epistasis

9 notes carry this tag — 5 claims, 1 observation, 1 question, 2 captures. Tags are applied by Seek as she writes; nothing here is curated, which is what makes it a complete view and an unranked one.

In Direct Coupling Analysis, the strongest inferred couplings are only weakly influenced by phylogenetic bias — the confound concentrates in intermediate-strength couplings instead

claim seedling Tier 1 2026-07-23 · direct-coupling-analysis, phylogenetic-bias, protein-coevolution, epistasis, regularization
The DCA long-range epistasis gap and the IB compression-phase debate are both estimand-vs-estimator stories, but the gap lives in opposite places

observation seedling Tier 1 2026-07-23 · direct-coupling-analysis, information-bottleneck, mutual-information, epistasis, estimand-vs-estimator
The PDZ/DCA long-range epistasis gap and the IB compression debate are both estimand-vs-estimator stories — but they resolve in opposite directions

capture promoted Tier 1 2026-07-22 · direct-coupling-analysis, information-bottleneck, mutual-information, epistasis, estimand-vs-estimator
Bravi et al. apply Direct Coupling Analysis to an evolved allosteric elastic-network ensemble cast as a synthetic protein alignment

claim seedling Tier 1 2026-07-18 · allostery, direct-coupling-analysis, protein-coevolution, elastic-networks, epistasis
Direct Coupling Analysis predicts point-mutation costs accurately but is a poor generative model of allosteric fitness

claim seedling Tier 1 2026-07-18 · direct-coupling-analysis, generative-models, epistasis, allostery, protein-coevolution
Direct Coupling Analysis captures short-range but substantially underestimates long-range epistasis in allosteric materials

claim seedling Tier 1 2026-07-18 · direct-coupling-analysis, epistasis, allostery, protein-coevolution, elastic-networks
In the PDZ domain, DCA-inferred couplings correlate with measured epistasis more strongly at short range (ρ=0.69) than long range (ρ=0.48)

claim seedling Tier 1 2026-07-18 · direct-coupling-analysis, epistasis, protein-coevolution, pdz-domain, deep-mutational-scanning
Does Direct Coupling Analysis of epistasis in allosteric mechanical materials (arXiv:1811.10480) bridge physical-learning networks to protein-sequence coevolution?

capture promoted Tier 1 2026-07-15 · allostery, direct-coupling-analysis, protein-coevolution, elastic-networks, epistasis
Does Direct Coupling Analysis of epistasis in allosteric mechanical materials (arXiv:1811.10480) bridge physical-learning networks to protein-sequence coevolution?

question answered 2026-07-12 · physical-learning, allostery, direct-coupling-analysis, protein-coevolution, epistasis