bornberglab.org

Projects

Click on the link to learn more about the projects. The classifications of the projects (Forschungsmodul, summerschool, BSc-thesis and MSc-thesis) are suggestive. If a project interests you for a Forschungsmodul but has a MSc-thesis classification, you are still strongly encouraged to contact the relevant supervisor to discuss the project.

Open Projects

• In silico selection and directed evolution of bioactive de novo emerged proteins
• Supervisor: Lars Eicholt
• Project type: BA/FM/MA



• Laboratory Evolution of de novo proteins
• Supervisor: Bharat Ravi
• Project type: MA/FM



• In silico evolution of newly emerging proteins
• Supervisor: Bharat Ravi
• Project type: MA/FM



• Finding evidence of de novo proteins using mass spectrometry data analysis
• Supervisor: Bharat Ravi
• Project type: BA/FM



• Ancestral reconstruction - Characterization of ancestral proteins of a possible de novo protein from Homo sapiens
• Supervisor: Andreas Lange
• Project type: BA/FM



• Understanding de novo gene emergence using a stochastic mathematical model of mutagenesis, selection and population growth
• Supervisor: Bharat Ravi
• Project type: MA



• Purification of putative de novo proteins from inclusion bodies
• Supervisor: Andreas Lange
• Project type: FM



• Analysing effects of ageing on co-expression networks in Drosophila
• Supervisor: Mark Harrison
• Project type: FM/ BSc/ MSc-thesis



• Discovering the secrets of a long life in eusocial animals with co-expression network analyses
• Supervisor: Mark Harrison
• Project type: FM/ BSc/ MSc-thesis



• Caste-specific role of transposable elements in gene regulation in termites.
• Supervisor: Mark Harrison
• Project type: FM/ BSc/ MSc-thesis



• The role of alternative splicing in the evolution of eusociality in Blattodea
• Supervisor: Mark Harrison
• Project type: FM/BSc/MSc-thesis



• Investigating the Molecular Footprints of Eusociality with Machine Learning.
• Supervisor: Mark Harrison
• Project type: FM/ BSc/ MSc-thesis



• A quest for the missing piece in the puzzle of epithelial junctions
• Supervisor: Erich Bornberg-Bauer and Prof. Stefan Luschnig (Institute of Neuro- and Behavioural Biology)
• Project type: FM/BSc-thesis



• Developing algorithms for the analysis of domains and their arrangements
• Supervisor: Carsten Kemena
• Project type: BSc/Msc-thesis



• Conservation analysis of protein domain arrangements
• Supervisor: Carsten Kemena
• Project type: FM



• The evolution of a social transcription factor
• Supervisor: Alun Jones
• Project type: FM/BSc/MSc-thesis (students welcome)



• Transcription factor intron and isoform dynamics in eusocial evolution
• Supervisor: Alun Jones
• Project type: FM/BSc/MSc-thesis (students welcome)

Ongoing Projects

• Are de novo genes real? Characterization of possible de novo genes from Homo sapiens (lab-based)
• Supervisor: Andreas Lange
• Project type: FM/BSc/MSc-thesis (students welcome)

Previous Projects

Genome assembly of Drosophila melanogaster

• Supervisor: Anna Grandchamp
• Project type: FoM/BSc/MSc

Studying the way of emergence of the de novo genes in Drosophila melanogaster

• Supervisor: Anna Grandchamp
• Project type: FoM/BSc/MSc

Chemosensory genes and mate perception in the viviparous cockroach /Diploptera punctata/

• Supervisor: Bertrand Fouks
• Project type: FoM / BSc

Regulation of Gene Expression & Transposable Elements

• Supervisor: Bertrand Fouks
• Project type: FM

Sociality Impact on Genome Evolution

• Supervisor: Bertrand Fouks
• Project type: FM/ BSc/ MSc-thesis

Transposable Elements families & Functional Categories

• Supervisor: Bertrand Fouks
• Project type: FM

Sequencing Techniques & the Discovery of Transposable Elements

• Supervisor: Bertrand Fouks
• Project type: FM/ BSc/ MSc-thesis

Purification and analysis (in vitro & in silico) of putative de novo proteins

• Supervisor: Lars Eicholt
• Project type: BA/FM/MA

• Expression, purification, analysis of putative de novo proteins
• Supervisor: Margaux Aubel & Lars Eicholt
• Project type: BA/FM/MA



• Role of phase separation in the activity of de novo proteins
• Supervisor: Lars Eicholt
• Project type: BA/FM



• Using AlphaFold2 to identify promising de novo protein candidates
• Supervisor: Lars Eicholt
• Project type: MA



• Improving RADIANT
• Supervisor: Carsten Kemena
• Project type: BSc/Msc-thesis



• Implementing porthoDom
• Supervisor: Carsten Kemena
• Project type: BSc



• Genome annotation of slave-maker ants and their hosts for comparative analyses
• Supervisor: Alice Séguret
• Project type: MSc thesis



• Development of a high-throughput assay to identify possible foldable de novo proteins
• Supervisor: Margaux Aubel & Lars Eicholt
• Project type: BA/FM



• Chaperones - The holy grail for soluble expression of de novo proteins from D. melanogaster in E.coli? (lab-based)
• Supervisor: Andreas Lange
• Project type: FM/BSc/MSc-thesis (students welcome)



• Adaptive Laboratory Evolution: Mapping Epistatic Mutations Within Ancestral Sulfatases
• Supervisor: Berndjan Eenink
• Project type: FoM/BSc-thesis



• Adaptive Laboratory Evolution: Disentangling and Combining Mutations to Reveal Epistatic Effects
• Supervisor: Bert van Loo
• Project type: FoM/BSc/MSc-thesis



• Identifying the transcriptional regulators of two insulin peptides, important in the development of termite queens.
• Supervisor: Mark Harrison/Alice Séguret
• Project type: FM/BSc/MSc-thesis



• Does methylation target transposable elements in the termite Macrotermes natalensis?
• Supervisor: Alice Séguret/Mark Harrison
• Project type: FM



• The evolution of gene network properties during slavemaker evolution
• Supervisor: Alice Séguret
• Project type: FM



• The potential role of repeats in the evolution of slave-making
• Supervisor: Alice Séguret
• Project type: FM



• Immunity gene family evolution in the European Beewolf
• Supervisor: Evelien Jongepier
• Project type: MSc project



• Historical Enzyme Evolution: Emergence of Sulfatases in the Metallo-β-Lactamase Superfamily
• Supervisor: Bert van Loo
• Project type: FoM/BSc/MSc-thesis



• Reading frame extension as potential domain emergence mechanism
• Supervisors: Andreas Lange/Brennen Haemes
• Project type: MSc-thesis



• Evolution of RNA structure.
• Supervisor: Jasmin Kurafeiski
• Project type: FM/BSc/MSc



• Effects of Epistasis on Transcription Factor Binding
• Supervisor: Jasmin Kurafeiski
• Project type: Summer School Project



• Comparative analysis of chemoreceptors in cockroaches
• Supervisor: Mark Harrison
• Project type: MSc-thesis



• Inference of C- and N-terminus protein extensions
• Supervisor: April Kleppe
• Project type: BSc-thesis



• Evolution-Inspired Protein Engineering and Design: Learning from the Evolutionary History of Haloalcohol Dehalogenases?Comparative analysis of chemoreceptors in cockroaches
• Supervisor: Bert van Loo
• Project type: BSc-thesis



• Evolution-Inspired Protein Engineering and Design: the Effect of Selection Pressure on Secondary Activities
• Supervisor: Bert van Loo
• Project type: FoM/BSc/MSc-thesis



• Investigating proto-genic ORFs
• Supervisor: Brennen Heames
• Project type: Forschungsmodul



• Creating a Benchmark for RADS
• Supervisor: Carsten Kemena
• Project type: BSc-thesis



• Fast domain annotation
• Supervisor: Carsten Kemena
• Project type: Forschungsmodul



• New Proteins out of Thin Air?
• Supervisor: Jonathan Schmitz
• Project type: BSc-thesis



• Evolutionary rate of novel genes
• Supervisor: Jonathan Schmitz
• Project type: Forschungsmodul



• Evolution-Inspired Protein Engineering and Design: Learning from the Evolutionary History of Haloalkane Dehalogenases?
• Supervisor: Bert van Loo
• Project type: BSc-thesis



• Identifying regulatory elements associated with de novo genes
• Supervisor: Brennen Heames
• Project type: Summer School Project



• Genomic adaptations in the Wolbachia endosymbiont of the European beewolf
• Supervisor: Evelien Jongepier
• Project type: Forschungsmodule



• The genomics of enemy recognition in the slaves of slavemaker ants
• Supervisor: Evelien Jongepier
• Project type: MSc



• Domain-Exon Overlap
• Supervisor: Carsten Kemena
• Project type: Forschungsmodule



• Partial Domain inclusion into Dogma
• Supervisor: Carsten Kemena
• Project type: Forschungsmodule



• Are de novo genes real? Characterization of possible de novo drosophila genes (lab-based)
• Supervisor: Andreas Lange
• Project type: FM/BSc/MSc-thesis



• Finding de novo genes in human populations
• Supervisor: Daniel Dowling
• Project type: Forschungsmodule



• Testing the evolutionary theory of ageing on eusocial insects
• Supervisor: Mark Harrison
• Project type: FM/MSc-thesis



• Atlas - a de novo gene important for spermatogenesis in male Drosophila melanogaster? (lab-based)
• Supervisor: Andreas Lange
• Project type: FM/BSc