CSTB team: Complex Systems and Translational Bioinformatics

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'''Team activities in 2023''' | ''[[Activites archives|Previous years]]''
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'''Team activities in 2024''' | ''[[Activites archives|Previous years]]''
  
 
= Scientific highlights =
 
= Scientific highlights =
 +
== March ==
  
== May ==
+
25/03: Article "Meyer et al. IMPatienT: an Integrated web application to digitize, process and explore Multimodal PATIENt daTa" accepted for publication in Journal of Neuromuscular Diseases.</br>
11/05 : Discrete mathematics seminaire : Spanning trees in regular graphs, KIT - Karlsruher Institut für Technologie, J.-S. Sereni.
+
21/03: Seminars by PhD students concerning the topic 'détection pour la cybersécurité' with Sherbrooke University (follow up of their visit in February)</br>
12/05 : Publication of a document for the general public : 'Enseignement supérieur et désinformation: quel bilan dans les écoles d’ingénieur ?', in 'Lutte contre les manipulations de l’information: Regards croisés de spécialistes et d’acteurs du domaine' White paper from the Pôle d’Excellence Cyber, contribution from P. Parrend. <br>
+
21/03: Presentations accepted in RESSI (Rendez-Vous de la Recherche et de l'Enseignement de la Sécurité des Systèmes d'Information; mai) for PhD students of Pierre Parrend: Julien Michel, Majed Jaber, Côme Frappé-Vialatoux</br>
 
+
11/03: The project for a Junior Professor Chair 'Atlas comparatif des répertoires de gènes et relations génotype-phénotype' led by Odile Lecompte is accepted. </br>
== April ==
 
6/04 : Article accepted in Frontiers in Bioinformatics : Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events, A. Kress et al. 2023<br />
 
15/4 : Start of PhD thesis by Côme Frappé-Vialatoux, ANR project Correau (detection of attacks on water networks)<br />
 
19/04 : Invited talk by P. Parrend : Trusted Graph for explainable detection of cyberattacks, au Cyber CNI Lecture Series (TALK.cybercni.fr) which aims to raise awareness of cybersecurity issues among all audiences and to enable a permanent dialogue between industry and academic experts and the general public.<br />
 
26/04 : "Best Paper Award" at the conference Complex Computational Ecosystems 2023, Baku : "Metrics for Evaluating Interface Explainability Models for Cyberattack Detection in IoT Data”, Amani Abou Rida <br />
 
<br />
 
 
 
== March ==
 
6/03 : Submission of a co-supervised thesis between Laurence Choulier (Laboratoire de Bioimagerie et Pathologies, UMR7021) and Odile Lecompte<br />
 
6/03 : Submission of a co-supervised thesis betweene Jean Louis Mandel (IGBMC) and Julie Thompson<br />
 
13/03 : Presentation at the first working group meeting "Aspects Computationnels de l'Éthique" (GDR RADIA) at LIP6, Paris : "Éléments d'épistémologie et d'éthique des systèmes d’apprentissage automatique", Anne Jeannin-Girardon<br />
 
14/03 : Submission of a project SMART4CBT (Sciences sociales, Microenvironnement & analyses multiomiques dans la résistance au RadioThérapie dans les tumeurs cérébrales de l'enfant) pour la création d'un Centre de Recherche Intégrée Nord-Est en Oncopédiatrie (National AAP INCA), Olivier Poch<br />
 
15/03 : Meeting with members of SATT CONECTUS concerning valorisation of tools developed by CSTB and BiGEst-ICube, Olivier Poch, Arnaud Kress/Luc Mouliner<br />
 
26/03 : Submission of the plan for the new Bioinformatics and Structural Bioimaging course of the Strasbourg Master in Life Sciences (co-head : O. Lecompte)<br />
 
27-31/03 : Presentation of J.-S. Sereni at the online symposium « χ-boundedness », in the context of the network ''A Sparse (Graphs) Coalition''<br />
 
29/03 : Article published in Journal of Fungi : C. Mayer et al. CeGAL: Redefining a Widespread Fungal-Specific Transcription Factor Family Using an In Silico Error-Tracking Approach<br />
 
  
 
== February ==
 
== February ==
02/02 : Work meeting with Emmanuelle Leize (Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes) to discuss a collaboration on the use of AI approaches in proteomics. J. Thompson, K. Chennen.<br />
+
23/02 : Article accepted : C. Frappé--Vialatoux et P. Parrend, Combining Physical and Network Data for Attack Detection in Water Distribution Networks, Water Distribution Systems Analysis (WDSA)/Computing and Control Water Industry (CCWI) Joint Conference, Ferrara, Italy.</br>
02-03/02 : Participation of Dorine Merlat at the conference Omics Days 2023 (Montpellier)<br />
+
20/02 : Project meeting of CILRET-PASS (PIA and ITMO Génétique Génomique et Bioinformatique d'AVIESAN): Work in progress and perspectives.</br>
8/02 : Participation in mentoring circle (O. Lecompte)
+
12/02 : Invited seminar by Prof Lennart Martens, Ghent University. Lennart is head of the CompOmics [https://www.compomics.com] team  and a specialist in the development of tools for proteomics data analysis, including AI approaches.</br>
  
 
== January ==
 
== January ==
09/01 : Invited talk by D. Merlat - ERGA Annotation Committee<br />
+
24/01 : PhD thesis defense of Amani Abou-Rida, "Enhancing Detection and Explainability in Cybersecurity: A Shift from Machine Learning to Graph Learning.", supervised by Rabih Amhaz and Pierre Parrend</br>
11/01: intervention at [https://esbs.unistra.fr/acces-directs/actualites/actualite/default-ae15da7018 conference Artificial Intelligence at ESBS] : "Intelligence artificielle, éthique et santé" (A. Jeannin-Girardon)
+
09/01 : Article “Impact of Decentralized Autonomous Organizations (DAO) on society 5.0” accepted in 8th International Conference on Networks and Communications, Rabih Amhaz</br>
12/01: Participation at Journées des Universités (O. Lecompte)<br />
+
29/01 : Project CZI (Chan Zuckerberg Initiative) Collaborative Pairs Pilot Project Awards: "Moonlighting functions in neurodegenerative aaRSopathies", proposition rejected</br>
23-25/01 : Presentation of a poster at ALPHY meeting (Grenoble) by Dorine Merlat
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05/01 : Article "Pathogenic missense variation in PABPC1L/EPAB causes female infertility due to oocyte maturation arrest at the germinal vesicle stage" Journal of Assisted Reproduction and Genetics (accepted in december) publishe on line (C. Mayer, K. Chennen)</br>
<br />
 
  
 
= Visitors =
 
= Visitors =
04-08/04 : Visit by J. Volec (Czech Technical University, Czech Republic). <br />
 
 
<br />
 
<br />
  
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= Internships =
 
= Internships =
15/03 : Start of M1 internship by Burak Arti, M1 BSIB, supervised by Julie Thompson and Laetitia Poidevin <br />
+
11/03 : Start of internship of Jérémie Carabin, M2 BSIB Supervisors: Kirsley Chennen and Olivier Poch<br />
15/03 : Start of M1 internship by Julien Schaffer, M1 BSIB, supervised by Julie Thompson and Kirsley Chennen <br />
+
11/03 : Start of internship of Mathilda Moser, M1 BSIB Supervisor: Odile Lecompte<br />
15/03 : Start of M1 internship by Dehelia Chettouf, M1 BSIB, supervised by Claudine Mayer, Kirsley Chennen and Olivier Poch <br />
+
11/03 : Start of internship of Marie Siroux, M1 BSIB Supervisor: Kirsley Chennen<br />
15/03 : Start of M1 internship by Migena Bejko, M1 BSIB, supervised by Kirsley Chennen, Claudine Mayer and Olivier Poch <br />
+
11/03 : Start of internship of Céline Masson, M1 BSIB Supervisor: Julie Thompson<br />
15/03 : Start of M1 internship by Deborah Antonio, M1 BSIB, supervised by Claudine Mayer and Olivier Poch <br />
+
01/02 : Start of internship of Adem Boukhari, M2 Intelligence en données de santé, Supervisor: Kirsley Chennen<br />
<br />
+
01/02 : Start of internship of Hugues Petitjean, ICAM Data Scientist, Supervisor: Kirsley Chennen<br />
27/02 : Start of M1 internship by Fazil Mammadov, UFAZ, Baku, supervised by Rabih Amhaz <br />
+
07/01 : Start of internship of Zephyrin Enaux, M2 BSIB. Supervisors: Julie Thompson and Anne Jeannin-Girardon<br />
<br />
+
07/01 : Start of internship of Laura Billard, M1 Biologie Santé. Supervisor: Kirsley Chennen <br />
 
 
15/01 : Start of M2 internship by Lucille Herbay (Science de la vie, biologie moléculaire) supervised by Julie Thompson, Arnaud Kress<br />
 
 
<br />
 
<br />
  
 
= Administrative activities =
 
= Administrative activities =
 
9/02 : Meeting of workgroup RDA Unistra (J. Thompson, Paulette Lieby)<br />
 
10/02 : Steering committee Science Ouverte de l'Unistra (J. Thompson)<br />
 
<br />
 
20/01 : Meeting to organise the new master Unistra in bioinformatics and structural bioimaging, for 2024 (O. Lecompte, J. Thompson)<br />
 
23/01 : RDA organisational assembly (J. Thompson)<br />
 
 
<br />
 
<br />
  
 
= Miscellaneous =
 
= Miscellaneous =
7/02 : First session of a training course on Sexual and Gender-Based Violence and Homophobia <br />
+
 
21/03 : Second session of a training course on Sexual and Gender-Based Violence and Homophobia <br />
 
 
<br />
 
<br />
  
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'''(*) Every Tuesday 13h30 to 15h30'''<br />
 
'''(*) Every Tuesday 13h30 to 15h30'''<br />
1st Tuesday of the month : Reports of members A-G<br />
+
1st Tuesday of the month : Reports of members A-M<br />
2nd Tuesday of the month : Reports of members H-N<br />
+
2nd Tuesday of the month : Journal Club<br />
3rd Tuesday of the month : Reports of members O-Z<br />
+
3rd Tuesday of the month : Reports of members M-Z<br />
 
4th Tuesday of the month : Meeting for permanent members<br />
 
4th Tuesday of the month : Meeting for permanent members<br />
  
Each Thursday 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).<br />
+
Every second Tuesday at 15h00 :  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).<br />
 
 
23/02 : (*) Meeting to discuss the organisation of the presentations<br />
 
 
 
13/04 : (*) Session "Jeun's" Presentation by Arnaud Kress<br />
 
06/04 : (*) Session "Jeun's" Presentation by Ihsane Errami<br />
 
30/03 : (*) Session "Jeun's" Presentation by  Corentin Meyer<br />
 
23/03 : (*) Session "Jeun's" Presentation by  Deborah Antonio, Burak Arti, Migena Bejko, Dehelia Chettouf and Julien Schaffer<br />
 
16/03 : (*) Session "Jeun's" Presentation by Anne Jeannin-Girardon et Hiba Khodji<br />
 
  
  
 
[[fr:Faits_marquants]]
 
[[fr:Faits_marquants]]

Latest revision as of 12:22, 8 April 2024

Team activities in 2024 | Previous years

Scientific highlights

March

25/03: Article "Meyer et al. IMPatienT: an Integrated web application to digitize, process and explore Multimodal PATIENt daTa" accepted for publication in Journal of Neuromuscular Diseases.
21/03: Seminars by PhD students concerning the topic 'détection pour la cybersécurité' with Sherbrooke University (follow up of their visit in February)
21/03: Presentations accepted in RESSI (Rendez-Vous de la Recherche et de l'Enseignement de la Sécurité des Systèmes d'Information; mai) for PhD students of Pierre Parrend: Julien Michel, Majed Jaber, Côme Frappé-Vialatoux
11/03: The project for a Junior Professor Chair 'Atlas comparatif des répertoires de gènes et relations génotype-phénotype' led by Odile Lecompte is accepted.

February

23/02 : Article accepted : C. Frappé--Vialatoux et P. Parrend, Combining Physical and Network Data for Attack Detection in Water Distribution Networks, Water Distribution Systems Analysis (WDSA)/Computing and Control Water Industry (CCWI) Joint Conference, Ferrara, Italy.
20/02 : Project meeting of CILRET-PASS (PIA and ITMO Génétique Génomique et Bioinformatique d'AVIESAN): Work in progress and perspectives.
12/02 : Invited seminar by Prof Lennart Martens, Ghent University. Lennart is head of the CompOmics [1] team and a specialist in the development of tools for proteomics data analysis, including AI approaches.

January

24/01 : PhD thesis defense of Amani Abou-Rida, "Enhancing Detection and Explainability in Cybersecurity: A Shift from Machine Learning to Graph Learning.", supervised by Rabih Amhaz and Pierre Parrend
09/01 : Article “Impact of Decentralized Autonomous Organizations (DAO) on society 5.0” accepted in 8th International Conference on Networks and Communications, Rabih Amhaz
29/01 : Project CZI (Chan Zuckerberg Initiative) Collaborative Pairs Pilot Project Awards: "Moonlighting functions in neurodegenerative aaRSopathies", proposition rejected
05/01 : Article "Pathogenic missense variation in PABPC1L/EPAB causes female infertility due to oocyte maturation arrest at the germinal vesicle stage" Journal of Assisted Reproduction and Genetics (accepted in december) publishe on line (C. Mayer, K. Chennen)

Visitors


Doctoral students

Internships

11/03 : Start of internship of Jérémie Carabin, M2 BSIB Supervisors: Kirsley Chennen and Olivier Poch
11/03 : Start of internship of Mathilda Moser, M1 BSIB Supervisor: Odile Lecompte
11/03 : Start of internship of Marie Siroux, M1 BSIB Supervisor: Kirsley Chennen
11/03 : Start of internship of Céline Masson, M1 BSIB Supervisor: Julie Thompson
01/02 : Start of internship of Adem Boukhari, M2 Intelligence en données de santé, Supervisor: Kirsley Chennen
01/02 : Start of internship of Hugues Petitjean, ICAM Data Scientist, Supervisor: Kirsley Chennen
07/01 : Start of internship of Zephyrin Enaux, M2 BSIB. Supervisors: Julie Thompson and Anne Jeannin-Girardon
07/01 : Start of internship of Laura Billard, M1 Biologie Santé. Supervisor: Kirsley Chennen

Administrative activities


Miscellaneous



Team life

Team meetings

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

Every second Tuesday at 15h00 : 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).