Dehaene N, Boussardon C, Andrey P, Charif D, Brandt D, Gilouppe Taillefer C, Nietzel T, Ricou A, Simon M, Tran J, Vezon D, Camilleri C, Arimura SI, Schwarzländer M, Budar F (2024). The mitochondrial orf117Sha gene desynchronizes pollen development and causes pollen abortion in Arabidopsis Sha cytoplasmic male sterility. J Exp Bot, 75(16):4851-4872. PubMed | DOI

Cromer L, Tiscareño Andrade M, Lefranc S, Chambon A, Hurel A, Brogniez M, Guérin J, Le Masson I, Adam G, Charif D, Andrey P, Grelon M (2024). Rapid meiotic prophase chromosome movements in Arabidopsis thaliana are linked to essential reorganization at the nuclear envelope. Nat Commun, 15(1):5964. PubMed | DOI

Chelysheva L, Morin H, Biot E, Nicolas A, Rech P, Da Costa M, Barel L, Laufs P, Palauqui JC (2024). M2WISH: An easy and efficient protocol for whole-mount mRNA in situ hybridization that allows 3D cell resolution of gene expression in Arabidopsis thaliana. Plant J, doi: 10.1111/tpj.16792. PubMed | DOI

Keller D, Stinus S, Umlauf D, Gourbeyre E, Biot E, Olivier N, Mahou P, Beaurepaire E, Andrey P, Crabbe L (2024). Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF. iScience, 27(4):109343. PubMed | DOI

Laruelle E, Palauqui JC, Andrey P, Trubuil A (2023). TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images. Plant Methods, 19(1):128. PubMed | DOI

Oughou M, Biot E, Arnaud N, Maugarny A, Laufs P, Andrey P, Burguet J (2023). Model-based reconstruction of whole organ growth dynamics reveals invariant patterns in leaf morphogenesis. Quant Plant Biol, 4:e1, 1-11. DOI

Xiao G, Kumar Ro, Komuro Y, Burguet J, Kakarla V, Azizkhanian I, Sheth SA, Williams CK, Zhang XR, Macknicki R, Brumm A, Kawaguchi R, Mai P, Kaneko N, Vinters HV, Carmichael ST, Havton LA, DeCarli C, Hinman JD (2022). IL-17/CXCL5 signaling within the oligovascular niche mediates human and mouse white matter injury. Cell Rep, 41(12):111848. PubMed | DOI

Laruelle E, Belcram K, Trubuil A, Palauqui JC, Andrey P (2022). Large-scale analysis and computer modeling reveal hidden regularities behind variability of cell division patterns in Arabidopsis thaliana embryogenesis. Elife, 11:e79224. PubMed | DOI

Bellec Y, Guyon-Debast A, Francois T, Gissot L, Biot E, Nogué F, Faure JD, Tepfer M (2022). New Flowering and Architecture Traits Mediated by Multiplex CRISPR-Cas9 Gene Editing in Hexaploid Camelina sativa. Agronomy, 12(8): 1873. DOI

Rampin O, Saint Albin Deliot A, Ouali C, Burguet J, Gry E, Champeil Potokar G, Jérôme N, Davidenko O, Darcel N, Bombail V, Andrey P, Denis I (2022). Dopamine Modulates the Processing of Food Odour in the Ventral Striatum. Biomedicines, 10(5):1126. PubMed | DOI

Bouré N, Peaucelle A, Goussot M, Adroher B, Soubigou-Taconnat L, Borrega N, Biot E, Tariq Z, Martin-Magniette ML, Pautot V, Laufs P, Arnaud N (2022). A cell wall-associated gene network shapes leaf boundary domains. Development, 149(11):dev200359. PubMed | DOI

Arpòn J, Sakai K, Gaudin V, Andrey P (2021). Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin. Sci Rep, 11(1):323. PubMed | DOI

Haddad-Tovolli R, Altirriba J, Obri A, Sanchez EE, Chivite I, Mila-Guasch M, Ramirez S, Gomez-Valades AG, Pozo M, Burguet J, Velloso LA, Claret M (2020). Pro-opiomelanocortin (POMC) neuron translatome signatures underlying obesogenic gestational malprogramming in mice. Mol Metab, 36:100963. PubMed | DOI

Burguet J, Andrey P (2020). Edge correction for intensity estimation of 3D heterogeneous point processes from replicated data. Spat Stat, 36:100421. DOI

Farmer DGS, Pracejus N, Dempsey B, Turner A, Bokiniec P, Paton JFR, Pickering AE, Burguet J, Andrey P, Goodchild AK, Mcallen RM, Mcmullan S (2019). On the presence and functional significance of sympathetic premotor neurons with collateralized spinal axons in the rat. J Physiol, 597:3407-3423. PubMed | DOI

Moukhtar J, Trubuil A, Belcram K, Legland D, Khadir Z, Urbain A, Palauqui JC, Andrey P (2019). Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos. PLoS Comput Biol, 15:e1006771. PubMed | DOI

Selka F, Burguet J, Biot E, Blein T, Laufs P, Andrey P (2019). Surface parameterization and registration for statistical multiscale atlasing of organ development. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops, pp. 134-139, Long Beach, CA. DOI

Oughou M, Cunha E, Biot E, Arnaud N, Laufs P, Andrey P, Burguet J (2019). Dynamic atlasing of gene expression domains from individual images. In 16th IEEE International Symposium on Biomedical Imaging (ISBI 2019): From Nano to Macro, pp. 662-665, Venice, Italy, 8-11 April. DOI

Arganda-Carreras I, Manoliu T, Mazuras N, Schulze F, Iglesias JE, Buhler K, Jenett A, Rouyer F, Andrey P (2018). A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain. Front Neuroinform, 12:13. PubMed | DOI

Arpòn J, Gaudin V, Andrey P (2018). A Method for Testing Random Spatial Models on Nuclear Object Distributions. Methods Mol Biol, 1675:493-507. PubMed | DOI

Fernandes JB, Duhamel M, Seguela-Arnaud M, Froger N, Girard C, Choinard S, Solier V, De Winne N, De Jaeger G, Gevaert K, Andrey P, Grelon M, Guerois R, Kumar R, Mercier R (2018). FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination. PLoS Genet, 14:e1007317. PubMed | DOI

Serra L, Arnaud N, Selka F, Rechenmann C, Andrey P, Laufs P (2018). Heterogeneity and its multiscale integration in plant morphogenesis. Curr Opin Plant Biol, 46:18-24. PubMed | DOI

Arganda-Carreras I, Andrey P (2017). Designing Image Analysis Pipelines in Light Microscopy: A Rational Approach. Methods Mol Biol, 1563:185-207. PubMed | DOI

Chehensse C, Facchinetti P, Bahrami S, Andrey P, Soler JM, Chretien F, Bernabe J, Clement P, Denys P, Giuliano F (2017). Human spinal ejaculation generator. Ann Neurol, 81:35-45. PubMed | DOI

Schaefer E, Belcram K, Uyttewaal M, Duroc Y, Goussot M, Legland D, Laruelle E, De Tauzia-Moreau ML, Pastuglia M, Bouchez D (2017). The preprophase band of microtubules controls the robustness of division orientation in plants. Science, 356:186-189. PubMed | DOI

Selka F, Blein T, Burguet J, Biot E, Laufs P, Andrey P (2017). Towards a spatio-temporal atlas of 3D cellular parameters during leaf morphogenesis. In Proceedings of the IEEE International Conference on Computer Vision (ICCV), pp. 56-63, Venice, Italy. DOI

Bastien R, Legland D, Martin M, Fregosi L, Peaucelle A, Douady S, Moulia B, Höfte H (2016). KymoRod: a method for automated kinematic analysis of rod-shaped plant organs. Plant J, 88:468-475. PubMed | DOI

Biot E, Cortizo M, Burguet J, Kiss A, Oughou M, Maugarny-Calès A, Goncalves B, Adroher B, Andrey P, Boudaoud A, Laufs P (2016). Multiscale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis. Development, 143:3417-3428. PubMed | DOI

Biot E, Crowell E, Burguet J, Höfte H, Vernhettes S, Andrey P (2016). Strategy and software for the statistical spatial analysis of 3D intracellular distributions. Plant J, 87:230-242. PubMed | DOI

Legland D, Arganda-Carreras I, Andrey P (2016). MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics, 32:3532-3534. PubMed | DOI

Molitor AM, Latrasse D, Zytnicki M, Andrey P, Houba-Herin N, Hachet M, Battail C, Del Prete S, Alberti A, Quesneville H, Gaudin V (2016). The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes. Plant Cell, 28:2197-2211. PubMed | DOI

Poulet A, Arganda-Carreras I, Legland D, Probst AV, Andrey P, Tatout C (2015). NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. Bioinformatics, 31:1144-1146. PubMed | DOI

Silva JVC, Legland D, Cauty C, Kolotuev I, Floury J (2015). Characterization of the microstructure of dairy systems using automated image analysis. Food Hydrocolloids, 44:360-371. PubMed | DOI

Burguet J, Andrey P (2014). Statistical comparison of spatial point patterns in biological imaging. PLoS One, 9:e87759. PubMed | DOI

Del Prete S, Arpòn J, Sakai K, Andrey P, Gaudin V (2014). Nuclear architecture and chromatin dynamics in interphase nuclei of Arabidopsis thaliana. Cytogenet Genome Res, 143:28-50. PubMed | DOI

Gul-Mohammed J, Arganda-Carreras I, Andrey P, Galy V, Boudier T (2014). A generic classification-based method for segmentation of nuclei in 3D images of early embryos. BMC Bioinformatics, 15:9. PubMed | DOI

Legland D, Devaux MF, Guillon F (2014). Statistical mapping of maize bundle intensity at the stem scale using spatial normalisation of replicated images. PLoS One, 9:e90673. PubMed | DOI

Miart F, Desprez T, Biot E, Morin H, Belcram K, Höfte H, Gonneau M, Vernhettes S (2014). Spatio-temporal analysis of cellulose synthesis during cell plate formation in Arabidopsis. Plant J, 77:71-84. PubMed | DOI

Vain T, Crowell EF, Timpano H, Biot E, Desprez T, Mansoori N, Trindade LM, Pagant S, Robert S, Höfte H, Gonneau M, Vernhettes S (2014). The Cellulase KORRIGAN Is Part of the Cellulose Synthase Complex. Plant Physiol, 165:1521-1532. PubMed | DOI

Burguet J, Mailly P, Andrey P (2013). Statistical groupwise comparison of spatial point patterns in biological imaging. In 2013 International Symposium on Biomedical Imaging: From Nano to Macro, pp. 456-459, San Francisco, 7-11 April. DOI

Ernoult-Lange M, Baconnais S, Harper M, Minshall N, Souquere S, Boudier T, Benard M, Andrey P, Pierron G, Kress M, Standart N, Le Cam E, Weil D (2012). Multiple binding of repressed mRNAs by the P-body protein Rck/p54. RNA, 18:1702-1715. PubMed | DOI

Burguet J, Mailly P, Maurin Y, Andrey P (2011). Reconstructing the three-dimensional surface of a branching and merging biological structure from a stack of coplanar contours. In Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011): From Nano to Macro, pp. 602-605, Chicago, March 30-April 2. DOI

Andrey P, Kieu K, Kress C, Lehmann G, Tirichine L, Liu Z, Biot E, Adenot PG, Hue-Beauvais C, Houba-Herin N, Duranthon V, Devinoy E, Beaujean N, Gaudin V, Maurin Y, Debey P (2010). Statistical analysis of 3D images detects regular spatial distributions of centromeres and chromocenters in animal and plant nuclei. PLoS Comput Biol, 6:e1000853. PubMed | DOI

Simon A, Biot E (2010). ANAIS: analysis of NimbleGen arrays interface. Bioinformatics, 26:2468-2469. PubMed | DOI

Gaudin V, Andrey P, Devinoy E, Kress C, Kieu K, Beaujean N, Maurin Y, Debey P (2009). Modeling the 3D functional architecture of the nucleus in animal and plant kingdoms. C R Biol, 332:937-946. PubMed | DOI

Tirichine L, Andrey P, Biot E, Maurin Y, Gaudin V (2009). 3D fluorescent in situ hybridization using Arabidopsis leaf cryosections and isolated nuclei. Plant Methods, 5:11. PubMed | DOI

Biot E, Crowell E, Höfte H, Maurin Y, Vernhettes S, Andrey P (2008). A new filter for spot extraction in N-dimensional biological imaging. In Fifth IEEE International Symposium on Biomedical Imaging (ISBI'08): From Nano to Macro, pp. 975-978, Paris, May 14-17. DOI