Quantitative Biology

Authors and titles for February 2020

[1] arXiv:2002.00019 [pdf, other]

Title: A large deviation principle linking lineage statistics to fitness in microbial populations

Ethan Levien, Trevor GrandPre, Ariel Amir

Journal-ref: Phys. Rev. Lett. 125, 048102 (2020)

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph)

[2] arXiv:2002.00070 [pdf, other]

Title: Analysis and optimal control of a malaria mathematical model under resistance and population movement

Cristhian Montoya, Jhoana P. Romero-Leiton

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

[3] arXiv:2002.00094 [pdf, other]

Title: Relations between large scale brain connectivity and effects of regional stimulation depend on collective dynamical state

Lia Papadopoulos, Christopher W. Lynn, Demian Battaglia, Danielle S. Bassett

Comments: Main Text: 32 pages, 10 figures; Supplement: 14 pages, 10 figures

Journal-ref: PLoS Computational Biology, 16-9 (2020)

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

[4] arXiv:2002.00130 [pdf, other]

Title: Higher Criticism Tuned Regression For Weak And Sparse Signals

Tao Jiang, Stephanie J. London, Mi Kyeong Lee, Josyf C. Mychaleckyj, Alison A. Motsinger-Reif

Subjects: Quantitative Methods (q-bio.QM); Methodology (stat.ME)

[5] arXiv:2002.00151 [pdf, other]

Title: What will computational modelling approaches have to say in the era of atomistic cryo-EM data?

James S. Fraser, Kresten Lindorff-Larsen, Massimiliano Bonomi

Comments: 10 pages

Subjects: Quantitative Methods (q-bio.QM); Biomolecules (q-bio.BM)

[6] arXiv:2002.00200 [pdf, other]

Title: Energetic Controls are Essential: New and Notable Note for Biophysical Journal

Robert S. Eisenberg

Comments: Biophysical Journal (2020)

Subjects: Biomolecules (q-bio.BM)

[7] arXiv:2002.00245 [pdf, other]

Title: Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction

Mandev S. Gill, Philippe Lemey, Marc A. Suchard, Andrew Rambaut, Guy Baele

Comments: 20 pages, 3 figures

Subjects: Populations and Evolution (q-bio.PE); Methodology (stat.ME)

[8] arXiv:2002.00363 [pdf, other]

Title: From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

Susanna Manrubia, José A. Cuesta, Jacobo Aguirre, Sebastian E. Ahnert, Lee Altenberg, Alejandro V. Cano, Pablo Catalán, Ramon Diaz-Uriarte, Santiago F. Elena, Juan Antonio García-Martín, Paulien Hogeweg, Bhavin S. Khatri, Joachim Krug, Ard A. Louis, Nora S. Martin, Joshua L. Payne, Matthew J. Tarnowski, Marcel Weiß

Comments: 111 pages, 11 figures uses elsarticle latex class

Journal-ref: Physics of Life Reviews 38, 55-106 (2021)

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

[9] arXiv:2002.00418 [pdf, other]

Title: A Time Delay Dynamical Model for Outbreak of 2019-nCoV and the Parameter Identification

Yu Chen, Jin Cheng, Yu Jiang, Keji Liu

Comments: 11 pages, 7 figures. arXiv admin note: text overlap with arXiv:2002.02590

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

[10] arXiv:2002.00426 [pdf, other]

Title: A Simple Prediction Model for the Development Trend of 2019-nCov Epidemics Based on Medical Observations

Ye Liang, Dan Xu, Shang Fu, Kewa Gao, Jingjing Huan, Linyong Xu, Jia-da Li

Comments: Written on February 1, 2020 at 15:00 (GMT+08:00) 12 pages, 7 figures

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

[11] arXiv:2002.00448 [pdf, other]

Title: Stability of synchronous states in sparse neuronal networks

Afifurrahman, Ekkehard Ullner, Antonio Politi

Comments: 9 pages, 7 figures

Subjects: Neurons and Cognition (q-bio.NC); Dynamical Systems (math.DS); Adaptation and Self-Organizing Systems (nlin.AO)

[12] arXiv:2002.00582 [pdf, other]

Title: Persistent spectral based machine learning (PerSpect ML) for drug design

Zhenyu Meng, Kelin Xia

Comments: 17 pages; 8 Figures; 3 tables

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

[13] arXiv:2002.00731 [pdf, other]

Title: Executable Biochemical Space for Specification and Analysis of Biochemical Systems

Matej Troják, David Šafránek, Luboš Brim

Comments: 18 pages, 5 figures

Subjects: Molecular Networks (q-bio.MN); Logic in Computer Science (cs.LO)

[14] arXiv:2002.00895 [pdf, other]

Title: Inferring population statistics of receptor neurons sensitivities and firing-rates from general functional requirements

Carlo Fulvi Mari

Comments: 9 pages, 2+1 figures (PDF). Minor modifications

Journal-ref: BioSystems (2020) 104153

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Biological Physics (physics.bio-ph)

[15] arXiv:2002.00931 [pdf, other]

Title: Stochastic reaction networks in dynamic compartment populations

Lorenzo Duso, Christoph Zechner

Comments: 9 pages, 3 figures, appendix included

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

[16] arXiv:2002.00951 [pdf, other]

Title: Improving Pest Monitoring Networks in order to reduce pesticide use in agriculture

Marie-Josée Cros, Jean-Noël Aubertot, Sabrina Gaba, Xavier Reboud, Régis Sabbadin, Nathalie Peyrard

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

[17] arXiv:2002.01299 [pdf, other]

Title: Mass-Resolved Electronic Circular Dichroism Ion Spectroscopy

Steven Daly, Frederic Rosu, Valerie Gabelica

Comments: main text (7 pages, 2 figures) + supporting information (20 pages, 11 figures)

Subjects: Biomolecules (q-bio.BM); Biological Physics (physics.bio-ph)

[18] arXiv:2002.01467 [pdf, other]

Title: Making Sense of Computational Psychiatry

LR Mujica-Parodi, HH Strey

Comments: 16 pages, 5 figures. Int J Neuropsychopharmacol. 2020 Mar 27

Subjects: Neurons and Cognition (q-bio.NC); Applications (stat.AP)

[19] arXiv:2002.01475 [pdf, other]

Title: Ripeline and Rmanual speed up biological research and reporting

Alexey Shipunov

Comments: 3 figures

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

[20] arXiv:2002.01563 [pdf, other]

Title: Discovery of Self-Assembling $\pi$-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Kirill Shmilovich, Rachael A. Mansbach, Hythem Sidky, Olivia E. Dunne, Sayak Subhra Panda, John D. Tovar, Andrew L. Ferguson

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft); Machine Learning (cs.LG)

[21] arXiv:2002.01727 [pdf, other]

Title: Cardiac kinematic parameters computed from video of $\textit{in situ}$ beating heart

Lorenzo Fassina, Giacomo Rozzi, Stefano Rossi, Simone Scacchi, Maricla Galetti, Francesco Paolo Lo Muzio, Fabrizio Del Bianco, Piero Colli Franzone, Giuseppe Petrilli, Giuseppe Faggian, Michele Miragoli

Journal-ref: Scientific Reports 2017;7:46143

Subjects: Tissues and Organs (q-bio.TO); Medical Physics (physics.med-ph); Quantitative Methods (q-bio.QM)

[22] arXiv:2002.01889 [pdf, other]

Title: Automated Deep Abstractions for Stochastic Chemical Reaction Networks

Tatjana Petrov, Denis Repin

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

[23] arXiv:2002.01986 [pdf, other]

Title: On the validation of Newcomb-Benford law and Weibull distribution in neuromuscular transmission

A. J. da Silva, S. Floquet, D. O. C. Santos, R. F. Lima

Comments: 16 pages, 4 figures, submitted to publication

Subjects: Subcellular Processes (q-bio.SC); Biological Physics (physics.bio-ph)

[24] arXiv:2002.02156 [pdf, other]

Title: Understanding evolutionary and ecological dynamics using a continuum limit

Peter Czuppon, Arne Traulsen

Comments: updated version

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

[25] arXiv:2002.02364 [pdf, other]

Title: Different approaches to unveil biomolecule configurations and their mutual interactions

Rosaria Benedetti, Francesco Bajardi, Salvatore Capozziello, Vincenzo Carafa, Mariarosaria Conte, Maria Rosaria Del Sorbo, Angela Nebbioso, Manjot Singh, Hendrik Gerard Stunnenberg, Mohammadhassan Valadan, Lucia Altucci, Carlo Altucci

Comments: 33 pages, 5 figures

Journal-ref: Analytical Letters 54, no.1-2, 40-56 (2020)

Subjects: Biomolecules (q-bio.BM)

[26] arXiv:2002.02367 [pdf, other]

Title: Geo-information system of spread of tuberculosis based on inversion and prediction

Sergey Kabanikhin, Olga Krivorotko, Aliya Takuadina, Darya Andornaya, Shuhua Zhang

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

[27] arXiv:2002.02381 [pdf, other]

Title: Boundary solution based on rescaling method: recoup the first and second-order statistics of neuron network dynamics

Cecilia Romaro, Antonio Carlos Roque, Jose Roberto Castilho Piqueira

Subjects: Neurons and Cognition (q-bio.NC); Dynamical Systems (math.DS); Numerical Analysis (math.NA)

[28] arXiv:2002.02394 [pdf, other]

Title: FPGA Acceleration of Sequence Alignment: A Survey

Sahand Salamat, Tajana Rosing

Subjects: Quantitative Methods (q-bio.QM); Hardware Architecture (cs.AR); Genomics (q-bio.GN)

[29] arXiv:2002.02425 [pdf, other]

Title: A mean field approach to model levels of consciousness from EEG recordings

Marco Alberto Javarone, Olivia Gosseries, Daniele Marinazzo, Quentin Noirhomme, Vincent Bonhomme, Steven Laureys, Srivas Chennu

Comments: 23 pages, 6 figures. Accepted for publication in Journal of Statistical Mechanics: Theory and Experiment

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech)

[30] arXiv:2002.02496 [pdf, other]

Title: Implementing Inductive bias for different navigation tasks through diverse RNN attractors

Tie Xu, Omri Barak

Comments: Main text: 11 pages, 5 figures. Supplementary: 16 pages, 14 figures, 3 tables. Accepted as a conference paper for ICLR 2020

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

[31] arXiv:2002.02530 [pdf, other]

Title: Machine learning on DNA-encoded libraries: A new paradigm for hit-finding

Kevin McCloskey, Eric A. Sigel, Steven Kearnes, Ling Xue, Xia Tian, Dennis Moccia, Diana Gikunju, Sana Bazzaz, Betty Chan, Matthew A. Clark, John W. Cuozzo, Marie-Aude Guié, John P. Guilinger, Christelle Huguet, Christopher D. Hupp, Anthony D. Keefe, Christopher J. Mulhern, Ying Zhang, Patrick Riley

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

[32] arXiv:2002.02642 [pdf, other]

Title: The weakest link bridging germinal center B cells and follicular dendritic cells limits antibody affinity maturation

Rajat Desikan, Rustom Antia, Narendra M. Dixit

Journal-ref: BioEssays, 2021

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

[33] arXiv:2002.02721 [pdf, other]

Title: Assessing biophysical and socio-economic impacts of climate change on avian biodiversity

Simon Kapitza, Pham Van Ha, Tom Kompas, Nick Golding, Natasha C. R. Cadenhead, Payal Bal, Brendan A. Wintle

Comments: 4 figures, 30 pages double-spaced

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

[34] arXiv:2002.02803 [pdf, other]

Title: Model of Algal Growth Depending on Nutrients and Inorganic Carbon in a Poorly Mixed Water Column

Jimin Zhang, Junping Shi, Xiaoyuan Chang

Comments: 27 pages, 7 figures

Subjects: Populations and Evolution (q-bio.PE); Analysis of PDEs (math.AP)

[35] arXiv:2002.02807 [pdf, other]

Title: Adaptive control for hindlimb locomotion in a simulated mouse through temporal cerebellar learning

T. P. Jensen, S. Tata, A. J. Ijspeert, S. Tolu

Comments: To be published in NICE '20: Proceedings of the 8th Annual Neuro-inspired Computational Elements Workshop. 8 pages, 13 figures

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

[36] arXiv:2002.02936 [pdf, other]

Title: Neurogenetics of the Human Adenosine Receptor Genes: Genetic Structures and Involvement in Brain Diseases

Vincent Huin (JPArc - U1172 Inserm), Claire-Marie Dhaenens (JPArc - U837 Inserm), Mégane Homa (JPArc - U1172 Inserm), Kévin Carvalho, Luc Buée, Bernard Sablonnière

Journal-ref: Journal of Caffeine and Adenosine Research, New Rochelle, N.Y. : Mary Ann Liebert, Inc., [2018]-, 2019, 9 (3), pp.73-88

Subjects: Quantitative Methods (q-bio.QM); Neurons and Cognition (q-bio.NC)

[37] arXiv:2002.03034 [pdf, other]

Title: Population pharmacokinetics and dosing regimen optimization of tacrolimus in Chinese lung transplant recipients

Xiaojun Cai, Huizhu Song, Zheng Jiao, Hang Yang, Min Zhu, Chengyu Wang, Dong Wei, Lingzhi Shi, Bo Wu, Jinyu Chen

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

[38] arXiv:2002.03173 [pdf, other]

Title: Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1

Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang

Comments: Structure models for 2019-nCoV proteins are available at this https URL

Journal-ref: J. Proteome Res. 2020, 19, 4, 1351-1360

Subjects: Genomics (q-bio.GN); Biomolecules (q-bio.BM)

[39] arXiv:2002.03211 [pdf, other]

Title: Appreciating the variety of goals in computational neuroscience

Konrad P. Kording, Gunnar Blohm, Paul Schrater, Kendrick Kay

Comments: Accepted for publication in Neurons, Behavior, Data Analysis, and Theory

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

[40] arXiv:2002.03268 [pdf, other]

Title: The Novel Coronavirus, 2019-nCoV, is Highly Contagious and More Infectious Than Initially Estimated

Steven Sanche, Yen Ting Lin, Chonggang Xu, Ethan Romero-Severson, Nicolas W. Hengartner, Ruian Ke

Comments: 8 pages, 3 figures, 1 Supplementary Text, 6 Supplementary figures, 2 Supplementary tables

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

[41] arXiv:2002.03288 [pdf, other]

Title: A Thermodynamic Model for Active Ion Transport

Xiang Zou

Comments: 13 pages, 3 figures

Subjects: Subcellular Processes (q-bio.SC); Molecular Networks (q-bio.MN)

[42] arXiv:2002.03383 [pdf, other]

Title: Prediction of native contacts in proteins from an out--of--equilibrium coevolutionary process

D. Oriani, M. Cagiada, G. Tiana

Subjects: Biomolecules (q-bio.BM)

[43] arXiv:2002.03410 [pdf, other]

Title: Learning graph representations of biochemical networks and its application to enzymatic link prediction

Julie Jiang, Li-Ping Liu, Soha Hassoun

Comments: 6 pages, 5 figures

Subjects: Molecular Networks (q-bio.MN)

[44] arXiv:2002.03419 [pdf, other]

Title: The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

Razvan V. Marinescu, Neil P. Oxtoby, Alexandra L. Young, Esther E. Bron, Arthur W. Toga, Michael W. Weiner, Frederik Barkhof, Nick C. Fox, Arman Eshaghi, Tina Toni, Marcin Salaterski, Veronika Lunina, Manon Ansart, Stanley Durrleman, Pascal Lu, Samuel Iddi, Dan Li, Wesley K. Thompson, Michael C. Donohue, Aviv Nahon, Yarden Levy, Dan Halbersberg, Mariya Cohen, Huiling Liao, Tengfei Li, Kaixian Yu, Hongtu Zhu, Jose G. Tamez-Pena, Aya Ismail, Timothy Wood, Hector Corrada Bravo, Minh Nguyen, Nanbo Sun, Jiashi Feng, B.T. Thomas Yeo, Gang Chen, Ke Qi, Shiyang Chen, Deqiang Qiu, Ionut Buciuman, Alex Kelner, Raluca Pop, Denisa Rimocea, Mostafa M. Ghazi, Mads Nielsen, Sebastien Ourselin, Lauge Sorensen, Vikram Venkatraghavan, Keli Liu, Christina Rabe, Paul Manser, Steven M. Hill, James Howlett, Zhiyue Huang, Steven Kiddle, Sach Mukherjee, Anais Rouanet, Bernd Taschler, Brian D. M. Tom, Simon R. White, Noel Faux, Suman Sedai, Javier de Velasco Oriol, Edgar E. V. Clemente, Karol Estrada, Leon Aksman, Andre Altmann, Cynthia M. Stonnington, Yalin Wang, Jianfeng Wu, Vivek Devadas, Clementine Fourrier, Lars Lau Raket, Aristeidis Sotiras, Guray Erus, Jimit Doshi, Christos Davatzikos, Jacob Vogel, Andrew Doyle, Angela Tam, Alex Diaz-Papkovich, Emmanuel Jammeh, Igor Koval, Paul Moore, Terry J. Lyons, John Gallacher, Jussi Tohka, Robert Ciszek, Bruno Jedynak, Kruti Pandya, Murat Bilgel, William Engels, Joseph Cole, Polina Golland, Stefan Klein, Daniel C. Alexander

Comments: Presents final results of the TADPOLE competition. 60 pages, 7 tables, 14 figures

Journal-ref: Machine Learning for Biomedical Imaging (MELBA), Dec 2021

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

[45] arXiv:2002.03420 [pdf, other]

Title: Mapping low-dimensional dynamics to high-dimensional neural activity: A derivation of the ring model from the neural engineering framework

Omri Barak, Sandro Romani

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

[46] arXiv:2002.03445 [pdf, other]

Title: The architecture of co-culture spheroids regulates tumor invasion within a 3D extracellular matrix

Yu Ling Huang, Carina Shiau, Cindy Wu, Jeffrey E. Segall, Mingming Wu

Comments: 15 pages, 5 figures, and 2 pages of supplementary information

Subjects: Cell Behavior (q-bio.CB)

[47] arXiv:2002.03540 [pdf, other]

Title: A wave-pulse neural network for quasi-quantum coding

Wen-Zhuo Zhang

Comments: 5 pages, 2 figures

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

[48] arXiv:2002.03638 [pdf, other]

Title: Piecewise quadratic growth during the 2019 novel coronavirus epidemic

Axel Brandenburg

Comments: 9 pages, 14 figures, 2 tables, published in Infectious Disease Modelling

Journal-ref: Infectious Disease Modelling 5, 681-690 (2020)

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

[49] arXiv:2002.03640 [pdf, other]

Title: microRNA-mediated noise processing in cells: a fight or a game?

Elsi Ferro, Chiara Enrico Bena, Silvia Grigolon, Carla Bosia

Comments: 10 pages, 1 figure

Subjects: Molecular Networks (q-bio.MN)

[50] arXiv:2002.03738 [pdf, other]

Title: Human Creativity and Consciousness: Unintended Consequences of the Brain's Extraordinary Energy Efficiency?

T.N.Palmer

Comments: Based on invited talk at Models of Consciousness Conference, Mathematical Institute, University of Oxford, September 2019

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