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Found 12 papers, 3 papers with code
Dissecting endogeneous genetic circuits from first principles
These parameters include binding site copy number, where a large number of binding sites may titrate away transcription factors, as well as overlapping binding sites, which may affect analysis of the mutual dependence between mutations in the regulatory region and expression levels.
Schrödinger's "What is Life?" at 75
2019 marked the 75th anniversary of the publication of Erwin Schr\"{o}dinger's "What is Life?
Programming Boundary Deformation Patterns in Active Networks
Studying a large set of shapes, we observe that the active networks contract in a shape-preserving manner that persists over the course of contraction.
Soft Condensed Matter
Quantitative clarification of key questions about COVID-19 epidemiology
Modeling the spread of COVID-19 is crucial for informing public health policy.
Reconciling Kinetic and Equilibrium Models of Bacterial Transcription
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease.
A quantitative compendium of COVID-19 epidemiology
Accurate numbers are needed to understand and predict viral dynamics.
Allostery and Kinetic Proofreading
Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond, and typically requires the free energy of nucleotide hydrolysis for its operation.
Proofreading through spatial gradients
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity.
First-principles prediction of the information processing capacity of a simple genetic circuit
We then predict the information processing capacity of the genetic circuit for a suite of biophysical parameters such as protein copy number and protein-DNA affinity.
SARS-CoV-2 (COVID-19) by the numbers
The current SARS-CoV-2 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers.
Deciphering the regulatory genome of $\textit{Escherichia coli}$, one hundred promoters at a time
Then, we examine the regulatory architectures for more than 80 promoters in the ${\it E. coli}$ genome which previously had no known regulation.
How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression
We show that this the refined energy matrix model can characterize the full suite of gene expression data and explore several applications of this framework, namely, how multivalent binding at the -35 and -10 sites can buffer RNAP kinetics against mutations and how promoters that bind overly tightly to RNA polymerase can inhibit gene expression.
