Organismal Systems Biology
Organismal Systems Biology Lab
Research
Our laboratory explores the fundamental design principles governing molecular circuits at the multicellular level. We aim to learn how organisms maintain robustness within an environment yet remain plastic across different environments.
Our current research focuses on :
1. how the robustness of development emerges from the communication between cells, and
2. how phenotypic plasticity optimzes performance under starvation.
We employ a combination of quantitative experiments and computational approaches, using the nematode C. elegans as our model organism. Our technical strengths lie in in quantitative live imaging and computational image analysis, high-throughput screens, and in the precise spatio-temporal perturbation of molecular circuits.
We value interdisciplinary exchange and collaboration to create new opportunities at the interface of disciplines.
Current Research Focus
1. Developmental Robustness: Orchestrating Cellular Growth
Key Question: How do an animal's cells coordinate their growth to consistently produce an appropriate body plan?
During development, organs grow exponentially by orders of magnitude. Therefore, small fluctuations in the growth rate can, in principle, amplify to significant size discrepancies. Yet, in nature, organ proportions are remarkably consistent across individuals. We investigate the molecular mechanisms that coordinate growth across different organs and thereby ensure this robustness.
Growth of individual animals
Individuals of C. elegans were imaged every 10 minutes throughout their development and computationally straightened. green marks the pharynx, red the total body. Our research asks how fluctuations in organ growth rates are correted to nevertheless yield robust body plan proportions.
References:
2023, Nature Communications
Klement Stojanovski, Ioana Gheorghe, Peter Lenart, Anne Lanjuin, William B Mair, Benjamin D Towbin
2022, Nature Communications
Klement Stojanovski, Helge Großhans & Benjamin D. Towbin
2. Developmental Plasticity: Thriving under Nutritional Fluctuations
Key Question: How do animals optimize their fitness in response to changing nutritional conditions?
Animals must navigate environments where food availability fluctuates. This requires a delicate balance between rapid growth during abundance and survival during scarcity. We investigate the molecular mechanisms that sense nutritional cues, how they alter gene expression, and how this regulation ultimately impacts organism-scale phenotypes, such as growth, reproduction, and aging. We thereby thrive to understand the molecular underpinnings of tradeoffs between these fundamental life history traits and how animals navigate these tradeoffs to make the best out of their environment.
Together, we aim to learn how organisms maintain robustness within an environment yet remain plastic across different environments.
Individuals of C. elegans growing in arrayed of micro chambers.
References:
2024, bioRxiv
Joel Tuomaala, Devanarayanan Siva Sankar, Julie Perey, Sacha Psalmon, Nicholas Stroustrup, Joern Dengjel, Benjamin D. Towbin
Team
Benjamin Towbin, PhD
Principal investigator
Benjamin carried out a PhD in Genetics with Prof. Susan Gasser at the FMI in Switzerland, where he studied epigenetic mechanisms of gene control using C. elegans. As a postdoc, he joined the group of Prof. Uri Alon at the Weizmann Institute in Israel, studying optimality principles in bacterial growth control. Since November 2019, he has been an SNSF Eccellenza Professor at the University of Bern. In his lab, he applies quantitative systems biology approaches to study optimality principles at a multi-cellular scale using C. elegans.
Klement Stojanovski, PhD
Lab manager
During his PhD, Klement studied prion formation, using S. cerevisiae. He continued working with yeast as a postdoc studying a kinase signalling pathway, before switching to mammalian cell cultures to study drug targets in the endocannabinoid system. In our group, he studies body size homeostasis and makes sure that everything runs smoothly in the lab.
Dirk Beuchle
Lab manager
Dirk has joined us in 2023 after being trained as a Drosophila geneticist in the laboratory of Prof. Beat Suter. We are fortunate that his golden hands can inject worms and flies alike. In his free time he explores the world by bike.
Peter Lenart, PhD
SNSF Swiss Postdoctoral fellow (MSCA replacement)
During his PhD, Peter developed his primary expertise in theoretical and computational biology, focusing mainly on the evolution of aging. He also acquired a rich experience in interdisciplinary research that ultimately led him to the decision to return to lab work so he could experimentally test his theoretical concepts. In our group, Peter studies the information contained in the developmental trajectories of individual C. elegans and asks various evolutionary questions along the way.
Anna Slesarchuk
PhD student
Anna is a Russian MSc graduate in chemistry with a deep fascination for life's molecular intricacies. A thought-provoking idea—‘In the beginning was the word, and the word was RNA’—sparked her transition from bioorganic chemistry to molecular biology. Now, as a PhD researcher, she explores the mechanisms of gene regulation in organ growth and development, aiming to uncover fundamental principles that shape life at the molecular level.
Sigma Pradhan
PhD student
Sigma comes from India with graduation from IISER Kolkata. She did her masters on regulation of HER2-induced oncogenicity and HER3 expression in breast epithelial cell lines at IISER Pune. Her interest in interdisciplinary sciences led her to organismal systems biology lab. During her Ph.D. she is studying the parental effects of dietary restriction in C. elegans on ribosome expression and growth dynamics, and the regulatory mechanisms involved.
Ioana Gheorghe
PhD student
Born in Romania, Ioana obtained her Bachelor of Science in Molecular Life Sciences from Radboud University in the Netherlands, where she worked with S. lycopersicum plants on reproductive heat tolerance. She chose to continue her studies in Molecular Life Sciences at Bern University, focusing on the coordination of tissue growth during C. elegans development in her MSc thesis and stayed for PhD.
Sacha Psalmon
PhD student
Born in France, Sacha studied engineering at the Polytech Nice-Sophia engineering school. Specialized in Applied Mathematics and Modelling, he is developing new image analysis pipelines using neural networks, and analysing mathematical models on the evolution of ageing.
Sacha Psalmon
PhD student
Ferdinand studied biology at the University of Innsbruck and the Technical University of Munich, focusing on cell biology, zoology and biomedicine. Wanting to focus on basic research in an interdisciplinary environment, he joined the organismal systems biology lab. During his PhD, he is studying starvation responses in C. elegans, with an emphasis on an evolutionary tradeoff between growth and survival.
Alumni
Artur Luzgin (internship)
Franziska Schmid (MSc, MLS)
Aaditya Saxena (BSc, ThinkSwiss scholar)
Stefano von Wyttenbach (BSc)
Garima Yadav (MSc intern)
Julie Perey (MSc, MLS)
Boris Gusev (MSc, Computational Biology)
Simeon Streit (BSc Biology)
Adriel Ysamin (BSc Biology)
Silvan Pauls (BSc BIology)
Delia Bogenstätter (BSc Biology)
Urs Nösberger (MSc, MLS)
Noelia Gerber (MSc, MLS)
Souvik Mandal (BSc, ThinkSwiss scholar)
Joel Tuomaala (PhD student)
Selected Publications
2022, Nature Communications
Klement Stojanovski, Helge Großhans & Benjamin D. Towbin
2023, Nature Communications
Klement Stojanovski, Ioana Gheorghe, Peter Lenart, Anne Lanjuin, William B Mair, Benjamin D Towbin
2023, bioRxiv
Peter Lenart, Sacha Psalmon, Benjamin D. Towbin
2024, bioRxiv
Joel Tuomaala, Devanarayanan Siva Sankar, Julie Perey, Sacha Psalmon, Nicholas Stroustrup, Joern Dengjel, Benjamin D. Towbin
2025, bioRxiv
Sigma Pradhan, Klement Stojanovski, Joel Tuomaala, Nicholas Stroustrup, Benjamin D Towbin
Join us!
We always welcome personalized unsolicited applications that consider the following:
PostDocs: We are always interested in motivated talent and can explore possible projects and funding opportunities, including postdoctoral fellowships from EMBO, MSCA, HFSP, or FEBS. Please get in touch by email providing your CV, a motivation letter, and a statement of research interests.
PhD students: Please get in touch if you are interested by sending an email with your CV and a cover letter describing:
(i) who you are
(ii) what you hope to learn/achieve by doing a PhD
(iii) what makes you interested in my lab.
Check out these guidelines for writing a cover letter that let's me evaluate if there is a match between our lab and you:
https://threadreaderapp.com/thread/1642327392122474496.html
Undergraduates (MSc/BSc): Please get in touch by email for training opportunities. We usually have wet or dry lab projects available. Include a CV and a cover letter with brief statement of your research interests (e.g. a lecture topic you particularly liked during your studies) and how you see a project in myl lab help you foster your interests.
Undergraduates from Europe (except Switzerland) can be funded through the SEMP/Erasmus program. International students may e.g. apply to the ThinkSwiss or ThinkSwiss-Asia programs. Check if you are eligible for those before applying.
Worm cinema
Individuals of C. elegans growing in micro chambers
Individual animals of C. elegans were recorded simultaneously in arrayed micro chambers from birth to adulthood at a time resolution of 10 minutes.
Worm race
Individuals of C. elegans were imaged every 10 minutes throughout their development and computationally straightened. green marks the pharynx, red the total body.
Germline growth
The two gonadal arms of the germline of C. elegans was marked GFP and imaged from birth to adulthood.
chewing worm
The pharynx of a worm was imaged at 30 frames per second to visualize the movements of the pharyngeal muscle. Movie plays in real time.
reproducing worms
Single animal was imaged hourly over 7 days. Eggs were genetically prevented from hatching to count progeny.
singaling dynamics
An animal expressing the transcription factor DAF-16:GFP is shown. DAF-16 shuttles in and out of th nucleus when activated.