Main Peer-reviewed Publications				Manfroi B, Dang VD, Bui-Thi C, Jungmann A, Borzakian S, Tong Y, Beauvineau C, Dupuis L, Guffart E, Borst K, Nguyen NT, Alvarez-Simon D, Chyzak G, Schaefer S, Gerlach RG, Frischbutter S, Hamann A, Salem Wehbe L, El Behi M, Luka M, Menager M, Jouneau L, Boudinot P, Jung S, Winkler TH, Liblau R, Marignier R, Isambert H, Prinz M, von Kries P, Specker E, Walter J, Mahuteau-Betzer F, Fillatreau S: Induced regulatory B cells stably expressing IL-10 cure CNS autoimmunity by targeting local myeloid cells Immunity, in press (2026). Pubmed | DOI | pdf
					Donada A, Hermange G, Tocci T, Midoun A, Prevedello G, Hadj Abed L, Dupre D, Sun W, Milo I, Tenreira Bento S, Pospori C, Innes A, Willekens C, Vargaftig J, Michonneau D, Lo Celso C, Servant N, Duffy KR, Isambert H, Cournede PH, Laplane L, Perie L: Clonal memory of cell division in humans diverges between healthy haematopoiesis and acute myeloid leukaemia Nature Commun, in press (2026). Pubmed | DOI | bioRxiv
					Fusilier Z, Clement A, Simon F, Calvente I, Jean-Marie R, Mathieu M, Calmettes V, Piastra-Facon F, Quintana-Perez Y, George Clement J, Crestey L, Lumineau E, Henninger R, Tonani M, Manriquez V, Lacerda L, Bensaid L, de Villemagne P, Piaggio E, Semetey V, Coscoy S, Martini E, Scita G, Gelly J-C, Ivaska J, Isambert H, Goudot C, Pierobon P, Lennon-Dumenil A-M, Moreau HD: Macrophages restrict tumor immune infiltration by controlling collagen topography Science Immunology, 11 (117):eadw8291 (2026). Pubmed | DOI | bioRxiv | pdf
					Buvat I, Aarntzen E, Badawi RD, Ballesta A, Bock C, Chuah C-N, Fisher J, Graff J-P, Ilan Y, Isambert H, Ivanov P, Izu LT, Koenen HJPM, Langevin H, Lewis DY, Pires M, Sundar LKS, Tawakol A, ter Horst R, van Cranenbroek B, Weigelin B, Cherry SR, Beyer T: Cross-Disciplinary Methodologies for Whole-Person Research - Insights from EMPOWER2024 npj Imaging, 4, 19 (2026). Pubmed | DOI | pdf
					Lagrange N, Isambert H: An efficient search-and-score algorithm for ancestral graphs using multivariate information scores for complex non-linear and categorical data Proceedings of the 42nd International Conference on Machine Learning (ICML2025), PMLR 267:32164-32187 (2025). Pubmed | DOI | ICML | pdf
					Dupuis L, Debeaupuis O, Simon F, Isambert H: CausalCCC: a web server to explore intracellular causal pathways enabling cell-cell communication Nucleic Acids Res, 53, W125 (2025). Pubmed | DOI | pdf
					Jeanpierre M, Debeaupuis O, Brunaud C, Yancoski J, Riller Q, Hadjadj J, Stolzenberg M-C, Villarreal G, Katsicas MM, Villa M, Neves JF, Stephan J-L, Leonard C, Lazaro E, Ciron J, Boussard C, Mazerolles F, Magerus A, Pelle O, Masson C, Schmitt Y, Hoareau B, Vinit A, Neven B, Quartier P, Isambert H, Oleastro M, Danielian S, Parlato M, Rieux-Laucat F: In silico modeling guides identification of novel JAK1 variants associated with immune dysregulation EMBO Mol Med, 17 (12), 3275 (2025). Pubmed | DOI | pdf
					Sella N, Guinot F, Lagrange N, Albou LP, Desponds J, Isambert H: Preserving information while respecting privacy through an information theoretic framework for synthetic health data generation npj Digital Medicine, 8, 49 (2025). Pubmed | DOI | pdf
					Parent C, Honari H, Tocci T, Simon F, Zaidi S, Jan A, Aubert V, Delattre O, Isambert H, Wilhelm C, Viovy J-L: Label-free Machine Learning prediction of chemotherapy on tumor spheroids using a microfluidics droplet platform Small Science, 2500173 (2025). Pubmed | DOI | pdf| supp
					Donada A, Hermange G, Tocci T, Midoun A, Prevedello G, Hadj Abed L, Dupre D, Sun W, Milo I, Tenreira Bento S, Pospori C, Innes A, Willekens C, Vargaftig J, Michonneau D, Lo Celso C, Servant N, Duffy KR, Isambert H, Cournede PH, Laplane L, Perie L: Clonal memory of cell division in humans diverges between healthy haematopoiesis and acute myeloid leukaemia bioRxiv, 2025.06.24.660535 (2025). Pubmed | DOI | bioRxiv
					Simon F, Comes MC, Tocci T, Dupuis L, Cabeli V, Lagrange N, Mencattini A, Parrini MC, Martinelli E, Isambert H: CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data eLife, 13:RP95485 (2025). Pubmed | DOI | bioRxiv | pdf | pdf+supp [press release]
					Fusilier Z, Simon F, Calvente I, Crestey L, Clement A, Mathieu M, Jean-Marie R, Piastra-Facon F, George Clement J, Lumineau E, Tonani M, Manriquez V, Lacerda L, de Villemagne P, Piaggio E, Semetey V, Coscoy S, Martini E, Scita G, Gelly J-C, Ivaska J, Isambert H, Goudot C, Pierobon P, Lennon-Dumenil A-M, Moreau HD: Macrophages restrict tumor permissiveness to immune infiltration by controlling local collagen topography through a Tcf4-Collagen3 fibrotic axis bioRxiv, 2025.01.17.633527 (2025). Pubmed | DOI | bioRxiv | pdf | pdf+supp
					Lagrange N, Isambert H: An efficient search-and-score algorithm for ancestral graphs using multivariate information scores opt-in article at NeurIPS 2024, arXiv, 2412.17508 (2024). Pubmed | DOI | arXiv | pdf
					Miladinovic O, Canto P-Y, Pouget C, Piau O, Radic N, Freschu P, Megherbi A, Prats CB, Jacques S, Hirsinger E, Geeverding A, Dufour S, Petit L, Souyri M, North T, Isambert H, Traver D, Jaffredo T, Charbord P, Durand C: A multistep computational approach reveals a neuro-mesenchymal cell population in the embryonic hematopoietic stem cell niche Development, 151, dev202614 (2024). Pubmed | DOI| pdf| supp
					Ribeiro-Dantas MdC, Li H, Cabeli V, Dupuis L, Simon F, Hettal L, Hamy A-S and Isambert H: Learning interpretable causal networks from very large datasets, application to 400,000 medical records of breast cancer patients iScience 27(5):109736 (2024). Pubmed | DOI | arxiv | pdf | pdf+supp
					Cosgrove J, Lyne A-M, Rodriguez I, Cabeli V, Conrad C, Tenreira-Bento S, Tubeuf E, Russo E, Tabarin F, Belloucif Y, Maleki-Toyserkani S, Reed S, Monaco F, Ager A, Lobry C, Bousso P, Fernandez-Marcos PJ, Isambert H, Arguello RJ, Perie L: Metabolically primed multipotent hematopoietic progenitors fuel innate immunity bioRxiv 2023.01.24.525166 (2023). Pubmed | bioRxiv | pdf | supp
					Sella N, Hamy AS, Cabeli V, Darrigues L, Lae M, Reyal F, Isambert H: Interactive exploration of a global clinical network from a large breast cancer cohort npj Digital Medicine 5, 113 (2022). Pubmed | DOI | pdf | supp
					Cabeli V, Li H, Ribeiro-Dantas M, Simon F, Isambert H: Reliable causal discovery based on mutual information supremum principle for finite dataset Why21 @ NeurIPS2021 (2021). Pubmed | DOI | pdf | supp
					Mencattini A, Spalloni A, Casti P, Comes MC, Di Giuseppe D, Antonelli G, D Orazio M, Filippi J, Corsi F, Isambert H, Di Natale C, Longone P, Martinelli E: NeuriTES. Monitoring neurite changes through transfer entropy and semantic segmentation in bright-field time-lapse microscopy Patterns 2(6):100261 (2021). Pubmed | DOI | pdf | supp
					Vial A, Taveneau C, Costa L, Chauvin B, Nasrallah H, Godefroy C, Dosset P, Isambert H, Ngo KX, Mangenot S, Levy D, Bertin A, Milhiet PE: Correlative AFM and fluorescence imaging demonstrate nanoscale membrane remodeling and ring-like and tubular structure formation by septins Nanoscale 13, 12484-12493 (2021). Pubmed | DOI | pdf | supp
					Cabeli V, Verny L, Sella N, Uguzzoni U, Verny M, Isambert H: Learning clinical networks from medical records based on information estimates in mixed-type data PLoS Comput Biol 16(5):e1007866 (2020). Pubmed | DOI | pdf | supp
					Desterke C, Petit L, Sella N, Chevallier N, Cabeli V, Coquelin L, Durand C, Oostendorp RAJ, Isambert H, Jaffredo T, Charbord P: Inferring gene networks in bone marrow Hematopoietic Stem Cell-supporting stromal niche populations iScience 23(6):101222 (2020). Pubmed | DOI | pdf | supp
					Singh PP, Isambert H: Ohnologs v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates Nucleic Acid Res 48(D1):D724-D730 (2020). Pubmed | DOI | pdf | supp | bioRxiv | Ohnologs server [recommended by F1000Prime]
					Arbabian A, Iftinca M, Altier C, Singh PP, Isambert H, Coscoy S: Mutations in calmodulin-binding domains of TRPV4/6 channels confer invasive properties to colon adenocarcinoma cells. Channels 14(1):101-109 (2020). Pubmed | DOI | pdf | supp
					Li H, Cabeli V, Sella N, Isambert H: Constraint-based causal structure learning with consistent separating sets. Advances in Neural Information Processing Systems (NeurIPS) 32, 14257-14266 (2019). Pubmed | DOI | pdf | supp
					Beber A, Taveneau C, Nania M, Tsai F-C, Di Cicco A, Bassereau P, Levy D, Cabral JT, Isambert H, Mangenot S, Bertin A: Membrane reshaping by micrometric curvature sensitive septin filaments. Nat Commun 10: 420 (2019). Pubmed | DOI | pdf | supp
					Sella N, Verny L, Uguzzoni G, Affeldt S, Isambert H: MIIC online: a web server to reconstruct causal or non-causal networks from non-perturbative data. Bioinformatics 34(13):2311-2313 (2018). Pubmed | OUP | pdf | MIIC online server
					Verny L, Sella N, Affeldt S, Singh PP, Isambert H: Learning causal networks with latent variables from multivariate information in genomic data. PLoS Comput Biol 13(10):e1005662 (2017). Pubmed | PLOS | pdf | supp [recommended by F1000]
					Affeldt S, Verny L, Isambert H: 3off2: A network reconstruction algorithm based on 2-point and 3-point information statistics. BMC Bioinformatics, 17 Suppl 2:12 (2016). Pubmed | BMC | pdf | supp
					Singh P-P, Arora J, Isambert H: Identification of ohnolog genes originating from whole genome duplication in early vertebrates, based on synteny comparison across multiple genomes. PLoS Comput Biol, 11(7):e1004394 (2015). Pubmed | PLOS | pdf | supp | Ohnologs server
					Affeldt S, Isambert H: Robust reconstruction of causal graphical models based on conditional 2-point and 3-point information. Proceedings of the 31th conference on Uncertainty in Artificial Intelligence (UAI), Amsterdam. Morgan Kaufmann (2015). [peer reviewed article] AUAI | pdf | supp
					Singh PP, Affeldt S, Malaguti G, Isambert H: Human dominant disease genes are enriched in paralogs originating from whole genome duplication. PLoS Comput Biol, 10(7):e1003754 (2014). Pubmed | PLOS | pdf
					Malaguti G, Singh PP, Isambert H. On the retention of gene duplicates prone to dominant deleterious mutations. Theor Popul Biol, 93:38-51 (2014). Pubmed | ScienceDirect | pdf
					Affeldt S, Singh PP, Cascone I, Selimoglu R, Camonis J, Isambert H: Evolution and cancer: expansion of dangerous gene repertoire by whole genome duplications. Med Sci, 29(4), 358-61 (2013) [french]. Pubmed | EDPSciences | pdf
					Singh PP, Affeldt S, Cascone I, Selimoglu R, Camonis J, Isambert H: On the expansion of "dangerous" gene repertoires by whole genome duplications in early vertebrates. Cell Rep, 2(5), 1387-1398 (2012). Pubmed | CellPress | pdf | supp [featured by Le Point, Biofutur, CNRS]
					Stein RR, Isambert H: Logistic map analysis of biomolecular network evolution. Phys Rev E, 84, 051904 (2011). Pubmed | APS | pdf
					Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulmé JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA: A boost for the emerging field of RNA nanotechnology. ACS Nano, 5(5):3405-18 (2011). Pubmed | ACS | pdf
					Viasnoff V, Bockelmann U, Isambert H, Laufer L, Tsori Y: Localized Joule heating produced by ion current focusing through micron-size holes. Appl Phys Lett, 96, 163701 (2010). AIP | pdf
					Cayrol B, Nogues C, Dawid A, Sagi I, Silberzan P, Isambert H: A nanostructure made of a bacterial noncoding RNA. J Am Chem Soc, 131(47):17270-6 (2009). Pubmed | ACS | pdf | supp [featured by HFSP]
					Isambert H, Stein RR: On the need for widespread horizontal gene transfers under genome size constraint. Biol Direct, 4:28 (2009). Pubmed | BMC | pdf
					Dawid A, Cayrol B, Isambert H: RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation. Phys Biol, 6(2):025007 (2009). Pubmed | IOP | pdf
					Isambert H: The jerky and knotty dynamics of RNA. Methods, 49(2):189-96 (2009). [review] Pubmed | ScienceDirect | pdf
					Sellerio AL, Bassetti B, Isambert H, Cosentino Lagomarsino M: A comparative evolutionary study of transcription networks. The global role of feedback and hierachical structures. Mol Biosyst, 5(2):170-9 (2009). Pubmed | RSC | pdf
					Evlampiev K, Isambert H: Conservation and topology of protein interaction networks under duplication-divergence evolution. Proc Natl Acad Sci USA, 105(29):9863-8 (2008). Pubmed | PNAS | pdf | supp
					Evlampiev K, Isambert H: Modeling protein network evolution under genome duplication and domain shuffling. BMC Syst Biol, 1:49 (2007). Pubmed | BMC | pdf | supp
					Cosentino Lagomarsino M, Jona P, Bassetti B, Isambert H: Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc Natl Acad Sci USA, 104(13):5516-20 (2007). Pubmed | PNAS | pdf | supp [featured by F1000]
					Xayaphoummine A, Viasnoff V, Harlepp S, Isambert H: Encoding folding paths of RNA switches. Nucleic Acids Res, 35(2):614-22 (2007). Pubmed | OXFORD | pdf [featured by HFSP]
					Viasnoff V, Meller A, Isambert H: DNA nanomechanical switches under folding kinetics control. Nano Lett, 6(1):101-4 (2006). Pubmed | ACS | pdf [featured by Nanowerk]
					Xayaphoummine A, Bucher T, Isambert H: Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res, 33:W605-10 (2005). Pubmed | OXFORD | pdf | supp | Kinefold server
					Harlepp S, Marchal T, Robert J, Léger JF, Xayaphoummine A, Isambert H, Chatenay D: Probing complex RNA structures by mechanical force. Eur Phys J E, 12(4):605-15 (2003). Pubmed | Springer | pdf
					Xayaphoummine A, Bucher T, Thalmann F, Isambert H: Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc Natl Acad Sci USA, 100(26):15310-5 (2003). Pubmed | PNAS | pdf
					Sens P, Isambert H: Undulation instability of lipid membranes under an electric field. Phys Rev Lett, 88(12):128102 (2002). Pubmed | APS | pdf [featured by NaturePhysics]
					Isambert H: Voltage addressable nanomemories in DNA? C R Physique, 3, 391-396 (2002). ScienceDirect | pdf
					Isambert H, Siggia ED: Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc Natl Acad Sci USA, 97(12):6515-20 (2000). Pubmed | PNAS | pdf [featured by Science]
					Magnúsdóttir S, Isambert H, Heller C, Viovy JL: Electrohydrodynamically induced aggregation during constant and pulsed field capillary electrophoresis of DNA. Biopolymers, 49(5):385-401 (1999). Pubmed | Wiley | pdf
					Isambert H: Understanding the electroporation of cells and artificial bilayer membranes. Phys Rev Lett, 80 (15), 3404 (1998). APS | pdf
					Ladoux B, Isambert H, Léger JF, Viovy JL: A new rectifying electrohydrodynamic instability at the boundary of charged gels. Phys Rev Lett, 81, 3793 (1998). APS | pdf
					Isambert H, Ajdari A, Viovy JL, Prost J: Electrohydrodynamic patterns in macroion dispersions under a strong electric field. Phys Rev E, 56, 5688 (1997). APS | pdf
					Isambert H, Ajdari A, Viovy JL, Prost J: Electrohydrodynamic patterns in charged colloidal solutions. Phys Rev Lett, 78 (5), 971 (1997). APS | pdf
					Isambert H, Maggs AC: Dynamics and rheology of actin solutions. Macromolecules, 29(3), 1036 (1996). ACS | pdf
					Isambert H, Maggs AC: Bending of actin filaments. Europhys Lett, 31, 263 (1995). IOP | pdf
					Isambert H, Venier P, Maggs AC, Fattoum A, Kassab R, Pantaloni D, Carlier MF: Flexibility of actin filaments derived from thermal fluctuations. J Biol Chem, 270(19):11437-44 (1995). Pubmed | ASBMB | pdf