I focus on designing parameterized algorithms
for hard problems in RNA bioinformatics, with a particular
emphasis on graph width parameters such as treewidth.
My research interests more largely include graph theory,
graph algorithms, general bioinformatics and quantum computing (see CV).
Preprints
Fernandez-de-Cossio-Diaz, J., Hardouin, P., Lyonnet du Moutier, F.-X., Di Gioacchino, A., Marchand, B., Ponty, Y., Sargueil, B., Monasson, R., & Cocco, S. (2023). Designing molecular RNA switches with Restricted Boltzmann machines. BioRxiv, 2023–2005.
@article{fernandez2023designing,
title = {Designing molecular RNA switches with Restricted Boltzmann machines},
author = {Fernandez-de-Cossio-Diaz, Jorge and Hardouin, Pierre and Lyonnet du Moutier, Francois-Xavier and Di Gioacchino, Andrea and Marchand, Bertrand and Ponty, Yann and Sargueil, Bruno and Monasson, Remi and Cocco, Simona},
journal = {bioRxiv},
pages = {2023--05},
year = {2023},
group = {preprint},
fulltext = {https://www.biorxiv.org/content/10.1101/2023.05.10.540155v1.full.pdf},
publisher = {Cold Spring Harbor Laboratory}
}
Boury, T., Bulteau, L., Marchand, B., & Ponty, Y. (2023). Independent set reconfiguration: general and RNA-focused parameterized algorithms.
@article{boury2023independent,
title = {Independent set reconfiguration: general and RNA-focused parameterized algorithms},
author = {Boury, Th{\'e}o and Bulteau, Laurent and Marchand, Bertrand and Ponty, Yann},
fulltext = {https://hal.science/hal-04094405/},
group = {preprint},
year = {2023}
}
Marchand, B., Will, S., Berkemer, S., Ponty, Y., & Bulteau, L. (2023). Automated design of dynamic programming schemes for RNA folding with pseudoknots.
@article{marchand2023automated,
title = {Automated design of dynamic programming schemes for RNA folding with pseudoknots},
author = {Marchand, Bertrand and Will, Sebastian and Berkemer, Sarah and Ponty, Yann and Bulteau, Laurent},
fulltext = {https://hal.science/hal-04103565/},
group = {preprint},
year = {2023}
}
Conference Publications
Marchand, B., Will, S., Berkemer, S., Bulteau, L., & Ponty, Y. (2022). Automated design of dynamic programming schemes for RNA folding with pseudoknots. WABI 2022.
@article{marchand2022automated,
title = {Automated design of dynamic programming schemes for RNA folding with pseudoknots},
author = {Marchand, Bertrand and Will, Sebastian and Berkemer, Sarah and Bulteau, Laurent and Ponty, Yann},
year = {2022},
fulltext = {https://pastel.archives-ouvertes.fr/LIX/hal-03676377v1},
code = {https://gitlab.inria.fr/bmarchan/auto-dp},
group = {conference},
journal = {WABI 2022}
}
Bulteau, L., Marchand, B., & Ponty, Y. (2021). A new parametrization for independent set reconfiguration and applications to RNA kinetics. IPEC 2021.
@article{bulteau2021new,
title = {A new parametrization for independent set reconfiguration and applications to RNA kinetics.},
author = {Bulteau, Laurent and Marchand, Bertrand and Ponty, Yann},
year = {2021},
fulltext = {https://hal.inria.fr/hal-03272963/document},
group = {conference},
link = {https://drops.dagstuhl.de/opus/volltexte/2021/15394/pdf/LIPIcs-IPEC-2021-11.pdf},
code = {https://gitlab.inria.fr/amibio/barriers},
journal = {IPEC 2021}
}
Marchand, B., Ponty, Y., & Bulteau, L. (2021). Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. WABI 2021.
@article{marchand2021tree,
title = {Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics},
author = {Marchand, Bertrand and Ponty, Yann and Bulteau, Laurent},
year = {2021},
fulltext = {https://hal.inria.fr/hal-03206132/document},
link = {https://drops.dagstuhl.de/opus/volltexte/2021/14360/pdf/LIPIcs-WABI-2021-7.pdf},
long = {https://almob.biomedcentral.com/articles/10.1186/s13015-022-00213-z},
code = {https://gitlab.inria.fr/amibio/tree-diet},
group = {conference},
journal = {WABI 2021}
}
Journal Publications
Marchand, B., Ponty, Y., & Bulteau, L. (2022). Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics. Algorithms for Molecular Biology, 17(1), 8.
@article{marchand2022tree,
title = {Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics},
author = {Marchand, Bertrand and Ponty, Yann and Bulteau, Laurent},
journal = {Algorithms for Molecular Biology},
volume = {17},
number = {1},
pages = {8},
year = {2022},
islong = {true},
group = {journal},
link = {https://almob.biomedcentral.com/articles/10.1186/s13015-022-00213-z},
code = {https://gitlab.inria.fr/amibio/tree-diet},
fulltext = {https://hal.science/hal-03608412},
publisher = {Springer}
}
Serret, M. F., Marchand, B., & Ayral, T. (2020). Solving optimization problems with Rydberg analog quantum computers: Realistic requirements for quantum advantage using noisy simulation and classical benchmarks. Physical Review A, 102(5), 052617.
@article{serret2020solving,
title = {Solving optimization problems with Rydberg analog quantum computers: Realistic requirements for quantum advantage using noisy simulation and classical benchmarks},
author = {Serret, Michel Fabrice and Marchand, Bertrand and Ayral, Thomas},
journal = {Physical Review A},
volume = {102},
number = {5},
pages = {052617},
year = {2020},
fulltext = {https://arxiv.org/pdf/2006.11190.pdf},
link = {https://journals.aps.org/pra/abstract/10.1103/PhysRevA.102.052617},
group = {journal},
publisher = {APS}
}