Representative publications

• W. Saelens^$, O. Pushkareva, B. Deplancke^$.
  ChromatinHD connects single-cell accessibility and conformation to gene expression through scale-adaptive machine learning,
  BioRxiv; Nature Coomunications, 16:317, 2025.

• J.F. Kribelbauer^$, O. Pushkareva, V. Gardeux, J. Russeil, G. van Mierlo, B. Deplancke^$.
  Context transcription factors establish cooperative enironments and mediate enhancer communication,
  BioRxiv; Nature Genetics, 56:2199-2212, 2024.

• R. Ferrero*, P.Y. Rainer*, J. Russeil, M. Zachara, J. Pezoldt, G. van Mierlo, V. Gardeux, W. Saelens, D. Alpern, L. Favre, S. Mantziari, T. Znigg, N. Pitteloud, M. Suter, M. Matter, C. Canto, B. Deplancke.
  A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion,
  BioRxiv; Cell Metabolism, 36:1566-1585.e9, 2024.
  
  Highlighted on 15 news outlets including MSN news, TheParadise.ng, AZO Life Sciences, Genetic Engineering news, My Science as well as on RTS Audio & Podcast (French) and swissinfo.ch news (French).

• M. Polychronidou^$, J. Hou^$, M. Babu^$, P. Liberali^$, I. Amit^$, B. Deplancke^$, G. Lahav^$, S. Itzkovitz^$, M. Mann^$, J. Seaz-Rodriguez^$, F. Theis^$, R. Eils^$.
  Single-cell biology: what does the future hold?
  Molecular Systems Biology, 19:e11799, 2023. (Perspective)

• G. van Mierlo*, O. Pushkarev*, J.F. Kribelbauer, B. Deplancke.
  Chromatin modules and their implication in genomic organization and gene regulation,
  Trends in Genetics, S0168-9525(22)00290-6, 2022. (Review)

• M. Zachara^#, P.Y. Rainer^#, J.M. Russeil, H. Hashimi, D. Alpern, R. Ferrero, M. Litovchenko, B. Deplancke.
  Mammalian adipogenesis regulator (Areg) cells use retinoic acid signalling to be non- and anti-adipogenic in age-dependent manner,
  BioRxiv, 2021; EMBO Journal, 41:e108206, 2022.

• W. Chen^*, O. Guillaume-Gentil*, R. Dainese, P.Y. Rainer, M. Zachara, C.G. Gäbelein, J.A. Vorholt^$, B. Deplancke^$.
  Live cell transcriptome profiling using Live-seq,
  BioRxiv, 2021; Nature, 608: 733–40, 2022.
  
  Highlighted on preLights (Preprints selected by the Biology Community); Covered by >30 news outlets such as Le Monde (French), German and Swiss National Radio (German), Genome Web, and Genetic Engineering & Biotechnology, PubReading, as well as highlighted by both Nature Biotechnology , Nature Methods and Cell Reports Methods. Altmetric ~ 900.

• G. Llimos, V. Gardeux, U. Koch, J.F. Kribelbauer, A. Hafner, D. Alpern, J. Pezoldt, M. Litovchenko, J. Russeil, R. Dainese, R. Moia, A.M. Mahmoud, D. Rossi, G. Gaidano, C. Plass, P. Lutsik, C. Gerhauser, S.M. Waszak, A. Boettiger, F. Radtke, B. Deplancke.
  A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation,
  Nature Communications, 13:2042, 2022.
  
  Editors’ highlight in the Cancer section.

• J. Bues*, M. Biočanin*, J. Pezoldt, R. Dainese, A. Chrisnandy, S. Rezakhani, W. Saelens, V. Gardeux, R. Gupta, J. Russeil, Y. Saeys , E. Amstad, M. Claassen, M. Lutolf, B. Deplancke.
  Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition,
  BioRxiv, 2020; Nature Methods, 19:323-330, 2022.
  
  News and Views: Single-cell, single-organoid phenotypic landscapes, Press coverage: Mirage News, Tech Explorist, bioengineer.org, Discussed in The Stem Cell Podcast.

• H. Li*, J. Janssens*, M. De Waegeneer, S. Saroja Kolluru, K. Davie, V. Gardeux, W. Saelens, F. David, M. Brbić, J. Leskovec, (22 co-authors), FCA Consortium, H. Jasper, B. Oliver, N. Perrimon^#, B. Deplancke^#, S.R. Quake^#, L. Luo^#, S. Aerts^#. Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly,
  BioRxiv, 2021; Science, 375:eabk2432, 2022.
  
  Press coverage: MSN Nieuws (Dutch), GenomeWeb, Mirage News.

• M. Litovchenko, A.C.A Meireles-Filho, M.V. Frochaux, R.P.J Bevers, A. Prunetto, A.M. Anduaga, B. Hollis, V. Gardeux, V.S. Braman, J.M.C. Russeil, S. Kadener, M. Dal Peraro, B. Deplancke.
  Extensive tissue-specific expression variation and novel regulators underlying circadian behavior,
  Science Advances, 7:eabc3781, 2021.
  
  Video summary; Press Coverage: Interview on Swiss National Radio; Mirage News; Pourquoi Docteur

• R. Ferrero*, P. Rainer*, B. Deplancke.
  Toward a consensus view of mammalian adipocyte stem and progenitor cell heterogeneity,
  Trends in Cell Biology, 12:937-50, 2020. (Review)

• F. David, B. Deplancke^$, V. Gardeux^$.
  ASAP: an open, scalable and interactive web-based portal for (single-cell) omics analyses,
  Nucleic Acids Research, 48:W403-414, 2020.
  
  ASAP is among most widely used scRNA-seq analysis platforms (2020)

• R.P.J. Bevers*, M. Litovchenko*, A. Kapopoulou, V.S. Braman, V.M. Lemos Da Silva, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke.
  Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,
  BioRxiv, 2018; Nature Metabolism, 1:226–1242, 2019.

• W. Chen*, P.C. Schwalie*, E.V. Pankevich, C. Gubelmann, S.K. Raghav, R. Dainese, M. Cassano, M. Imbeault, S. Min Jang, J. Russeil, T. Delessa, D. Trono, C. Wolfrum, B. Deplancke.
  ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer,
  Nature Communications, 10:1809, 2019.

• D. Alpern, V. Gardeux, J. Russeil, B. Mangeat, A.C.A. Meireles-Filho, R. Breysse, D. Hacker, B. Deplancke.
  BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing,
  bioRxiv, 2018; Genome Biology, 20:71, 2019.
  
  Highlighted as “among the 10 most accessed Genome Biology papers in 2019” (out of 300). Foundation for our start-up Alithea Genomics.

• P.C. Schwalie^*, H. Dong^*, M. Zachara^*, J. Russeil, D. Alpern, N. Akchiche, C. Caprara, W. Sun, K.U. Schlaudraff, G. Soldati, C. Wolfrum^#, B. Deplancke^#.
  A stromal cell population that inhibits adipogenesis in mammalian fat depots,
  Nature, 559:103-108, 2018
  
  Highlighted >10 international news outlets (incl. Newsweek, Wired) and News and Views: Unexpected cell population gives fat a brake; Biomedical Picture of the Day (MRC London Institute of Medical Sciences Initiative). Two Faculty of 1000 Recommendations: https://f1000.com/prime/733479878

• A. Isakova, R. Groux, M. Imbeault, P. Rainer, D. Alpern, R. Dainese, A. Giovanna, D. Trono, P. Bucher, B. Deplancke.
  SMiLE-seq identifies binding motifs of single and dimeric transcription factors,
  Nature Methods, 14:316-322, 2017.
  
  Highlighted in: Nature Reviews Genetics, 18, 145, 2017; GenomeWeb: https://www.genomeweb.com/proteomics-protein-research/swiss-team-looks-market-dna-protein-binding-assay-transcription-factor ; Three Faculty of 1000 recommendations.

• B. Deplancke^#, D. Alpern, V. Gardeux.
  The genetics of transcription factor DNA binding variation,
  Cell, 166:538-554, 2016. (review)

• S.M. Waszak*, O. Delaneau*, A.R. Gschwind, H. Kilpinen, S.K. Raghav, R.M. Witwicki, A. Orioli, M. Wiederkehr, N.I. Panousis, A. Yurovsky, L. Romano-Palumbo, A. Planchon, D. Bielser, I. Padioleau, G. Udin, S. Thurnheer, D. Hacker, N. Hernandez, A. Reymond, B. Deplancke^#, E.T. Dermitzakis^#.
  Population variation and genetic control of modular chromatin architecture in humans,
  Cell, 162:1039-1050, 2015.
  
  Perspective: A. Denker, W. de Laat. A long-distance chromatin affair. Cell, 162:942-43, 2015. Highlighted @ Nature Reviews Genetics: L. Koch. Genomics. Adding another dimension to gene regulation, September 2015.

• M.S. Bou Sleiman*, D. Osman*,^#, A. Massouras, A.A. Hoffmann, B. Lemaitre^#, B. Deplancke^#.
  Multiple genetic and transcriptional changes mediate high levels of natural variation in gut immunocompetence in Drosophila melanogaster,
  Nature Communications, 6:7829, 2015.

• H. Kilpinen*, S.M. Waszak*, A. Gschwind*, S.K. Raghav, R.M. Witwicki, A. Orioli, E. Migliavacca, M. Wiederkehr, M. Gutierrez-Arcelus, N. Panousis, A. Yurovsky, T. Tappalainen, L. Romano-Palumbo, A. Planchon, D. Bielser, J. Bryois, I. Padioleau, G. Udin, S. Thurnheer, D. Hacker, L.J. Core, J.T. Lis, N. Hernandez^#, A. Reymond^#, B. Deplancke^#, E.T. Dermitzakis^#.
  Coordinated effects of sequence variation on chromatin structure, DNA binding and transcription,
  Science, 342:744-747, 2013.
  
  Perspective: T.S. Furey, P. Sethupathy. Genetics. Genetics driving epigenetics. Science, 342:705-6, 2013; Highlighted @ Nature Reviews Genetics, 14:824, 2013.

• J. Simicevic*, A.W. Schmid*, P. Gilardoni*, B. Zoller, S.K. Raghav, I. Krier, C. Gubelmann, F. Lisacek, F. Naef, M. Moniatte^#, B. Deplancke^#.
  Absolute quantification of transcription factors during cellular differentiation using multiplexed, targeted proteomics,
  Nature Methods, 10:570-576, 2013.
  
  Featured as a Nature Biotechnology Highlight (@NatureBiotech, April 15^th 2013)

• S.K. Raghav*, S.M. Waszak*, I. Krier, A. Isakova, C. Gubelmann, T.S. Mikkelsen, and B. Deplancke.
  Integrative genomics identifies SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPb and KAISO,
  Molecular Cell, 46:335-350, 2012.