Members

This group is part of the EMBL/CRG Research Unit in Systems Biology.

Group Leader:

Johannes Jaeger

Technician/Lab manager :

Hilde Janssens

Technician/Programmer :

Damjan Cicin-Sain

Postdoctoral Fellows :

Anton Crombach, Eva Jiménez-Guri, Bàrbara Negre, Karl Wotton

Interpod Fellows :

Juan José Fraire-Zamora (with Jerôme Solon)

PhD Students :

Berta Verd

Graduate Intern:

Helena Roca

Undergratuate Students:

Anna Alcaine Colet, Núria Bosch

Selected Publications

Jaeger J and Monk N.
“Everything flows: a process perspective on life.”
EMBO Rep, 16:1064–67 (2015).

Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine Colet A, Lemke S, Schmidt-Ott U, Jaeger J.
“Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita.”
eLIFE, 4:e04785 (2015).

Wotton KR, Jiménez-Guri E, Jaeger J.
“Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita.”
PLoS Genet, 11: e1005042 (2015).

Wotton KR, Jiménez-Guri E, Crombach A, Cicin-Sain D, Jaeger J.
“High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita.”
Sci Data, 2:150005 (2015).

Cicin-Sain D, Hermoso Pulido A, Crombach A, Wotton KR, Jiménez-Guri E, Taly J-F, Roma G, Jaeger J.
“SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos.”
Nucl Acids Res, 43(Database Issue):D752–6 (2015).

Jaeger J, Laubichler M, Callebaut W.
“The comet cometh: evolving developmental systems.”
Biol Theory, 10:36–49 (2015).

Green S, Fagan M, Jaeger J.
“Explanatory integration challenges in evolutionary systems biology.”
Biol Theory, 10:18–35 (2015).

Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR.
“BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.”
BMC Syst Biol, 9:8 (2015).

Summary

The diversity of biological form depends on the processes of development and evolution. Our group tries to understand the principles that govern these processes using an interdisciplinary approach based on experimental work and quantitative mathematical modelling of gene regulatory networks. As our experimental system, we study and compare pattern formation during early development of three dipteran insects: the fruit fly (Drosophila melangoaster), a scuttle fly (Megaselia abdita), and a moth midge (Clogmia albipuncata). In 2015, we have published an extensive quantitative data set for spatio-temporal expression patterns of the gap genes in Megaselia. These data are accessible through our SuperFly database (superfly.crg.eu), and were used for two detailed functional analyses of maternal co-ordinate and gap gene regulation based on gene knock-down by RNA interference. In early 2016, we have also published comparative study of gene network models between Drosophila and Megaselia. This work reveals that the gap genes evolve through system drift along a genotype network, to compensate changing maternal inputs through compensatory evolution. Finally, over the last two years we have published numerous theoretical papers that explore the implications of our work for evolutionary systems biology and the philosophy of biology.

Research projects

A quantitative, comparative study of gap gene regulation in dipterans (Karl Wotton, Eva Jiménez-Guri, Anton Crombach, Brenda Gavilán, Núria Bosch, Damjan Cicin-Sain)

Modelling the evolutionary dynamics of the gap gene network (Anton Crombach)

Phase space analysis of evolving regulatory networks (Berta Verd, Anton Crombach)

Development of new optimization and model analysis tools (BioPreDyn) (Anton Crombach, Damjan Cicin-Sain)

A systems-level analysis of giant (gt) regulation in Drosophila melanogaster (Astrid Hörmann)

A quantitative study of gap gene mutants in Drosophila melanogaster (Hilde Janssens)

Analysis of dorso-ventral patterning in the moth midge Clogmia albipunctata (Eva Jiménez-Guri, Anna Alcaine Colet)