I focus on designing parameterized algorithms for hard problems in bioinformatics. Application areas include RNA bioinformatics and evolution, with my current post-doctoral project being about the comparison of phylogenetic networks.
My research interests more largely include graph theory, graph algorithms, general bioinformatics and quantum computing (see CV).
PhD thesis
Marchand, B. (2023). Exact Parameterized Algorithmics for Structural RNA Bioinformatics [PhD thesis]. Ecole Polytechnique.
@phdthesis{marchand2023exact,
title = {Exact Parameterized Algorithmics for Structural RNA Bioinformatics},
author = {Marchand, Bertrand},
year = {2023},
fulltext = {https://hal.science/tel-04404102},
group = {thesis},
school = {Ecole Polytechnique}
}
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 (under review). BioRxiv, 2023–2005.
@article{fernandez2023designing,
title = {Designing molecular RNA switches with Restricted Boltzmann machines (under review)},
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}
}
Journal Publications
Yao, H.-T., Marchand, B., Berkemer, S. J., Ponty, Y., & Will, S. (2024). Infrared: a declarative tree decomposition-powered framework for bioinformatics. Algorithms for Molecular Biology, 19(1), 13.
@article{yao2024infrared,
title = {Infrared: a declarative tree decomposition-powered framework for bioinformatics},
author = {Yao, Hua-Ting and Marchand, Bertrand and Berkemer, Sarah J and Ponty, Yann and Will, Sebastian},
journal = {Algorithms for Molecular Biology},
volume = {19},
number = {1},
pages = {13},
year = {2024},
group = {journal},
link = {https://almob.biomedcentral.com/articles/10.1186/s13015-024-00258-2},
code = {https://gitlab.inria.fr/amibio/Infrared},
publisher = {Springer}
}
Marchand, B., Will, S., Berkemer, S. J., Ponty, Y., & Bulteau, L. (2023). Automated design of dynamic programming schemes for RNA folding with pseudoknots. Algorithms for Molecular Biology, 18(1), 18.
@article{marchand2023automated,
title = {Automated design of dynamic programming schemes for RNA folding with pseudoknots},
author = {Marchand, Bertrand and Will, Sebastian and Berkemer, Sarah J and Ponty, Yann and Bulteau, Laurent},
journal = {Algorithms for Molecular Biology},
volume = {18},
number = {1},
pages = {18},
year = {2023},
islong = {true},
fulltext = {https://hal.science/hal-04103565/document},
link = {https://almob.biomedcentral.com/articles/10.1186/s13015-023-00229-z},
code = {https://gitlab.inria.fr/bmarchan/auto-dp},
group = {journal},
publisher = {Springer}
}
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}
}
Conference Publications
Marchand, B., Tahiri, N., Tremblay-Savard, O., & Lafond, M. (2024). Finding Maximum Common Contractions Between Phylogenetic Networks. WABI 2024. https://doi.org/10.4230/LIPIcs.WABI.2024.16
@inproceedings{marchand2024finding,
title = {Finding Maximum Common Contractions Between Phylogenetic Networks},
author = {Marchand, Bertrand and Tahiri, Nadia and Tremblay-Savard, Olivier and Lafond, Manuel},
journal = {WABI 2024},
year = {2024},
fulltext = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.16},
doi = {10.4230/LIPIcs.WABI.2024.16},
annote = {Keywords: Phylogenetic networks, contractions, algorithms, weakly galled trees},
group = {conference}
}
Marchand, B., Anselmetti, Y., Lafond, M., & Ouangraoua Aı̈da. (2024). Median and Small Parsimony Problems on RNA trees. ISMB 2024.
@article{marchand2024median,
title = {Median and Small Parsimony Problems on RNA trees},
author = {Marchand, Bertrand and Anselmetti, Yoann and Lafond, Manuel and Ouangraoua, A{\"\i}da},
journal = {ISMB 2024},
group = {conference},
fulltext = {https://academic.oup.com/bioinformatics/article/40/Supplement_1/i237/7700894},
year = {2024}
}
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},
link = {https://drops.dagstuhl.de/storage/00lipics/lipics-vol242-wabi2022/LIPIcs.WABI.2022.7/LIPIcs.WABI.2022.7.pdf},
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. In A. Carbone & M. El-Kebir (Eds.), WABI 2021 (Vol. 201, pp. 7:1–7:23). Schloss Dagstuhl – Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2021.7
@inproceedings{marchan2021tree,
author = {Marchand, Bertrand and Ponty, Yann and Bulteau, Laurent},
title = {Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics},
journal = {WABI 2021},
pages = {7:1--7:23},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
isbn = {978-3-95977-200-6},
issn = {1868-8969},
year = {2021},
volume = {201},
code = {https://gitlab.inria.fr/amibio/tree-diet},
group = {conference},
editor = {Carbone, Alessandra and El-Kebir, Mohammed},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
fulltext = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.7},
urn = {urn:nbn:de:0030-drops-143604},
doi = {10.4230/LIPIcs.WABI.2021.7},
annote = {Keywords: RNA, treewidth, FPT algorithms, RNA design, structure-sequence alignment}
}
Patents
Marchand, B. (2024). Positioning atoms using optical tweezer traps.
US Patent 11,869,678
@misc{marchand2024positioning,
title = {Positioning atoms using optical tweezer traps},
author = {Marchand, Bertrand},
year = {2024},
link = {https://patents.google.com/patent/US11869678B2/en},
group = {patents},
note = {US Patent 11,869,678}
}
