A. Goyal

Energy-ordered resource stratification as an agnostic signature of life

This paper proposes a new biosignature for extraterrestrial life based on energy-ordered resource stratification, independent of specific metabolic processes.

Genome-Wide Transcription Response of Staphylococcus epidermidis to Heat Shock and Medically Relevant Glucose Levels

This study quantifies gene expression changes in Staphylococcus epidermidis under varying glucose and temperature conditions, identifying glucose-responsive genes and a heat-shock response similar to related species.

A universal niche geometry governs the response of ecosystems to environmental perturbations

The paper introduces a theoretical framework to calculate ecosystem responses to environmental perturbations using geometric transformations in consumer-resource models.

The proteome is a terminal electron acceptor

The paper develops a mathematical model showing microbial proteins adapt to maintain redox balance, improving growth by aligning biomass redox state with nutrients.

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.

Closed ecosystems extract energy through self-organized nutrient cycles

The paper introduces a conceptual model explaining how closed microbial ecosystems self-organize to stabilize nutrient cycles and extract energy efficiently.

Mixing selects for predation resistance in lab-evolved communities of bacterial prey and social predator Myxococcus xanthus

This study shows that repeated mixing in predator-prey communities increases prey resistance to predation but does not affect predator efficiency.

Air channels create a directional light signal to regulate hypocotyl phototropism

The paper shows that air channels in Arabidopsis hypocotyls enhance light scattering, creating a gradient that regulates phototropism through auxin distribution.

Annotation-free discovery of functional groups in microbial communities

This paper introduces an unsupervised method to identify functional groups in microbial communities based on abundance patterns and environmental data, validated across soil, ocean, and gut microbiome datasets.

Community interactions drive the evolution of antibiotic tolerance in bacteria

This study shows that ecological interactions in bacterial communities can drive the evolution of antibiotic tolerance in susceptible strains.

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.

The chemical basis of metabolic interdependence in microbial communities

This study investigates the conditions under which cross-feeding between microbial species is beneficial, finding that certain nonlinearities in metabolic flux distribution allow cross-feeding pairs to outperform autonomous networks.

Functional classification and validation of yeast prenylation motifs using machine learning and genetic reporters

This study improves prenylation predictions in yeast using machine learning, identifying new motifs and distinguishing cleaved from shunted sequences.

Particle foraging strategies promote microbial diversity in marine environments

The paper models how varying detachment rates from particles allow microbial populations to coexist in marine environments by balancing growth and mortality risks.

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.

Interactions between strains govern the eco-evolutionary dynamics of microbial communities

The paper tracks microbial communities over generations to show that strain-level interactions drive eco-evolutionary dynamics, with fine-scale genetic differences affecting community behavior.

Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism

The paper investigates how resource diversity affects microbial community diversity by analyzing metabolic networks and cross-feeding interactions in soil-derived bacterial communities.

Horizontal gene transfer becomes disadvantageous in rapidly fluctuating environments

The paper shows that horizontal gene transfer (HGT) can be disadvantageous in rapidly fluctuating environments, as it creates a trade-off between adaptation speed and fitness, leading to an optimal HGT rate that decreases with environmental fluctuation speed.

Mathematical modeling explains differential SARS CoV-2 kinetics in lung and nasal passages in remdesivir treated rhesus macaques

The paper develops a mathematical model to explain why remdesivir reduces SARS-CoV-2 viral loads more in lungs than nasal passages in rhesus macaques.

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.

In Arabidopsis, low blue light enhances phototropism by releasing cryptochrome 1-mediated inhibition of PIF4 expression

Horizontal gene transfer drives the evolution of dependencies in bacteria

The paper shows horizontal gene transfer drives metabolic dependency evolution in bacteria by enabling new catabolic routes and promoting gene loss.

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.

Metabolic adaptations underlying genome flexibility in prokaryotes

The paper analyzes accessory genes in prokaryotes and finds that ~40% contribute beneficial metabolic functions, enhancing biosynthetic potential and reducing auxotrophies through intra-species exchanges.

PIF transcription factors link a neighbor threat cue to accelerated reproduction in Arabidopsis

This study identifies PIF transcription factors as mediators of accelerated reproduction in Arabidopsis in response to neighbor proximity light cues.

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.