Sequence logos are visually compelling ways of illustrating the biological properties of DNA,
RNA and protein sequences, yet it is currently difficult to generate and customize such …

Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep
mutational scanning experiments on proteins and massively parallel reporter assays on gene …

The adoption of deep learning techniques in genomics has been hindered by the difficulty
of mechanistically interpreting the models that these techniques produce. In recent years, a …

In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with
RNA polymerase (RNAP), makes sequence-specific protein–DNA interactions with a …

How might a smooth probability distribution be estimated with accurately quantified uncertainty
from a limited amount of sampled data? Here we describe a field-theoretic approach that …

Signal transduction networks can form highly interconnected systems within cells due to
crosstalk between constituent pathways. To better understand the evolutionary design principles …

Multiplex assays of variant effect (MAVEs) are being rapidly adopted in many areas of biology
including gene regulation, protein science, and evolution. However, inferring quantitative …

Polygonal loops are interesting both as classical geometric objects and in modeling practical
engineering systems, eg, grasping systems with fingers having planar revolute joints. …

MAVE-NN 1 enables the rapid quantitative modeling of genotype-phenotype (GP) maps from
the data produced by multiplex assays of variant effect (MAVEs). Such assays include deep …

Here we show that Ivar provides a variational lower bound on Ipre. This fact was previously
described by Barber and Agakov (2003) in the general context of mutual information …