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

16/05/2019: Watch recent Bart's interview on the topic of storage of information in DNA:

07/05/2019: Congratulations to Marjan Biočanin, Johannes Bues and Dr. Riccardo Dainese on publishing their research about a systematic re-engineering and optimization of Drop-seq in Lab on a Chip:
Marjan Biočanin, Johannes Bues, Riccardo Dainese, Esther Amstadc and Bart Deplancke

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip



brb-seq

19/04/2019: Congratulations to Drs. Daniel Alpern and Vincent Gardeux on publishing their research on developing an ultra-affordable high-throughput bulk RNA-sequencing approach "brb-seq":
Daniel Alpern, Vincent Gardeux, Julie Russeil, Bastien Mangeat, Antonio C. A. Meireles-Filho, Romane Breysse, David Hacker and Bart Deplancke

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing



brb-seq

18/04/2019: Congratulations to Drs. Wanze Chen and Petra Schwalie on publishing their research demonstrating that the ZFP30-KAP1 axis has a pro-adipogenic function in adipogenesis by directly activating PPARg expression:
Wanze Chen, Petra C. Schwalie, Eugenia V. Pankevich, Carine Gubelmann, Sunil K. Raghav, Riccardo Dainese, Marco Cassano, Michael Imbeault, Suk Min Jang, Julie Russeil, Tenagne Delessa, Julien Duc, Didier Trono, Christian Wolfrum and Bart Deplancke

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer



wanze paper

16/04/2019: Congratulations to Dr. Sachi Inukai on publishing her research on the mapping of an integrated fly TF-TF interactome:
Leila Shokri, Sachi Inukai, Antonina Hafner, Kathryn Weinand, Korneel Hens, Anastasia Vedenko, Stephen S.Gisselbrecht, Riccardo Dainese, Johannes Bischof, Edy Furger, Jean - Daniel Feuz, Konrad Basler, BartDeplancke and Martha L.Bulyk

A Comprehensive Drosophila melanogaster Transcription Factor Interactome



sachi paper


Representative Publications

    2019

  1. 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).
  2. 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.
  3. 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.
  4. 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.
  5. 2018

  6. 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.
  7. 2017

  8. 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.
  9. 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)
  10. 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.
  11. Pradhan, R. N.#, M. Zachara, and B. Deplancke. A systems perspective on brown adipogenesis and metabolic activation. Obesity Reviews 18.S1 (2017): 65-81.
  12. 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).
  13. 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.
  14. 2016

  15. B. Deplancke#, D. Alpern, V. Gardeux. The genetics of variable transcription factor DNA binding. Cell, 166:538-554, 2016. (review)
  16. 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.
  17. 2015

  18. 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.
  19. 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.
  20. 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.
  21. 2014

  22. 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.
  23. 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.
  24. 2013

  25. S.M. Waszak, B. Deplancke. Rounding up natural gene expression variation during development, Dev Cell, 27:601-3, 2013.
  26. 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.
  27. 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
  28. 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.
  29. 2012

  30. 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.
  31. 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.
  32. B. Deplancke, K.J. Verstrepen. Variable outcome of mutations, Science, 335:44-45, 2012.
  33. 2011

  34. 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.
  35. 2010

  36. 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:

21/06/2018: Our paper "A stromal cell population that inhibits adipogenesis in mammalian fat depots" got intensive coverage in press: press release from Nature, articles in Swiss RJB and SwissInfo, French Sciences et Avenir, Italian Wired, Russian RIA novosti, Greek Egno, US Gene News, Newsweek and Stat Morning:
Nature wired RIA StatMorning GenLogo NewsweekLogo RJB Logo Egno Logo swissInfo Logo sciencesetavenir Logo

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