Gasper Tkacik

Abstract Cis-regulatory elements (CREs), such as enhancers and promoters, control gene expression by binding regulatory proteins. In contrast to their bacterial counterparts, eukaryotic CREs typically bind transcription factors with short recognition motifs across multiple functional yet often weak binding sites. The evolutionary origin of this genetic architecture remains unclear. Here we study adaptive evolution of entire CREs under selection for controllable gene expression.

Abstract Evolution of gene regulatory sequences is shaped by their genotype-phenotype (GP) map, but this map itself can evolve via changes in the molecular machinery that reads out the regulatory sequences. Using population genetics theory, we derive an optimality principle, implying that the evolved GP maps will associate fit phenotypes with larger numbers of possible genotypes.

Abstract A key feature of biological and artificial neural networks is the progressive refinement of their neural representations with experience. In neuroscience, this fact has inspired several recent studies in sensory and motor systems. However, less is known about how higher associational cortical areas, such as the hippocampus, modify representations throughout the learning of complex tasks.