LABORATORY OF
SYSTEMS
BIOLOGY AND
GENETICS


Speciality of LSBG

The LSBG is using microfluidics, high-throughput sequencing, single cell genomics, large-scale yeast screens, and computational approaches to characterize the regulatory code in Drosophila and mammals and to examine how variations in this code affect molecular and organismal diversity.


Latest news


Representative Publications

    2017

  1. Pradhan, R. N.#, M. Zachara, and B. Deplancke. A systems perspective on brown adipogenesis and metabolic activation. Obesity Reviews 18.S1 (2017): 65-81.
  2. 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).
  3. 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.
  4. 2016

  5. B. Deplancke#, D. Alpern, V. Gardeux. The genetics of variable transcription factor DNA binding. Cell, 166:538-554, 2016. (review)
  6. 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.
  7. 2015

  8. 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.
  9. 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.
  10. 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.
  11. 2014

  12. 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.
  13. 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.
  14. 2013

  15. S.M. Waszak, B. Deplancke. Rounding up natural gene expression variation during development, Dev Cell, 27:601-3, 2013.
  16. 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.
  17. 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
  18. 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.
  19. 2012

  20. 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.
  21. 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.
  22. B. Deplancke, K.J. Verstrepen. Variable outcome of mutations, Science, 335:44-45, 2012.
  23. 2011

  24. 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.
  25. 2010

  26. 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:

28/02/2017: Bart was featured in the Nature Methods Author File section.
31/01/2017: In collaboration with the Bucher and Trono Labs, we published a new microfluidic technology in Nature Methods, SMiLE-seq aimed at profiling the DNA binding behavior of TF monomers and dimers in quantitative fashion. Congrats to Alina and the entire team for 4 years of hard but productive work! SMiLE-seq also appeared in Science Daily.
29/09/2016: Bart presents “A primer to single cell gene expression analyses” including our newly developed Automated Single cell Analysis Platform ASAP for the Swiss Institute of Bioinformatics Virtual Seminar Series.
27/09/2016: Congratulations to Magda who was awarded the prize for best poster t the 2016 LIMNA symposium – muscle stem cells, metabolism, and ageing.

Software

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

Junior European Drosophilia Investigators (JEDI)

Jedi Website