M. Mani

Functional regimes define the response of the soil microbiome to environmental change

The paper uses microcosm experiments and modeling to identify three functional regimes governing soil microbiome responses to pH changes, revealing distinct metabolic dynamics and underlying mechanisms.

A physically inspired approach to coarse-graining transcriptomes reveals the dynamics of aging: multiscale description of gene expressions and a spectral view of aging dynamics

This study applies physics-inspired methods to single-cell RNA sequencing data to uncover multiscale patterns in aging transcriptomes and provides a spectral view of aging dynamics.

Bayesian inference of relative fitness on high-throughput pooled competition assays

This paper introduces a Bayesian framework to infer microbial fitness from lineage tracking assays, accounting for noise and scaling to large datasets.

The Physical Biology of Nucleolus Disassembly

The paper investigates the physical mechanisms of nucleolus disassembly during mitosis, identifying two distinct phases and proposing a universal design principle for biomolecular condensate disassembly.

Global patterns in gene content of soil microbiomes emerge from microbial interactions

The paper shows that environmental filtering alone cannot explain global patterns in soil microbiome gene content, as ecological interactions between genotypes drive observed associations with pH.

A dynamical systems treatment of transcriptomic trajectories in hematopoiesis

This paper applies a dynamical systems framework to transcriptomic data from hematopoiesis, identifying bifurcations in neutrophil differentiation and uncovering key gene contributors.

Genomic structure predicts metabolite dynamics in microbial communities

The paper shows that genomic structure can predict metabolite dynamics in microbial communities using machine learning and consumer-resource models.

Evolution of generalists by phenotypic plasticity

This study shows that selection for faster migration in one sugar environment leads to phenotypic plasticity allowing faster migration in all sugars, suggesting plasticity aids in evolving generalist traits.

A jump distance based parameter inference scheme for particulate trajectories in biological settings

This paper introduces a parameter inference scheme based on jump distance distribution to analyze particulate trajectories, showing improved model selection and parameter estimation compared to mean square displacement analysis.

QuBiT: A quantitative tool for epithelial tubes reveals cell dynamics and unexpected patterns of organization during Drosophila tracheal morphogenesis

QuBiT quantifies cell geometry and organization in Drosophila tracheal tubes, revealing new A-P gradients and periodic cell patterns during morphogenesis.

Distinct contributions of tensile and shear stress on E-cadherin levels during morphogenesis

The paper investigates how tensile and shear stresses affect E-cadherin levels during Drosophila embryo axis elongation, finding distinct impacts on adhesion.

The Role of Cytoplasmic Interactions in the Collective Polarization of Tissues and its Interplay with Cellular Geometry

The paper uses a reaction-diffusion model to show that cytoplasmic interactions are essential for tissue-wide polarization and detect weak directional signals, and demonstrates their interplay with tissue geometry.

A scheme for 3-dimensional morphological reconstruction and force inference in the early C. elegans embryo

This study presents a method for 3D morphological reconstruction and force inference in early C. elegans embryos, showing deviations of 7% and 10% from force balance and Young-Laplace relations.

Matrix Production In Bacillus subtilis Biofilms Is Localized To A Propagating Front

This study shows that EPS matrix production in Bacillus subtilis biofilms occurs at a propagating front, with gene expression waves coordinating sporulation and matrix production.