Quantitative Biology

Authors and titles for June 2008

[1] arXiv:0806.0084 [pdf, other]

Title: Muscle fatigue degrades force sense at the ankle joint

Nicolas Vuillerme (TIMC), Matthieu Boisgontier (TIMC)

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

[2] arXiv:0806.0087 [pdf, other]

Title: Postural destabilization induced by trunk extensor muscles fatigue is suppressed by use of a plantar pressure-based electro-tactile biofeedback

Nicolas Vuillerme (TIMC), Nicolas Pinsault (TIMC), Olivier Chenu (TIMC), Anthony Fleury (TIMC), Yohan Payan (TIMC), Jacques Demongeot (TIMC)

Journal-ref: Arbeitsphysiologie (2008) epub ahead of print

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

[3] arXiv:0806.0108 [pdf, other]

Title: The C-value enigma and timing of the Cambrian explosion

Dirson Jian Li, Shengli Zhang

Comments: 46 pages, 10 figures

Journal-ref: Biochemical and Biophysical Research Communications 392, 240-245 (2010)

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

[4] arXiv:0806.0205 [pdf, other]

Title: Prediction of genomic properties and classification of life by protein length distributions

Dirson Jian Li, Shengli Zhang

Comments: 5 pages, 3 figures

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

[5] arXiv:0806.0215 [pdf, other]

Title: Reconstruction of biological networks by supervised machine learning approaches

Jean-Philippe Vert (CBIO)

Subjects: Quantitative Methods (q-bio.QM)

[6] arXiv:0806.0276 [pdf, other]

Title: Symbolic dynamics of biological feedback networks

Simone Pigolotti, Sandeep Krishna, Mogens H. Jensen

Comments: 4 pages, 4 figures

Journal-ref: Phys. Rev. Lett. 102(8), 088701 (2009)

Subjects: Quantitative Methods (q-bio.QM); Chaotic Dynamics (nlin.CD)

[7] arXiv:0806.0449 [pdf, other]

Title: Anapedesis: Implications and Applications of Bio-Structural Robustness

Nicanor I. Moldovan

Subjects: Other Quantitative Biology (q-bio.OT); Cell Behavior (q-bio.CB)

[8] arXiv:0806.0514 [pdf, other]

Title: Conformation of Circular DNA in 2 Dimensions

G. Witz, K. Rechendorff, J. Adamcik, G. Dietler

Comments: 4 pages, 5 figures

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

[9] arXiv:0806.0537 [pdf, other]

Title: Flexible Logic from Neuronal Dynamics

Abraham Miliotis, Sachin S. Talathi, William L. Ditto

Comments: 5 pages, 5 Figures

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

[10] arXiv:0806.0690 [pdf, other]

Title: Phase Transitions, Chaos and Joint Action in the Life Space Foam

Vladimir Ivancevic, Eugene Aidman, Leong Yen, Darryn Reid

Comments: 20 pages, no figures, elsart

Subjects: Neurons and Cognition (q-bio.NC); Other Quantitative Biology (q-bio.OT)

[11] arXiv:0806.0691 [pdf, other]

Title: Ricci Flow and Entropy Model for Avascular Tumor Growth and Decay Control

Tijana T. Ivancevic

Comments: 24 pages, 2 figures, Latex, revised

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

[12] arXiv:0806.0744 [pdf, other]

Title: Bacterial tracking of motile algae assisted by algal cell's vorticity field

Janos Tobias Locsei, Timothy J Pedley

Comments: 21 pages, 15 figures

Subjects: Cell Behavior (q-bio.CB); Quantitative Methods (q-bio.QM)

[13] arXiv:0806.0856 [pdf, other]

Title: New Proposed Mechanism of Actin-Polymerization-Driven Motility

Kun-Chun Lee, Andrea J. Liu

Comments: 31 pages, 5 figures

Subjects: Cell Behavior (q-bio.CB); Subcellular Processes (q-bio.SC)

[14] arXiv:0806.0979 [pdf, other]

Title: Pruning the Tree of Life: k-core Percolation as Selection Mechanism

Peter Klimek, Stefan Thurner, Rudolf Hanel

Comments: 6 pages, 3 eps figures

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

[15] arXiv:0806.1029 [pdf, other]

Title: Group theory of icosahedral virus capsids: a dynamical top-down approach

Kasper Peeters, Anne Taormina

Comments: 35 pages, many figures, animations available at this http URL

Journal-ref: J. Theor. Biol., 256 4, (2009), 607- 624

Subjects: Biomolecules (q-bio.BM)

[16] arXiv:0806.1063 [pdf, other]

Title: A cellular automata model for avascular solid tumor growth under the effect of therapy

E. A. Reis, L. B. L. Santos, S. T. R. Pinho

Comments: 18 pages, 15 figures (jpeg)

Subjects: Tissues and Organs (q-bio.TO); Cellular Automata and Lattice Gases (nlin.CG)

[17] arXiv:0806.1103 [pdf, other]

Title: On the Approximability of Comparing Genomes with Duplicates

Sébastien Angibaud (LINA), Guillaume Fertin (LINA), Irena Rusu (LINA), Annelyse Thevenin (LRI), Stéphane Vialette (IGM)

Subjects: Quantitative Methods (q-bio.QM); Computational Complexity (cs.CC)

[18] arXiv:0806.1264 [pdf, other]

Title: Can a Plantar Pressure-Based Tongue-Placed Electrotactile Biofeedback Improve Postural Control Under Altered Vestibular and Neck Proprioceptive Conditions?

Nicolas Vuillerme (TIMC), Olivier Chenu (TIMC), Nicolas Pinsault (TIMC), Anthony Fleury (TIMC), Jacques Demongeot (TIMC), Yohan Payan (TIMC)

Journal-ref: Neuroscience / Neurosciences (2008)

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

[19] arXiv:0806.1267 [pdf, other]

Title: Rapid divergence of the ecdysone receptor in Diptera and Lepidoptera suggests coevolution between ECR and USP-RXR

François Bonneton (CGMC), Dominique Zelus (LBMC), Thomas Iwema (CGMC), Marc Robinson-Rechavi (LBMC), Vincent Laudet (LBMC)

Journal-ref: Molecular Biology and Evolution 4, 20 (2003) 541-553

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

[20] arXiv:0806.1287 [pdf, other]

Title: Quasi-cycles in a spatial predator-prey model

Carlos A. Lugo, Alan J. McKane

Comments: 18 pages, 4 figures

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

[21] arXiv:0806.1292 [pdf, other]

Title: A standalone version of IsoFinder for the computational prediction of isochores in genome sequences

Pedro Bernaola-Galván, Pedro Carpena, José L. Oliver

Comments: 7 pages, 3 figures

Subjects: Genomics (q-bio.GN)

[22] arXiv:0806.1297 [pdf, other]

Title: On the Estimation of the Proportion of True Recent Infections Using the BED Capture Enzyme Immunoassay

T.A. McWalter, A. Welte

Comments: 8 pages, 1 figure

Subjects: Quantitative Methods (q-bio.QM)

[23] arXiv:0806.1322 [pdf, other]

Title: Stroke volume estimation by thoracocardiography is better when glottis is closed

Enas Abdulhay (TIMC), Pierre Baconnier (TIMC)

Journal-ref: Conference proceedings : Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 2007 (2007) 1074-7

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

[24] arXiv:0806.1378 [pdf, other]

Title: Hadamard Phylogenetic Methods and the n-taxon process

David Bryant

Comments: 20 pages, 2 figures

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

[25] arXiv:0806.1382 [pdf, other]

Title: Extra-auditory effects of noise in laboratory animals: the relationship between noise and sleep

Arnaud Rabat (IMNSSA)

Journal-ref: J Am Assoc Lab Anim Sci 46, 1 (2007) 35-41

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

[26] arXiv:0806.1551 [pdf, other]

Title: First-principles calculation of DNA looping in tethered particle experiments

Kevin B. Towles, John F. Beausang, Hernan G. Garcia, Rob Phillips, Philip C. Nelson

Comments: See the supplement at this http URL . This revised version accepted for publication at Physical Biology

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

[27] arXiv:0806.1649 [pdf, other]

Title: Effect of spatial structure on the evolution of cooperation

Carlos P. Roca, José A. Cuesta, Angel Sánchez

Comments: Final version, 20 pages, 14 figures

Journal-ref: Phys. Rev. E 80, 046106 (2009)

Subjects: Populations and Evolution (q-bio.PE); Computer Science and Game Theory (cs.GT); Physics and Society (physics.soc-ph)

[28] arXiv:0806.1685 [pdf, other]

Title: Activity-dependent stochastic resonance in recurrent neuronal networks

Vladislav Volman, Herbert Levine

Comments: 4 pages, 4 figures, published in Physical Review E

Subjects: Neurons and Cognition (q-bio.NC); Populations and Evolution (q-bio.PE)

[29] arXiv:0806.1733 [pdf, other]

Title: A dynamic logic method for determining behaviors of biological networks

Suping Lyu

Comments: 29 pages, 5 figures, 2008 APS poster

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

[30] arXiv:0806.1860 [pdf, other]

Title: Concentration and Length Dependence of DNA Looping in Transcriptional Regulation

Lin Han, Hernan G. Garcia, Seth Blumberg, Kevin B. Towles, John F. Beausang, Philip C. Nelson, Rob Phillips

Subjects: Biomolecules (q-bio.BM)

[31] arXiv:0806.1872 [pdf, other]

Title: Contact switching as a control strategy for epidemic outbreaks

Sebastian Risau-Gusman, Damian H. Zanette

Comments: 21 pages, 8 figures

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

[32] arXiv:0806.1955 [pdf, other]

Title: Observation of Cholesterol Dissolved in Microscopic Deposits of Free Fatty Acids in the Lumen of an Aorta of a Mouse Model for Human Atherosclerosis

Fran Adar

Comments: 5 pages, 3 figures

Journal-ref: SPIE 7 5321A-11 (2004)

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

[33] arXiv:0806.1988 [pdf, other]

Title: Statistical Characterization of a 1D Random Potential Problem - with applications in score statistics of MS-based peptide sequencing

Gelio Alves, Yi-Kuo Yu

Comments: 14 pages, 1 figure

Subjects: Quantitative Methods (q-bio.QM)

[34] arXiv:0806.2005 [pdf, other]

Title: SAPHIR - a multi-scale, multi-resolution modeling environment targeting blood pressure regulation and fluid homeostasis

S. Randall Thomas (IBISC), Enas Abdulhay (TIMC), Pierre Baconnier (TIMC), Julie Fontecave (TIMC), Jean-Pierre Francoise (LJLL), Francois Guillaud, Patrick Hannaert, Alfredo Hernandez (LTSI), Virginie Le Rolle (LTSI), Pierre Maziere (CPBS), Fariza Tahi, Farida Zehraoui (LIPN)

Journal-ref: Conference proceedings : Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 2007 (2007) 6649-52

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

[35] arXiv:0806.2035 [pdf, other]

Title: Nodal distances for rooted phylogenetic trees

Gabriel Cardona, Merce Llabres, Francesc Rossello, Gabriel Valiente

Comments: 26 pages, Supplementary Material available at this http URL

Subjects: Populations and Evolution (q-bio.PE); Computational Engineering, Finance, and Science (cs.CE); Discrete Mathematics (cs.DM)

[36] arXiv:0806.2059 [pdf, other]

Title: Segmentation of DNA sequences into twostate regions and melting fork regions

Eivind Tøstesen, Geir Kjetil Sandve, Fang Liu, Eivind Hovig

Comments: 17 pages, 8 figures; new introduction, added refs, minor changes

Journal-ref: J. Phys.: Condens. Matter 21 (2009) 034109

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

[37] arXiv:0806.2069 [pdf, other]

Title: The information capacity of hypercycles

Daniel A. M. M. Silvestre, Jose F. Fontanari

Comments: 4 pages, 1 figure, submitted to J. Theor. Biol

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

[38] arXiv:0806.2099 [pdf, other]

Title: Metabolic scaling law for fetus and placenta

Carolyn M. Salafia, Michael Yampolsky

Subjects: Tissues and Organs (q-bio.TO); Quantitative Methods (q-bio.QM)

[39] arXiv:0806.2108 [pdf, other]

Title: How Xenopus laevis embryos replicate reliably: investigating the random-completion problem

Scott Cheng-Hsin Yang, John Bechhoefer

Comments: 16 pages, 9 figures, submitted to Physical Review E

Journal-ref: Phys. Rev. E 78, 041917 (2008)

Subjects: Cell Behavior (q-bio.CB); Biological Physics (physics.bio-ph)

[40] arXiv:0806.2181 [pdf, other]

Title: The Evolutionary Reduction Principle for Linear Variation in Genetic Transmission

Lee Altenberg

Comments: 22 pages, 1 figure

Journal-ref: Bulletin of Mathematical Biology, Volume 71, Number 5, 1264-1284 (2009)

Subjects: Populations and Evolution (q-bio.PE); Spectral Theory (math.SP)

[41] arXiv:0806.2308 [pdf, other]

Title: Dynamics and Steady States in excitable mobile agent systems

Fernando Peruani, Gustavo J. Sibona

Journal-ref: Phys. Rev. Lett. 100, 168103 (2008)

Subjects: Populations and Evolution (q-bio.PE); Other Quantitative Biology (q-bio.OT)

[42] arXiv:0806.2331 [pdf, other]

Title: Optimal Control of Evolutionary Dynamics

Raj Chakrabarti, Herschel Rabitz, George McLendon

Comments: Extends "Mutagenic evidence for the optimal control of evolutionary dynamics" (accepted, Physical Review Letters)

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

[43] arXiv:0806.2373 [pdf, other]

Title: Coexistence of amplitude and frequency modulations in intracellular calcium dynamics

Maurizio De Pitta, Vladislav Volman, Herbert Levine, Giovanni Pioggia, Danilo De Rossi, Eshel Ben-Jacob

Comments: 4 pages, 4 figures

Journal-ref: Physical Review E, 77, 030903(R), March 2008

Subjects: Cell Behavior (q-bio.CB); Subcellular Processes (q-bio.SC)

[44] arXiv:0806.2394 [pdf, other]

Title: Phylogenetic Profiles as a Unified Framework for Measuring Protein Structure, Function and Evolution

Kyung Dae Ko (1,4), Yoojin Hong (2,4), Gue Su Chang (1,4), Gaurav Bhardwaj (1), Damian B. van Rossum (1,3), Randen L. Patterson (1,3), ((1) Department of Biology, The Pennsylvania State University, (2) Department of Computer Science and Engineering, The Pennsylvania State University, (3) Center for Computational Proteomics, The Pennsylvania State University)

Comments: 21 Pages, 10 Figures

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

[45] arXiv:0806.2500 [pdf, other]

Title: Sequence length bounds for resolving a deep phylogenetic divergence

Mareike Fischer, Mike Steel

Comments: 13 pages, 1 figure

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

[46] arXiv:0806.2594 [pdf, other]

Title: Towards quantitative prediction of proteasomal digestion patterns of proteins

Denis S. Goldobin, Alexey Zaikin

Comments: 14 pages, 4 figures, submitted to J. Stat. Mech. (Special issue for proceedings of 5th Intl. Conf. on Unsolved Problems on Noise and Fluctuations in Physics, Biology & High Technology, Lyon (France), June 2-6, 2008)

Journal-ref: J. Stat. Mech.: Theory Exp., P01009 (2009)

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

[47] arXiv:0806.2636 [pdf, other]

Title: Evolutionary game dynamics in phenotype space

Tibor Antal, Hisashi Ohtsuki, John Wakeley, Peter D. Taylor, Martin A. Nowak

Comments: version 2: minor changes; equivalent to final published version

Journal-ref: PNAS 106, 8597 (2009)

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

[48] arXiv:0806.2685 [pdf, other]

Title: RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics

Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu

Comments: 34 pages, 10 figures, 1 supplementary information file (this http URL). To view the supplementary file, please download and extract the gzipped tar source file listed under "Other formats"

Subjects: Quantitative Methods (q-bio.QM)

[49] arXiv:0806.2694 [pdf, other]

Title: Thermodynamics of natural images

Greg J Stephens, Thierry Mora, Gasper Tkacik, William Bialek

Subjects: Neurons and Cognition (q-bio.NC); Statistical Mechanics (cond-mat.stat-mech); Quantitative Methods (q-bio.QM)

[50] arXiv:0806.2763 [pdf, other]

Title: Substance graphs are optimal simple-graph representations of metabolism

Petter Holme, Mikael Huss

Journal-ref: Chinese Sci. Bull. 55, 3161-3168 (2010)

Subjects: Molecular Networks (q-bio.MN)