Biology, Computation and Engineering

Today’s questions in biology are increasingly being tackled using methods and concepts from mathematics, physics, computer science, and engineering. Massively parallel experiments provide the opportunity to study complex biological systems in their entirety, generating enormous data sets that require sophisticated computational analyses. Advances in physics and optical engineering open up new possibilities for looking into cells and organisms with unprecedented spatial and temporal resolution, and are complemented by methods from computer vision and mathematics for automated and quantative analyses of image and video data. And with methods from microfluidics and bioengineering, biologists can now design experimental systems to automatically manipulate single animals or cells, or even the biochemical processes inside living cells. More than ever, biology offers exciting new challenges and opportunities for researchers from mathematics, physics, computer science and engineering.

The IMP brings biology together with expertise in these fields to form a collaborative and stimulating research environment. Groups that bridge these fields work in bioinformatics, computer vision, data visualization, virtual reality, microfluidics, and optical engineering. They are supported by outstanding scientific services, a large and fully administered compute cluster, and a state-of-the-art technical workshop. Together, these groups offer unique opportunities for highly interdisciplinary research projects.

Dickson Group

The Dickson group uses methods from computer vision to derive quantitative descriptions of the behaviour of the fruit fly Drosophila, and uses statistics and machine learning approaches to investigate the structure of these behaviours and infer the neural algorithms that generate them. The group is also developing interactive 3D atlases of the neuronal networks in the fly’s brain, and collaborates with the Stark group to identify unique genetic addresses for each distinct neuronal class within these networks.

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Rumpel Group

The Rumpel group applies computational approaches to analyze data on the dynamics of synapses and neuronal firing patterns obtained from in vivo imaging studies in mice. Furthermore, we use optogenetic approaches to interface with ongoing brain activity to interrogate the function of neocortical circuits.

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Stark Group

The Stark group uses experimental and computational techniques to study how gene regulatory information is encoded in the genome sequence. Using ChIP-Seq, in vivo and in vitro enhancer screens, sequence analyses, and machine learning, we aim to “crack” the regulatory code by predicting enhancer activity from DNA sequence, and thus to understand how transcriptional networks define cellular and developmental programs.

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Straw Group

The Straw group uses methods in realtime computer vision, computer graphics, and electronic circuits to dynamically interact with the feedback driven sensory-motor pathways in the brain of insects, especially the visual behaviors of the fruit fly Drosophila. Quantitative behavioral experiments performed in a free flight virtual reality apparatus aim to describe new behaviors and extract algorithmic descriptions with the assistance of machine learning techniques and automated experiment design.

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Vaziri Group

The Vaziri group brings approaches and methods from physics to biological problems, aiming to understand the principles of biological function on a multi-level scales. We are interested in problems ranging from the mechanisms of selectivity and transport in ion-channels and mechanism of protein-protein recognition to understanding how the dynamic interaction of defined neuronal circuits with sensory information generates behavior. We use advanced spectroscopy techniques and develop methods based on ultrafast and non-linear optics which are used in collaboration with other IMP groups for structural and functional imaging and interrogation of biological processes at unprecedented speed, spatial and temporal resolution.

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Zimmer Group

The Zimmer group engineers microfluidic lab-on-a-chip devices to study neural circuits and behavior in the nematode worm C. elegans. These devices constrain animals onto microscope stages while controlling a precise chemosensory environment, such as oxygen levels. Using optical imaging of behavior and neural activity followed by sophisticated image processing analysis, we decipher how environmental changes lead to changes in the activity patterns of neuronal ensembles that are translated into patterns of appropriate behavioral output.

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