Publications:
B. T. Analikwu, A. Deshayes, J. van der Torre, T. Guérin, A. J. Katan, C. Béneut, R. Barth, J. Phipps, V. Scolari, X. Veaute, C. Barrington, D. Busso, F. Uhlmann, K. Dubrana, S. Mattarocci&, C. Dekker, S. Marcand. Telomere protein arrays stall DNA loop extrusion by condensin. Cell Reports (2025). https://doi.org/10.1016/j.celrep.2025.115900
A. Banderas, M. Hofmann, C. Cordier, M. Le Bec, C. Elizondo, L. Chiron, S. Pouzet, V. Scolari, P. Hersen. Optogenetic control of pheromone gradients and mating behavior in budding yeast, Life Science Alliance (2025). https://doi.org/10.26508/lsa.202403078
Q. Chaboche, G. Campos-Villalobos, G. Giunta, M. Dijkstra, M. Cosentino-Lagomarsino, V. Scolari. A mean-field theory for predicting single polymer collapse induced by neutral crowders. Soft Matter (2024). https://doi.org/10.1039/d3sm01522j
M. Le Bec, S. Pouzet, C. Cordier, S. Barral, V. Scolari, B. Sorre, A. Banderas and P. Hersen. Optogenetic spatial patterning of cooperation in yeast populations. Nature communications 15, 75 (2024). 10.1038/s41467-023-44379-5. https://doi.org/10.1038/s41467-023-44379-5
V. I. P. Keizer, S. Grosse-Holz, M. Woringer, L. Zambon, K. Aizel, M. Bongaerts, F. Delille, L. Kolar-Znika, V.F. Scolari, S. Hoffmann, E. J. Banigan, L. A. Mirny, M. Dahan, D. Fachinetti, A. Coulon. Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics. Science, Vol 377, Issue 6605, pp. 489-495. https://doi.org/10.1126/science.abi9810 . Press: https://www.lefigaro.fr/sciences/les-chromosomes-sont-fluides-dans-le-noyau-des-cellules-20220731
M. Ruault, V. F. Scolari, L. Lazar-Stefanita, A. Hocher, I. Loiodice, C. Nous, R. Koszul, A. Taddei. Sir3 mediates long-range chromosome interactions in budding yeast. Genome Research 31, no. 3 (2021): 411–25. https://doi.org/10.1101/gr.267872.120
G. Pagani, A. Giacomelli, F. Conti, D. Bernacchia, R. Rondanin, A. Prina, V. Scolari, A. Rizzo, M. Beltrami, C. Caimi, C.E. Gandolfi, S. Castaldi, B.A. Rivieccio, G. Buonanno, G. Marano, C. Ottomano, P. Boracchi, E. Biganzoli, M. Galli. Prevalence of SARS-CoV-2 in an area of unrestricted viral circulation: Mass seroepidemiological screening in Castiglione d’Adda, Italy. PloS one 16 (2), e0246513, 2021, https://doi.org/10.1371/journal.pone.0246513
C. Matthey-Doret, L. Baudry, A. Breuer, N. Guiglielmoni, P.Moreau, A. Vigouroux, R.Montagne, V. Scolari, L. Politis, A. Meot, E. Oriol, P. Chanut, A. Campeas, E. Jean, R. Koszul, A. Cournac. Chromosight: A computer vision program for pattern detection in chromosome contact maps. Nature Communications volume 11, 5795 (2020), https://doi.org/10.1038/s41467-020-19562-7
G. Pagani, F. Conti, A. Giacomelli, D. Bernacchia, R. Rondanin, A. Prina, V. Scolari, C. E. Gandolfi, S. Castaldi, G. Marano, C. Ottomano, P. Boracchi, E. M. Biganzoli, M. Galli. Seroprevalence of SARS-CoV-2 IgG significantly varies with age: Preliminary results from a mass population screening. Journal of Infection, Sept. 2020, https://doi.org/10.1016/j.jinf.2020.09.021
L. Baudry, G. A. Millot, A. Thierry, R. Koszul and V.F. Scolari. Serpentine: a flexible 2D binning method for differential Hi-C analysis. Bioinformatics, 36(12), 2020, 3645–3651, https://doi.org/10.1093/bioinformatics/btaa249
V.F. Scolari, G. Mercy, R. Koszul, A. Lesne, J. Mozziconacci. Kinetic Signature of Cooperativity in the Irreversible Collapse of a Polymer. Physical Review Letter, 2018, 121, 057801, https://arxiv.org/abs/1804.04099, https://doi.org/10.1103/PhysRevLett.121.057801
H. Muller, V.F. Scolari, N. Agier, A. Piazza, A. Thierry, G. Mercy, S. Descorps-Declere, L. Lazar-Stefanita, O. Espeli, B. Llorente, G. Fischer, J. Mozziconacci, R. Koszul. Characterizing meiotic chromosomes’ structure and pairing using a designer sequence optimized for Hi-C. Molecular Systems Biology, 2018, 14, e8293, featured on the cover, https://doi.org/10.15252/msb.20188293
L. Lazar-Stefanita, V.F. Scolari, G. Mercy, H. Muller, T. M. Guérin, A. Thierry, J. Mozziconacci, R. Koszul. Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle. The EMBO journal, 2017, e201797342, featured on the cover, https://doi.org/10.15252/embj.201797342
G. Mercy, J. Mozziconacci, V.F. Scolari, K. Yang, G. Zhao, A. Thierry, Y. Luo, L.A. Mitchell, M. Shen, Y. Shen, R. Walker, W. Zhang, Yi Wu, Z. Xie, Z. Luo, Y. Cai, J. Dai, H. Yang, Y.Yuan, J.D. Boeke, J. S. Bader, H. Muller, R. Koszul. 3D organization of synthetic and scrambled chromosomes. Science 355.6329, 2017, eaaf4597, featured on the cover, https://doi.org/10.1126/science.aaf4597, Press: https://www.repubblica.it/scienze/2017/03/09/news/vita_artificiale_cromosomi_lievito-160157902/
V.F. Scolari, B. Sclavi, M. Cosentino-Lagomarsino. The nucleoid as a smart polymer. Front. Microbiol., 2015, 6:424, https://doi.org/10.3389%2Ffmicb.2015.00424
V.F. Scolari and M. Cosentino-Lagomarsino. Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid. Soft Matter, 2015, 11, 1677-1687, featured on the cover, https://arxiv.org/pdf/1408.2391.pdf, https://doi.org/10.1039/C4SM02434F
R. Srinivasan, V.F. Scolari, M. Cosentino-Lagomarsino, A.S.N Seshasayee. The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli. Nucleic Acid Research, 2015, 43, 295308, https://doi.org/10.1093/nar/gku1229
R. Srinivasan, D. Chandraprakash, R. Krishnamurthi, P. Singh, V.F. Scolari, S. Krishna, A.S.N. Seshasayee. Genomic analysis reveals epistatic silencing of “expensive” genes in Escherichia coli. Mol. BioSyst., 2013, 9, 2021-2033, https://doi.org/10.1039/c3mb70035f
V.G. Benza, K.D. Dorfman, V.F. Scolari, K. Bromek, P. Cicuta, M. Cosentino-Lagomarsino. Physical descriptions of the bacterial nucleoid at large scales, and their biological implications. Rep. Prog. Phys. 2012, 75 076602, https://doi.org/10.1088/0034-4885/75/7/076602
V.F. Scolari, M.Zarei, M. Osella, M. Cosentino-Lagomarsino. NuST: analysis of the interplay between nucleoid organization and gene expression. Web-tool http://www.lcqb.upmc.fr/nust/ Bioinformatics, 2012, 28 (12): 1643-1644, https://doi.org/10.1093/bioinformatics/bts201
V.F. Scolari, B. Bassetti, B. Sclavi, M. Cosentino-Lagomarsino. Gene clusters reflecting macrodomain structure respond to nucleoid perturbations. Mol. BioSyst., 2011, 7, 878-888, https://doi.org/10.1039/c0mb00213e
Research monographs, chapters:
M. Gherardi, V.F. Scolari, R.T. Dame, M. Cosentino-Lagomarsino. Chromosome Structure and Dynamics in Bacteria: Theory and Experiments. Modeling the 3D Conformation of Genomes. Edited by G. Tiana and L. Giorgetti. (CRC Press, ISBN 9781138500792), Here
PhD thesis:
Physics of bacterial nucleoid organization and large-scale gene expression