62 citations · 93 across the 11 of their papers we have counts for
13 papers
Information-Theoretical Measures for Developmental Cell-Fate Proportioning Processes
Michael A. Ramirez-Sierra, Thomas R. Sokolowski
Self-organization is a fundamental process of complex biological systems, particularly during the early stages of development. In the mammalian embryo, blastocyst formation exempli…
Initial Luminally Deposited FGF4 Critically Influences Blastocyst Patterning
Michael A. Ramirez-Sierra, Thomas R. Sokolowski
Luminogenesis, the formation of a fluid-filled cavity (lumen), is an essential process in early mammalian embryonic development, coinciding with the second cell-fate decision that…
Unifying Physics- and Data-Driven Modeling via Novel Causal Spatiotemporal Graph Neural Network for Interpretable Epidemic Forecasting
Shuai Han, Lukas Stelz, Thomas R. Sokolowski +2
Accurate epidemic forecasting is crucial for effective disease control and prevention. Traditional compartmental models often struggle to estimate temporally and spatially varying…
Comparing AI versus Optimization Workflows for Simulation-Based Inference of Spatial-Stochastic Systems
Michael A. Ramirez-Sierra, Thomas R. Sokolowski
Model parameter inference is a universal problem across science. This challenge is particularly pronounced in developmental biology, where faithful mechanistic descriptions require…
AI-powered simulation-based inference of a genuinely spatial-stochastic model of early mouse embryogenesis
Michael A. Ramirez-Sierra, Thomas R. Sokolowski
Understanding how multicellular organisms reliably orchestrate cell-fate decisions is a central challenge in developmental biology. This is particularly intriguing in early mammali…
Stable developmental patterns of gene expression without morphogen gradients
Maciej Majka, Nils B. Becker, Pieter Rein ten Wolde +2
Gene expression patterns (GEPs) are established by cross-regulating target genes that interpret morphogen gradients. However, as development progresses, morphogen activity is reduc…
Deriving a genetic regulatory network from an optimization principle
Thomas R Sokolowski, Thomas Gregor, William Bialek +1
Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nev…
A Tight Upper Bound on Mutual Information
Michal Hledík, Thomas R. Sokolowski, Gašper Tkačik
We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bo…
eGFRD in all dimensions
Thomas R. Sokolowski, Joris Paijmans, Laurens Bossen +7
Biochemical reactions typically occur at low copy numbers, but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical…
Spatial-Stochastic Simulation of Reaction-Diffusion Systems
Thomas R. Sokolowski, Pieter Rein ten Wolde
Biochemical networks play a crucial role in biological systems, implementing a broad range of vital functions. They normally operate at low copy numbers and in spatial settings, bu…
Extending the dynamic range of transcription factor action by translational regulation
Thomas R. Sokolowski, Aleksandra M. Walczak, William Bialek +1
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar c…
Optimizing information flow in small genetic networks. IV. Spatial coupling
Thomas R. Sokolowski, Gašper Tkačik
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate.…
Mutual Repression enhances the Steepness and Precision of Gene Expression Boundaries
Thomas R. Sokolowski, Thorsten Erdmann, Pieter Rein ten Wolde
Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic…