* Co-corresponding author.

Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivation
Moritz Bauer, Enrique Vidal, Eduard Zorita, Nil Üresin, Stefan F Pinter, Guillaume J Filion*, Bernhard Payer
Nature Communications, 2021 (Article)

The chromatin landscape at the HIV-1 provirus integration site determines viral expression
Gerlinde Vansant, Heng-Chang Chen, Eduard Zorita, Katerina Trejbalová, Dalibor Miklík, Guillaume Filion, Zeger Debyser
Nucleic acids research, 2020 (Article)

Calibrating Seed-Based Heuristics to Map Short Reads With Sesame
Guillaume J Filion, Ruggero Cortini, Eduard Zorita
Frontiers in genetics, 2020 (Article)

Mapping short reads, faithfully
Eduard Valera Zorita, Ruggero Cortini, Guillaume J Filion
BioRxiv, 2020 (Article)

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration
Bojana Lucic, Heng-Chang Chen, Maja Kuzman, Eduard Zorita, Julia Wegner, Vera Minneker, Wei Wang, Raffaele Fronza, Stefanie Laufs, Manfred Schmidt, Ralph Stadhouders, Vassilis Roukos, Kristian Vlahovicek, Guillaume J Filion*, Marina Lusic
Nature communications, 2019 (Article)

Transcription factors and 3D genome conformation in cell-fate decisions
Ralph Stadhouders, Guillaume J Filion, Thomas Graf
Nature, 2019 (Article)

An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape
Victoria O Pokusaeva, Dinara R Usmanova, Ekaterina V Putintseva, Lorena Espinar, Karen S Sarkisyan, Alexander S Mishin, Natalya S Bogatyreva, Dmitry N Ivankov, Arseniy V Akopyan, Sergey Ya Avvakumov, Inna S Povolotskaya, Guillaume J Filion, Lucas B Carey, Fyodor A Kondrashov
PLoS genetics, 2019 (Article)

Strand asymmetry influences mismatch repair during single-strand annealing
Victoria O Pokusaeva, Aránzazu Rosado Diez, Lorena Espinar, Guillaume J Filion
bioRxiv, 2019 (Article)

OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes
Enrique Vidal, François le Dily, Javier Quilez, Ralph Stadhouders, Yasmina Cuartero, Thomas Graf, Marc A Marti-Renom, Miguel Beato, Guillaume J Filion
Nucleic acids research, 2018 (Article)

A new quinoline BRD4 inhibitor targets a distinct latent HIV-1 reservoir for reactivation from other “shock” drugs
Erik Abner, Mateusz Stoszko, Lei Zeng, Heng-Chang Chen, Andrea Izquierdo-Bouldstridge, Tsuyoshi Konuma, Eduard Zorita, Elisa Fanunza, Qiang Zhang, Tokameh Mahmoudi, Ming-Ming Zhou, Guillaume J Filion, Albert Jordan
Journal of virology, 2018 (Article)

Theoretical principles of transcription factor traffic on folded chromatin
Ruggero Cortini, Guillaume J Filion
Nature communications, 2018 (Article)

Using Barcoded HIV Ensembles (B‐HIVE) for Single Provirus Transcriptomics
Heng‐Chang Chen, Eduard Zorita, Guillaume J Filion
Current protocols in molecular biology, 2018 (Article)

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming
Ralph Stadhouders, Enrique Vidal, François Serra, Bruno Di Stefano, François Le Dily, Javier Quilez, Antonio Gomez, Samuel Collombet, Clara Berenguer, Yasmina Cuartero, Jochen Hecht, Guillaume J Filion, Miguel Beato, Marc A Marti-Renom, Thomas Graf
Nature genetics, 2018 (Article)

Analytic combinatorics for computing seeding probabilities
Guillaume J Filion
Algorithms, 2018 (Article)

Methylation of DNA ligase 1 by G9a/GLP recruits UHRF1 to replicating DNA and regulates DNA methylation
Laure Ferry, Alexandra Fournier, Takeshi Tsusaka, Guillaume Adelmant, Tadahiro Shimazu, Shohei Matano, Olivier Kirsh, Rachel Amouroux, Naoshi Dohmae, Takehiro Suzuki, Guillaume J Filion, Wen Deng, Maud de Dieuleveult, Lauriane Fritsch, Srikanth Kudithipudi, Albert Jeltsch, Heinrich Leonhardt, Petra Hajkova, Jarrod A Marto, Kyohei Arita, Yoichi Shinkai, Pierre-Antoine Defossez
Molecular cell, 2017 (Article)

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J Filion, Marc A Marti-Renom
PLoS computational biology, 2017 (Article)

Clustering of Drosophila housekeeping promoters facilitates their expression
Marc Corrales, Aránzazu Rosado, Ruggero Cortini, Joris van Arensbergen, Bas van Steensel, Guillaume J Filion
Genome research, 2017 (Article)

Parallel sequencing lives, or what makes large sequencing projects successful
Javier Quilez, Enrique Vidal, François Le Dily, Francois Serra, Yasmina Cuartero, Ralph Stadhouders, Thomas Graf, Marc A Marti-Renom, Miguel Beato, Guillaume Filion
GigaScience, 2017 (Article)

Analytic combinatorics for bioinformatics I: seeding methods
Guillaume J Filion
bioRxiv, 2017 (Article)

Position effects influence HIV latency reversal
Heng-Chang Chen, Javier P Martinez, Eduard Zorita, Andreas Meyerhans, Guillaume J Filion
Nature structural & molecular biology, 2017 (Article)

Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control
Pol Cuscó, Guillaume J Filion
Bioinformatics, 2016 (Article)

Starcode: sequence clustering based on all-pairs search
Eduard Zorita, Pol Cusco, Guillaume J Filion
Bioinformatics, 2015 (Article)

The signed Kolmogorov-Smirnov test: why it should not be used
Guillaume J Filion
Gigascience, 2015 (Article)

Machine learning: how much does it tell about protein folding rates?
Marc Corrales, Pol Cuscó, Dinara R Usmanova, Heng-Chang Chen, Natalya S Bogatyreva, Guillaume J Filion, Dmitry N Ivankov
PloS one, 2015 (Article)

3D genome structure. Organization of the nucleus in space and time
Guillaume J Filion, Miguel Beato
FEBS letters, 2015 (Article)

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation
François Le Dily, Davide Bau, Andy Pohl, Guillermo P Vicent, François Serra, Daniel Soronellas, Giancarlo Castellano, Roni HG Wright, Cecilia Ballare, Guillaume Filion, Marc A Marti-Renom, Miguel Beato
Genes & development, 2014 (Article)

A network model of the molecular organization of chromatin in Drosophila
Joke G Van Bemmel, Guillaume J Filion, Arantxa Rosado, Wendy Talhout, Marcel De Haas, Tibor Van Welsem, Fred van Leeuwen, Bas van Steensel
Molecular cell, 2013 (Article)

The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe
Babett Steglich, Guillaume Filion, Bas van Steensel, Karl Ekwall
Nucleus, 2012 (Article)

Les cinq couleurs de la chromatine de drosophile
Guillaume Filion
médecine/sciences, 2011 (Article)

Bayesian network analysis of targeting interactions in chromatin
Bas Van Steensel, Ulrich Braunschweig, Guillaume J Filion, Menzies Chen, Joke G van Bemmel, Trey Ideker
Genome research, 2010 (Article)

Systematic protein location mapping reveals five principal chromatin types in Drosophila cells
Guillaume J Filion, Joke G van Bemmel, Ulrich Braunschweig, Wendy Talhout, Jop Kind, Lucas D Ward, Wim Brugman, Inês J de Castro, Ron M Kerkhoven, Harmen J Bussemaker, Bas van Steensel
Cell, 2010 (Article)

Reply to “Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells”
Bo Wen, Hao Wu, Yoichi Shinkai, Rafael A Irizarry, Andrew P Feinberg
Nature genetics, 2010 (Article)

The human protein kinase HIPK2 phosphorylates and downregulates the methyl-binding transcription factor ZBTB4
D Yamada, R Perez-Torrado, G Filion, M Caly, B Jammart, V Devignot, N Sasai, P Ravassard, J Mallet, X Sastre-Garau, ML Schmitz, P-A Defossez
Oncogene, 2009 (Article)

Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic
S Augui, GJ Filion, S Huart, E Nora, M Guggiari, M Maresca, AF Stewart, E Heard
Science, 2007 (Article)

Transmission and immunity: the importance of heterogeneity in the fight against malaria
Guillaume JP Filion, Richard EL Paul, Vincent Robert
Trends in parasitology, 2006 (Article)

Epigénétique et cancer
Guillaume JP Filion, Pierre-Antoine Defossez
Bulletin du cancer, 2006 (Article)

Using reverse electrophoretic mobility shift assay to measure and compare protein–DNA binding affinities
Guillaume JP Filion, Lucie Fouvry, Pierre-Antoine Defossez
Analytical biochemistry, 2006 (Article)

A family of human zinc finger proteins that bind methylated DNA and repress transcription
Guillaume JP Filion, Svetlana Zhenilo, Sergey Salozhin, Daisuke Yamada, Egor Prokhortchouk, Pierre-Antoine Defossez
Molecular and cellular biology, 2006 (Article)

The human enhancer blocker CTC-binding factor interacts with the transcription factor Kaiso
Pierre-Antoine Defossez, Kevin F Kelly, Guillaume JP Filion, Roberto Pérez-Torrado, Frédérique Magdinier, Hervé Menoni, Curtis L Nordgaard, Juliet M Daniel, Eric Gilson
Journal of Biological Chemistry, 2005 (Article)

Les protéines se liant à l’ADN méthylé: interprètes du code épigénétique
Guillaume Filion, Pierre-Antoine Defossez
médecine/sciences, 2004 (Article)

Méthylation de l’ADN et activité du génome: Actualités sur l’épigénétique
Guillaume FILION, Pierre-Antoine DEFOSSEZ
Biofutur (Puteaux), 2004 (Article)