Balaramane D*, Spill YG*, Weber M#, Bardet AF#. MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole-genome datasets. BioRxiv (2023) – PREPRINT – CODE
Al Adhami H, Vallet J, Schaal C, Schumacher P, Bardet AF, Dumas M, Chicher J, Hammann P, Daujat S#, Weber M#. Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells. Nucleic Acid Research (2023) 11;gkad071 – PAPER
Detilleux D*, Spill YG*, Balaramane D, Weber M#, Bardet AF#. Pan-cancer predictions of transcription factors mediating aberrant DNA methylation. Epigenetics & Chromatin (2022) 15:10 – PAPER – WEB SERVER – DATA
Al Adhami H, Bardet AF, Dumas M, Cleroux E, Guibert S, Fauque P, Acloque H, Weber M. A comparative methylome analysis reveals conservation and divergence of DNA methylation patterns and functions in vertebrates. BMC Biology (2022) 20(1):70 – PAPER
Dahlet T, Truss M, Frede U, Al Adhami H, Bardet AF, Dumas M, Vallet J, Chicher J, Hammann P, Kottnik S, Hansen P, Luz U, Alvarez G, Auclair G, Hecht J, Robinson PN, Hagemeier C, Weber M. E2F6 initiates stable epigenetic silencing of germline genes during embryonic development. Nature Communications (2021) 12:3582 – PAPER
Leporcq C, Spill Y, Balaramane D, Toussaint C, Weber M, Bardet AF#. TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions. Nucleic Acid Research (2020) 48:W208-W217 – PAPER – WEB SERVER
Dahlet T, Argüeso Lleida A, Al Adhami H, Dumas M, Bender A, Ngondo RP, Tanguy M, Vallet J, Auclair G, Bardet AF, Weber M. Genome-wide Analysis in the Mouse Embryo Reveals the Importance of DNA Methylation for Transcription Integrity. Nature Communications (2020) 11:3153 – PAPER
Bruschi M, Garnier L, Cleroux E, Giordano A, Dumas M, Bardet AF, Kergrohen T, Quesada S, Cesses P, Weber M, Gerbe F, Jay P. Loss of APC Rapidly Impairs DNA Methylation Programs and Cell Fate Decisions in LGR5+ Intestinal Stem Cells. Cancer Research (2020) 80(11):2101-2113 – PAPER
Héberlé É, Bardet AF#. Sensitivity of transcription factors to DNA methylation. Essays Biochem. (2019) 63(6):727-741 – REVIEW
Book: Mifsud B, Zarnack K, Bardet AF. Practical Guide to ChIP-seq Data Analysis. CRC Press (2018) ISBN 9781138596528 – BOOK – CODE
Work as a postdoctoral fellow:
Olivieri D, Paramanathan S, Bardet AF, Hess D, Smallwood SA, Elling U, Betschinger J. The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency. JBC (2021) 100947 – PAPER
Domcke S*, Bardet AF*, Ginno P, Hartl D, Burger L, Schübeler D. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature (2015) 528(7583):575-9 – PAPER – DATA
Stein C*, Bardet AF*, Roma G, Bergling S, Clay I, Agarinis C, Schmelzle T, Bouwmeester T, Schübeler D, Bauer A. YAP1 exerts its transcriptional control via TEAD-mediated activation of enhancers. PLoS Genetics (2015) 11(8):e1005465 – PAPER – DATA
Work as a PhD student:
Meireles-Filho ACA, Bardet AF, Yanez-Cuna JO, Stampfel G, Stark A. Cis-regulatory requirements for tissue-specific programs of the circadian clock. Current Biology (2014) 24(1):1-10 – PAPER – DATA – DISPATCH
Bardet AF*, Steinmann J*, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high-resolution. Bioinformatics (2013) 29(21):2705-13- PAPER – CODE
Hnisz D, Bardet AF, Nobile CJ, Petryshyn A, Glaser W, Schöck U, Stark A, Kuchler K. A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis. PLoS Genetics (2012) 8(12):e1003118
Bardet AF, He Q, Zeitlinger J, Stark A. A computational pipeline for comparative ChIP-seq analyses. Nature Protocols (2012) 7(1):45-61- PAPER – DATA
He Q*, Bardet AF*, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nature Genetics (2011) 43(5):414-20 – PAPER – DATA – CODE
Work as a research assistant:
Labaj PP, Leparc GG, Bardet AF, Kreil G, Kreil DP. Single amino acid repeats in signal peptides. FEBS J. (2010) 277(15):3147-57
Leitner J, Klauser C, Pickl WF, Stöckl J, Majdic O, Bardet AF, Kreil DP, Dong C, Yamazaki T, Zlabinger G, Pfistershammer K, Steinberger P. B7-H3 is a potent inhibitor of human T-cell activation: No evidence for B7-H3 and TREML2 interaction. Eur J Immunol. (2009) 39(7):1754-64