Gašper Tkačik

PhD, Physics (Princeton University)

I joined IST Austria in 2011. Previously I was a postdoc with Vijay Balasubramanian and Phil Nelson at University of Pennsylvania, working on the theory of neural coding and specifically exploring population coding and adaptation in the retina. I finished my PhD at Princeton with Bill Bialek and Curt Callan in 2007, studying how biological networks can reliably transmit and process information in the presence of intrinsic noise and corrupted signals. I am broadly interested in uncovering general principles that underlie efficient biological computation.

[ CV pdf ]


Michal Hledík

Graduate Student, co-advised by Nick Barton

Mutations can affect the expression of a gene either directly (e.g. mutations in its promoter region) or indirectly, by first perturbing other genes upstream in a regulatory network. We can see many such indirect effects in the data as trans-eQTLs. I study how the properties of the regulatory network shape genetic variation in expression levels of many genes across a population. In particular, I am interested in what the network needs to be like for the indirect/trans effects to contribute substantially to expresion variation. To do this, I use simple biophysics-inspired models of gene regulation and genotype + expression data analysis.

Reka Körei

Graduate Student

I started at IST Austria in 2019 as a graduate student. A few months later I joined Gasper’s group aiming for a deeper understanding of regulatory networks.
We represent interacting genes inside of a cell often as a regulatory network. In this network, each node corresponds to a specific gene and two genes are connected with a directed link if one regulates the other (regulation happens when at least one gene is a transcription factor). These interactions between genes lead to complex behavior, which enables the cell to adapt to its environment and to function properly. I am interested in how evolution drives the system towards the emergence of a particular behavior. To gain a better knowledge I use a biophysical model, which operates in the discrete space of regulatory sequences, but is still simple enough to be understandable.

Natália Ružičková

Graduate Student

I joined the group in 2020 after starting as a PhD student at IST in 2019. I am broadly interested in the function of regulatory networks in biology, at various scales. On the intracellular level, I ask how we can incorporate experimental findings about gene regulatory networks into genotype-phenotype predictive models, aiming towards a biophysically interpretable form of genome-wide association studies (GWAS). On the intercellular level, I am trying to understand how cells in the pancreatic islets of Langerhans interact to collectively ensure precise measurement of blood glucose and subsequent release of insulin. As a physicist by training, I use a combination of modelling and inference from data.

Mantas Gabrielaitis

IST Fellow
PhD (MPI-DS and University of Göttingen)

I joined the group as an IST Fellow in 2017. My research interests include acoustic information processing in the nervous system. Applying tools and concepts from signal processing, statistics, and information theory, I study how various biophysical structures in the peripheral auditory system are adapted to efficiently encode and transmit information to the brain. Answering these questions poses unsolved inverse problems of general interest in signal processing and statistical learning theory. Solving these problems and developing corresponding numerical methods constitute another active branch of my work program.

Wiktor Mlynarski

IST Fellow
PhD (MPI for Mathematics in the Sciences)

I joined the group as an IST Plus fellow in October 2018. Before that I was a postdoc at MIT Brain and Cognitive Sciences Department, and got my PhD at the Max-Planck Institute for Mathematics in the Sciences. In my work I try to understand fundamental limits and principles which govern the function of sensory systems. To that end I analyze the statistical structure of natural stimuli, develop optimal processing strategies which might be approximated by biological systems and verify theoretical predictions through experimental data analysis. To read more about my work please see my homepage.

Fabrizio Lombardi

IST Fellow
PhD (ETH Zurich)

I joined the group in May 2019 as an ISTplus fellow, moving from Boston University, where I was postdoc at the Department of Physics. My research interests fall into the realm of theoretical and computational statistical physics, with a particular inclination towards non-equilibrium phenomena and emergent collective behaviors in biological, ecological and physiological systems. Recently I have been focusing on criticality in brain dynamics and non-equilibrium effects in homeostatic sleep regulation, and in developing a holistic approach to human physiology that aims to associate distinct conditions with networks of interactions inferred from synchronous recordings of several organs across the human body and predict their evolution in response to perturbations (e.g. organ failure, medical treatments). I approach problems at the interface of physics and life sciences combining data analysis and computational modeling, and make use of concepts and methods from statistical mechanics, non-linear dynamics and theory of stochastic processes, with the objective of explaining large scale collective behaviors in term of key properties that characterize basic constituents and their interactions.

David Brückner

Nomis Fellow, joint with Edouard Hannezo
PhD (LMU Munich)

I joined the group as an NOMIS Postdoctoral Fellow in August 2021. Following undergraduate studies at the University of Cambridge, I did my PhD in the group of Chase Broedersz at the LMU in Munich. In my work, I seek to understand the physical principles governing complex biological systems, with a focus on developmental biology. To this end, I use a mix of data-driven inference methods, mechanistic biophysical models, and normative approaches based on information theory. My current projects focus on fate decision making of stem cells in development, as well as the interplay of chromosome structure and transcriptional regulation. To read more about my work please visit my homepage.

Former group members

Anna M Andersson, postdoc, 2019 starting as a data scientist at Equiniti
Katarína Boďová, postdoc, cosupervised with Nick Barton; 2017 starting as Assistant Professor at the Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava
Vicent Botella-Soler, postdoc, 2016 starting as freelance data analysis consultant, now at ForwardKeys
Remy Chait, IST Fellow, cosupervised with Calin Guet, 2019 starting as Lecturer in the biosciences department, University of Exeter
Matthew Chalk, postdoc, 2018 starting as INSERM Researcher at Institute of Vision, Paris
Sarah Anhala Cepeda-Humerez, PhD student (defended Feb 27, 2019), 2021 starting as data scientist at United Nations
Rok Grah, PhD student, cosupervised with Calin Guet (defended June 8, 2020), 2020 starting as Research Associate at Stockholm Environment Institute (SEI), now at European Centre for Disease Prevention and Control (ECDC), Stockholm
Jan Humplik, PhD student, 2019/2020 starting at DeepMind, London
Bor Kavčič, PhD student & postdoc (defended September 9, 2020), 2022 starting as Postdoc at Biozentrum Basel
Daniele De Martino, postdoc, 2019 starting as Postdoc at Jozsef Stefan Institute, Ljubljana; Winter 2019 starting as Assistant Professor at Basque Center for Biophysics
Tamar Friedlander, IST Fellow, 2017 starting as Assistant Professor at Hebrew University of Jerusalem
Aditya Gilra, IST Fellow, 2020 starting as Lecturer at Department of Computer Science, University of Sheffield
Anna Levina, IST Fellow, 2017 starting as Group Leader at University of Tübingen, recipient of Sofja Kovalevskaja Award (2017)
Georg Martius, IST Fellow, 2017 starting as Max Planck Group Leader at MPI for Biological Cybernetics
Gabriel Mitchell, postdoc
Roshan Prizak, PhD student, cosupervised with Nick Barton (defended Jan 14, 2019), since 2019 postdoc with Lennart Hilbert at KIT Karlsruhe
Georg Rieckh, PhD student (defended June 28, 2016); 2016 starting as postdoc with Sergey Kryazhimskiy at UC San Diego, now at Accenture Vienna
Jakob Ruess, IST Fellow, 2016 starting as INRIA Palaiseau Researcher at Institut Pasteur
Cristina Savin, IST Fellow, 2017 starting as Assistant Professor at NYU in Neuroscience and Data Science
Thomas R Sokolowski, Postdoc, 2020 starting as Group Leader at Frankfurt Institute for Advanced Studies
Murat Tugrul, PhD student, cosupervised with Nick Barton (defended June 27, 2016); 2016 starting as postdoc at St. Anna Kinderspital, Vienna