Transcription factors and 3D genome conformation in cell-fate decisions von Stadhouders, Ralph, Filion, Guillaume J., Graf, Thomas

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

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Starcode: sequence clustering based on all-pairs search von Zorita, Eduard, Cuscó, Pol, Filion, Guillaume J

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

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Theoretical principles of transcription factor traffic on folded chromatin von Cortini, Ruggero, Filion, Guillaume J.

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Heterochromatin: did H3K9 methylation evolve to tame transposons? von Kabi, Manisha, Filion, Guillaume J

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Position effects influence HIV latency reversal von Chen, Heng-Chang, Martinez, Javier P, Zorita, Eduard, Meyerhans, Andreas, Filion, Guillaume J

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Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells von Filion, Guillaume J., van Bemmel, Joke G., Braunschweig, Ulrich, Talhout, Wendy, Kind, Jop, Ward, Lucas D., Brugman, Wim, de Castro, Inês J., Kerkhoven, Ron M., Bussemaker, Harmen J., van Steensel, Bas

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Methylation of DNA Ligase 1 by G9a/GLP Recruits UHRF1 to Replicating DNA and Regulates DNA Methylation von Ferry, Laure, Fournier, Alexandra, Tsusaka, Takeshi, Adelmant, Guillaume, Shimazu, Tadahiro, Matano, Shohei, Kirsh, Olivier, Amouroux, Rachel, Dohmae, Naoshi, Suzuki, Takehiro, Filion, Guillaume J., Deng, Wen, de Dieuleveult, Maud, Fritsch, Lauriane, Kudithipudi, Srikanth, Jeltsch, Albert, Leonhardt, Heinrich, Hajkova, Petra, Marto, Jarrod A., Arita, Kyohei, Shinkai, Yoichi, Defossez, Pierre-Antoine

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Correction: Filion, G.J. Analytic Combinatorics for Computing Seeding Probabilities. Algorithms 2018, 11, 3 von Filion, Guillaume J.

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

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

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Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivation von Bauer, Moritz, Vidal, Enrique, Zorita, Eduard, Üresin, Nil, Pinter, Stefan F., Filion, Guillaume J., Payer, Bernhard

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A Family of Human Zinc Finger Proteins That Bind Methylated DNA and Repress Transcription von Filion, Guillaume J. P., Zhenilo, Svetlana, Salozhin, Sergey, Yamada, Daisuke, Prokhortchouk, Egor, Defossez, Pierre-Antoine

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Strand asymmetry influences mismatch resolution during a single-strand annealing von Pokusaeva, Victoria O, Diez, Aránzazu Rosado, Espinar, Lorena, Pérez, Albert Torelló, Filion, Guillaume J

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A New Quinoline BRD4 Inhibitor Targets a Distinct Latent HIV-1 Reservoir for Reactivation from Other "Shock" Drugs von Abner, Erik, Stoszko, Mateusz, Zeng, Lei, Chen, Heng-Chang, Izquierdo-Bouldstridge, Andrea, Konuma, Tsuyoshi, Zorita, Eduard, Fanunza, Elisa, Zhang, Qiang, Mahmoudi, Tokameh, Zhou, Ming-Ming, Filion, Guillaume J, Jordan, Albert

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Metabolic Tumor Volume Predicts for Recurrence and Death in Head-and-Neck Cancer von La, Trang H., M.D, Filion, Edith J., M.D, Turnbull, Brit B., Ph.D, Chu, Jackie N, Lee, Percy, M.D, Nguyen, Khoa, B.S, Maxim, Peter, Ph.D, Quon, Andy, M.D, Graves, Edward E., Ph.D, Loo, Billy W., M.D., Ph.D, Le, Quynh-Thu, M.D

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Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells von Filion, Guillaume J, van Steensel, Bas

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A Network Model of the Molecular Organization of Chromatin in Drosophila von van Bemmel, Joke G., Filion, Guillaume J., Rosado, Arantxa, Talhout, Wendy, de Haas, Marcel, van Welsem, Tibor, van Leeuwen, Fred, van Steensel, Bas

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Calibrating Seed-Based Heuristics to Map Short Reads With Sesame von Filion, Guillaume J, Cortini, Ruggero, Zorita, Eduard

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