bioRxiv SysBio

Geometric Evaluation and Optimization of Maize Leaf Morphology and Canopy Architecture https://www.biorxiv.org/content/10.1101/2025.08.01.668074v1

Data Driven Disease Dynamics Models https://www.biorxiv.org/content/10.1101/2025.08.01.668106v1

A Multi-Layered Transcriptomic Analysis Sheds Light on Antisense Transcription, RNA Processing, and SmAP Interactions in Sulfolobus acidocaldarius https://www.biorxiv.org/content/10.1101/2025.07.28.667248v1

Rapid remodeling of the human gut microbiome in response to short-term animal product restriction https://www.biorxiv.org/content/10.1101/2025.07.30.667695v1

The interplay between biomechanics and cell kinetics explains the spatial pattern in liver fibrosis https://www.biorxiv.org/content/10.1101/2025.07.31.667562v1

Elementary vectors reveal minimal interactions in microbial communities https://www.biorxiv.org/content/10.1101/2025.07.30.667663v1

Transcriptomic profiling and machine learning uncover gene signatures of psoriasis endotypes and disease severity https://www.biorxiv.org/content/10.1101/2025.07.29.666780v1

The ten dollar proteome: low-cost, deep and quantitative proteome profiling of limited sample amounts using the Orbitrap Astral and timsTOF Ultra 2 mass spectrometers https://www.biorxiv.org/content/10.1101/2025.07.29.667408v1

Superior batch alignment and hyper-dimensional cytometry representations allow ultra-sensitive classification of disease phenotypes https://www.biorxiv.org/content/10.1101/2025.07.28.666458v1

Efficient Data Collection for Establishing Practical Identifiability via Active Learning https://www.biorxiv.org/content/10.1101/2025.07.28.667128v1

ACMTF-R: supervised multi-omics data integration uncovering shared and distinct outcome-associated variation https://www.biorxiv.org/content/10.1101/2025.07.28.667162v1

Genome-scale metabolic modelling of trimethoprim's mode of action reveals free ATP salvaged to restore purine pool https://www.biorxiv.org/content/10.1101/2025.07.25.666800v1

Signatures of digital Polycomb regulation in functional iPSC heterogeneity between individuals https://www.biorxiv.org/content/10.1101/2025.07.25.666753v1

Entangled stoichiometric objectives shape microbial catabolism https://www.biorxiv.org/content/10.1101/2025.07.29.667445v1

Comprehensive Network of Signaling Pathways in Hepatocellular Carcinoma and Network Analysis Reveals PTK2, GSK3β, and β-catenin to be Crucial for Cancer Progression https://www.biorxiv.org/content/10.1101/2025.07.25.666714v1

Mouse, pig, and human atherosclerotic lesions have common and distinct mesenchymal cell populations https://www.biorxiv.org/content/10.1101/2025.07.24.666663v1

Integral Synthesis and Clearance Analysis via DIA (ISDia) Reveals Coordinated Protein Dynamics Regulation during Endoplasmic Reticulum Stress https://www.biorxiv.org/content/10.1101/2025.07.23.666381v1

Benchmarking of signaling networks generated by large language models https://www.biorxiv.org/content/10.1101/2025.07.28.667217v1

Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication https://www.biorxiv.org/content/10.1101/2025.07.26.666918v1

SIMPLICITY: an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution. https://www.biorxiv.org/content/10.1101/2025.07.28.667187v1

Spatial Dynamics in the Yeast Galactose Switch Revealed Through RDME-ODE Hybrid 4D Simulations https://www.biorxiv.org/content/10.1101/2025.07.23.666409v1

Estimating flux dynamics from metabolite concentration time courses with dynafluxr https://www.biorxiv.org/content/10.1101/2025.07.22.666125v1

Pairwise Causal Discovery in Biochemical Network: A Survey on Directionality Inference within Complex Networks from Stationary Observations https://www.biorxiv.org/content/10.1101/2025.07.22.666141v1

A Co-Evolutionary Multi-Objective Framework for Joint Topology and Parameter Discovery in Gene Regulatory Networks https://www.biorxiv.org/content/10.1101/2025.07.22.666158v1

RASGRP4 is a key factor in KRAS activation mediated by SOS in Y1 mouse tumor cell line https://www.biorxiv.org/content/10.1101/2025.07.23.663512v1

Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis https://www.biorxiv.org/content/10.1101/2025.07.22.666210v1

Tuning regimes in ant foraging dynamics depend on the existence of bistability https://www.biorxiv.org/content/10.1101/2025.07.22.666247v1

The fecal microbiota of lactating Holstein dairy cows: a meta-analysis highlighting key microbial profiles and methodological challenges https://www.biorxiv.org/content/10.1101/2025.07.21.666008v1

Community-based biomedical context to unlock agentic systems https://www.biorxiv.org/content/10.1101/2025.07.21.665729v1

Modular cyanobacterial regulatory architecture enables dynamic graded responses to oxidative stress https://www.biorxiv.org/content/10.1101/2025.07.21.665879v1