Quantitative Biology

Authors and titles for Apr 2019, skipping first 25

[26]  arXiv:1904.02049 [pdf, other]

Title: No evidence of fish biodiversity effects on coral reef ecosystem functioning across scales

Authors: Tarik C. Gouhier, Pradeep Pillai

Journal-ref: Frontiers in Ecology and Evolution 7 (2019) 212

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

[27]  arXiv:1904.02145 [pdf, other]

Title: Fitting stochastic predator-prey models using both population density and kill rate data

Authors: Frederic Barraquand, Olivier Gimenez

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

[28]  arXiv:1904.02523 [pdf, other]

Title: Explaining versus Describing Human Decisions. Hilbert Space Structures in Decision Theory

Authors: Sandro Sozzo

Comments: 16 pages, 1 figure, LateX

Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Quantum Physics (quant-ph)

[29]  arXiv:1904.02576 [pdf, ps, other]

Title: The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA

Authors: Jack W Shepherd, Robert J Greenall, Matt I J Probert, Agnes Noy, Mark C Leake

Subjects: Biomolecules (q-bio.BM)

[30]  arXiv:1904.02600 [pdf, ps, other]

Title: Large-scale Species Tree Estimation

Authors: Erin Molloy, Tandy Warnow

Comments: 25 pages, no figures, submitted as a chapter for a book edited by Lacey Knowles and Laura Kubatko

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

[31]  arXiv:1904.02610 [pdf, other]

Title: Diverse communities behave like typical random ecosystems

Authors: Wenping Cui, Robert Marsland III, Pankaj Mehta

Comments: 24 pages

Journal-ref: Phys. Rev. E 104, 034416 (2021)

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

[32]  arXiv:1904.02741 [pdf, other]

Title: Modeling Bottom-Up and Top-Down Attention with a Neurodynamic Model of V1

Authors: David Berga, Xavier Otazu

Comments: 27 pages, 19 figures

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

[33]  arXiv:1904.02866 [pdf, other]

Title: The nature of the animacy organization in human ventral temporal cortex

Authors: Sushrut Thorat, Daria Proklova, Marius V. Peelen

Comments: 16 pages, 5 figures, code+data at - this https URL Update - added supplementary results and edited abstract

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

[34]  arXiv:1904.02979 [pdf, other]

Title: A stochastic individual-based model to explore the role of spatial interactions and antigen recognition in the immune response against solid tumours

Authors: Fiona R Macfarlane, Mark AJ Chaplain, Tommaso Lorenzi

Subjects: Cell Behavior (q-bio.CB); Dynamical Systems (math.DS)

[35]  arXiv:1904.02983 [pdf, ps, other]

Title: A proof of unlimited multistability for phosphorylation cycles

Authors: Elisenda Feliu, Alan D. Rendall, Carsten Wiuf

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

[36]  arXiv:1904.02995 [pdf, ps, other]

Title: When is an action caused from within? Quantifying the causal chain leading to actions in simulated agents

Authors: Bjørn Erik Juel, Renzo Comolatti, Giulio Tononi, Larissa Albantakis

Comments: Submitted and accepted to Alife 2019 conference. Revised version: edits include adding more references to relevant work and clarifying minor points in response to reviewers

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

[37]  arXiv:1904.03093 [pdf, ps, other]

Title: Structure Learning in Coupled Dynamical Systems and Dynamic Causal Modelling

Authors: Amirhossein Jafarian, Peter Zeidman, Vladimir Litvak, Karl Friston

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

[38]  arXiv:1904.03102 [pdf, ps, other]

Title: Passive Cervical Spine Ligaments Provide Stability during Head Impacts in Vivo

Authors: Calvin Kuo, Jodie Sheffels, Michael Fanton, Ina Bianca Yu, Rosa Hamalainen, David Camarillo

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

[39]  arXiv:1904.03133 [pdf, other]

Title: Global Small-Angle Scattering Data Analysis of Inverted Hexagonal Phases

Authors: Moritz P. K. Frewein, Michael Rumetshofer, Georg Pabst

Journal-ref: J. Appl. Cryst. 52, 403-414 (2019)

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

[40]  arXiv:1904.03236 [pdf, other]

Title: Transmission of danger information past physical barriers by ants

Authors: A. Reyes, M. Curbelo, F. Tejera, A. Rivera, G. Simon, O. Ramos, M.S. Turner, E. Altshuler

Comments: 12 pages, 6 figures

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

[41]  arXiv:1904.03290 [pdf, other]

Title: Dynamics of a birth-death process based on combinatorial innovation

Authors: Mike Steel, Wim Hordijk, Stuart A. Kauffman

Comments: 21 pages, 4 figures

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

[42]  arXiv:1904.03328 [pdf, other]

Title: Mitigating Gyral Bias in Cortical Tractography via Asymmetric Fiber Orientation Distributions

Authors: Ye Wu, Yoonmi Hong, Yuanjing Feng, Dinggang Shen, Pew-Thian Yap

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

[43]  arXiv:1904.03399 [pdf, other]

Title: Functional Geometry of Human Connectome and Robustness of Gender Differences

Authors: Bosiljka Tadic, Miroslav Andjelkovic, Roderick Melnik

Comments: 13 pages, 7 figures

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Algebraic Topology (math.AT)

[44]  arXiv:1904.03410 [pdf, ps, other]

Title: The role of dose-density in combination cancer chemotherapy

Authors: Álvaro G. López, Kelly C. Iarosz, Antonio M. Batista, Jesús M. Seoane, Ricardo L. Viana, Miguel A. F. Sanjuán

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

[45]  arXiv:1904.03531 [pdf, ps, other]

Title: Decoding hand kinematics from population responses in sensorimotor cortex during grasping

Authors: Elizaveta V. Okorokova, James M. Goodman, Nicholas G. Hatsopoulos, Sliman J. Bensmaia

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

[46]  arXiv:1904.03653 [pdf, ps, other]

Title: Conformational catalysis of cataract-associated aggregation by interacting intermediates in a human eye lens crystallin

Authors: Eugene Serebryany, Rostam Razban, Eugene I Shakhnovich

Comments: 26 pages, 6 figures+Supplementary

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

[47]  arXiv:1904.03675 [pdf, other]

Title: Trivial pursuits

Authors: Tarik C. Gouhier, Pradeep Pillai

Journal-ref: Frontiers in Ecology and Evolution 7 (2019) 236

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

[48]  arXiv:1904.03801 [pdf, other]

Title: pdbmine: A Node.js API for the RCSB Protein Data Bank (PDB)

Authors: Newlyn N. Joseph, Raktim N. Roy, Thomas A. Steitz

Comments: 1 figure

Subjects: Genomics (q-bio.GN)

[49]  arXiv:1904.03826 [pdf, other]

Title: Species Tree Estimation Using ASTRAL: Practical Considerations

Authors: Siavash Mirarab

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

[50]  arXiv:1904.03910 [pdf, ps, other]

Title: The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks

Authors: Bence Agg, Andrea Csaszar, Mate Szalay-Beko, Daniel V. Veres, Reka Mizsei, Peter Ferdinandy, Peter Csermely, Istvan A. Kovacs

Journal-ref: Bioinformatics 2019 35, 4490-4492

Subjects: Molecular Networks (q-bio.MN); Disordered Systems and Neural Networks (cond-mat.dis-nn); Computer Vision and Pattern Recognition (cs.CV); Biological Physics (physics.bio-ph)