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 – PAPERWEB SERVERDATA

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) 12:3582PAPER

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 – PAPERWEB 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) 11:3153PAPER

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 – BOOKCODE

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