LABORATORY OF
SYSTEMS
BIOLOGY AND
GENETICS

Speciality of LSBG

The central research focus of the LSBG is to understand genome organization, regulation, and variation and is broadly partitioned according to three major research pillars:

In the "Techo" pillar, we are developing novel microfluidic, high-throughput sequencing, single cell omic, and computational approaches, which are used to address biological questions in the other two pillars.
In the "Adipo" pillar, we are characterizing the regulatory mechanisms driving mesenchymal stromal cell heterogeneity and function in adipose biology and other metabolically relevant processes.
In the "Geno" pillar, we are examining how variation in the regulatory code affects molecular and organismal diversity.

Latest news

14.02.2020 Congratulations to Dr. Sachi Inukai and Dr. Judith Kribelbauer on being awarded with the prestigious Marie Curie and EMBO fellowships!
MarieCurieLogo EMBO

17.01.2020 Congratulations to Dr. Michael Frochaux and Dr. Maroun Bou Sleiman on publishing two research papers about Drosophila immunity in Genome biology:

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

and

Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes





Representative Publications

    2020

  1. Frochaux, M.V., Bou Sleiman, M., Gardeux, V. et al. cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel. Genome Biol 21, 6 (2020)
  2. Bou Sleiman, M., Frochaux, M.V., Andreani, T. et al. Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes. Genome Biol 21, 4 (2020).
  3. 2019

  4. Yongguo Li, Petra C.Schwalie, Andrea Bast-Habersbrunner, Sabine Mocek, Julie Russeil, Tobias Fromme, Bart Deplancke, Martin Klingenspor. Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning. Cell Reports, 2019.
  5. Bevers, R. P., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J. & Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism, 1-17.
  6. Dali Ma, Maroun Bou-Sleiman, Pauline Joncour, Claire-Emmanuelle Indelicato, Michael Frochaux, Virginie Braman, Maria Litovchenko, Gilles Storelli, Bart Deplancke, François Leulier. Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress. iScience (2019).
  7. Biočanin, Marjan, Johannes Bues, Riccardo Dainese, Esther Amstad, and Bart Deplancke.Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip. Lab on a Chip (2019).
  8. Alpern, Daniel, Vincent Gardeux, Julie Russeil, Bastien Mangeat, Antonio CA Meireles-Filho, Romane Breysse, David Hacker, and Bart Deplancke. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome biology 20, no. 1 (2019): 71.
  9. Chen, Wanze, Petra C. Schwalie, Eugenia V. Pankevich, Carine Gubelmann, Sunil K. Raghav, Riccardo Dainese, Marco Cassano et al. ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer.Nature communications 10, no. 1 (2019): 1809.
  10. Shokri, Leila, Sachi Inukai, Antonina Hafner, Kathryn Weinand, Korneel Hens, Anastasia Vedenko, Stephen S. Gisselbrecht et al. A Comprehensive Drosophila melanogaster Transcription Factor Interactome.Cell reports 27, no. 3 (2019): 955-970.
  11. 2018

  12. P.C. Schwalie#, Hua Dong, Magda Zachara, Julie Russeil, Daniel Alpern, Nassila Akchiche, Christian Caprara, Wenfei Sun, Kai-Uwe Schlaudraff, Gianni Soldati, Christian Wolfrum and Bart Deplancke. A stromal cell population that inhibits adipogenesis in mammalian fat depots , Nature, 2018.
  13. 2017

  14. P.C. Schwalie#, P.O. Moran, J. Huelsken, B. Deplancke. Cross-tissue identification of somatic stem and progenitor cells using a single-cell RNA-seq derived gene signature, Stem Cells, 35:2390-2402, 2017.
  15. Vincent Gardeux#, Fabrice P. A. David, Adrian Shajkofci, Petra C. Schwalie, Bart Deplancke ASAP: a Web-based platform for the analysis and inter-active visualization of single-cell RNA-seq data Bioinformatics (2017)
  16. J.A. Sobel #, I. Krier, T. Andersin, S. Raghav, D. Canella,F. Gilardi, A.S. Kalantzi, G.Rey, B. Weger, F. Gachon, M.Dal Peraro, N. Hernandez, U. Schibler,B.Deplancke#, F. Naef#, and the CycliX consortium. Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biology, 5:e2001069, 2017.
  17. Pradhan, R. N.#, M. Zachara, and B. Deplancke. A systems perspective on brown adipogenesis and metabolic activation. Obesity Reviews 18.S1 (2017): 65-81.
  18. Pradhan, Rachana N.#, Johannes J. Bues, Vincent Gardeux, Petra C. Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, and Bart Deplancke. Dissecting the brown adipogenic regulatory network using integrative genomics. Scientific Reports 7 (2017).
  19. Isakova, A.#, Groux, R., Imbeault, M., Rainer, P., Alpern, D., Dainese, R., ..., Deplancke, B. (2017). SMiLE-seq identifies binding motifs of single and dimeric transcription factors. Nature methods, 14(3), 316-322.
  20. 2016

  21. B. Deplancke#, D. Alpern, V. Gardeux. The genetics of variable transcription factor DNA binding. Cell, 166:538-554, 2016. (review)
  22. A. Isakova, Y. Berset, V. Hatzimanikatis#, B. Deplancke#. Quantification of cooperativity in heterodimer-DNA binding improves the accuracy of binding specificity models, Journal of Biological Chemistry, 291:10293-10306, 2016.
  23. 2015

  24. S.M. Waszak*, O. Delaneau*, A.R. Gschwind, H. Kilpinen, S.K. Raghav, R.M. Witwicki, A. Orioli, 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#. Variation and genetic control of chromatin architecture in humans, Cell, 162:1039-1050, 2015.
  25. M.S. Bou Sleiman*, D. Osman*,#, A. Massouras, A.A. Hoffmann, B. Lemaitre#, B. Deplancke#. Multiple genetic and transcriptionalchanges mediate high levels of natural variation in gut immunocompetence in Drosophila melanogaster, Nature Communications,6:7829, 2015.
  26. C. Schertel*, M. Albarca*, C. Rockel-Bauer, N.W. Kelley, J. Bischof, K. Hens, E. van Nimwegen#, K. Basler# and B. Deplancke#. A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development, Genome Research, 25:514-23, 2015.
  27. 2014

  28. C. Gubelmann *, P.C. Schwalie*, S.K. Raghav*, E. Röder, T. Delessa, E. Kielmann, S.M. Waszak, A. Corsinotti, G. Udin, W. Holcombe, G. Rudofsky, D. Trono, C. Wolfrum#, B. Deplancke#. Identification of ZEB1 as a central component of the adipogenic gene regulatory network, eLife, 3:e03346, 2014.
  29. W. Huang*, A. Massouras *, Y. Inoue, J. Peiffer, M. Ràmia, A. Tarone, L. Turlapati, T. Zichner, D. Zhu, (31 co-authors), R. Anholt, J. Korbel, D. Mittelman, D. Muzny, R. Gibbs, A. Barbadilla$, S. Johnston$, E. Stone$, S. Richards$, B. Deplancke$, T.F.C. Mackay$,#. Natural Variation in Genome Architecture Among 205 Drosophila melanogaster Genetic Reference Panel Lines, Genome Research, 24:1193-1208, 2014.
  30. 2013

  31. S.M. Waszak, B. Deplancke. Rounding up natural gene expression variation during development, Dev Cell, 27:601-3, 2013.
  32. 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.
  33. C. Gubelmann, A. Isakova, S.M. Waszak, A. Iagovitina, K. Hens, S.M. Waszak, J.D. Feuz, S.K. Raghav, J. Simicevic, B. Deplancke. A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory elements, Molecular Systems Biology, 9:682 (Article #), 2013
  34. 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.
  35. 2012

  36. A. Massouras*, S.M. Waszak*, M. Albarca, W. Westhal, K. Hens, J.F. Ayroles, E.T. Dermitzakis, E.A. Stone, T.F.C. Mackay, and B. Deplancke. Genomic variation and its impact on gene expression in Drosophila melanogaster, PLoS Genetics, 8:e1003055, 2012.
  37. 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.
  38. B. Deplancke, K.J. Verstrepen. Variable outcome of mutations, Science, 335:44-45, 2012.
  39. 2011

  40. K. Hens, J Feuz, A. Isakova, A. Iagovitina, A. Massouras, J. Bryois, P. Callaerts, S.E. Celniker, B. Deplancke. Automated protein-DNA interaction screening of Drosophila regulatory elements, Nature Methods, 8:1065-70, 2011.
  41. 2010

  42. A. Massouras, K. Hens, C. Gubelmann, C. Chidley, S. Uplekar, F. Decouttere, J. Rougemont, K. Johnsson, S.T. Cole, B. Deplancke. Primer-Initiated Sequence Synthesis to detect and assemble structural variants, Nature Methods, 7: 485-486, 2010.

Press about us:

Our paper "Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel" got intensive coverage in press: articles in Medical Express, Eurekalert, Science Daily, Technology Networks and Phys.org
mito1 mito2
mito3 mito4 mito5

Software

Check our github for the latest updates on our software.
Check our youtube channel for the latest tutorials on our software.

Catalyze4Life

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Junior European Drosophilia Investigators (JEDI)

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