Publications - IFB

Last publications
Mention IFB infrastructure

Regarding open science publications, IFB/ELIXIR-FR is committed to openly sharing the results of internal research. In this context, we publish and encourage publications on HAL.

IFB/ELIXIR-FR Collection on HAL

An IFB/ELIXIR-FR collection on HAL is currently being prepared. While waiting for its launch, we invite you to discover the collections of our various platforms and our coordinating unit.

IFB-core Collection on HAL

All IFB-core publications are available in our collection, from which the latest publications below are taken.

Find the entire collection on HAL

Latest IFB-core publications

Zoé Le Roux, Alessandra Merlotti, Francesco Durrazi, Daniel Remondini, Sandra Dérozier, et al.

Community detection in a plant-based fermentation knowledge graph.

FOODSIM 2026 - 14th biennial FOODSIM'2026, EUROSIS, Apr 2026, Gand, Belgium. ⟨hal-05540516⟩.

Cameron Hyde, Anna Syme, Bérénice Batut, Paul Zierep, Winnie Mok, et al.

Community-curated Galaxy interfaces with the Galaxy Labs Engine.

GigaScience, 2026, ⟨10.1093/gigascience/giag041⟩. ⟨hal-05589198⟩.

Lucie Khamvongsa-Charbonnier, Robert Aboukhalil, Hélène Chiapello, Thomas Denecker, Pierre Poulain, et al.

Training biologists in Unix command-line skills: From curriculum to interactive online tutorials.

PLoS Computational Biology, 2026, 22 (4), pp. e1014133. ⟨10.1371/journal.pcbi.1014133⟩. ⟨hal-05583485⟩.

Messak Imane, Rousseau Baptiste, Seiler Julien, Denecker Thomas.

madbot.

The metadata and data brokering online tool. C2RI seminar Pasteur, Apr 2026, Paris, France. ⟨hal-05577097⟩.

Marie Schmit, Ulysse Le Clanche, George Marchment, Sarah Cohen-Boulakia, Olivier Dameron, et al.

A Standards-Based Knowledge Graph that Bridges Scientific Workflows, Run-Time Provenance, and Tool Registries.

SWAT4HCLS 2026, Mar 2026, Amsterdam, Netherlands. ⟨hal-05517640⟩.

Acknowledgments and affiliations in publications

Affiliations in publications for IFB-core staff (UAR3601)

The writing of affiliations in publications for Unit UAR3601 staff must be done in this format:

IFB-core, Institut Français de Bioinformatique (IFB), CNRS, INSERM, INRAE, CEA, 94800 Villejuif, France.

Affiliations in publications for the use of NNCR hardware and software resources

Affiliations in publications that have benefited from the use of the servers from NNCR (cluster et cloud) must be written in this format :

The bioinformatics analyses were performed on the HPC facilities of the National Network of Computing Resources of the Institut Français de Bioinformatique (IFB), funded by the Programme d’Investissements d’Avenir (PIA), grant Agence Nationale de la Recherche number ANR-11-INBS-0013

Publication resulting from PIA1 IFB funding

Pour toute publication ayant bénéficié du financement PIA1 IFB, nous demandons d’inclure la phrase suivante dans la section “Funding” ou “Acknowledgement” selon le cas :

The French Institute of Bioinformatics (IFB) was founded by the Future Investment Program subsidized by the National Research Agency, number ANR-11-INBS-0013.

Oral communication media, poster communications and websites must also display the France 2030 logo. Download the logo

Publication resulting from MUDIS4LS funding

For any publication that has benefited from PIA4 ESR/Equipex+ MUDIS4LS funding, we ask that the following sentence be included in the “Funding” or “Acknowledgement” section as appropriate:

This work received state aid managed by the National Research Agency under France 2030 for structural research equipment / EQUIPEX+ with reference ANR-21-ESRE-0048.

Oral communication media, poster communications and websites must also display the France 2030 logo. Download the logo

Publication resulting for projects IFB or MUDIS4LS funding

For any publication that has benefited from the funding PIA1 IFB et PIA4 ESR/Equipex+ MUDIS4LS, we request that the following sentence be included in the “Funding” or “Acknowledgement” section, as appropriate: :

This work received state aid managed by the National Research Agency under France 2030 for the French Institute of Bioinformatics (IFB), founded by the Investments for the Future Program, number ANR-11-INBS-0013, as well as for structural research equipment / EQUIPEX+ with reference ANR-21-ESRE-0048.

Oral communication media, poster communications and websites must also display the France 2030 logo. Download the logo

Publication resulting from ABBA Funding

For any publication that has benefited from PI4 ABBA project (Accelerating Bioinformatics for Biology Applications) funding, we request that the following sentence be included in the “Funding” or “Acknowledgement” section, as appropriate:

This work received state aid managed by the National Research Agency under France 2030 as part of the “Jouvence” program of the Health Plan, for the ABBA project with reference ANR-24-INBS-0010 IFB-ABBA..

Publication resulting from ABRomics Funding

For any publication that has benefited from ABRomics funding, we request that the following sentence be included in the “Funding” or “Acknowledgement” section, as appropriate:

This (type of publication) received financial support from the Priority Research Program on Antibiotic Resistance (PPR Antibiorésistance), coordinated by Inserm and funded by the General Secretariat for Investment (SGPI).

Publication resulting from BYTE-Sea Funding

For any publication that has benefited from PEPR ATLASea funding – Priority Research Program and Equipment for Exploratory Research, we request that the following sentence be included in the “Funding” or “Acknowledgement” section, as appropriate:

The exploratory research program “ATLASea: Atlas of Marine Genomes” and the targeted project BYTE-Sea (ANR-22-EXAT-0004) benefit from state aid managed by the National Research Agency (ANR) as part of the “France 2030” future investment plan.

Oral communication media, poster communications and websites must also display the France 2030 logo. Download the logo

Publication resulting from Cloud4SAMS Funding

For any publication that has benefited from Cloud4SAMS funding – a targeted project of the SAMS Priority Research Program and Equipment, we request that the following sentence be included in the “Funding” or “Acknowledgement” section, as appropriate:

This work received state aid managed by the National Research Agency under France 2030 with reference “ANR-24-PESA-0003”.

Oral communication media, poster communications and websites must also display the France 2030 logo. Download the logo

Using the madbot tool

If you use madbot in your work, please cite it as follows:

Laurent BOURI, Imane MESSAK, Baptiste ROUSSEAU, Anakim GUALDONI, Elora VIGO, Matéo HIRIART, Nadia GOUÉ, Julien SEILER, Thomas DENECKER. Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context. Gitlab repository, IFB ELIXIR France, 2025. https://gitlab.com/ifb-elixirfr/madbot

Publication Resulting from NEUROVASC Funding

For any publication that has benefited from PEPR Digital Health funding – Involvement in the NeuroVasc axis, we request that the following sentence be included in the “Funding” or “Acknowledgement” section, as appropriate:

This project received state aid managed by the National Research Agency under France 2030 with reference “ANR-22-PESN-0008”.

Oral communication media, poster communications and websites must also display the France 2030 logo. Download the logo

Publication for other Projects

The maDMP4LS project (machine-actionable Data Management Plans for Life Sciences) received funding ANR-19-DATA-0017-01 as part of the Flash call “Open Science: research practices and open data”.

The OpenLink project (A gateway between imaging data management tools to apply FAIR principles) received funding ANR-19-DATA-0011-01 as part of the Flash call “Open Science: research practices and open data”.