Publications
Unraveling spatial cellular pattern by computational tissue shuffling
E. Laruelle, N. Spassky✉, A. Genovesio✉
2020, Communications Biology, doi : 10.1038/s42003-020-01323-3
In vivo large-scale analysis of Drosophila neuronal calcium traces by automated tracking of single somata
F Delestro*, L Scheunemann*, M Pedrezzani, P Tchenio, T Preat✉, A Genovesio✉
2020, Scientific Reports, doi : 10.1038/s41598-020-64060-x
Artificially decreasing cortical tension generates aneuploidy in mouse oocytes
I Bennabi, F Crozet, E Nikalayevich, A Chaigne, G Letort, M Manil-Ségalen, C Campillo, C Cadart, A Othmani, R Attia, A Genovesio, M-H Verlhac✉, M-E Terret✉
2020, Nature communications, doi : 10.1038/s41467-020-15470-y
Coordination of transcriptional and translational regulations in human cells infected by Listeria monocytogenes
V. Besic, F. Habibolahi*, B. Noël*, S. Rupp, A. Genovesio and A. Lebreton✉
2020, RNA Biology, doi : 10.1080/15476286.2020.1777380.
PhaeoNet : a holistic RNAseq-based portrait of transcriptional coordination in the model diatom Phaeodactylum tricornutum
O Ait-Mohamed, AMG Novák Vanclová, N Joli, Y Liang, X Zhao, A Genovesio, L Tirichine✉, C Bowler✉, R Dorrell
2020, Front. Plant Sci. doi : 10.3389/fpls.2020.590949
PySpacell : A Python Package for Spatial Analysis of Cell Images.
F Rose, L Rappez, SH Triana, T Alexandrov, A Genovesio✉
2019, Cytometry Part A, doi : 10.1002/cyto.a.23955
Active Fluctuations of the Nuclear Envelope Shape the Transcriptional Dynamics in Oocytes
M Almonacid, A Al Jord, S El-Hayek, A Othmani, F Coulpier, S Lemoine, K Miyamoto, R Grosse, C Klein, T Piolot, P Mailly, R Voituriez, A Genovesio✉, M-H Verlhac✉
2019, Developmental Cell, doi:10.1016/j.devcel.2019.09.010
m5C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants
L Yang, V Perrera, E Saplaoura, F Apelt, M Bahin, A Kramdi, J Olas, B Mueller-Roeber, E Sokolowska, W Zhang, R Li, N Pitzalis, M Heinlein, S Zhang, A Genovesio, V Colot, F Kragler✉
2019, Current Biology, doi:10.1016/j.cub.2019.06.042
ALFA : annotation landscape for aligned reads
M Bahin*, B F Noel*, V Murigneux, C Bernard, L Bastianelli, H Le Hir, A Lebreton✉, A Genovesio✉
2019, BMC Genomics, doi:10.1186/s12864-019-5624-2
Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members
Ortiz-Álvarez G*, Daclin M*, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti ME, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N✉
2019 Neuron, doi.org/10.1016/j.neuron.2019.01.051.
Monitored eCLIP : high accuracy mapping of RNA-protein interactions
R Hocq*, J Paternina*, Q Alasseur, A Genovesio✉, H Le Hir✉
2018, Nucleic Acid Research, doi.org/10.1093/nar/gky858
High‐Throughput Optical Mapping of Replicating DNA
F De Carli*, N Menezes*, W Berrabah, V Barbe, A Genovesio✉, O Hyrien✉
2018, Small Methods, doi.org/10.1002/smtd.201800146
DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis
A Nassrallah, M Rougée, C Bourbousse, S Drevensek, S Fonseca, E Iniesto, O Ait-Mohamed, A-F Deton-Cabanillas, G Zabulon, I Ahmed, D Stroebel, V Masson, B Lombard, D Eeckhout, K Gevaert, D Loew, A Genovesio, C Breyton, G de Jaeger, C Bowler✉, V Rubio✉, F Barneche✉
2018, eLIFE, doi:10.7554/eLife.37892
FastSME : faster and smoother manifold extraction from 3D stack
S Basu, E Rexhepaj, N Spassky, A Genovesio, R R Paulsen, ASM Shihavuddin✉
2018, IEEE Computer Vision and Pattern Recognition Conference (CVPR)
Ependymal cilia beating induces an actin network to protect centrioles against shear stress
A Mahuzier, A Shihavuddin, C Fournier, P Lansade, M Faucourt, N Menezes, A Meunier, M Garfa-Traoré, M-F Carlier, R Voituriez, A Genovesio, N Spassky✉, N Delgehyr✉
2018, Nature Communications, doi:doi.org/10.1038/s41467-018-04676-w
Compound Functional Prediction Using Multiple Unrelated Morphological Profiling Assays
F Rose*, S Basu*, E Rexhepaj, A Chauchereau, E Del Nery, A Genovesio✉
2017, SLAS Technology, doi:10.1177/2472630317740831
Calibrated mitotic oscillator drives motile ciliogenesis
A Al Jord, A Shihavuddin, R Servignat d’Aout, M Faucourt, A Genovesio, A Karaiskou, J Sobczak-Thépot, N Spassky, A Meunier✉
2017, Science, doi : 10.1126/science.aan8311
Smooth 2D manifold extraction from 3D image stack
A Shihavuddin*, S Basu*, E Rexhepaj, F Delestro, N Menezes, SM Sigoillot, E Del Nery, F Selimi, N Spassky, A Genovesio✉
2017, Nature Communications, doi:10.1038/ncomms15554
An RNAi Screen in a Novel Model of Oriented Divisions Identifies the Actin-Capping Protein Z β as an Essential Regulator of Spindle Orientation
F di Pietro, L Valon, Y Li, R Goïame, A Genovesio, X Morin✉
2017, Current Biology, Volume 27, Issue 16, 21 August, Pages 2452-2464.e8 doi.org/10.1016/j.cub.2017.06.055
Translation in astrocyte distal processes sets molecular heterogeneity at the gliovascular interface
Boulay AC, Saubaméa B, Adam N, Chasseigneaux S, Mazaré N, Gilbert A, Bahin M, Bastianelli L, Blugeon C, Perrin S, Pouch J, Ducos B, Le Crom S, Genovesio A, Chrétien F, Declèves X, Laplanche JL, Cohen-Salmon M.✉
2017 Cell Discov. doi : 10.1038/celldisc.2017.5
mTORC1 signaling and primary cilia are required for brain ventricle morphogenesis
P Foerster, M Daclin, A Shihavuddin, M Faucourt, A Boletta, A Genovesio, N Spassky✉
2016, Development : doi : 10.1242/dev.138271
Detection and tracking of overlapping cell nuclei for large scale mitosis analyses
Y Li*, F Rose*, F di Pietro, X Morin, A Genovesio✉
2016, BMC bioinformatics 17 (1), 1, doi:10.1186/s12859-016-1030-9
High-throughput in vivo genotoxicity testing : an automated readout system for the somatic mutation and recombination test (SMART)
B Lombardot*, CT Oh*, J Kwak, A Genovesio, M Kang, MAE Hansen✉, SJ Han✉
2015, PloS one 10 (4), e0121287
Increasing the content of high-content screening an overview
S Singh, AE Carpenter✉, A Genovesio✉
2014, Journal of biomolecular screening 19 (5), 640-650
Dimerization, oligomerization, and aggregation of human amyotrophic lateral sclerosis Copper/Zinc superoxide dismutase 1 protein mutant forms in live cells
J Kim*, H Lee*, JH Lee, D Kwon, A Genovesio, D Fenistein, A Ogier, V Brondani, R Grailhe✉
2014, Journal of Biological Chemistry 289 (21), 15094-15103
Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment
V Ljosa, PD Caie, R ter Horst*, KL Sokolnicki*, EL Jenkins, S Daya, ME Roberts, TR Jones, S Singh, A Genovesio, PA Clemons, NO Carragher, AE Carpenter✉
2013, Journal of biomolecular screening, 1087057113503553
Development of a multiplex phenotypic cell-based high throughput screening assay to identify novel hepatitis C virus antivirals
HY Kim, X Li, CT Jones, CM Rice, JM Garcia, A Genovesio, MAE Hansen, MP Windisch✉
2013, Antiviral research 99 (1), 6-11
Transcription Sites Are Developmentally Regulated during the Asexual Cycle of Plasmodium falciparum
CB Moraes, T Dorval, M Contreras-Dominguez, FM Dossin, MAE Hansen, A Genovesio, LH Freitas-Junior✉
2013, PloS one 8 (2)
An image-based drug susceptibility assay targeting the placental sequestration of Plasmodium falciparum-infected erythrocytes
MJ Ku*, FM Dossin*, MAE Hansen*, A Genovesio, L Ayong, LH Freitas-Junior✉
2012, PloS one 7 (8), e41765
An image-based high-content screening assay for compounds targeting intracellular Leishmania donovani amastigotes in human macrophages
JL Siqueira-Neto*, S Moon*, J Jang*, G Yang, C Lee, HK Moon, E Chatelain, A Genovesio✉, J Cechetto✉, LH Freitas-Junior✉
2012, PLoS Negl Trop Dis 6 (6), e1671
A high-content subtractive screen for selecting small molecules affecting internalization of GPCRs
YJ Kwon, W Lee, A Genovesio, N Emans✉
2012, Journal of biomolecular screening 17 (3), 379-385
Quantification of protein interaction in living cells by two‐photon spectral imaging with fluorescent protein fluorescence resonance energy transfer pair devoid of acceptor bleed‐through
J Kim, X Li, MS Kang, KB Im✉, A Genovesio, R Grailhe✉
2012, Cytometry Part A 81 (2), 112-119
A novel specific edge effect correction method for RNA interference screenings
JP Carralot✉, A Ogier, A Boese, A Genovesio, P Brodin, P Sommer, T Dorval✉
2012, Bioinformatics 28 (2), 261-268
Automated Identification and Analysis of Visual Micro-experiments on Cellular Microarray
A Genovesio✉
2012, Advances in Bio-Imaging : From Physics to Signal Understanding Issues, 27-33
Automated genome-wide visual profiling of cellular proteins involved in HIV infection
A Genovesio*✉, YJ Kwon*, MP Windisch*, NY Kim, SY Choi, HC Kim, S Jung, F Mammano, V Perrin, AS Boese, N Casartelli, O Schwartz, U Nehrbass, N Emans✉
2011, Journal of biomolecular screening 16 (9), 945-958
A method for discontinuous neurite reconstruction based on diffusion tensor, Hessian eigenvector, and diffused gradient vector fields
HC Kim, G Stamon, A Genovesio✉
2011, ICIP. Proceedings of the 18th IEEE International Conference on Image Processing, 1401-1404
Visual genome-wide RNAi screening to identify human host factors required for Trypanosoma cruzi infection
A Genovesio*, MA Giardini*, YJ Kwon*, F de Macedo Dossin, SY Choi, NY Kim, HC Kim, SY Jung, S Schenkman, IC Almeida, N Emans✉, LH Freitas-Junior✉
2011, PLoS One 6 (5), e19733
3D Detection of Mutant Hairs in Drosophila Wing Images
J Kwak, CT Oh, SJ Han, M Hansen, A. Genovesio✉, M Kang✉
2011, 한국산업응용수학회 학술대회 논문집 Vol. 6 No. 1 6 (1), 221-224
A modified fluorescence in situ hybridization protocol for Plasmodium falciparum greatly improves nuclear architecture conservation
M Contreras-Dominguez*, CB Moraes*, T Dorval, A Genovesio, F de Macedo Dossin, LH Freitas-Junior✉
2010, Molecular and biochemical parasitology 173 (1), 48-52
High content phenotypic cell-based visual screen identifies Mycobacterium tuberculosis acyltrehalose-containing glycolipids involved in phagosome remodeling
P Brodin*, Y Poquet*, F Levillain*, I Peguillet*, G Larrouy-Maumus, M Gilleron, F Ewann, T Christophe, D Fenistein, J Jang, MS Jang, SJ Park, J Rauzier, JP Carralot, R Shrimpton, A Genovesio, JA Gonzalo-Asensio, G Puzo, C Martin, R Brosch, GR Stewart, B Gicquel, O Neyrolles✉
2010, PLoS Pathog 6 (9), e1001100
Contextual automated 3D analysis of subcellular organelles adapted to high-content screening
T Dorval✉, A Ogier, A Genovesio, HK Lim, JH Lee, HJ Worman, W Dauer, R Grailhe✉
2010, Journal of biomolecular screening 15 (7), 847-857
Antileishmanial high-throughput drug screening reveals drug candidates with new scaffolds
JL Siqueira-Neto*, OR Song*, H Oh*, JH Sohn, G Yang, J Nam, J Jang, J Cechetto, CB Lee, S Moon, A Genovesio, E Chatelain, T Christophe, LH Freitas-Junior✉
2010, PLoS Negl Trop Dis 4 (5), e675
Spatially adaptive relaxation for active contour cell segmentation
A Ogier, T Dorval, B Kim, A Genovesio✉
2010, Proceedings of the 2010 IEEE international conference on Biomedical imaging : from nano to Macro
Hair Separation and Detection in Mutant Drosophila Hair Images
J Kwak, CT Oh, SJ Han, M Kang✉, A Genovesio
2010, Proceedings of the Korean Society for Industrial and Applied Mathmatics 5 (1)
Active vector graph for regularized tesselation
A Genovesio✉
2009, ICIP. Proceedings of the 16th IEEE International Conference on Image Processing, 2429-2432
High content screening identifies decaprenyl-phosphoribose 2′ epimerase as a target for intracellular antimycobacterial inhibitors
T Christophe, M Jackson, HK Jeon, D Fenistein, M Contreras-Dominguez, J Kim, A Genovesio, JP Carralot, F Ewann, EH Kim, SY Lee, S Kang, MJ Seo, EJ Park, H Škovierová, H Pham, G Riccardi, JY Nam, L Marsollier, M Kempf, ML Joly-Guillou, T Oh, WK Shin, ZN, U Nehrbass, R Brosch, ST Cole, P Brodin✉
2009, PLoS Pathog 5 (10), e1000645
In vivo colocalisation of oskar mRNA and trans-acting proteins revealed by quantitative imaging of the Drosophila oocyte
MM Mhlanga*✉, DP Bratu*, A Genovesio, A Rybarska, N Chenouard, U Nehrbass, JC Olivo-Marin
2009, PloS one 4 (7), e6241
3D spatial drift correction using Kalman filtering for fluorescence based imaging
T Dorval, CB Moraes, A Ogier, LH Freitas, A Genovesio✉
2009, ISBI. Proceedings of the IEEE International Symposium on Biomedical Imaging : From Nano to Macro
Automated high-throughput siRNA transfection in raw 264.7 macrophages : a case study for optimization procedure
JP Carralot✉, TK Kim, B Lenseigne, AS Boese, P Sommer, A Genovesio, P Brodin
2009, Journal of biomolecular screening
Neuron branch detection and description using random walk
HC Kim, A Genovesio✉
2009, Proceedings of the IEEE Engineering in Medicine and Biology Society.
A fast, fully automated cell segmentation algorithm for high‐throughput and high‐content screening
D Fenistein✉, B Lenseigne, T Christophe, P Brodin, A Genovesio
2008, Cytometry part A 73 (10), 958-964
Im. Grid, a grid computing approach for image mining of high throughput-high content screening
HK Moon, A Genovesio✉
2008, Proceedings of the 9th IEEE/ACM International Conference on Grid Computing
Automated nuclear analysis of Leishmania major telomeric clusters reveals changes in their organization during the parasite’s life cycle
FM Dossin*, A Dufour*, E Dusch*, JL Siqueira-Neto, CB Moraes, GS Yang, MI Cano, A Genovesio, LH Freitas-Junior✉
2008, PloS one 3 (6), e2313
Inhomogeneous deconvolution in a biological images context
A Ogier, T Dorval, A Genovesio✉
2008, ISBI. Proceedings of the 5th IEEE International Symposium on Biomedical Imaging : From Nano to Macro
Three‐dimensional point spread function model for line‐scanning confocal microscope with high‐aperture objective
E Dusch✉, T Dorval, N Vincent, M Wachsmuth, A Genovesio✉
2007, Journal of microscopy 228 (2), 132-138
Bias image correction via stationarity maximization
T Dorval, A Ogier, A Genovesio✉
2007, MICCAI. Medical Image Computing and Computer-Assisted Intervention, 693-700
3D automated nuclear morphometric analysis using Active Meshes
A Dufour✉, JH Lee, N Vincent, R Grailhe, A Genovesio✉
2007, Pattern Recognition in Bioinformatics, 356-367
3D fluorescent spots detection in line-scanning confocal microscopy
E Dusch, N Vincent, A Genovesio✉
2007, ICIP. Proceedings of the IEEE International Conference on Image Processing, 6, VI-241-VI-244
Biased image correction based on empirical mode decomposition
A Ogier, T Dorval, A Genovesio✉
2007, ICIP 2007. Proceedings of the IEEE International Conference on Image Processing, 1, I-533-I-536
A new color representation for intensity independent pixel classification in confocal microscopy images
B Lenseigne, T Dorval, A Ogier, A Genovesio✉
2007, Advanced Concepts for Intelligent Vision Systems, 597-606
High-content classification of nucleocytoplasmic import or export inhibitors
YJ Kwon, A Genovesio, NY Kim, HC Kim, S Jung, B David-Watine, U Nehrbass, N Emans✉
2007, Journal of biomolecular screening
Bias free features detection for high content screening
T Dorval, A Ogier, E Dusch, N Emans, A Genovesio✉
2007, ISBI. IEEE International Symposium on Biomedical Imaging : From Nano to Macro, 2007.
Support vector machines for automatic detection of tuberculosis bacteria in confocal microscopy images
B Lenseigne, P Brodin, HK Jeon, T Christophe, A Genovesio✉
2007, ISBI. IEEE International Symposium on Biomedical Imaging : From Nano to Macro, 2007.
3D Mumford-Shah based active mesh
A Dufour✉, N Vincent, A Genovesio
2006, Progress in Pattern Recognition, Image Analysis and Applications, 208-217
Automated confocal microscope bias correction
T Dorval, A Genovesio✉
2006, Information Optics : Proceedings of the 5th International Workshop on Information Optics (WIO’06)
Quantitative four-dimensional tracking of cytoplasmic and nuclear HIV-1 complexes
N Arhel*, A Genovesio*, KA Kim, S Miko, E Perret, JC Olivo-Marin✉, S Shorte, P Charneau✉
2006, Nature methods 3 (10), 817-824
Cerebral microcirculation shear stress levels determine Neisseria meningitidis attachment sites along the blood–brain barrier
E Mairey, A Genovesio, E Donnadieu, C Bernard, F Jaubert, E Pinard, J Seylaz, JC Olivo-Marin, X Nassif, G Duménil✉
2006, The Journal of experimental medicine 203 (8), 1939-1950
SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope
GG Cabal*, A Genovesio*, S Rodriguez-Navarro, C Zimmer, O Gadal, A Lesne, H Buc, F Feuerbach-Fournier, JC Olivo-Marin, E C Hurt✉, U Nehrbass✉
2006, Nature 441 (7094), 770-773
Multiple particle tracking in 3-D+ t microscopy : method and application to the tracking of endocytosed quantum dots
A Genovesio, T Liedl, V Emiliani, WJ Parak, M Coppey-Moisan, JC Olivo-Marin✉
2006, IEEE Transactions on Image Processing, 15 (5), 1062-1070
Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region
P Therizols, C Fairhead, GG Cabal, A Genovesio, JC Olivo-Marin, B Dujon, E Fabre✉
2006, The Journal of cell biology 172 (2), 189-199
Adaptive gating in Gaussian Bayesian multi-target tracking
A Genovesio✉, Z Belhassine, JC Olivo-Marin✉
2004, ICIP. International Conference on Image Processing, 1, 147-150
Split and merge data association filter for dense multi-target tracking
A Genovesio✉, JC Olivo-Marin
2004, ICPR, Proceedings of the 17th International Conference on Pattern Recognition
Interacting multiple model based method to track moving fluorescent biological spots
A Genovesio✉, B Zhang, JC Olivo-Marin✉
2004, ISBI. Proceedings of the IEEE International Symposium on Biomedical Imaging : Nano to Macro.
Tracking of multiple fluorescent biological objects in three dimensional video microscopy
A Genovesio✉, B Zhang, JC Olivo-Marin✉
2003, ICIP Proceedings of the International Conference on Image Processing
Tracking fluroescent spots in biological video microscopy
A Genovesio✉, JC Olivo-Marin✉
2003, Biomedical Optics 2003, 98-105
Patents
Anti-infective compounds
P Brodin, T Christophe, Z No, J Kim, A Genovesio, DPC Fenistein, H Jeon, FA Ewann, S Kang, S Lee, MJ Seo, P Eunjung, M Contreras Dominguez, JY Nam, EH Kim
2014, US Patent 8,785,452
Genome Wide Visual Identification of Human Co-Factors of HIV-1 Infection
N Emans, A Genovesio, MP Windisch, YJ Kwon, S Jung, HC Kim, NY Kim, S Yeon
2014, European Patent 2307568, 2011 US Patent app 20110183313
Method and apparatus for imaging of features on a substrate
A Genovesio, N Emans
2014, US Patent 8,692,876
Anti-infective compounds
Z No, J Kim, P Brodin, MJ Seo, YM Kim, J Cechetto, H Jeon, A Genovesio, S Lee, S Kang, FA Ewann, JY Nam, T Christophe, DPC Fenistein, J Heo, J Jiyeon
2013, US Patent 8,865,734
Anti-infective pyrido (1, 2-a) pyrimidines
Z No, J Kim, P Brodin, MJ Seo, P Eunjung, J Cechetto, H Jeon, EH Kim, J Heo, JY Nam, DPC Fenistein, T Christophe, MC Dominguez, A Genovesio, S Lee, S Kang, FA Ewann
2013, US Patent App. 20130012506
