04 : First meeting of GT Données EST, RDG (Recherche Data Gouv) : 'Atelier de la donnée' projects (J. Thompson)

02/03 : Project RainRARE, transcriptomic data reception and analysis ((Wojciech Krezel, Kirsley Chennen)
14/03 : Participation of O. Lecompte in the HDR jury of Anaïs Bardet, Université de Strasbourg
16/03 : Meeting NMD (Non-Sens mediated mRNA decay) - Thérapies de Translecture (Olivier Poch, Kirsley Chennen, Nicolas Hass, Jean-Paul Renaud, Fabrice Lejeune)
23-24/03 : Kick-off meeting of ANR PRCI GEODE at LOEWE Centre for Translational Biodiversity Genomics (Francfort) (O. Lecompte, C Rutz, D Merlat)
23/03 : Participation of J. Thompson in the HDR jury of Pierre Poulain, Université de Paris Diderot
29/03 : I Invitation to CAGI6 meeting (Challenge Critical Assessment of Genome Interpretation VIth version) : results to be announced

18/02 : Work meetings with SDC, CSIP, FEMTO-ST, Mob-ion and AAQIUS in the context of project AI-ReFuel ANR 2022 (preparation of a detailed proposal for the transition to phase 2), Ali Ayadi project coordinator.
23/02 : Meeting with Laurence Choulier (faculté de pharmacie) to discuss potential co-supervision of thesis (Quentin Rott), Julie Thompson, Odile Lecompte
24/02 : Meeting with Prof. Bourcier and Emilia Koestel, Ophtalmologue, CHU de Strasbourg to discuss potential collaboration as a follow-up of project Myo-XIA, with Corentin Meyer, Julie Thompson, Olivier Poch, Pierre Collet

03-07/01 : Participation (online) of J.-S. Sereni at the colloque Graph Theory à Oberwolfach (Allemagne)
17/01 : Participation of O. Lecompte in the meeting organised by european consortium ERGA (European Reference Genome ATlas)
18-19/01 : Meeting Institut de Myologie Paris; Project: AI and multi-level knowledge base for the diagnosis of congenital myopathies (Corentin Meyer/Olivier Poch/Kirsley Chennen)
21/01 : Meeting with CInflows e-solutions for medical workflows, on the use of AI to determine the size of heart valves and on the anonymization of medical files
24/01 : Meeting with Urania Therapeutics, on the creation of a knowledge base dedicated to therapies for genetic diseases with false-sense technology of 'Read-Through' molecules within ribosomes (Olivier Poch/Kirsley Chennen/Nicolas Haas)

Visitors

18-19/08 : Visit of Mikhail Isaev (School of Mathematics, Monash University)
18/08 : Presentation by M. Isaev at the séminaire de calcul stochastique (IRMA) : The expected number of spanning trees in random graphs with given degrees.

18-22/07 : Visit of Ugo Giocanti (G-SCOP, Université Grenoble Alpes)

25-29/04 : Visit of Z. Dvořák & B. Moore (Université Charles de Prague, République tchèque)

07-11/02 : Visit of J. Volec (Czech Technical University, République tchèque).
10/02 : Presentation by J. Volec at the séminaire de calcul stochastique (IRMA) : Graph limits, common graphs and Sidorenko's conjecture.

Doctoral students

13/06 : Presentation for the PhD monitoring committee by Hiba Khodji, co-supervised by Pierre Collet / Anne Jeannin and Julie Thompson
15/06 : Presentation for the PhD monitoring committee by Christelle Rutz, supervised by Odile Lecompte
20/06 : Presentation for the PhD monitoring committee by Alix Simon, co-supervised by Jocelyn Laporte (IGBMC) and Julie Thompson

24/05 : PhD defense of Anna Leonteva 'Evolutionary and Quantum-inspired Algorithms for the Optimization of Magnetic Cooling Systems', co-supervised by Pierre Collet, Pierre Parrend and Anne Jeannin
30/05 : Presentation for the PhD monitoring committee by Corention Meyer, co-supervised by Olivier Poch and Pierre Collet

01/03 : Start of PhD of Lena Bonassin - supervisor: O. Lecompte, co-supervisor: K. Theissinger (Francfort)
01/03 : Start of PhD of Ljudevit Luka Boštjančić - supervisor: K. Theissinger (Francfort), co-supervisor: O. Lecompte

11/01 : Start of PhD by Julien Michel on the project Damiage, supervised by Pierre Parrend (programme RAPID, led by EPITA)
25/01 : Work session 'Anomaly detection in networks' with PhD and post-doc students of 'Réseau' team (Cristel Pelsser) and CSTB (Pierre Parrend)

Internships

01/06 : Début du stage volontaire L2 de Inès Wurch (Science de la vie, biologie moléculaire) encadrée par Julie Thompson, Nicolas Scalzitti et Corentin Meyer
01/06 : Début du stage volontaire L2 de Jérémie Carabin (Science de la vie, biologie moléculaire) encadré par Julie Thompson, Olivier Poch
06/06 : Début du stage de Pierre Michel, M1 SdV, Biologie structurale intégrative et bio-informatique, Université de Strasbourg encadré par Julie Thompson, Kirsley Chennen, Nicolas Scalzitti

01/04 : End of Freezer project, with EPITA students (reaction tool in case of computer attack, which allows to prevent the connection of new users, the opening of new network accesses), supervised by Pierre Parrend

01/03 : Start of M2 internship by Henri Joel Azemena (Université de Lorraine) supervised by Ali Ayadi

28/02 : Start of M1 internship by Tuba Uslu (Master Biologie Structurale Intégrative et Bionformatique) supervised by Julie Thompson
28/02 : Start of internship by Souliman El Moussaoui (ECAM formation Data Science) supervised by Julie Thompson, Kirlsey Chennen, Nicolas Scalzitti, collaboration Jean Muller, Laboratoire de diagnostic génétique, CHU de Strasbourg
28/02 : Start of M1 internship by Timothé Benoît (Master Biologie Structurale Intégrative et Bionformatique) supervised by Claudine Mayer
28/02 : Start of M1 internship by Anthony Seyller (Master Biologie Structurale Intégrative et Bionformatique) supervised by Claudine Mayer and Kirsley Chennen
28/02 : Start of M2 internship by Khayala Gaybaliyeva, M2 Sciences de Données et Intelligence Artificielle, Université Franco-Azerbaidjanaise, supervised by Nathalie Al Makdessi
28/02 : Start of M2 internship by Mahir Israyilov, M2 Sciences de Données et Intelligence Artificielle, Université Franco-Azerbaidjanaise, supervised by Ali Ayadi, Anne Jeannin-Girardon and Pierre Collet

03/01 : Start of M2 internship by Dorine Merlat (Master Biologie Structurale Intégrative et Bionformatique) supervised by O. Lecompte
03/01 : Start of M2 internship by Nicolas Haas (Master Biologie Structurale Intégrative et Bionformatique) supervised by O. Poch and K. Chennen
03/01 : Start of M2 internship by Arthur Vogt (Master Biologie Structurale Intégrative et Bionformatique) supervised by C. Mayer


Administrative activities

23/06 : Meeting to discuss the evolution of the Schéma Directeur du Numérique (J. Thompson)
24/06 : Steering committee, Science Ouverte de l'Unistra (J. Thompson)

23/05 : Preparatory meeting for UnivOAK 2 (Julie Thompson)

05/04 : Meeting of steering committee Mentorat en Alsace - Université de Strasbourg and Université de Haute Alsace (O. Lecompte)
08/04 : Meeting of steering committee Open Science Unistra (J. Thompson)
28/04 : Meeting with Société Urania Therapeutics-CSTB in the context of application for PhD funding CIFRE : "Development of an artificial intelligence algorithm dedicated to trans-reading therapies: Application to rare genetic diseases" (25/04/2022) (N. Haas, K. Chennen, O. Poch)

09/03 : Meeting with Urania Therapeutics to discuss the scope of a PhD funding CIFRE (Olivier Poch, Kirsley Chennen, Nicolas Hass, Jean-Paul Renaud)
14/03 : Meeting to discuss participation of CSTB in the UE Master Omiques, Bioinbfo, données de santé (Olivier Poch, Kirsley Chennen, Agnes Bloch-Zupan)
24/03 : Submission of project ANR Correau on the cybersecurity of water networks (Pierre Parrend)
28/03 : Meeting with Google Cloud to discuss a possible collaboration on the OrthoInspector project, and use of IA for integration of 3D structure data in the analysis of genetic variants (Olivier Poch, Kirsley Chennen, Arnaud Kress, Julie Thompson, Pierre Collet)
31/03 : Meeting with Professor Seiamak BAHRAM, PUPH Immunologie biologique, and Vincent Noblet, to discuss a possible collaboration on a project in AI analysis of multi-omics data (Julie Thompson, Olivier Poch, Pierre Collet).

02-03/02 : Organisation of meetings Coalition Café (en ligne) by S. Cambie, R. J. Kang, J.-S. Sereni & Y. Yuditski
04/02 : End of project MedCTF - medical data management application for cybersecurity challenge, internship of Tayyip Gedik (supervised by Pierre Parrend)
09/02 : Submission of a response to Appel à manifestation d’intérêt - Chaire de professeur junior "GROOT: atlas of Gene RepertOire evOluTion", Odile Lecompte
16/02 : Submission of a pre-proposal "RAinMARK : New tools and predictive markers for better patient care and treatment solutions in MCOPS12" to AP European Joint Programme Rare Diseases, in collaboration with Wojciech KREZEL, IGBMC
16/02 : Submission of a pre-proposal "Development of new analytic tools and pathways to accelerate diagnosis and facilitate diagnostic monitoring of rare diseases" to AP European Joint Programme Rare Diseases, in collaboration with Amélie Piton, IGBMC.
21/02 : Meeting to prepare project Correau, ANR phase 2 (INRAE, Eurométropole, CNAM, ICube)
25/02 : Acceptation of project RARETIA ANR-20-MRB-00XX-03 (ANR/Investissements d'Avenir: Accelerating Research and Innovation on Rare Diseases through Databases)

11/01 : Annual meeting of French Bioinformatics Institute, to discuss roadmap for 2022-2027
20/01 : Meeting to prepare project for European Joint Programme RARE DISEASES (Olivier Poch/Kirsley Chennen)
31/01 : Meeting to prepare project RDG AMI Atelier de la donnée (Julie Thompson)

Miscellaneous

17/05 : Installation of our servers in the DataCenter


Team life

Team meetings

(*) Every Tuesday 13h30 to 15h30
1st Tuesday of the month : Reports of members A-G
2nd Tuesday of the month : Reports of members H-N
3rd Tuesday of the month : Reports of members O-Z
4th Tuesday of the month : Meeting for permanent members

Last Thusrday of the month at 14h00 : Presentations of trainees/students followed by questions (2 to 3 presentations of 12 min for trainees and 1st and 2nd year PhD students, 20 min for 3rd year PhD students).

25/04 : (*) Session "Jeun's" Presentations by Quentin Christoffel, Nicolas Haas and Arthur Vogt
06/04 : (*) Session "Jeun's" Presentations by Dorine Merlat, Tuba Uslu, Thimothé Benoit and Antony Seyller
27/01 : (*) Session "Jeun's" Presentations by Lalla Aicha Koné and Yohan Solon