227 citations · 547 across the 14 of their papers we have counts for
14 papers
Random permutations from -Demazure products
Mikhail Tikhonov
We study the -deformation of the Demazure product model from arXiv:2407.21653. Consider the longest element in written as a reduced word in simple transpositions. In…
Emergent predictability in microbial ecosystems
Jacob Moran, Lucas C. Graham, Mikhail Tikhonov
Microbial ecosystems exhibit a surprising amount of functionally relevant diversity at all levels of taxonomic resolution, presenting a significant challenge for most modeling fram…
Energy-ordered resource stratification as an agnostic signature of life
Akshit Goyal, Mikhail Tikhonov
The search for extraterrestrial life hinges on identifying biosignatures, often focusing on gaseous metabolic byproducts as indicators. However, most such biosignatures require ass…
Generalized end-product feedback circuit senses high dimensional environmental fluctuations
Fang Yu, Mikhail Tikhonov
Understanding computational capabilities of simple biological circuits, such as the regulatory circuits of single-cell organisms, remains an active area of research. Recent theoret…
Global epistasis on fitness landscapes
Juan Diaz-Colunga, Abigail Skwara, Karna Gowda +4
Epistatic interactions between mutations add substantial complexity to adaptive landscapes, and are often thought of as detrimental to our ability to predict evolution. Yet, patter…
A simple regulatory architecture allows learning the statistical structure of a changing environment
Stefan Landmann, Caroline M. Holmes, Mikhail Tikhonov
Bacteria live in environments that are continuously fluctuating and changing. Exploiting any predictability of such fluctuations can lead to an increased fitness. On longer timesca…
Improve it or lose it: evolvability costs of competition for expression
Jacob Moran, Devon Finlay, Mikhail Tikhonov
Expression level is known to be a strong determinant of a protein's rate of evolution. But the converse can also be true: evolutionary dynamics can affect expression levels of prot…
Innovation rather than improvement: a solvable high-dimensional model highlights the limitations of scalar fitness
Mikhail Tikhonov, Remi Monasson
Much of our understanding of ecological and evolutionary mechanisms derives from analysis of low-dimensional models: with few interacting species, or few axes defining "fitness". I…
A collective phase in resource competition in a highly diverse ecosystem
Mikhail Tikhonov, Remi Monasson
Organisms shape their own environment, which in turn affects their survival. This feedback becomes especially important for communities containing a large number of species; howeve…
Community-level cohesion without cooperation
Mikhail Tikhonov
Recent work draws attention to community-community encounters ("coalescence") as likely an important factor shaping natural ecosystems. This work builds on MacArthur's classic mode…
Theoretical ecology without species
Mikhail Tikhonov
Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic, and…
Only accessible information is useful: insights from gradient-mediated patterning
Mikhail Tikhonov, Shawn C. Little, Thomas Gregor
Information theory is gaining popularity as a tool to characterize performance of biological systems. However, information is commonly quantified without reference to whether or ho…
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
Mikhail Tikhonov, Robert W. Leach, Ned S. Wingreen
The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accurac…
Complexity in genetic networks: topology vs. strength of interactions
Mikhail Tikhonov, William Bialek
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relati…