Molecular Networks

Authors and titles for q-bio.MN in Mar 2023

[1]  arXiv:2303.01809 [pdf, other]

Title: A Concise and Formal Definition of RAF Sets and the RAF Algorithm

Authors: Wim Hordijk

Comments: 7 pages, 1 figure

Subjects: Molecular Networks (q-bio.MN)

[2]  arXiv:2303.02079 [pdf, other]

Title: Insights from number theory into the critical Kauffman model with connectivity one

Authors: F. C. Sheldon, T. M. A. Fink

Comments: 15 pages, 3 figures

Subjects: Molecular Networks (q-bio.MN); Disordered Systems and Neural Networks (cond-mat.dis-nn); Probability (math.PR)

[3]  arXiv:2303.07508 [pdf, other]

Title: QuTIE: Quantum optimization for Target Identification by Enzymes

Authors: Hoang M. Ngo, My T. Thai, Tamer Kahveci

Subjects: Molecular Networks (q-bio.MN)

[4]  arXiv:2303.08822 [pdf, ps, other]

Title: Nonequilibrium calcium dynamics optimizes the energetic efficiency of mitochondrial metabolism

Authors: Valérie Voorsluijs, Francesco Avanzini, Gianmaria Falasco, Massimiliano Esposito, Alexander Skupin

Subjects: Molecular Networks (q-bio.MN); Other Condensed Matter (cond-mat.other); Statistical Mechanics (cond-mat.stat-mech)

[5]  arXiv:2303.12526 [pdf, ps, other]

Title: COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Changes in Metabolic Interaction Networks

Authors: Jiahang Li, Steffen Waldherr, Wolfram Weckwerth

Comments: none

Journal-ref: https://academic.oup.com/bioinformatics/article/39/7/btad397/7218933 2023

Subjects: Molecular Networks (q-bio.MN); Optimization and Control (math.OC)

[6]  arXiv:2303.12651 [pdf, ps, other]

Title: Model Validation and Selection in Metabolic Flux Analysis and Flux Balance Analysis

Authors: Joshua A.M. Kaste, Yair Shachar-Hill

Comments: 23 pages, 2 figures, 1 table

Subjects: Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[7]  arXiv:2303.14193 [pdf, other]

Title: Quadratic Graph Attention Network (Q-GAT) for Robust Construction of Gene Regulatory Networks

Authors: Hui Zhang, Xuexin An, Qiang He, Yudong Yao, Yudong Zhang, Feng-Lei Fan, Yueyang Teng

Subjects: Molecular Networks (q-bio.MN); Computational Engineering, Finance, and Science (cs.CE)

[8]  arXiv:2303.14238 [pdf, other]

Title: Polyhedral geometry and combinatorics of an autocatalytic ecosystem

Authors: Praful Gagrani, Victor Blanco, Eric Smith, David Baum

Comments: 36 pages, 17 figures, 7 tables

Subjects: Molecular Networks (q-bio.MN); Dynamical Systems (math.DS)

[9]  arXiv:2303.14440 [pdf, ps, other]

Title: A Bioinformatics Study for Recognition of Hub Genes and Pathways in Pancreatic Ductal Adenocarcinoma

Authors: Atefeh Akbarnia Dafrazi, Tahmineh Mehrabi, Fatemeh Malekinejad

Subjects: Molecular Networks (q-bio.MN)

[10]  arXiv:2303.16361 [pdf, other]

Title: Dynamical Modularity in Automata Models of Biochemical Networks

Authors: Thomas Parmer, Luis M. Rocha

Comments: 42 pages, 7 figures; updated author information

Subjects: Molecular Networks (q-bio.MN); Computational Engineering, Finance, and Science (cs.CE)

[11]  arXiv:2303.00933 (cross-list from q-bio.GN) [pdf, ps, other]

Title: Spatial cancer systems biology resolves heterotypic interactions and identifies disruption of spatial hierarchy as a pathological driver event

Authors: Fabian V. Filipp

Comments: 7 pages, 2 figures

Subjects: Genomics (q-bio.GN); Cell Behavior (q-bio.CB); Molecular Networks (q-bio.MN); Tissues and Organs (q-bio.TO)

[12]  arXiv:2303.06423 (cross-list from q-bio.QM) [pdf, other]

Title: Learning interpretable causal networks from very large datasets, application to 400,000 medical records of breast cancer patients

Authors: Marcel da Câmara Ribeiro-Dantas, Honghao Li, Vincent Cabeli, Louise Dupuis, Franck Simon, Liza Hettal, Anne-Sophie Hamy, Hervé Isambert

Comments: 19 pages, 6 figures, 8 supplementary figures and 5 pages supporting information

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Data Analysis, Statistics and Probability (physics.data-an); Molecular Networks (q-bio.MN); Methodology (stat.ME)

[13]  arXiv:2303.01643 (cross-list from math.CT) [pdf, ps, other]

Title: Additive Invariants of Open Petri Nets

Authors: Benjamin Merlin Bumpus, Sophie Libkind, Jordy Lopez Garcia, Layla Sorkatti, Samuel Tenka

Comments: 20 pages

Subjects: Category Theory (math.CT); Molecular Networks (q-bio.MN)

[14]  arXiv:2303.03960 (cross-list from math.DS) [pdf, ps, other]

Title: On the connectedness of multistationarity regions of small reaction networks

Authors: Allison McClure, Anne Shiu

Comments: 16 pages, 1 figure; many edits following suggestions by reviewers; updated one author's last name

Subjects: Dynamical Systems (math.DS); Molecular Networks (q-bio.MN)

[15]  arXiv:2303.11723 (cross-list from cond-mat.soft) [pdf, other]

Title: Robust microphase separation through chemical reaction networks

Authors: Franco Blanchini, Elisa Franco, Giulia Giordano, Dino Osmanovic

Comments: 6 pages, 2 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Adaptation and Self-Organizing Systems (nlin.AO); Pattern Formation and Solitons (nlin.PS); Molecular Networks (q-bio.MN)