S. Maslov

SPLICER: A Highly Efficient Base Editing Toolbox That Enables In Vivo Therapeutic Exon Skipping

SPLICER improves exon skipping by editing both splice acceptor and donor sites, reducing aberrant splicing and enabling therapeutic applications in Alzheimer's disease.

Coarse-Grained Model of Serial Dilution Dynamics in Synthetic Human Gut Microbiome

The paper develops a model to predict serial dilution dynamics in a synthetic human gut microbiome using metabolomics data and validates it with high correlation.

The ecological consequences of microbial metabolic strategies in fluctuating environments

This study examines how different microbial metabolic strategies affect community resilience and feasibility in fluctuating environments, finding that sequential utilizers are more resilient but less feasible than co-utilizing communities.

Emergence of catalytic function in prebiotic information-coding polymers

This paper demonstrates how prebiotic information-coding polymers could evolve catalytic cleavage activity through cooperative networks, bridging information-first and autocatalytic origin of life theories.

Predicting metabolite response to dietary intervention using deep learning

This paper develops a deep learning model to predict individual metabolite responses to dietary interventions based on gut microbiota composition, showing improved performance over traditional methods.

Predicting metabolomic profiles from microbial composition through neural ordinary differential equations

This paper introduces mNODE, a neural ODE-based method predicting metabolomic profiles from microbial composition, showing superior performance and interpretability across human and environmental microbiomes.

Fine-scale diversity of microbial communities due to satellite niches in boom-and-bust environments

The paper uses a consumer-resource model to show that microbial strains can coexist in boom-and-bust environments by differentiating on Monod parameters, resulting in 1-3 strains coexisting despite theoretical limits.

Functional universality in slow-growing microbial communities arises from thermodynamic constraints

The paper develops a consumer-resource model to show that thermodynamic constraints drive functional convergence in slow-growing microbial communities, validated by experimental data from anaerobic digesters.

Complementary resource preferences spontaneously emerge in diauxic microbial communities

This study develops a model of diauxic microbial communities and finds that complementary resource preferences emerge spontaneously during community assembly.

Ligation of random oligomers leads to emergence of autocatalytic sequence network

This study shows how nontrivial sequence patterns emerge from random DNA strands through templated ligation and temperature cycling, resembling Darwinian evolution.

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome

The paper predicts hundreds of new cross-feeding interactions in the human gut microbiome using an ecology-based computational method called GutCP, supported by genome annotation evidence.

The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification

The paper models CRISPR-mediated host-virus interactions and shows empirical systems exhibit weighted-nested protection networks indicative of host suppression of virus diversification.

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence

The paper develops an intermediate-scale model to describe microbial cross-feeding interactions, showing it accurately captures community dynamics and species coexistence in experimental data.

Regime shifts in a phage-bacterial ecosystem and strategies for its control

The paper studies regime shifts in phage-bacterial ecosystems and proposes a phage therapy strategy using partially resistant host bacteria to control bacterial populations.

Evidence for a multi-level trophic organization of the human gut microbiome

The paper models the human gut microbiome as a multi-level trophic system, predicting four trophic levels and their metabolic interactions, which align with observed fecal metabolomes.

Multistability and regime shifts in microbial communities explained by competition for essential nutrients

This study explains multistability and regime shifts in microbial communities through a resource-explicit model and game-theoretical methods, showing that nutrient stoichiometry and supply balance influence stability and diversity.

Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems

The study analyzes phage genomes from horse feces to show that recombination events dominate over point mutations in phage evolution over a 7-year period.

Hitchhiking, collapse and contingency in phage infections of migrating bacterial populations

The paper studies phage infection dynamics in migrating bacterial populations and identifies a phage transition where bacteria shift from outrunning phages to evolving resistance.

Multiple stable states in microbial communities explained by the stable marriage problem

The paper introduces a model based on the stable marriage problem to predict and control transitions between stable states in microbial communities.

Diversity, stability, and reproducibility in stochastically assembled microbial ecosystems

This study presents a conceptual model showing microbial ecosystems can be diverse, stable, and partially reproducible through resource competition and metabolic commensalism.

Recombination-driven genome evolution and stability of bacterial species

This study uses a computational model to show that bacterial evolution is shaped by two regimes—divergent and metastable—determined by recombination frequency and barriers, affecting genome diversity and species stability.