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RepliFlow infers cell cycle dynamics from flow cytometry data, capturing changes in DNA replication program alterations.

The paper integrates multi-omics data to explore host-pathogen interactions in severe Pseudomonas aeruginosa infection, identifying key molecular mechanisms and interactions.

This paper compares multivariate and univariate resilience indicators for early warning of West Nile virus outbreaks, finding multivariate indicators perform better in data-poor scenarios.

The paper develops an algorithm to analyze human tissue microanatomy and finds age-related changes in domain abundance and resilience.

The paper identifies mechanisms of NRT1.1 phosphorylation switch in plants, showing how phosphorylation and conformational changes regulate nitrate uptake modes.

The paper introduces a surrogate workflow for faster virtual population development by using a convex quadratic objective function as a proxy for nonlinear goodness-of-fit, improving efficiency in calibration.

The paper develops a mechanistic model of the HPA axis to explain the cortisol paradox in PTSD, showing that enhanced GR sensitivity leads to low cortisol with normal ACTH and elevated GR activity.

This paper introduces PhenoSCoP, a framework that uses single-cell proteomics and microscopy to identify drug-resistant proteotypes in cancer cells and their progression in patient tissues.

The paper develops a linear model to predict chromatin dynamics based on transcription factor binding in C. elegans, identifying key regulators that schedule gene expression rhythms.

The paper develops a probability distribution for rare subclones in cancer and applies it to simulate dynamic precision medicine to improve treatment outcomes despite sequencing limitations.

This study uses multi-omics analysis to identify key biological changes in ASD children after microbiota transplant therapy, showing shifts in microbiome, metabolites, and symptoms.

The paper develops a mathematical framework showing intercellular signaling stabilizes cell fate and tissue patterning by suppressing spontaneous switching and inducing coordinated behaviors.

The paper shows that inhibiting PERK rewires host kinase networks to create an antiviral state during coronavirus infection.

The paper identifies a mitochondrial localization phenotype in psychosis patients and uses a cell-based assay to screen for compounds and genes affecting this phenotype.

The paper analyzes transcriptome diversity in alcohol-related liver disease to identify novel pathways and genes not detected by differential expression analysis.

This study shows that African green monkeys exposed to synthetic Aβ oligomers exhibit persistent Alzheimer's-like proteomic changes without cognitive decline.

This paper introduces a proteogenomic framework combining genetic perturbations and proteomics to map phospho-signaling pathways in primary human T cells, validated with inflammatory stimuli.

The paper develops a framework to integrate multiplexed immunofluorescence data with mathematical models to study cell cycle dynamics and arrest, validated on MCF-10A cells exposed to arresting agents.

The paper demonstrates population cycles in a cross-feeding microbial community using an engineered system and a nonlinear dynamical model.

The paper introduces a compositional model to predict protein interactions, showing that functional group composition can reliably predict survivin binding without relying on amino acid sequences.