Below is a list of my publications with a short descriptions of the respective projects (last update 23/01/2022). Please visit my google scholar or orcid profile for the most up-to-date list of publications.
Article | Hulse BK*, Haberkern H*, Franconville R*, Turner-Evans DB*, Takemura S, Wolff T, Noorman M, Dreher M, Dan C, Parekh R, Hermundstad AM, Rubin GM, Jayaraman V (2021). *shared first-author A connectome of the Drosophila central complex reveals network motifs suitable for flexible navigation and context-dependent action selection. eLife 2021;10:e66039 DOI: 10.7554/eLife.66039 |
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Article | Haberkern H, Basnak MA, Ahanonu B, Schauder D, Cohen JD, Bolstad M, Bruns C, Jayaraman V (2019). Visually guided behavior and optogenetically induced learning in head-fixed flies exploring a virtual landscape. Current Biology 29(10) 1647-1659. e8 |
Combining behavioral studies with genetic tools in highly controlled sensory environments using virtual reality (VR) has a long tradition fly neurobiology. More recently, VR has been used to record neural activity, which requires small animals like flies to be head-fixed. Neurophysiology in behaving head-fixed flies enabled important insights into navigational circuit function, though so far simulated sensory environments have been highly reduced and behaviors relatively simple. We developed a novel VR system and behavioral paradigms that allow study of complex behaviors that unfold in two-dimensional environments. This will increase the scope of possible studies of neural mechanisms underlying navigation in flies.
Article | Haberkern H, Hedwig B (2016). Behavioural integration of auditory and antennal stimulation during phonotaxis in the field cricket Gryllus bimaculatus. J Exp Biol. 219(Pt 22):3575-3586. |
In this study we investigated how crickets following conspecific male’s calling song in search of a mating partner (phonotaxis) respond to simulated obstacles in their path (antennal stimuli). Following the hypothesis that animals need to flexibly respond to environmental stimuli without compromising behavioral consistency we expected that crickets would only briefly interrupt phonotaxis during antennal stimulation. Surprisingly, mechanosensory stimulation suppressed phonotaxis for extended time periods. This was likely the consequence of incomplete sensory feedback under laboratory conditions causing the behavioral sequence to stall. This hints at mechanisms underlying generation of behavioral sequences.
Review | Haberkern H, Jayaraman V (2016). Studying small brains to understand the building blocks of cognition. Curr Opin Neurobiol. 37:59-65. |
This review was part of the issue “Neurobiology of cognitive behavior”, which focused on experimental and theoretical approaches for studying complex, cognitive behavior and its neural underpinnings. Most of the issue was focused on studying cognition in vertebrate models. Our review provided a perspective on what could be learned about the neural basis of cognition from studying small invertebrate brains. We argued that insects show a range of cognitive behaviors and describe methods that have been used to probe the underlying neural mechanisms – with a special focus on studies in fruit flies.
Article | Milde F, Tauriello G, Haberkern H, Koumoutsakos P (2014). SEM++: a particle model of cellular growth, signaling and migration. Computational Particle Mechanics 1 (2), 211-227 |
Subcellular Element Models use a collection of computational particles with short-range interactions to model biological cells and tissues. They are computationally efficient and intuitive. This work extends the previously described subcellular elements modeling approach to explicitly consider different cellular components such as the nucleus or the cell membrane. Computational particles used to model these different compartments can have different properties and rules according to which they interact. This does not only permit modeling of cell growth and motility, but also cell-cell signaling through interactions between “membrane particles” of different simulated cells.
Article | Wang D, Freitag F, Gattin Z, Haberkern H, Jaun B, Siwko M, Vyas R, van Gunsteren W F, Dolenc J (2012). Validation of the GROMOS 54A7 Force Field Regarding Mixed α/β -Peptide Molecules. Helvetica Chimica Acta 95 (12), 2562- 577 |
To experimentally determine molecular structures involves averaging over time. This is problematic when measuring flexible molecules that rapidly transition through multiple configurations. Simulating molecular dynamics provides a valuable tool to assess the full potential range of structural conformations. However, simulating large molecules like proteins based on first principle physical models is computationally expensive. So-called forcefields can be used as an approximative method but they have to be validated. Here we validated a new force field by simulating folding of two small peptides and demonstrating that the most commonly obtained confirmations matched experimental data.
Article | Eschbach C, Cano C, Haberkern H, Schraut K, Guan C, Triphan T, Gerber B (2011). Associative learning between odorants and mechanosensory punishment in larval Drosophila. J Exp Biol. 214(Pt 23):3897-905. |
Previous work had shown that Drosophila melanogaster larvae can be trained to avoid an odor after pairing it with an unpleasant taste or electric shock. This study establishes mechanical vibration of the substrate on which larvae are moving as a new type of punishment for olfactory conditioning. Olfactory conditioning in fruit fly larvae is used as a model system to study the cellular mechanisms underlying learning. Being able to compare how olfactory memories are formed using different types of punishment stimuli may help to identify the principles according to which larvae form associative memories.
Preprint | Hulse BK*, Haberkern H*, Franconville R*, Turner-Evans DB*, Takemura S, Wolff T, Noorman M, Dreher M, Dan C, Parekh R, Hermundstad AM, Rubin GM, Jayaraman V (2020). A connectome of the Drosophila central complex reveals network motifs suitable for flexible navigation and context-dependent action selection. bioRxiv. DOI: 10.1101/2020.12.08.413955. (*) co-first author.
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Preprint | Haberkern H, Basnak MA, Ahanonu B, Schauder D, Cohen JD, Bolstad M, Bruns C, Jayaraman V (2018). On the adaptive behavior of head-fixed flies navigating in two-dimensional, visual virtual reality. bioRxiv.DOI: 10.1101/462028. -> now published in Current Biology (see above)
Combining behavioral studies with genetic tools in highly controlled sensory environments using virtual reality (VR) has a long tradition fly neurobiology. More recently, VR has been used to record neural activity, which requires small animals to be head-fixed, in behaving flies. This enabled important insights into navigational circuit function, though so far simulated sensory environments have been highly reduced and behaviors relatively simple. We developed a novel VR system and behavioral paradigms that allow study of complex behaviors that unfold in two-dimensional environments. This will increase the scope of possible studies of neural mechanisms underlying navigation in flies.
PhD Thesis | Haberkern H (2017). Multisensory navigation in tethered walking insects. |