Molecular Networks

Authors and titles for November 2019

[1] arXiv:1911.00356 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Kinetic foundation of the zero-inflated negative binomial model for single-cell RNA sequencing data Show Chinese title

Title: 零膨胀负二项分布模型的运动学基础用于单细胞RNA测序数据

Chen Jia

Comments: 19 pages, 5 figures

Subjects: Molecular Networks (q-bio.MN) ; Biological Physics (physics.bio-ph) ; Quantitative Methods (q-bio.QM) ; Applications (stat.AP)

[2] arXiv:1911.03032 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Dissipation in non-steady state regulatory circuits Show Chinese title

Title: 非稳态调控回路中的耗散

P. Szymańska-Rożek, D. Villamaina, J. Miȩkisz, A.M. Walczak

Subjects: Molecular Networks (q-bio.MN)

[3] arXiv:1911.03517 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: N-terminal domain Increases Activation of Elephant Shark Glucocorticoid and Mineralocorticoid Receptors Show Chinese title

Title: N端结构域增强象鲨糖皮质激素和盐皮质激素受体的激活

Yoshinao Katsu, Islam MD Shariful, Xiaozhi Lin, Wataru Takagi, Hiroshi Urushitani, Satomi Kohno, Susumu Hyodo, Michael E. Baker

Comments: 17 pages, 6 figures

Subjects: Molecular Networks (q-bio.MN) ; Biomolecules (q-bio.BM)

[4] arXiv:1911.04046 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Network Inference in Systems Biology: Recent Developments, Challenges, and Applications Show Chinese title

Title: 系统生物学中的网络推断：最新进展、挑战与应用

Michael M. Saint-Antoine, Abhyudai Singh

Subjects: Molecular Networks (q-bio.MN)

[5] arXiv:1911.04895 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Communication in Plants: Comparison of Multiple Action Potential and Mechanosensitive Signals with Experiments Show Chinese title

Title: 植物中的通信：多动作电位和机械敏感信号与实验的比较

Hamdan Awan, Kareem Zeid, Raviraj S. Adve, Nigel Wallbridge, Carrol Plummer, Andrew W. Eckford

Comments: 12 Pages, 15 Figures, Accepted for Publication in IEEE Transactions on NanoBioscience

Journal-ref: IEEE Transactions on NanoBioscience 2019

Subjects: Molecular Networks (q-bio.MN) ; Information Theory (cs.IT) ; Neurons and Cognition (q-bio.NC)

[6] arXiv:1911.05259 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Weighted Network Analysis of Biologically Relevant Chemical Spaces Show Chinese title

Title: 生物相关化学空间的加权网络分析

Mariko I. Ito, Takaaki Ohnishi

Comments: 12 pages, 4 figures

Subjects: Molecular Networks (q-bio.MN) ; Physics and Society (physics.soc-ph) ; Biomolecules (q-bio.BM)

[7] arXiv:1911.05895 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Pleiotropy enables specific and accurate signaling in the presence of ligand cross talk Show Chinese title

Title: 多效性在配体交叉对话存在的情况下实现了特定和准确的信号传递

Duncan Kirby, Jeremy Rothschild, Matthew Smart, Anton Zilman

Journal-ref: Phys. Rev. E 103, 042401 (2021)

Subjects: Molecular Networks (q-bio.MN)

[8] arXiv:1911.06659 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Large-Scale Survey of Cell-Differentiation Programs in a Generative Model Reveals Regeneration as an Epiphenomenon of Development Show Chinese title

Title: 大规模生成模型中细胞分化程序的调查揭示了再生是发育的副现象

Somya Mani, Tsvi Tlusty

Subjects: Molecular Networks (q-bio.MN) ; Biological Physics (physics.bio-ph) ; Populations and Evolution (q-bio.PE)

[9] arXiv:1911.10133 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: An introductory guide to aligning networks using SANA, the Simulated Annealing Network Aligner Show Chinese title

Title: 使用SANA对齐网络的入门指南，SANA是模拟退火网络对齐器

Wayne B. Hayes

Journal-ref: In Protein-Protein Interaction Networks, pp. 263-284. Humana, New York, NY, 2020

Subjects: Molecular Networks (q-bio.MN) ; Biomolecules (q-bio.BM)

[10] arXiv:1911.10252 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Biological Regulatory Networks are Minimally Frustrated Show Chinese title

Title: 生物调控网络是最小挫折的

Shubham Tripathi, David A. Kessler, Herbert Levine

Comments: 5 pages, 4 figures

Journal-ref: Phys. Rev. Lett. 125, 088101 (2020)

Subjects: Molecular Networks (q-bio.MN)

[11] arXiv:1911.10316 (cross-list from q-bio.MN) [cn-pdf, pdf, other]

Title: Deep graph embedding for prioritizing synergistic anticancer drug combinations Show Chinese title

Title: 深度图嵌入用于优先排序协同抗癌药物组合

Peiran Jiang, Shujun Huang, Zhenyuan Fu, Zexuan Sun, Ted M. Lakowski, Pingzhao Hu

Subjects: Molecular Networks (q-bio.MN)

[12] arXiv:1911.00978 (cross-list from q-bio.QM) [cn-pdf, pdf, other]

Title: Solving the chemical master equation for monomolecular reaction systems analytically: a Doi-Peliti path integral view Show Chinese title

Title: 解析求解单分子反应系统的化学主方程：Doi-Peliti路径积分视角

John J. Vastola

Comments: 61 pages

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

[13] arXiv:1911.02175 (cross-list from stat.ML) [cn-pdf, pdf, other]

Title: Integrating Markov processes with structural causal modeling enables counterfactual inference in complex systems Show Chinese title

Title: 将马尔可夫过程与结构因果建模相结合，可在复杂系统中进行反事实推断

Robert Osazuwa Ness, Kaushal Paneri, Olga Vitek

Comments: Accepted to Thirty-third Conference on Neural Information Processing Systems (2019)

Subjects: Machine Learning (stat.ML) ; Machine Learning (cs.LG) ; Molecular Networks (q-bio.MN) ; Applications (stat.AP)

[14] arXiv:1911.04673 (cross-list from physics.bio-ph) [cn-pdf, pdf, other]

Title: Kinetic Proofreading and the Limits of Thermodynamic Uncertainty Show Chinese title

Title: 动能校对与热力学不确定性的极限

William D. Piñeros, Tsvi Tlusty

Comments: Main text: 9 pages, 6 figures. 2 tables; no supplementary information

Journal-ref: Phys. Rev. E 101, 022415 (2020)

Subjects: Biological Physics (physics.bio-ph) ; Molecular Networks (q-bio.MN)

[15] arXiv:1911.05732 (cross-list from eess.SY) [cn-pdf, pdf, other]

Title: Antithetic integral feedback for the robust control of monostable and oscillatory biomolecular circuits Show Chinese title

Title: 单稳态和振荡生物分子电路的抗对称积分反馈鲁棒控制

Noah Olsman, Fulvio Forni

Comments: 7 pages, 7 figures

Subjects: Systems and Control (eess.SY) ; Molecular Networks (q-bio.MN)

[16] arXiv:1911.06684 (cross-list from q-bio.SC) [cn-pdf, pdf, other]

Title: New Approaches in Synthetic Biology: Abiotic Organelles and Artificial Cells Powered and Controlled by Light Show Chinese title

Title: 合成生物学的新方法：由光供能和控制的非生物细胞器和人工细胞

Günther Knör

Subjects: Subcellular Processes (q-bio.SC) ; Biomolecules (q-bio.BM) ; Molecular Networks (q-bio.MN) ; Tissues and Organs (q-bio.TO)

[17] arXiv:1911.07125 (cross-list from cs.AI) [cn-pdf, pdf, other]

Title: Opportunities for artificial intelligence in advancing precision medicine Show Chinese title

Title: 人工智能在推进精准医学中的机会

Fabian V. Filipp

Subjects: Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG) ; Biomolecules (q-bio.BM) ; Genomics (q-bio.GN) ; Molecular Networks (q-bio.MN)

[18] arXiv:1911.09959 (cross-list from q-bio.QM) [cn-pdf, pdf, other]

Title: Alignment of Protein-Protein Interaction Networks Show Chinese title

Title: 蛋白质-蛋白质相互作用网络的对齐

Sarra Ghanjeti

Comments: 57 pages, in French, 9 figures

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