4 papers
Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges
Elia Mascolo, Réka Borbély, Noa Ottilie Borst +3
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yi…
Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype-phenotype maps
Elia Mascolo, Réka Borbély, Santiago Herrera-Álvarez +3
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yi…
Meta-Learning Theory-Informed Inductive Biases using Deep Kernel Gaussian Processes
Bahti Zakirov, Gašper Tkačik
Normative and task-driven theories offer powerful top-down explanations for biological systems, yet the goals of quantitatively arbitrating between competing theories, and utilizin…
ML-PWS: Estimating the Mutual Information Between Experimental Time Series Using Neural Networks
Manuel Reinhardt, Gašper Tkačik, Pieter Rein ten Wolde
The ability to quantify information transmission is crucial for the analysis and design of both natural and engineered systems. For systems driven by time-varying signals, the fund…