Quantitative Biology

Authors and titles for November 2020

[1] arXiv:2011.00002 [pdf, other]

Title: Molecular Communications in Viral Infections Research: Modelling, Experimental Data and Future Directions

Michael Taynnan Barros, Mladen Veletić, Masamitsu Kanada, Massimiliano Pierobon, Seppo Vainio, Ilangko Balasingham, Sasitharan Balasubramaniam

Comments: Submitted for journal publication

Subjects: Other Quantitative Biology (q-bio.OT); Signal Processing (eess.SP)

[2] arXiv:2011.00088 [pdf, other]

Title: Towards a perceptual distance metric for auditory stimuli

Sarah Oh, Elijah FW Bowen, Antonio Rodriguez, Damian Sowinski, Eva Childers, Annemarie Brown, Laura Ray, Richard Granger

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

[3] arXiv:2011.00089 [pdf, other]

Title: EUKulele: Taxonomic annotation of the unsung eukaryotic microbes

Arianna I. Krinos, Sarah K. Hu, Natalie R. Cohen, Harriet Alexander

Comments: Software paper submitted to JOSS

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

[4] arXiv:2011.00163 [pdf, other]

Title: Distraction by auditory novelty during reading: Evidence for disruption in saccade planning, but not saccade execution

Martin R. Vasilev, Fabrice B. R. Parmentier, Julie A. Kirkby

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

[5] arXiv:2011.00257 [pdf, other]

Title: Temporary changes in large-scale memory neural networks after fear learning and extinction in healthy adults

Kirill V. Efimov, Alina O. Tetereva, Aleksey M. Ivanitskiy, Sergey I. Kartashov, Olga V. Martynova

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

[6] arXiv:2011.00297 [pdf, other]

Title: Generalisation of neuronal excitability allows for the identification of an excitability change parameter that links to an experimentally measurable value

Jantine A.C. Broek, Guillaume Drion

Comments: 21 pages, 10 main figures, 3 supplementary figures

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

[7] arXiv:2011.00304 [pdf, other]

Title: Digital image processing to detect subtle motion in stony coral

Shuaifeng Li, Liza M. Roger, Lokander Kumar, Nastassja Lewinski, Judith Klein, Alex Gagnon, Hollie M. Putnam, Jinkyu Yang

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

[8] arXiv:2011.00378 [pdf, other]

Title: The approximately universal shapes of epidemic curves in the Susceptible-Exposed-Infectious-Recovered (SEIR) model

Kevin Heng, Christian L. Althaus

Comments: This is a post-peer-review, pre-copyedit version of an article published in Scientific Reports (Springer Nature; this http URL). The final authenticated version is available online at: this https URL

Subjects: Populations and Evolution (q-bio.PE); Biological Physics (physics.bio-ph); Medical Physics (physics.med-ph)

[9] arXiv:2011.00485 [pdf, other]

Title: Comparing Machine Learning Algorithms with or without Feature Extraction for DNA Classification

Xiangxie Zhang, Ben Beinke, Berlian Al Kindhi, Marco Wiering

Comments: 17 pages

Subjects: Other Quantitative Biology (q-bio.OT); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[10] arXiv:2011.00659 [pdf, other]

Title: Survival prediction and risk estimation of Glioma patients using mRNA expressions

Navodini Wijethilake, Dulani Meedeniya, Charith Chitraranjan, Indika Perera

Comments: Presented at the 20th IEEE International Conference on BioInformatics And BioEngineering (BIBE 2020)

Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)

[11] arXiv:2011.00829 [pdf, other]

Title: A Generic Trauma Severity Computer Method Applied to Pedestrian Collisions

Christophe Bastien, Clive Neal-Sturgess, Huw Davies

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

[12] arXiv:2011.01002 [pdf, other]

Title: RRScell method for automated single-cell profiling of multiplexed immunofluorescence cancer tissue

Alvason Zhenhua Li, Karsten Eichholz, Anton Sholukh, Daniel Stone, Michelle A. Loprieno, Keith R. Jerome, Khamsone Phasouk, Kurt Diem, Jia Zhu, Lawrence Corey

Comments: 8 pages, 6 figures, markerUMAP cell clustering

Subjects: Quantitative Methods (q-bio.QM); Image and Video Processing (eess.IV); Tissues and Organs (q-bio.TO); Applications (stat.AP)

[13] arXiv:2011.01069 [pdf, other]

Title: Describing the movement of molecules in reduced-dimension models

Natasha S. Savage

Comments: Main Text. Methods. Supplementary Text. References

Subjects: Quantitative Methods (q-bio.QM)

[14] arXiv:2011.01098 [pdf, other]

Title: Development of antibacterial compounds that block evolutionary pathways to resistance

Yanmin Zhang, Sourav Choudhury, Joao Rodrigues, Eugene Shakhnovich

Subjects: Biomolecules (q-bio.BM); Cell Behavior (q-bio.CB); Populations and Evolution (q-bio.PE)

[15] arXiv:2011.01294 [pdf, other]

Title: Studying evolution of the primary body axis in vivo and in vitro

Kerim Anlas, Vikas Trivedi

Subjects: Populations and Evolution (q-bio.PE); Cell Behavior (q-bio.CB); Tissues and Organs (q-bio.TO)

[16] arXiv:2011.01508 [pdf, other]

Title: Greetings from a Triparental Planet

Gizem Bacaksizlar, Stefani Crabtree, Joshua Garland, Natalie Grefenstette, Albert Kao, David Kinney, Artemy Kolchinsky, Tyler Marghetis, Michael Price, Maria Riolo, Hajime Shimao, Ashley Teufel, Tamara van der Does, Vicky Chuqiao Yang (Santa Fe Institute Postdocs)

Comments: The original version of this report was produced by a team in just 72 hours. This version includes additional edits for style and formatting

Subjects: Populations and Evolution (q-bio.PE); General Economics (econ.GN)

[17] arXiv:2011.01548 [pdf, other]

Title: Antibiotic treatment, duration of infectiousness, and disease transmission

Thomas Caraco

Comments: 25 pages of text, 5 figures, 1 table. arXiv admin note: substantial text overlap with arXiv:2001.06948

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

[18] arXiv:2011.01688 [pdf, other]

Title: Imaging the Beating Heart with Macroscopic Phase Stamping

Vikas Trivedi, Sara Madaan, Daniel B. Holland, Le A. Trinh, Scott E. Fraser, Thai V. Truong

Comments: 4 pages

Subjects: Quantitative Methods (q-bio.QM)

[19] arXiv:2011.01739 [pdf, other]

Title: Spatial autocorrelation and the dynamics of the mean center of COVID-19 infections in Lebanon

Omar El Deeb

Comments: 15 pages, 6 figures, 1 table

Journal-ref: Front. Appl. Math. Stat., 13 (2021)

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

[20] arXiv:2011.01750 [pdf, other]

Title: Formation of working memory in a spiking neuron network accompanied by astrocytes

Susanna Yu. Gordleeva, Yulia A. Tsybina, Mikhail I. Krivonosov, Mikhail V. Ivanchenko, Alexey A. Zaikin, Victor B. Kazantsev, Alexander N. Gorban

Journal-ref: Frontiers in Cellular Neuroscience, 15, 2021, Article 631485

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

[21] arXiv:2011.01795 [pdf, other]

Title: Vector Field Streamline Clustering Framework for Brain Fiber Tract Segmentation

Chaoqing Xu, Guodao Sun, Ronghua Liang, Xiufang Xu

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

[22] arXiv:2011.01873 [pdf, other]

Title: Self-Organized Networks: Darwinian Evolution of Myosin-1

J. C. Phillips

Comments: 20 pages, 9 figures

Subjects: Other Quantitative Biology (q-bio.OT); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

[23] arXiv:2011.01877 [pdf, other]

Title: Exploring the Synchrony Between Body Temperature and HR, RR, and Aortic Blood Pressure in Viral/Bacterial Disease Onsets with Signal Dynamics

Camille Dunning

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

[24] arXiv:2011.02000 [pdf, other]

Title: Detection of Maternal and Fetal Stress from the Electrocardiogram with Self-Supervised Representation Learning

Pritam Sarkar, Silvia Lobmaier, Bibiana Fabre, Diego González, Alexander Mueller, Martin G. Frasch, Marta C. Antonelli, Ali Etemad

Comments: this http URL registration number: NCT03389178. Code repo: this https URL

Journal-ref: Scientific Reports, December 2021

Subjects: Quantitative Methods (q-bio.QM); Signal Processing (eess.SP)

[25] arXiv:2011.02081 [pdf, other]

Title: A deep learning classifier for local ancestry inference

Matthew Aguirre, Jan Sokol, Guhan Venkataraman, Alexander Ioannidis

Comments: Accepted to Learning Meaningful Representations of Life (LMRL), Workshop at the 34th Conference on Neural Information Processing Systems (NeurIPS 2020), Vancouver, Canada

Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE)

[26] arXiv:2011.02103 [pdf, other]

Title: COMO: A Pipeline for Multi-Omics Data Integration in Metabolic Modeling and Drug Discovery

Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomáš Helikar, Bhanwar Lal Puniya

Subjects: Molecular Networks (q-bio.MN)

[27] arXiv:2011.02349 [pdf, other]

Title: Effectiveness of isolation measures with app support to contain COVID-19 epidemics: a parametric approach

Andrea Maiorana, Marco Meneghelli, Mario Resnati

Comments: 31 pages, 10 figures

Journal-ref: J. Math. Biol. 83, 46 (2021)

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

[28] arXiv:2011.02372 [pdf, other]

Title: A biomimetic kidney tubule model

Elod Mehes, Tana S Pottorf, Marton Gulyas, Sandor Paku, Pamela V. Tran, Andras Czirok

Comments: 11 pages, 4 figures

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

[29] arXiv:2011.02420 [pdf, other]

Title: Estimating effective infection fatality rates during the course of the COVID-19 pandemic in Germany

Christian Staerk, Tobias Wistuba, Andreas Mayr

Subjects: Populations and Evolution (q-bio.PE); Applications (stat.AP)

[30] arXiv:2011.02425 [pdf, other]

Title: Generalized Stoichiometry and Biogeochemistry for Astrobiological Applications

Christopher P. Kempes, Michael J. Follows, Hillary Smith, Heather Graham, Christopher H. House, Simon A. Levin

Comments: 18 pages, 5 figures

Subjects: Quantitative Methods (q-bio.QM); Earth and Planetary Astrophysics (astro-ph.EP)

[31] arXiv:2011.02460 [pdf, other]

Title: Phylogenetic reconstruction of the cultural evolution of electronic music via dynamic community detection (1975-1999)

Mason Youngblood, Karim Baraghith, Patrick E. Savage

Subjects: Populations and Evolution (q-bio.PE); Applications (stat.AP)

[32] arXiv:2011.02516 [pdf, other]

Title: On Key Epidemiological Metrics during Infectious Disease Outbreaks

Hernán De Battista (1), José García-Clúa (1), Sebastián Nuñez (1), Fernando Inthamoussou (1), Fabricio Garelli (1) ((1) Grupo de Control Aplicado GCA-LEICI. Facultad de Ingeniería, Universidad Nacional de La Plata - CONICET, Argentina)

Subjects: Populations and Evolution (q-bio.PE); Systems and Control (eess.SY)

[33] arXiv:2011.02534 [pdf, other]

Title: A tunable population timer in multicellular consortia

Carlos Toscano-Ochoa, Jordi Garcia-Ojalvo

Comments: 11 pages, 5 figures

Subjects: Molecular Networks (q-bio.MN)

[34] arXiv:2011.02597 [pdf, other]

Title: SBML2Julia: interfacing SBML with efficient nonlinear Julia modelling and solution tools for parameter optimization

Paul F. Lang, Sungho Shin, Victor M. Zavala

Comments: 4 pages, 1 figure

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

[35] arXiv:2011.02766 [pdf, other]

Title: Logistic growth model and modeling of factors for community case transmission

Massamba Diouf, Babacar Mbaye Ndiaye

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

[36] arXiv:2011.02893 [pdf, other]

Title: RetroXpert: Decompose Retrosynthesis Prediction like a Chemist

Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang

Comments: 17 pages, to appear in NeurIPS 2020

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

[37] arXiv:2011.03019 [pdf, other]

Title: Influence of autapses on synchronisation in neural networks with chemical synapses

P. R. Protachevicz, K. C. Iarosz, I. L. Caldas, C. G. Antonopoulos, A. M. Batista, J. Kurths

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

[38] arXiv:2011.03112 [pdf, other]

Title: Deep generative selection models of T and B cell receptor repertoires with soNNia

Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad

Subjects: Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[39] arXiv:2011.03260 [pdf, other]

Title: Phase transition in Kermack-McKendrick Model of Epidemic: Effects of Additional Nonlinearity and Introduction of Medicated Immunity

Agniva Datta, Muktish Acharyya

Comments: A few more referenced added

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

[40] arXiv:2011.03344 [pdf, other]

Title: Can We Detect Mastitis earlier than Farmers?

Cathal Ryan, Christophe Guéret, Donagh Berry, Brian Mac Namee

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

[41] arXiv:2011.03415 [pdf, other]

Title: Searching beyond the usual papillomavirus suspects in squamous carcinomas of the vulva, penis and head and neck

Marta Félez-Sánchez, Marleny Vergara, Silvia de Sanjosé, Xavier Castellsagué, Laia Alemany, Ignacio Bravo (MIVEGEC)

Journal-ref: Infection, Genetics and Evolution, Elsevier, 2016, 45, pp.198-204

Subjects: Populations and Evolution (q-bio.PE); Tissues and Organs (q-bio.TO)

[42] arXiv:2011.03419 [pdf, other]

Title: Design Of Drug-Like Protein-Protein Interaction Stabilizers Guided By Chelation-Controlled Bioactive Conformation Stabilization

Francesco Bosica (TU/e), Sebastian Andrei (TU/e), João Filipe Neves (ERL 9002 - BSI, RID-AGE), Peter Brandt, Anders Gunnarsson, Isabelle Landrieu (ERL 9002 - BSI, RID-AGE), Christian Ottmann (TU/e), Gavin O'Mahony

Journal-ref: Chemistry - A European Journal, Wiley-VCH Verlag, 2020, 26 (31), pp.7131-7139

Subjects: Biomolecules (q-bio.BM)

[43] arXiv:2011.03442 [pdf, other]

Title: DeepFoldit -- A Deep Reinforcement Learning Neural Network Folding Proteins

Dimitra N. Panou, Martin Reczko

Comments: 108 pages, 66 figures

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

[44] arXiv:2011.03443 [pdf, other]

Title: Is Transfer Learning Necessary for Protein Landscape Prediction?

Amir Shanehsazzadeh, David Belanger, David Dohan

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

[45] arXiv:2011.03518 [pdf, other]

Title: Transformer Based Molecule Encoding for Property Prediction

Prateeth Nayak, Andrew Silberfarb, Ran Chen, Tulay Muezzinoglu, John Byrnes

Comments: Machine Learning for Molecules Workshop, NeurIPs2020

Subjects: Quantitative Methods (q-bio.QM)

[46] arXiv:2011.03526 [pdf, other]

Title: Identifying Stress Responsive Genes using Overlapping Communities in Co-expression Networks

Camila Riccio, Jorge Finke, Camilo Rocha

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

[47] arXiv:2011.03759 [pdf, other]

Title: The Budapest Amyloid Predictor and its Applications

Laszlo Keresztes, Evelin Szogi, Balint Varga, Viktor Farkas, Andras Perczel, Vince Grolmusz

Subjects: Biomolecules (q-bio.BM)

[48] arXiv:2011.03767 [pdf, other]

Title: Tree species effects on topsoil carbon stock and concentration are mediated by tree species type, mycorrhizal association, and N-fixing ability at the global scale

Yan Peng, Inger Kappel Schmidt, Haifeng Zheng, Petr Heděnec, Luciana Ruggiero Bachega, Kai Yue, Fuzhong Wu, Lars Vesterdal

Comments: Authors Accepted Manuscript

Journal-ref: In: Forest Ecology and Management. 2020 ; Vol. 478

Subjects: Quantitative Methods (q-bio.QM)

[49] arXiv:2011.03852 [pdf, other]

Title: Anticipation in architectural experience: a computational neurophenomenology for architecture?

Zakaria Djebbara, Thomas Parr, Karl Friston

Comments: 1 title-page, 23 pages, 5 figures

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

[50] arXiv:2011.03913 [pdf, other]

Title: Neuro-PC: Causal Functional Connectivity from Neural Dynamics

Rahul Biswas, Eli Shlizerman

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