Systems Biology

yogi-jager
Comparative Analysis of Developmental Systems

Group Structure

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:
Besray Ünal (with Luis Serrano), Juan José Fraire-Zamora (with Jerôme Solon)
PhD STUDENTS:
Astrid Hörmann, Berta Verd
GRADUATE INTERN:
Heleia Roca
UNDERGRADUATE STUDENTS:
Anna Alcaine Colet, Brenda Gavilán

Summary

“Natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.” said the famous geneticist Hugo de Vries in 1904. Today, we still lack a clear idea of why organisms such as plants and animals look exactly the way they do. For example, why are there no back-boned animals with more than four legs? Why do most of these creatures have five or less toes on their feet? Why are there no insects with more than two pairs of wings? Part of these questions can be explained by adaptation of environmental conditions through natural selection. But biological form also depends on how organisms grow and develop. Understanding development is one of the fundamental challenges of modern biology. In our laboratory we try to understand the principles that govern this process, from egg to adult, and how these principles affect the way in which evolution by natural selection shapes the diversity of life.

Our group consists of experimentalists and computational researchers. We perform experiments on three species of flies and midges: the fruit fly (Drosophila melangoaster), a scuttle fly (Megaselia abdita), and a moth midge (Clogmia albipuncata). We study when and where genes are switched on or off during development of these animals. This is done by coloring the chemical products of gene regulation (RNA or protein), and visualizing the resulting patterns of gene expression by microscopy. We then simulate the interactions of these genes (how they regulate each other) using the Mare Nostrum supercomputer of the Barcelona Supercomputing Center (BSC: http://www.bsc.es). This approach is called gene network modeling and allows us to study how genes function in their organismic context and how this function has changed during evolution.


Research Projects

  • A quantitative, comparative study of gap gene regulation in dipterans
    Karl Wotton, Eva Jiménez-Guri, Anton Crombach, Brenda Gavilán, Damjan Cicin-Sain
  • Modeling 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
  • Inferring the thoracic bristle patterning network of Drosophila melanogaster
    Bárbara Negre, Heleia Roca
  • Comparative transcriptomics and genomics of dipteran species
    Bárbara Negre (with the CRG Genomics and Bioinformatics Cores)

Selected Publications

  1. Becker K, Balsa-Canto E, Cicin-Sain D, Hoermann A, Janssens H, Banga JR, Jaeger J.
    “Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster.”
    PLoS Comp Biol, 9: e1003281 (2013).
  2. Wotton KR, Alcaine Colet A, Jaeger J & Jiménez-Guri E.
    “Evolution and expression of BMP genes in flies.”
    Dev Genes Evol, 223: 335–340 (2013).
  3. Janssens H, Crombach A, Wotton KR, Cicin-Sain D, Surkova S, Lim CL, Samsonova M, Akam M & Jaeger J.
    “Lack of tailless leads to an increase in expression variability in Drosophila embryos.”
    Dev Biol, 377: 305–317 (2013).
  4. Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J.
    “Comparative transcriptomics of early dipteran development.”
    BMC Genomics 14: 123.
  5. Jaeger J & Monk N.
    “Keeping the gene in its place.”
    In: The Intuitive Way of Knowing: A Tribute to Brian Goodwin, Lambert D & Chetland C (eds.), Floris Books, Edinburgh, UK.