P. Mehta

A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits

This paper introduces a differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits, demonstrating its effectiveness with E. coli promoter models.

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.

Phosphoproteomic identification of Mos-MAPK targets in meiotic cell cycle and asymmetric oocyte divisions

The paper identifies Mos-MAPK targets in starfish oocytes using phosphoproteomics, revealing roles in mRNA polyadenylation and cytoskeletal regulation during meiosis.

Metabolic similarity and the predictability of microbial community assembly

The paper predicts microbial community composition based on metabolic similarities across environments by analyzing growth rates and secretion profiles of proteobacterial strains.

Multiplexed fluorescence and scatter detection with single cell resolution using on-chip fiber optics for droplet microfluidic applications

The paper introduces OptiDrop, a platform that enables multi-parametric optical sensing of microfluidic droplets with single-cell resolution using on-chip fiber optics.

Geometry of ecological coexistence and niche differentiation

The paper develops a geometric framework using convex polytopes to predict species coexistence and stable states in ecological systems based on consumer preferences.

scTOP: physics-inspired order parameters for cellular identification and visualization

scTOP uses physics-inspired order parameters to classify cells, visualize developmental trajectories, and assess engineered cells without feature selection or dimensionality reduction.

The emergence of goblet inflammatory or ITGB6hi nasal progenitor cells determines age-associated SARS-CoV-2 pathogenesis

The study identifies age-related differences in nasal epithelial cell responses to SARS-CoV-2 infection, showing distinct progenitor cell dynamics in children and elderly.

Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution

Root Walker quantifies root growth responses to environmental signals using automated imaging and analysis, revealing auxin concentration dependence and MAPK inhibitor specificity.

Durable alveolar engraftment of PSC-derived lung epithelial cells into immunocompetent mice

This study demonstrates the durable engraftment of PSC-derived lung epithelial cells into immunocompetent mice, showing long-term retention of both progenitor and differentiated cell phenotypes.

Cross-feeding shapes both competition and cooperation in microbial ecosystems

The paper analyzes how cross-feeding and competition influence microbial ecosystem properties using the Microbial Consumer Resource Model.

Re-assessing the phylogenetic status and evolutionary relationship of Forest Owlet using genomic data

The paper uses genomic data to reassess the phylogenetic status of the Forest Owlet, finding it as an early split from the Athene clade but sister to other Athene species.

Cellular-level phenotyping of tumor-immune microenvironment (TiME) in patients in vivo reveals distinct inflammation and endothelial anergy signatures

The paper uses in vivo cellular-level imaging to phenotype tumor-immune microenvironments, identifying distinct inflammation and endothelial anergy signatures linked to immunotherapy response.

The minimum land area requiring conservation attention to safeguard biodiversity

The paper estimates that 64 million km2 of terrestrial land requires conservation attention to safeguard biodiversity, with potential losses of 1.3 million km2 by 2030 under intensive land-use scenarios.

Signatures of processing complexity during global cognitive states in ventromedial prefrontal cortex

The paper examines neural activity during inter-trial intervals in macaques, finding increased mnemonic discriminability and processing complexity in the ventromedial prefrontal cortex.

The effect of resource dynamics on species packing in diverse ecosystems

The paper examines how resource dynamics influence species packing in ecosystems, showing species can occupy only half of available niches in certain conditions.

The Community Simulator: A Python package for microbial ecology

The paper introduces a Python package for simulating microbial community dynamics, showing improved performance using a new EM algorithm for finding equilibrium states.

Automated detection of glaucoma with interpretable machine learning using clinical data and multi-modal retinal images

This paper develops an interpretable machine learning model for glaucoma detection using clinical data and multi-modal retinal images, achieving high accuracy and identifying both known and novel disease-related features.

A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns

The paper shows a minimal model can reproduce ecological patterns in microbial communities observed in surveys like EMP and HMP.

The Minimum Environmental Perturbation Principle: A New Perspective on Niche Theory

The paper introduces the Minimum Environmental Perturbation Principle (MEPP) as a framework to analyze ecosystems and ecological invasions by minimizing environmental impact.

Single-cell analysis of intestinal immune cells during helminth infection

The paper optimizes a protocol to isolate immune cells from helminth-infected intestines and analyzes their characteristics during infection.

Diverse communities behave like typical random ecosystems

The paper extends May's theorem by showing that diverse ecosystems reorganize into stable states with random interactions beyond the May threshold.

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

This study shows that available energy fluxes drive a transition in microbial community diversity, stability, and function, shifting from resource-limited to preference-driven regimes.

Antimicrobial Efficacy and Safety of a Novel Gas Plasma-Activated Catheter Lock Solution

This study evaluates a novel antibiotic-free gas plasma-activated catheter lock solution, showing it effectively eradicates biofilm microbes and is less toxic to human cells than a standard solution.

Emergent Simplicity in Microbial Community Assembly

The paper shows that microbial communities re-assemble into predictable, stable communities through non-specific metabolic cross-feeding, even when grown in minimal environments.