20 citations · 41 across the 9 of their papers we have counts for
9 papers
Nonlocal decoding of positional and correlational information during development
Alex Chen Yi Zhang, Pablo Mateu Hoyos, David Brückner +1
In many developmental systems, cells differentiate into a tissue by reading out morphogen concentration fields, a process fundamentally limited by noise. How much can the precision…
Marr's three levels for embryonic development: information, dynamical systems, gene networks
David B. Brückner, Gašper Tkačik
Developmental patterning comprises processes that range from purely instructed, where external signals specify cell fates, to fully self-organized, where spatial patterns emerge au…
Invariant non-equilibrium dynamics of transcriptional regulation optimize information flow
Benjamin Zoller, Alexis Bénichou, Thomas Gregor +1
Eukaryotic gene regulation is based on stochastic yet controlled promoter switching, during which genes transition between transcriptionally active and inactive states. Despite the…
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…
Eukaryotic gene regulation at equilibrium, or non?
Benjamin Zoller, Thomas Gregor, Gašper Tkačik
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. How…
Action at a distance in transcriptional regulation
William Bialek, Thomas Gregor, Gašper Tkačik
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with t…
Semiparametric energy-based probabilistic models
Jan Humplik, Gašper Tkačik
Probabilistic models can be defined by an energy function, where the probability of each state is proportional to the exponential of the state's negative energy. This paper conside…
Retinal adaptation and invariance to changes in higher-order stimulus statistics
Gašper Tkačik, Anandamohan Ghosh, Elad Schneidman +1
Adaptation in the retina is thought to optimize the encoding of natural light signals into sequences of spikes sent to the brain. However, adaptation also entails computational cos…
From statistical mechanics to information theory: understanding biophysical information-processing systems
Gašper Tkačik
These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on u…