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. 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.
  2. 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)
  3. 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.
  4. Pradhan, R. N.#, M. Zachara, and B. Deplancke. A systems perspective on brown adipogenesis and metabolic activation. Obesity Reviews 18.S1 (2017): 65-81.
  5. 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).
  6. 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.
  7. 2016

  8. B. Deplancke#, D. Alpern, V. Gardeux. The genetics of variable transcription factor DNA binding. Cell, 166:538-554, 2016. (review)
  9. 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.
  10. 2015

  11. 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.
  12. 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.
  13. 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.
  14. 2014

  15. 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.
  16. 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.
  17. 2013

  18. S.M. Waszak, B. Deplancke. Rounding up natural gene expression variation during development, Dev Cell, 27:601-3, 2013.
  19. 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.
  20. 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
  21. 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.
  22. 2012

  23. 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.
  24. 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.
  25. B. Deplancke, K.J. Verstrepen. Variable outcome of mutations, Science, 335:44-45, 2012.
  26. 2011

  27. 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.
  28. 2010

  29. 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:

20/11/2017: Prof. Deplancke gave an interview about the influence of genes on longevity to RTS Radio Télévision Suisse (in French)
15/11/2017: Prof. Deplancke gave an interview about the power of single cell genomics to Belgian Knack magazine (in Dutch)
06/11/2017: Congratulations to Dr. Petra C. Schwalie and colleagues with publishing a new computational model that is able to accurately distinguish somatic stem cells from differentiated cells.
17/10/2017: Congratulations to Rachana Pradhan with successful graduation! Good luck, Dr. Pradhan!
05/07/2017: Our new software, ASAP was highlighted in the Nature toolbox section. Congratulations to Dr. Vincent Gardeux, Fabrice David and the rest of the team with well-deserved recognition of work!

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