Molecular Networks Papers

New Molecular Networks papers from gene regulation, signal transduction. Thank you to arXiv for use of its open access interoperability.

[Molecular Networks Papers @ENZN]

Systematic pathway comparison on the powerset of rule-based biochemical systems

Anne-Susann Abel, Sissel Banke, Erika M. Herrera Machado, Jakob Lykke Andersen, Peter Dittrich, Rolf Fagerberg, Daniel Merkle
https://t.co/1tkiaLQJ2z [𝚚-𝚋𝚒𝚘.𝙼𝙽]

[Molecular Networks Papers @ENZN]

Uncovering Cellular Resolution in scRNAseq via Unbiased Cell and Gene Network Analysis

Olga lanzetta, Luisa Cutillo, Bailey Andrew, Claudia Angelini
https://t.co/MudwUV6QLC [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚜𝚝𝚊𝚝.𝙰𝙿]

[Molecular Networks Papers @ENZN]

DigiPhen: a new paradigm for building predictive models of biological systems

H. Steven Wiley, Angela Cintolesi, Niaz Bahar Chowdhury, Jaydeep P Bardhan, Song Feng, Steven S. Andrews, Herbert M Sauro, Kristin E. Burnum-Johnson, …
https://t.co/rKfhEFLKWY [𝚚-𝚋𝚒𝚘.𝙼𝙽]

[Molecular Networks Papers @ENZN]

Motional Degrees of Freedom in Network Hamiltonian Models

Peng Huang, Elizabeth M. Diessner, Carter T. Butts
https://t.co/nOfz6RtqLv [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚌𝚘𝚗𝚍-𝚖𝚊𝚝.𝚜𝚝𝚊𝚝-𝚖𝚎𝚌𝚑]

[Molecular Networks Papers @ENZN]

Metabolic Network Properties: Comprehensive Analysis Across Domains

José Antônio Pellizzaro, Daniel Gamermann, Julian Triana Dopico
https://t.co/tc82kcZmAo [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚌𝚘𝚗𝚍-𝚖𝚊𝚝.𝚜𝚝𝚊𝚝-𝚖𝚎𝚌𝚑]

[Molecular Networks Papers @ENZN]

Reducing Boolean Networks via Analysis of Dynamic Network Subgraph Behavior

Soodabeh Zakeri, Mohieddin Jafari
https://t.co/vh3ComV5Cb [𝚚-𝚋𝚒𝚘.𝙼𝙽]
💬Code: https://t.co/MHBln9UG2h

[Molecular Networks Papers @ENZN]

Characterization of Minimal Degenerate Zero-One Reaction Networks

Yuanlin Chen, Xiaoxian Tang
https://t.co/zxMJIapDZx [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚖𝚊𝚝𝚑.𝙳𝚂]

[Molecular Networks Papers @ENZN]

Permutation theory governs long-term dynamics of critical Boolean networks

Venkata Sai Narayana Bavisetty, Matthew Wheeler, Julian Vignes, Matthew Stephen Jones, Ruodan Liu, Sean Campbell, Claus Kadelka
https://t.co/VNaIfjrpQi [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚙𝚑𝚢𝚜𝚒𝚌𝚜.𝚋𝚒𝚘-𝚙𝚑]

[Molecular Networks Papers @ENZN]

Simulating is not always understanding: When model complexity obscures biology

Lendert Gelens, Alejandro Fábregas-Tejeda, Grant Ramsey, Sylvia Wenmackers, Bart Smeets
https://t.co/N8Rnke9t3D [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚙𝚑𝚢𝚜𝚒𝚌𝚜.𝚋𝚒𝚘-𝚙𝚑]

[Molecular Networks Papers @ENZN]

Control-Anchored Residual Flow Matching Conditioned on Gene Geometry for Virtual Cell Perturbation Modeling

Quanquan Li, Yihe Chi, Liuyang Song, Hongbo Zhang, Jingyu Li, Xidong Xi, Conghua Wei, Yijie Sun, Yu Chen, Xin Liu, …
https://t.co/kKTYDTAI8c [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚌𝚜.𝙰𝙸]

[Molecular Networks Papers @ENZN]

On the realizability of abstract reaction networks with real molecules and reactions

Tuyet-Minh Phan, Daniel Merkle, Tieu-Long Phan, Christoph Flamm, Peter F. Stadler
https://t.co/OoShmuzqHl [𝚚-𝚋𝚒𝚘.𝙼𝙽]

[Molecular Networks Papers @ENZN]

Synergy and Complementarity: The Generative Basis of Chemical Organizations

Tomas Veloz
https://t.co/275ek7c3eL [𝚚-𝚋𝚒𝚘.𝙼𝙽]

[Molecular Networks Papers @ENZN]

Timescale disparity and the reduction of the chemical master equation: A geometric approach via the linear noise approximation

Justin Eilertsen, Wylie Stroberg
https://t.co/YgIkPMcN6s [𝚚-𝚋𝚒𝚘.𝙼𝙽]

[Molecular Networks Papers @ENZN]

On the Cost of Entrainment in Protein Translation

Ram Massas, Michael Margaliot
https://t.co/pqOH4EMrpG [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚚-𝚋𝚒𝚘.𝚀𝙼]

[Molecular Networks Papers @ENZN]

Variational kinetics: elementary reaction kinetics via conic optimisation

Ronan M. T. Fleming, Ines Thiele
https://t.co/c660lIcZ2f [𝚚-𝚋𝚒𝚘.𝙼𝙽]

[Molecular Networks Papers @ENZN]

A universal multi-turnpike principle for optimal allocation of translational resources

Ram Massas, Thomas Kriecherbauer, Lars Grüne, Tamir Tuller, Michael Margaliot
https://t.co/Iii6r3WiyW [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚚-𝚋𝚒𝚘.𝙶𝙽]

[Molecular Networks Papers @ENZN]

Construction of an Inducible TBCE Overexpression System to Probe Tubulin Cofactor-Mediated Microtubule Homeostasis

Faiza Hasib Khan
https://t.co/WUOHR4TBJy [𝚚-𝚋𝚒𝚘.𝙼𝙽]

[Molecular Networks Papers @ENZN]

Continuous surrogates versus threshold Boolean networks for modeling Arabidopsis ISR gene regulation

Gonzalo A. Ruz
https://t.co/520gOMHvIy [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚌𝚜.𝙻𝙶 𝚌𝚜.𝙽𝙴]
💬To be published in IEEE CIBCB 2026

[Molecular Networks Papers @ENZN]

From Berg-Purcell precision bounds to clock-limited information capacity

Michał Komorowski
https://t.co/I7rYsqjgre [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚌𝚜.𝙸𝚃 𝚜𝚝𝚊𝚝.𝙰𝙿]

[Molecular Networks Papers @ENZN]

A Reexamination of Noise-Driven Robustness Evolution in Gene Regulatory Networks

Momoko Amemiya, Ayaka Sakata
https://t.co/bQGuEDPJhD [𝚚-𝚋𝚒𝚘.𝙼𝙽 𝚗𝚕𝚒𝚗.𝙰𝙾]