Quantitative Biology

Authors and titles for September 2020

[101] arXiv:2009.07466 [pdf, other]

Title: The role of hydrophobic interactions in folding of $\beta$-sheets

Jiacheng Li, Xiaoliang Ma, Hongchi Zhang, Chengyu Hou, Liping Shi, Shuai Guo, Chenchen Liao, Bing Zheng, Lin Ye, Lin Yang, Xiaodong He

Subjects: Biomolecules (q-bio.BM)

[102] arXiv:2009.07479 [pdf, other]

Title: Accurate and efficient Simulation of very high-dimensional Neural Mass Models with distributed-delay Connectome Tensors

A. González-Mitjans, D. Paz-Linares, A. Areces-Gonzalez, M. Li, Y. Wang, ML. Bringas-Vega, P.A Valdés-Sosa

Comments: 12 pages, 6 figures, 2 tables

Subjects: Neurons and Cognition (q-bio.NC); Computational Engineering, Finance, and Science (cs.CE); Neural and Evolutionary Computing (cs.NE)

[103] arXiv:2009.07778 [pdf, other]

Title: Scaffold-constrained molecular generation

Maxime Langevin, Herve Minoux, Maximilien Levesque, Marc Bianciotto

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI)

[104] arXiv:2009.08023 [pdf, other]

Title: New mixture models for decoy-free false discovery rate estimation in mass-spectrometry proteomics

Yisu Peng (1), Shantanu Jain (1), Yong Fuga Li (2), Michal Gregus (3 and 4), Alexander R. Ivanov (3 and 4), Olga Vitek (1 and 4), Predrag Radivojac (1) ((1) Khoury College of Computer Sciences, Northeastern University, (2) Illumina Inc., (3) Department of Chemistry and Chemical Biology, Northeastern University, (4) Barnett Institute of Chemical and Biological Analysis, Northeastern University)

Subjects: Quantitative Methods (q-bio.QM)

[105] arXiv:2009.08101 [pdf, other]

Title: Attracting Sets in Perceptual Networks

Robert Prentner

Subjects: Neurons and Cognition (q-bio.NC); Neural and Evolutionary Computing (cs.NE)

[106] arXiv:2009.08176 [pdf, other]

Title: Resistance of the cell wall to degradation is a critical parameter for isolation of high quality RNA from natural isolates of Bacillus subtilis

Jean-Sebastien Guez (IP), François Coutte, Anne-Sophie Drucbert (IMPRT), Pierre-Marie Danzé (IMPRT), Philippe Jacques

Journal-ref: Archives of Microbiology, Springer Verlag, 2009, 191, pp.669 - 673

Subjects: Biomolecules (q-bio.BM)

[107] arXiv:2009.08296 [pdf, other]

Title: Identification of Biomarkers Controlling Cell Fate In Blood Cell Development

Maryam Nazarieh, Volkhard Helms, Marc P. Hoeppner, Andre Franke

Comments: 17 pages

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

[108] arXiv:2009.08309 [pdf, other]

Title: Unsupervised Image Classification Through Time-Multiplexed Photonic Multi-Layer Spiking Convolutional Neural Network

Menelaos Skontranis, George Sarantoglou, Stavros Deligiannidis, Adonis Bogris, Charis Mesaritakis

Comments: 4 pages, 3 figures

Subjects: Neurons and Cognition (q-bio.NC); Image and Video Processing (eess.IV)

[109] arXiv:2009.08356 [pdf, other]

Title: Stability analysis of a signaling circuit with dual species of GTPase switches

Lucas M. Stolerman, Pradipta Ghosh, Padmini Rangamani

Comments: 7 figures

Subjects: Subcellular Processes (q-bio.SC)

[110] arXiv:2009.08378 [pdf, other]

Title: Event-Based Backpropagation can compute Exact Gradients for Spiking Neural Networks

Timo C. Wunderlich, Christian Pehle

Subjects: Neurons and Cognition (q-bio.NC); Neural and Evolutionary Computing (cs.NE)

[111] arXiv:2009.08385 [pdf, other]

Title: Computational models in Electroencephalography

Katharina Glomb, Joana Cabral, Anna Cattani, Alberto Mazzoni, Ashish Raj, Benedetta Franceschiello

Subjects: Neurons and Cognition (q-bio.NC); Computational Engineering, Finance, and Science (cs.CE)

[112] arXiv:2009.08411 [pdf, other]

Title: Dynamic causal modelling of immune heterogeneity

Thomas Parr, Anjali Bhat, Peter Zeidman, Aimee Goel, Alexander J. Billig, Rosalyn Moran, Karl J. Friston

Subjects: Quantitative Methods (q-bio.QM); Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[113] arXiv:2009.08491 [pdf, other]

Title: Globular structure of the hypermineralized tissue in human femoral neck

Qiong Wang, Tengteng Tang, David Cooper, Felipe Eltit, Peter Fratzl, Pierre Guy, Rizhi Wang

Journal-ref: Journal of Structural Biology,Volume 212, Issue 2, 1 November 2020, 107606

Subjects: Tissues and Organs (q-bio.TO); Materials Science (cond-mat.mtrl-sci)

[114] arXiv:2009.08667 [pdf, other]

Title: Event-based update of synapses in voltage-based learning rules

Jonas Stapmanns, Jan Hahne, Moritz Helias, Matthias Bolten, Markus Diesmann, David Dahmen

Comments: 45 pages, 13 figures, 7 tables

Subjects: Neurons and Cognition (q-bio.NC)

[115] arXiv:2009.08672 [pdf, other]

Title: Setting up and modelling of overflowing fed-batch cultures of Bacillus subtilis for the production and continuous removal of lipopeptides

J.S Guez, S. Chenikher, J.Ph Cassar, P. Jacques

Journal-ref: Journal of Biotechnology, Elsevier, 2007, 131, pp.67 - 75

Subjects: Biomolecules (q-bio.BM)

[116] arXiv:2009.08687 [pdf, other]

Title: Chemical Property Prediction Under Experimental Biases

Yang Liu, Hisashi Kashima

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)

[117] arXiv:2009.08793 [pdf, other]

Title: GuessTheMusic: Song Identification from Electroencephalography response

Dhananjay Sonawane, Krishna Prasad Miyapuram, Bharatesh RS, Derek J. Lomas

Subjects: Neurons and Cognition (q-bio.NC); Sound (cs.SD)

[118] arXiv:2009.08802 [pdf, other]

Title: A computationally efficient physiologically comprehensive 3D-0D closed-loop model of the heart and circulation

Christoph M. Augustin, Matthias A. F. Gsell, Elias Karabelas, Erik Willemen, Frits W. Prinzen, Joost Lumens, Edward J. Vigmond, Gernot Plank

Comments: This project has received funding from the EU's H2020 programme under the Marie Sklodowska-Curie Action InsiliCardio, GA No. 750835 and under the ERA-NET co-fund action No. 680969 (ERA-CVD SICVALVES) funded by the Austrian Science Fund (FWF), GA I 4652-B to CMA. The research was supported by the Grants F3210-N18 and I2760-B30 from the FWF and a BioTechMed Graz flagship award ILearnHeart to GP

Journal-ref: Computer Methods in Applied Mechanics and Engineering 386 (2021) 114092

Subjects: Tissues and Organs (q-bio.TO)

[119] arXiv:2009.08868 [pdf, other]

Title: Review of Machine-Learning Methods for RNA Secondary Structure Prediction

Qi Zhao, Zheng Zhao, Xiaoya Fan, Zhengwei Yuan, Qian Mao, Yudong Yao

Comments: 25 pages, 5 figures, 1 table

Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Machine Learning (stat.ML)

[120] arXiv:2009.08869 [pdf, other]

Title: PANDA: Predicting the change in proteins binding affinity upon mutations using sequence information

Wajid Arshad Abbasi, Syed Ali Abbas, Saiqa Andleeb

Journal-ref: Journal of Bioinformatics and Computational Biology, 2021

Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Machine Learning (stat.ML)

[121] arXiv:2009.08940 [pdf, other]

Title: An infection process near criticality: Influence of the initial condition

P. L. Krapivsky

Comments: 13 pages, 3 figures

Journal-ref: J. Stat. Mech. 013501 (2021)

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Probability (math.PR); Physics and Society (physics.soc-ph)

[122] arXiv:2009.09150 [pdf, other]

Title: Population Susceptibility Variation and Its Effect on Contagion Dynamics

Christopher Rose, Andrew J. Medford, C. Franklin Goldsmith, Tejs Vegge, Joshua Weitz, Andrew A. Peterson

Comments: 12 pages, 2 figures

Subjects: Populations and Evolution (q-bio.PE); Social and Information Networks (cs.SI); Systems and Control (eess.SY)

[123] arXiv:2009.09250 [pdf, other]

Title: Frequency selectivity of neural circuits with heterogeneous transmission delays

Akke Mats Houben

Comments: 11 pages, 6 figures

Journal-ref: Neural Computation 33 (8) (2021) 2068-2086

Subjects: Neurons and Cognition (q-bio.NC)

[124] arXiv:2009.09317 [pdf, other]

Title: Reconciling Multiple Connectivity Scores for Drug Repurposing

Kewalin Samart, Phoebe Tuyishime, Arjun Krishnan, Janani Ravi

Comments: KS and PT contributed equally to this work. Corresponding authors: [email protected] (AK), [email protected] (JR). Preprint contains 24 pages, 3 figures, 8 tables

Subjects: Quantitative Methods (q-bio.QM); Genomics (q-bio.GN)

[125] arXiv:2009.09422 [pdf, other]

Title: Epidemic mitigation by statistical inference from contact tracing data

Antoine Baker, Indaco Biazzo, Alfredo Braunstein, Giovanni Catania, Luca Dall'Asta, Alessandro Ingrosso, Florent Krzakala, Fabio Mazza, Marc Mézard, Anna Paola Muntoni, Maria Refinetti, Stefano Sarao Mannelli, Lenka Zdeborová

Comments: 21 pages, 7 figures

Journal-ref: PNAS 2021 Vol. 118 No. 32 e2106548118

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[126] arXiv:2009.09589 [pdf, other]

Title: Coarse-Grained Nucleic Acid-Protein Model for Hybrid Nanotechnology

Jonah Procyk, Erik Poppleton, Petr Šulc

Comments: 8 pages, 6 figures

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

[127] arXiv:2009.09702 [pdf, other]

Title: On the verge of life: Distribution of nucleotide sequences in viral RNAs

Mykola Husev, Andrij Rovenchak

Journal-ref: Biosemiotics 14, No. 2, 253-269 (2021)

Subjects: Other Quantitative Biology (q-bio.OT)

[128] arXiv:2009.09911 [pdf, other]

Title: Are mouse and cat the missing link in the COVID-19 outbreaks in seafood markets?

Daniel H. Tao, Weitao Sun

Subjects: Other Quantitative Biology (q-bio.OT)

[129] arXiv:2009.09950 [pdf, other]

Title: Coupling between COVID-19 and seasonal influenza leads to synchronization of their dynamics

Jorge P. Rodríguez, Víctor M. Eguíluz

Journal-ref: Chaos 33, 021103 (2023)

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[130] arXiv:2009.10014 [pdf, other]

Title: Models for COVID-19 Pandemic: A Comparative Analysis

Aniruddha Adiga, Devdatt Dubhashi, Bryan Lewis, Madhav Marathe, Srinivasan Venkatramanan, Anil Vullikanti

Subjects: Populations and Evolution (q-bio.PE); Artificial Intelligence (cs.AI)

[131] arXiv:2009.10018 [pdf, other]

Title: Data-driven modeling for different stages of pandemic response

Aniruddha Adiga, Jiangzhuo Chen, Madhav Marathe, Henning Mortveit, Srinivasan Venkatramanan, Anil Vullikanti

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[132] arXiv:2009.10046 [pdf, other]

Title: A flux-limited model for glioma patterning with hypoxia-induced angiogenesis

Pawan Kumar, Christina Surulescu

Subjects: Tissues and Organs (q-bio.TO)

[133] arXiv:2009.10049 [pdf, other]

Title: Optimal Drug Regimen and Combined Drug Therapy and its Efficacy in the Treatment of COVID-19 : An Within-Host Modeling Study

Bishal Chhetri, Vijay M. Bhagat, D. K. K. Vamsi, Ananth V S, Bhanu Prakash, Swapna Muthuswamy, Pradeep Deshmukh, Carani B Sanjeevi

Comments: 16 pages, 13 figures

Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS); Optimization and Control (math.OC)

[134] arXiv:2009.10308 [pdf, other]

Title: Modularity allows classification of human brain networks during music and speech perception

Melia E. Bonomo, Christof Karmonik, Anthony K. Brandt, J. Todd Frazier

Comments: 17 pages, 6 figures, 5 tables

Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph)

[135] arXiv:2009.10375 [pdf, other]

Title: Temperature dependence of mycosubtilin homologue production in Bacillus subtilis ATCC6633

Patrick Fickers, Valérie Leclére, Jean-Sebastien Guez (IP), Max Béchet, Françoise Coucheney, Bernard Joris, Philippe Jacques

Comments: Research in Microbiology, Elsevier, 2008

Subjects: Biomolecules (q-bio.BM)

[136] arXiv:2009.10378 [pdf, other]

Title: Mycosubtilin Overproduction by Bacillus subtilis BBG100 Enhances the Organism's Antagonistic and Biocontrol Activities

Valérie Leclére, Max Béchet, Akram Adam, Jean-Sebastien Guez (IP), Bernard Wathelet, Marc Ongena, Philippe Thonart, Frédérique Gancel, Marléne Chollet-Imbert, Philippe Jacques

Journal-ref: Applied and Environmental Microbiology, American Society for Microbiology, 2005, 71, pp.4577 - 4584

Subjects: Biomolecules (q-bio.BM)

[137] arXiv:2009.10449 [pdf, other]

Title: A word recurrence based algorithm to extract genomic dictionaries

Vincenzo Bonnici, Giuditta Franco, Vincenzo Manca

Subjects: Genomics (q-bio.GN); Information Theory (cs.IT)

[138] arXiv:2009.10514 [pdf, other]

Title: Integration of Clinical Criteria into the Training of Deep Models: Application to Glucose Prediction for Diabetic People

Maxime De Bois, Mounîm A. El Yacoubi, Mehdi Ammi

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)

[139] arXiv:2009.10609 [pdf, other]

Title: Spinopelvic Anatomic Parameters Prediction Model of NSLBP based on data mining

Hua Cheng

Comments: 12 pages, 4 figures, Funding by "Science and Technology Bureau (Zhanjiang City) technological guidance special project(No. 2017A01014.)"

Subjects: Tissues and Organs (q-bio.TO)

[140] arXiv:2009.10615 [pdf, other]

Title: Computational capacity of pyramidal neurons in the cerebral cortex

Danko D. Georgiev, Stefan K. Kolev, Eliahu Cohen, James F. Glazebrook

Comments: 18 pages, 4 figures

Journal-ref: Brain Research 2020; 1748: 147069

Subjects: Neurons and Cognition (q-bio.NC)

[141] arXiv:2009.10621 [pdf, other]

Title: The fitness landscapes of translation

Mario Josupeit, Joachim Krug

Comments: 10 pages, 4 figures

Journal-ref: Physica A 569:125768 (2021)

Subjects: Subcellular Processes (q-bio.SC); Statistical Mechanics (cond-mat.stat-mech)

[142] arXiv:2009.10693 [pdf, other]

Title: The Moran process on 2-chromatic graphs

Kamran Kaveh, Alex McAvoy, Krishnendu Chatterjee, Martin A. Nowak

Comments: 19 pages

Journal-ref: PLOS Computational Biology (2020)

Subjects: Populations and Evolution (q-bio.PE)

[143] arXiv:2009.10706 [pdf, other]

Title: DiviK: Divisive intelligent K-Means for hands-free unsupervised clustering in big biological data

Grzegorz Mrukwa (1 and 2), Joanna Polanska (1) ((1) Silesian University of Technology, (2) Netguru)

Comments: 24 pages, 11 figures

Journal-ref: BMC Bioinformatics 23, 538 (2022)

Subjects: Quantitative Methods (q-bio.QM)

[144] arXiv:2009.10820 [pdf, other]

Title: Identifying and Analyzing Sepsis States: A Retrospective Study on Patients with Sepsis in ICUs

Chih-Hao Fang, Vikram Ravindra, Salma Akhter, Mohammad Adibuzzaman, Paul Griffin, Shankar Subramaniam, Ananth Grama

Subjects: Quantitative Methods (q-bio.QM)

[145] arXiv:2009.10931 [pdf, other]

Title: Drug repurposing for COVID-19 using graph neural network and harmonizing multiple evidence

Kanglin Hsieh, Yinyin Wang, Luyao Chen, Zhongming Zhao, Sean Savitz, Xiaoqian Jiang, Jing Tang, Yejin Kim

Comments: 13 pages

Journal-ref: Sci Rep 11, 23179 (2021)

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)

[146] arXiv:2009.10953 [pdf, other]

Title: Mechanical models of pattern and form in biological tissues: the role of stress-strain constitutive equations

Chiara Villa, Mark A. J. Chaplain, Alf Gerisch, Tommaso Lorenzi

Comments: 33 pages + 6 pages of supplementary material, 15 figures, 6 movies

Subjects: Tissues and Organs (q-bio.TO)

[147] arXiv:2009.11121 [pdf, other]

Title: An algorithm to represent inbreeding trees

C. Jarne, F A. Gómez Albarracín, M. Caruso

Subjects: Populations and Evolution (q-bio.PE)

[148] arXiv:2009.11168 [pdf, other]

Title: A multilayer interstitial fluid flow along vascular adventitia

Hongyi Li (1, 2), You Lv (2), Xiaoliang Chen (4), Bei Li (2), Qi Hua (1), Fusui Ji (2), Yajun Yin (5), Hua Li (6) ((1) Cardiology Department, Xuanwu Hospital, Capital Medical University, Xicheng, Beijing, China, (2) Cardiology Department, Radiology Department, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China (4) Radiology Department, China-Japan Friendship Hospital, Beijing Hospital, China, (5) Department of Engineering Mechanics, Tsinghua University, Beijing, China (6) Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China)

Comments: 28 pages, 8 figures

Subjects: Tissues and Organs (q-bio.TO)

[149] arXiv:2009.11241 [pdf, other]

Title: Deep learning for peptide identification from metaproteomics datasets

Xuan Guo, Shichao Feng

Subjects: Quantitative Methods (q-bio.QM)

[150] arXiv:2009.11288 [pdf, other]

Title: Spike conformation transition in SARS-CoV-2 infection

Liaofu Luo, Yongchun Zuo

Comments: 14 pages, 1 figure

Subjects: Biomolecules (q-bio.BM); Cell Behavior (q-bio.CB)