Janbain A, Reynès C, Assaghir Z, Zeineddine H, Sabatier R, Journot L (2021) TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules. NAR Genom Bioinform. 3:lqab103. doi: 10.1093/nargab/lqab103

Rèynes C, Kister G, Rohmer M, Bouschet T, Varrault A, Dubois E, Rialle S, Journot L, Sabatier R (2020) ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses. Bioinformatics. 36:504-13. doi: 10.1093/bioinformatics/btz564

Du K, Stöck M, Kneitz S, Klopp C, Woltering JM, Adolfi MC, Feron R, Prokopov D, Makunin A, Kichigin I, Schmidt C, Fischer P, Kuhl H, Wuertz S, Gessner J, Kloas W, Cabau C, Iampietro C, Parrinello H, Tomlinson C, Journot L, Postlethwait JH, Braasch I, Trifonov V, Warren WC, Meyer A, Guiguen Y, Schartl M (2020) The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol. 4:841-852. doi: 10.1038/s41559-020-1166-x.

Baudement MO, Cournac A, Court F, Seveno M, Parrinello H, Reynès C, Sabatier R, Bouschet T, Yi Z, Sallis S, Tancelin M, Rebouissou C, Cathala G, Lesne A, Mozziconacci J*, Journot L*, Forne T* (2018) High-salt Recovered Sequences are associated with the active chromosomal compartment and with large ribonucleoproteic complexes including nuclear bodies. Genome Res. 28:1733-46. doi: 10.1101/gr.237073.118

Varrault A, Eckardt S, Girard B, Le Digarcher A, Sassetti I, Meusnier C, Ripoll C, Badalyan A, Bertaso F, McLaughlin KJ, Journot L, Bouschet T (2018) Mouse Parthenogenetic Embryonic Stem Cells with Biparental-Like Expression of Imprinted Genes Generate Cortical-Like Neurons That Integrate into the Injured Adult Cerebral Cortex. Stem Cells. 36:192-205. doi: 10.1002/stem.2721.

Varrault A, Dantec C, Le Digarcher A, Chotard L, Bilanges B, Parrinello H, Dubois E, Rialle S, Severac D, Bouschet T, Journot L (2017) Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network. Nucleic Acids Res. 45:10466-80. doi: 10.1093/nar/gkx672.

Bouschet T, Dubois E, Reynès C, Kota SK, Rialle S, Maupetit-Méhouas S, Pezet M, Le Digarcher A, Nidelet S, Demolombe V, Cavelier P, Meusnier C, Maurizy C, Sabatier R, Feil R, Arnaud P, Journot L, Varrault A (2017) In Vitro Corticogenesis from Embryonic Stem Cells Recapitulates the In Vivo Epigenetic Control of Imprinted Gene Expression. Cereb Cortex. 27:2418-33. doi: 10.1093/cercor/bhw102.

Al Adhami H, Evano B, Le Digarcher A, Gueydan C, Dubois E, Parrinello H, Dantec C, Bouschet T, Varrault A, Journot L (2015) A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation. Genome Res. 25:353-67. doi: 10.1101/gr.175919.114.

Kota SK, Llères D, Bouschet T, Hirasawa R, Marchand A, Begon-Pescia C, Sanli I, Arnaud P, Journot L, Girardot M, Feil R (2014) ICR noncoding RNA expression controls imprinting and DNA replication at the Dlk1-Dio3 domain. Dev Cell. 31:19-33. doi: 10.1016/j.devcel.2014.08.009.

Seibt J, Armant O, Le Digarcher A, Castro D, Ramesh V, Journot L, Guillemot F, Vanderhaeghen P, Bouschet T (2012) Expression at the imprinted dlk1-gtl2 locus is regulated by proneural genes in the developing telencephalon. PLoS One. 7:e48675. doi: 10.1371/journal.pone.0048675.

Gabory A, Ripoche MA, Le Digarcher A, Watrin F, Ziyyat A, Forné T, Jammes H, Ainscough JF, Surani MA, Journot L, Dandolo L (2009) H19 acts as a trans regulator of the imprinted gene network controlling growth in mice. Development. 136:3413-21. doi: 10.1242/dev.036061.

Ma L, Cantrup R, Varrault A, Colak D, Klenin N, Götz M, McFarlane S, Journot L, Schuurmans C (2007) Zac1 functions through TGFbetaII to negatively regulate cell number in the developing retina. Neural Dev. 2:11.