Jordan C. Rozum

Cell State Transitions Drive Transcriptome-Proteome Alignment in a Minimal Photoautotroph

The paper investigates how cell state transitions in Prochlorococcus marinus MED4 affect transcriptome-proteome alignment through regulatory mechanisms involving RpaB and HimA.

Cyanophage CP12 Rewires Host Carbon Regulation through Interface Remodeling and Redox Buffering

This study investigates how cyanophage CP12 modulates host carbon regulation by remodeling interfaces and buffering redox changes during infection.

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

The paper develops a 4D whole-cell model of Prochlorococcus marinus MED4 to show how spatial organization and redox PTMs regulate carbon fixation under light disturbance.

ProteoMeter: A pipeline for integrating multi-PTM and limited proteolysis data to reveal modification-structure coupling at the residue level

ProteoMeter integrates multi-PTM and limited proteolysis data to map proteomic changes to residue level, demonstrating its use in analyzing HCoV-229E infection.

Extreme genome reduction selectively retains modular regulatory architecture in Prochlorococcus MED4: conserved transcriptional modules reveal core physiological regulatory programs

This paper identifies conserved transcriptional modules in Prochlorococcus MED4 using RNA-seq data and independent component analysis, revealing core regulatory programs that persist despite extreme genome reduction.

Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophage

The paper integrates AMGs and phage assembly into a genome-scale metabolic model to predict their impact on host metabolism and phage production, revealing synergistic and antagonistic effects.

Automated Model Refinement Using Perturbation-Observation Pairs

This paper introduces a genetic algorithm-based workflow for refining biological network models using perturbation-observation pairs, demonstrating its effectiveness in a plant signaling model.

Mapping the attractor landscape of Boolean networks

This paper introduces biobalm, a tool for constructing succession diagrams of Boolean networks, showing improved performance and demonstrating that non-random models have complex attractor landscapes.

Robustness of biomolecular networks suggests functional modules far from the edge of chaos

The paper analyzes experimentally-supported biomolecular networks to show they are ordered and far from the edge of chaos, with new measures and simulations revealing greater rigidity than previously thought.

Inferring gene regulatory networks using transcriptional profiles as dynamical attractors

This paper develops an ODE-based GRN inference method using dynamic transcriptional data and validates it on synthetic yeast and Candida albicans GRNs.

A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpoint

The paper analyzes a mammalian cell cycle model to show how conditionally stable motifs drive oscillations through cell cycle checkpoints.

Identifying (un)controllable dynamical behavior in complex networks

The paper introduces a method to identify control-robust subsystems in dynamical systems, demonstrating its application to biological networks like Drosophila and T-cell signaling.