Team CSTB : Complex Systems and Translational Bioinformatics

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TEAM PRESENTATION

Team meetings

(*) Every Tuesday 13h30 to 15h30, Room 526, Medical School, CSTB 5th floor - 11 rue Humann
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 N-Z
4th Tuesday of the month : Meeting for permanent members

DECEMBER 2016

  • 06/12 : Presentation of Y.Nevers on available complete proteomes
  • 07/12 : Presentation of J.Navarro Lara at SSCI (Symposium Series on Computational Intelligences) in Athens
  • 08/12 : Presentation of P.Willaume at SSCI (Symposium Series on Computational Intelligences) in Athens
  • 08/12 : Presentation at "BioWin days", Louvain-la-Neuve, BELGIUM (A.Jeannin-Girardon, P.Collet and O.Poch)
  • 13/12 : Presentation of K.Chennen on installation of a CSTB semantic web in the context of the Elixir project
  • 15/12 : Fête de Noël

NOVEMBER 2016

- 02/11 : Arrival of 2 Master 2 BSBB interns for 1 month : Audrey Fosset (supervisor Odile Lecompte) and Vincent Zilliox (supervisor Julie Thompson)
- 08/11 : (*) Presentation of progress, group A-M
- 14/11 : Y.Nevers is the new representant for CSTB doctoral students
- 14/11 : Integration of Catherine Guth (associated MCF)
- 15/11 : Half-day of presentations in "deep learning et réseaux de neurones"
- 15/11 : (*) Journal Club
- 16/11 : Return of Salma Aouled El Haj Mohamed for 2 months (thesis co-director Julie-Thompson)
- 16/11 : Y.Nevers organised a JeBiF pub meeting in Strasbourg
- 18/11 : Invited speech in Rennes (J.Thompson)
- 22/11 : (*) Presentation of progress, group N-Z
- 25/11 : Presentations of projects by 2 Master2 ILC students, Alexandre Bruyant and Marc Haegelin
- 25/11 : Presentation of CSTB for the CNRS DAS (O.Poch)
- 28/11 : Elixir conf-call, K.Chennen, O.Poch and J.Thompson
- 28/11 : Presentation of CSTB for new lab members (O.Poch)
- 29/11 : A.Jeannin and P.Collet at the ImmuniComplexIT network workshop in Paris
- 29/11 : (*) Meeting for permanent members (OJ : report of the CSTB presentation for the CNRS DAS; website: things to do; IT needs; infos concerning the new building)

OCTOBER 2016

- 04/10 : (*) Presentation of progress, group A-M
- 12/10 : (*) Journal Club
- 14/10 : Thesis of Kirsley Chennen Rare diseases and 'Big Data' : bioinformatics solutions for knowledge-guided analysis
- 15-16/10 : Participation in Fête de la Science in Strasbourg. Organisation of a booth by P. Collet, A. Jeannin, P. Parrend
- 18/10 : (*) Presentation of progress, group N-Z
- 24/10 : (*) Conf call ELIXIR --> Detailed discussions about obtaining a future BYOD (Bring Your Own Data) in Strasbourg
- 25/10 : (*) Meeting for permanent members (OJ : ANR projects submitted; new entrants; Elixir project)
- 25/10 : Medical thesis of Yvan Herenger (ex-intern) Cataractes congénitales génétiques : apport du séquençage haut débit dans le diagnostic et la prise en charge

SEPTEMBER 2016

- 01/09 : Arrival of Anne Jeannin, lecturer at University of Strasbourg
- 02/09 : Party for Anne Jeannin and promotion of Pierre Collet to PRCE
- 05-07/09 : Presentation of Pierre Masai at the 20th conference KES 2016 in York, UK
- 12/09 : CRBS gouvernance meeting, Olivier Poch
- 20/09 : (*) Presentation of progress, group A-M
- 20-23/09 : Poster presentation by Yannis Nevers at 20th Evolutionary Biology Meeting in Marseille
- 21/09 : Arrival of 2 Master2 ILC students, Alexandre Bruyant and Marc Haegelin
- 22/09 : 1 day meeting between CSTB and Dr. Partap Chauhan concerning project of modeling for Ayurvedic medicine
- 23/09 : 1articles accepted in international conferences, Pierre Willaume and Julio Navarro Lara
-26/09 : Restart of monthly conf call meetings for H2020 project "Elixir Excelerate"
- 27/09 : (*) Presentation of progress, group N-Z
- 28/09 : Visit of Dr. Christian Rolando from Université de Lille in the context of Master 2 internship of Marc Haegelin
- 30/09 : 1 day BIONICS meeting organised by Pierre Parrend at CSTB

AUGUST 2016

JULY 2016

- 08/07 : Front page of newsletter n°126 of University of Strasbourg, 08/07/2016.
Hélène Gass, Master2 intern in bioinformatics, ranked 4th in world apnea championships 2016 (16x 50m). Double champion of France 2015 (record and gold medal)

JUNE 2016

- 01/06 : Arrival of L3 intern, Laurine Huber (Supervisor Pierre Collet)
- 02/06 : IGMA meeting on IT for CRBS (Centre de Recherche en Biomédecine de Strasbourg)
- 07/06 : Presentation of UFAZ (Université franco-azerbaïdjanaise) project by the presidency (Pierre Collet co-rector)
- 07/06 : (*) Meeting for permanent members (OJ: preparation of weekly meetings; HCERES report; dates for annual team BBQ and SONIC meeting day)
- 14/06 : (*) Presentation of progress, group A
- 15/06 : (*) Meeting for permanent members to discuss HCERES "scientific strategies & perspectives"
- 15/06 : Arrival of intern (observation internship) Mickaël Wagner (Supervisor Olivier Poch)
- 21/06 : (*) Journal Club
- 23/06 : Mid thesis defence Salma Aouled El Haj Mohamed (thesis co-director Julie-Thompson)
- 23/06 : Scientific council of ECAM (Olivier Poch)
- 28/06 : Presentation by Yannis Nevers at Journées ouvertes en biologie informatique et mathématiques (JOBIM) in Lyon 28-30 June. Participation of Salma Aouled El Haj Mohamed.
- 27/06 : Presentation by intern Fantin Mesny (supervisor Odile Lecompte) "Analysis of interactions in protein networks"
- 28/06 : Annual team BBQ
- 30/06 : Promotion of Pierre Collet to PRCE

MAI 2016

- 03/05 : (*) Meeting for permanent members (OJ : preparation of weekly meetings ; team budgets and spending; 1st version of HCERES report)
- 10/05 : (*) Presentation of progress, group A
- 11-13/05 : Evaluation of INRA engineers(LEAN philosophy, EPST skills dashboard, constructive messages for engineers) (Olivier Poch)
- 12/05 : Anne Jeannin ranked 1st for the lecturer post in the team
- 17/05 : (*) Journal Club, presentation of Yann Hode (supervisor Aline Deruyver)
- 17/05 : Arrival of ESBS intern, Fantin Mesny (supervisor Odile Lecompte)
- 19/05 : Validation of thesis funding for Cédric Pupka by SYNOVO
- 19/05 : Validation of internship funding by fondation N-Light (management of JIVA Ayurveda cohort)
- 19/05 : (*) Meeting for permanent members : HCERES-SWOT
- 24/05 : (*) Presentation of progress, group B
- 30/05 : Arrival of BTS intern Mickaël Joly (supervisor, Raymond Ripp)
- 31/05 : Presentation by Fantin Mesny (supervisor Odile Lecompte) "Analysis of gene lists in bioinformatics"

APRIL 2016

- 05/04 : (*) Meeting for permanent members (OJ : preparation of weekly meetings ; upcoming intern presentations/competitions/mid-thesis defence)
- 07/04 : Course on circular codes in genes at Ecole des Jeunes Chercheurs en Informatique Mathématiques (EJCIM 16) (Christian Michel)
- 12/04 : (*) Presentation of progress, group A
- 19/04 : (*) Journal Club
- 26/04 : (*) Presentation of progress, group B
- 28/04 : Visit 'Introduction to research' (L3 students)
- 29/04 : Prssentations at quatrièmes journées scientifiques of the Fédération de Médecine Translationnelle Strasbourg (FMTS):

Carlos Bermejo Das Neves : "MODEX: An artificial intelligence engine designed for systems biomedicine"
Yannis Nevers : "Prediction and characterization of ciliary proteins by comparative genomics"

- Publications :
1) Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.
Nat Methods. 2016 [Epub ahead of print]

2) Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells.

Kole C, Berdugo N, Da Silva C, Aït-Ali N, Millet-Puel G, Pagan D, Blond F, Poidevin L, Ripp R, Fontaine V, Wincker P, Zack DJ, Sahel JA, Poch O, Léveillard T.
PLoS One. 2016;11(3):e0150758.

MARCH 2016

Starting in March, the weekly team meetings will be held on Tuesday at 14h00.
Programming of meetings for permanent members, every 1st Tuesday of the month at 14h00.

- 01/03 : (*) Meeting for permanent members (OJ : preparation of weekly meetings ; liste des points à aborder à la réunion préparatoire de l'HCERES le 03 mars ; bilan des entrées/sorties au CSTB ; bilan des financements
- 03/03 : (*) HCERES preparatory meeting
- 03/03 : HCERES, summary on the CSTB wiki
- 08/03 : ELIXIR All Hands meeting Barcelona 7-9 March (Julie Thompson/Olivier Poch)

https://www.elixir-europe.org/events/elixir-all-hands-2016

- 08/03 : (*) Presentation of progress, group A
- 11/03 : Presentation of Artifical Immun Systems by Cédric Pupka at 14h (supervisor Pierre Parrend)
- 15/03 : Arrival of intern Anna Leontova (supervisor Julie Thompson)
- 15/03 : (*) Presentation of progress, group B
- 16/03 : 4P Factory workshop, 4P-Factory e-room + Grand Amphi de Math Unistra (Pierre Parrend)

https://4pfactory.wordpress.com/4p-factory-workshop-2016-program/

- 17/03 : Annual general meeting of ANR Infrastructure BIPBIP in Strasbourg at CSTB Medical school (25 participants)
- 21/03 : Visit of Amy Gooch (University of Durham) (21/03 to 01/04)
- 22/03 : Presentations by 3 M2 BSBI interns
- 25/03 : « Science Days » of SANOFI - "Scientific innovation for patients"

Poster presentation of VarScrut, Centre de Congrès, Le Port-Marly (78) (Olivier Poch)

- 29/03 : (*) Journal Club
- Mission by Pierre Collet to Bakou to set up a new university, Université Franco-Azerbaïdjanaise (UFAZ)
- Finalisation of Springer Proceedings book on Complexity First Complex Systems Digital Campus World E-Conference 2015 (Edits P.Bourgine, P.Collet, P.Parrend).
- 2 Papers accepted at CEC and Gecco :
- CEC'16: Author(s): Jean Meunier, Julier Rohmer, Dominique Knittel and Pierre Collet

Title: Metaheuristic Based Battery Control Optimization of a Photovoltaic System with Grid Connexion

- GECCO'16: Author(s): N. Hamze, P. Collet, and C. Essert

Title: Introducing Pareto-based MOEA to Neurosurgery Preoperative Path Planning

FEBRUARY 2016

- 04/02 : (*) Meeting for permanent members (OJ : preparation of weekly meetings ; January activities : a- ComDir Icube 01/02 report, b- IFB general meeint 26/01 report; Funding / Project calls ; Other)
- 10/02 : (*) Presentation of progress, group A
- 12/02 : Meeting with SATT Connectus, VarScrut license
- 17/02 : (*) Journal Club
- 22/02 : Arrival Masters intern Cédric Pupka (supervisor Pierre Parrend)
- 24/02 : (*) Presentation of progress, group B
- 25/02 : ICube general meeting
- 2 ANR out of3 passed phase 1 - paper EvoBio accepted:

Authors: Elise Rosati, Morgan Madec, Abir Rezgui, Quentin Colman, Nicolas Toussaint, Christophe Lallement, Pierre Collet
Title: Application of Evolutionary Algorithms for the Optimization of Genetic Regulatory Networks

JANUARY 2016

Weekly team meeetings will take place on Thursdays starting in January.

- 04/01 : Arrival of Master2 intern Hélène Gass (supervisor Julie Thompson)
- 04/01 : Arrival of Master2 intern Morgane Gilg (supervisor Julie Thompson)
- 06/01 : (*) Meeting for permanent members CSTB (OJ: debriefing of Bingi Days team retreat 10/11 Dec, Maison des Associations Strasbourg ; Preparation of HCERES; funding)
- 11/01 : Arrival of Master2 intern Vanessa Fernandes-Cardoso (supervisor Olivier Poch)
- 13/01 : Presentation by skype by Salma Aouled El Haj
- 18/01 : (*) Meeting to discuss budget, themes and identification of information to prepare HCERES
- 20/01 : (*) Presentation of progress, group A
- 22/01 : Presentation of chairs and Unitwin UNESCO-Unistra at Institut Lebel (Pierre Collet)
- 25-26/01 : General meeting of the Institut français de bioinformatique, workshops on platform economic models and viability of participation in Infradev "Elixir Excelerate" project (Olivier Poch)
- 27/01 : Presentation by Alexis Allot (ex doctoral student)
- 28/01 : (*) Presentation of progress, group B

  • 9-11 December 2015 : CSTB retreat at the Maison des Associations, place des Orphelins
  • 9 October 2015 : Alexis ALLOT defended his PhD in bioinformacs.
  • 8 October 2015 : Carlos BERMEJO DAS NEVES defended his mid-PhD in bioinformacs.
  • 1st October 2015 : First students from the SONIC group move into the Medical School building.