R. Phillips

Melanization interacts with soil mineral and microbial properties to determine fungal carbon and nitrogen persistence in soils

This study shows that fungal melanin content and soil mineral properties interact to influence the formation of fungal-derived mineral-associated organic matter (MAOM) in soils.

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.

Specific cPRC1 complexes are co-opted to mediate oncogenic gene repression in diffuse midline glioma

The paper identifies specific cPRC1 complexes, CBX4/PCGF4, that mediate oncogenic gene repression in DMG cells downstream of H3K27M mutation.

Mechanistic implications of the ternary complex structural models for the photoenzyme protochlorophyllide oxidoreductase.

The paper investigates structural models of the POR-Pchlide-NADPH ternary complex and proposes an alternative model based on mutagenesis and computational analysis, identifying key residues involved in catalysis.

Flexibility and sensitivity in gene regulation out of equilibrium

This paper investigates how energy dissipation in gene regulatory networks enables nonmonotonic and sensitive gene expression behaviors not achievable at equilibrium.

Major axes of variation in tree demography across global forests

This study identifies key sources of variation in tree demography across global forests using a variance partitioning framework, finding species differences as a major driver of demographic variance.

Wildebeest Herds on Rolling Hills: Flocking on Arbitrary Curved Surfaces

This paper extends the Toner-Tu flocking theory to arbitrary curved surfaces using finite element methods, enabling analysis of collective motion in complex geometries.

Emergent Actin Flows Explain Diverse Parasite Gliding Modes

This study uses single-molecule imaging and modeling to show that F-actin flows in parasites self-organize to produce diverse gliding motility modes.

Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle

The paper models k-fiber anchorage in mammalian spindles and shows that spatially regulated anchorage creates distinct mechanical behaviors.

Anthroponumbers.org: A Quantitative Database Of Human Impacts on Planet Earth

The paper introduces a database of human impacts on Earth, providing curated quantitative data and analysis of their interconnected effects.

Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies

The paper investigates how motor protein properties affect microtubule assembly dynamics and structure, showing that motor speed and processivity determine aster size and contraction rates.

Reconciling Kinetic and Equilibrium Models of Bacterial Transcription

The paper compares seven models of bacterial transcriptional repression to determine which best explains gene expression data, finding a two-state model with burst size distribution most effective.

Proofreading through spatial gradients

This paper proposes a spatial gradient-based error correction mechanism that enhances specificity without requiring dedicated structural features, and quantifies its performance limitations.

First-principles prediction of the information processing capacity of a simple genetic circuit

The paper predicts the information processing capacity of a genetic circuit using a minimal model based on published data and compares it with experimental results in E. coli.

Deciphering the regulatory genome of Escherichiacoli, one hundred promoters at a time

The paper introduces a method to characterize promoter regulation in E. coli by analyzing 100 promoters across 12 growth conditions, identifying regulatory elements and transcription factors.

Physiological Adaptability and Parametric Versatility in a Simple Genetic Circuit

This study examines how growth rate and temperature affect gene expression in a genetic circuit, revealing robustness to nutrient changes but temperature-dependent effects not captured by thermodynamic models.

Theoretical investigation of a genetic switch for metabolic adaptation

The paper models a genetic switch in E. coli that uses membrane transport and enzymatic degradation to control metabolic enzyme production based on metabolite availability.

Sequence-Dependent Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination

The paper quantifies sequence-dependent dynamics of RAG-RSS interactions in V(D)J recombination, revealing how single-bp changes affect PC formation, stability, and cleavage.

Defining the Energetic Costs of Cellular Structures

The paper defines and separates energetic costs of molecular building blocks from opportunity costs to improve accuracy in estimating cellular structure energy requirements.

Differential Effects of Afferent and Efferent Vagus Nerve Stimulation on Gastric Motility Assessed with Magnetic Resonance Imaging

This study compares the effects of afferent and efferent vagus nerve stimulation on gastric motility using MRI in anesthetized rats, finding afferent stimulation more effective.

Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries

This paper demonstrates the use of optically-defined boundaries to control active matter systems of microtubules and motor proteins, enabling the creation of contractile networks and fluid flows.

Harnessing Avidity: Quantifying Entropic and Energetic Effects of Linker Length and Rigidity Required for Multivalent Binding of Antibodies to HIV-1 Spikes

This paper models synthetic diFabs with DNA linkers to quantify how linker length and rigidity affect antibody neutralization potency against HIV-1.

The Energetics of Molecular Adaptation in Transcriptional Regulation

The paper links mutations in a transcriptional repressor to biophysical parameters, showing how changes in free energy predict gene expression and epistasis.

How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression

This paper challenges energy matrix models of gene expression by showing that avidity between -35 and -10 promoter sites significantly affects gene expression and proposes a refined model incorporating this effect.

Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions

This study uses targeted sequencing of oral phage communities to show that phage compositions are individual-specific, stable over time, and not strongly influenced by geography or genetics.

Combinatorial Control through Allostery

This study develops a statistical mechanical model to analyze how allosteric molecules can implement different Boolean logic gates and ratiometric sensing based on the MWC model.

Measuring cis-regulatory energetics in living cells using allelic manifolds

The paper introduces a method to measure the Gibbs free energy of TF-DNA and TF-TF interactions in living cells using allelic manifolds and reporter assays, achieving precision of ~0.1 kcal/mol.

Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution

The paper quantifies the number of MscL channels required for E. coli survival after osmotic shock using single-cell fluorescence microscopy and finds that 500-700 channels per cell are needed for 80% survival.

Mapping DNA sequence to transcription factor binding energy in vivo

This study develops a method to map DNA sequences to transcription factor binding energy using in vivo data, achieving predictions within 1 kBT of measured values and exploring sequence-context relationships.

A systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

The paper introduces a systematic method combining assays and modeling to dissect bacterial promoter mechanisms at nucleotide resolution.