Quantitative Biology

Authors and titles for October 2005

[1] arXiv:q-bio/0510001 [pdf, other]

Title: Implications of Aging in Bacteria

Leah R. Johnson, Marc Mangel (University of California at Santa Cruz)

Comments: 16 pages, 6 figures submitted to Mechanisms of Aging and Development

Journal-ref: Mech. Age. Dev., Vol 127/10 pp 786-793, 2006

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

[2] arXiv:q-bio/0510002 [pdf, other]

Title: A p53 Oscillator Model of DNA Break Repair Control

Vijay Chickarmane, Ali Nadim, Animesh Ray, Herbert M. Sauro

Comments: 31 pages, 8 figures

Subjects: Molecular Networks (q-bio.MN)

[3] arXiv:q-bio/0510003 [pdf, other]

Title: Control of neural chaos by synaptic noise

J. M. Cortes, J. Marro, J. J. Torres

Comments: 6 pages, 3 figures. To appear in Biosystems, 2005

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

[4] arXiv:q-bio/0510004 [pdf, other]

Title: The simplest model of spatially distributed population with reasonable migration of organisms

Michael Sadovsky

Comments: 7 pages, 1 figure

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

[5] arXiv:q-bio/0510005 [pdf, other]

Title: Pair Approximation Models for Disease Spread

Jerome Benoit, Ana Nunes, Margarida Telo da Gama

Comments: 6 pages, 3 figures, LaTeX2e+SVJour+AmSLaTeX, NEXTSigmaPhi 2005; metadata title corrected wrt paper title

Journal-ref: Eur. Phys. J. B 50 (2006), no. 1-2, 177--181

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

[6] arXiv:q-bio/0510006 [pdf, other]

Title: Protein crystallization in vivo

Jonathan P.K. Doye, Wilson C.K. Poon

Comments: 17 pages, 1 figure

Journal-ref: Curr. Opin. Colloid In., 11, 40-46 (2006)

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

[7] arXiv:q-bio/0510007 [pdf, other]

Title: The fitness value of information

Carl T. Bergstrom, Michael Lachmann

Comments: 18 pages, 3 figures (included in text). Submitted to PNAS

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

[8] arXiv:q-bio/0510008 [pdf, other]

Title: The Tangled nature model with inheritance and constraint: Evolutionary ecology restricted by a conserved resource

Simon Laird, Henrik Jeldtoft Jensen

Comments: 18 pages and 9 figures

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

[9] arXiv:q-bio/0510009 [pdf, other]

Title: Network growth models and genetic regulatory networks

D. V. Foster (1), S. A. Kauffman (2), J. E. S. Socolar (1) ((1) Duke University, (2) University of Calgary)

Comments: 8 pages with 7 eps figures; uses revtex4. Added references, cleaner figures

Journal-ref: Phys. Rev. E, Vol. 73, 031912 (2006)

Subjects: Molecular Networks (q-bio.MN)

[10] arXiv:q-bio/0510010 [pdf, other]

Title: Role of transport performance on neuron cell morphology

E. Louis C. Degli Esposti Boschi G. J. Ortega E. Fernandez

Comments: 9 pages with 3 figures, submitted to Neuroscience Letters

Journal-ref: FASEB Journal 21, 866 (2007)

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

[11] arXiv:q-bio/0510011 [pdf, other]

Title: A new formalism for calculation of the partition function of single stranded nucleic acids

Roumen A. Dimitrov

Subjects: Biomolecules (q-bio.BM)

[12] arXiv:q-bio/0510012 [pdf, other]

Title: Gene Copy Number and Cell Cycle Arrest

Bhaswar Ghosh, Indrani Bose

Comments: 17 pages, 12 figures

Subjects: Molecular Networks (q-bio.MN); Other Quantitative Biology (q-bio.OT)

[13] arXiv:q-bio/0510013 [pdf, other]

Title: The protein map of Synechococcus sp. PCC 7942 - the first overlook

Olga A. Koksharova, Johan Klint, Ulla Rasmussen

Subjects: Genomics (q-bio.GN)

[14] arXiv:q-bio/0510014 [pdf, other]

Title: Predictive Models for Characterization of Ecological Data

Can Ozan Tan, Uygar Ozesmi, Bahtiyar Kurt

Comments: 14 pages, 1 figure. Submitted to Ecology as a Statistical Report

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

[15] arXiv:q-bio/0510015 [pdf, other]

Title: Participatory Ecosystem Management Planning at Tuzla Lake (Turkey) Using Fuzzy Cognitive Mapping

Filiz Dadaser Celik, Uygar Ozesmi, Asuman Akdogan

Comments: 43 pages, 4 figures

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

[16] arXiv:q-bio/0510016 [pdf, other]

Title: Generalizability of Artificial Neural Network Models in Ecological Applications: Predicting Nest Occurrence and Breeding Success of the Red-winged Blackbird Agelaius phoeniceus

Uygar Ozesmi, Can Ozan Tan, Stacy L. Ozesmi, Raleigh J. Robertson

Comments: 42 pages, 3 figures. Presented in ISEI3 conference (2002). Ecological Modeling in press

Journal-ref: Ecological Modelling, 195:94-104. 2006

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

[17] arXiv:q-bio/0510017 [pdf, other]

Title: Methodological Issues in Building, Training, and Testing Artificial Neural Networks

Stacy L. Ozesmi, Uygar Ozesmi, Can Ozan Tan

Comments: 22 pages, 2 figures. Presented in ISEI3 (2002). Ecological Modelling in press

Journal-ref: Ecological Modelling, 195:83-93. 2006

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

[18] arXiv:q-bio/0510018 [pdf, other]

Title: A Model Analyzing Life Cycle of Periodical Cicadas

Shi Chen, Sheng Bao, Jian-Xiu Chen

Comments: 4 pages,1 figure

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

[19] arXiv:q-bio/0510019 [pdf, other]

Title: Species Numbers versus Area in Chowdhury Ecosystems

D. Stauffer, A. Pekalski

Comments: 4 pages including 3 figures

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

[20] arXiv:q-bio/0510020 [pdf, other]

Title: $C_{E}PT$ Symmetry of the Simple Ecological Dynamical Equations

Vladan Pankovic, Rade Glavatovic, Milan Predojevic

Comments: 11 pages, no figures

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

[21] arXiv:q-bio/0510021 [pdf, other]

Title: Non-extensive Trends in the Size Distribution of Coding and Non-coding DNA Sequences in the Human Genome

Th. Oikonomou, A. Provata

Comments: 13 pages, 10 figures, 2 tables

Subjects: Genomics (q-bio.GN)

[22] arXiv:q-bio/0510022 [pdf, other]

Title: Content based network model with duplication and divergence

Yasemin Sengun, Ayse Erzan

Comments: 12 pages, 6 figures

Subjects: Molecular Networks (q-bio.MN)

[23] arXiv:q-bio/0510023 [pdf, other]

Title: The equilibrium theory of life evolution

D. Balciunas

Comments: 4 pages

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

[24] arXiv:q-bio/0510024 [pdf, other]

Title: Effect of pooling samples on the efficiency of comparative studies using microarrays

Shu-Dong Zhang, Timothy W. Gant

Comments: 8 pages, 1 figure, 2 tables; to appear in Bioinformatics

Journal-ref: Bioinformatics 2005 21(24):4378-4383.

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

[25] arXiv:q-bio/0510025 [pdf, other]

Title: NF-kappa B oscillations and cell-to-cell variability

F. Hayot, C. Jayaprakash

Comments: 14 pages, 9 figures, 1 table

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

[26] arXiv:q-bio/0510026 [pdf, other]

Title: Some Theoretical Investigations in EEG Studies

I.Mitra

Comments: 12 pages

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

[27] arXiv:q-bio/0510027 [pdf, other]

Title: Mathematical approaches to differentiation and gene regulation

C. Soulé (IHES)

Comments: To appear in Notes Comptes-Rendus Acad. Sc. Paris, Biologie

Subjects: Molecular Networks (q-bio.MN)

[28] arXiv:q-bio/0510028 [pdf, other]

Title: Classification of capped tubular viral particles in the family of Papovaviridae

T. Keef, A. Taormina, R. Twarock

Comments: 13 pages

Journal-ref: J.Phys.:Condens.Matter 18 (2006) S375-S387

Subjects: Biomolecules (q-bio.BM)

[29] arXiv:q-bio/0510029 [pdf, other]

Title: Vector space of DNA genomic sequences on a Genetic Code Galois Field

Robersy Sanchez, Eberto R Morgado, Ricardo Grau

Comments: 10 pages, 2 figures

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

[30] arXiv:q-bio/0510030 [pdf, other]

Title: Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes

Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam Margolin, Andrea Califano

Comments: 15 pages, 3 figures, 2 tables; minor changes following referees' comments; accepted to RECOMB06

Journal-ref: RECOMB'06 Proceedings, LNCS 3909, Springer, 2006

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

[31] arXiv:q-bio/0510031 [pdf, other]

Title: Statistical Predictive Models in Ecology: Comparison of Performances and Assessment of Applicability

Can Ozan Tan, Uygar Ozesmi, Meryem Beklioglu, Esra Per, Bahtiyar Kurt

Comments: 34 pages, 2 figures. Submitted to Ecological Informatics

Journal-ref: Ecological Informatics, 1:195-211. 2006

Subjects: Quantitative Methods (q-bio.QM)

[32] arXiv:q-bio/0510032 [pdf, other]

Title: Kernel methods in genomics and computational biology

Jean-Philippe Vert (ENSMP-CBG)

Subjects: Quantitative Methods (q-bio.QM)

[33] arXiv:q-bio/0510033 [pdf, other]

Title: Tropical rainforest bird community structure in relation to altitude, tree species composition, and null models in the Western Ghats, India

T. R. Shankar Raman, N. V. Joshi, R. Sukumar

Comments: 36 pages, 5 figures, two tables (including one in the appendix) Submitted to the Journal of the Bombay Natural History Society (JBNHS)

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

[34] arXiv:q-bio/0510034 [pdf, other]

Title: Bending a slab of neural tissue

Partha P. Mitra

Comments: 6 pages, 2 figures

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

[35] arXiv:q-bio/0510035 [pdf, other]

Title: Using the tangle: a consistent construction of phylogenetic distance matrices for quartets

J G Sumner, P D Jarvis

Comments: 18 Pges. Submitted to Mathematical Biosciences

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

[36] arXiv:q-bio/0510036 [pdf, other]

Title: When Response Variability Increases Neural Network Robustness to Synaptic Noise

Gleb Basalyga, Emilio Salinas

Comments: 26 pages, 7 figures, to appear in Neural Computation

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

[37] arXiv:q-bio/0510037 [pdf, other]

Title: Context-dependent selection of visuomotor maps

Emilio Salinas

Comments: 22 pages, 10 figures. Article available from: this http URL

Journal-ref: BMC Neuroscience 5:47, 2005

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

[38] arXiv:q-bio/0510038 [pdf, other]

Title: Are structural biases at protein termini a signature of vectorial folding?

Alessandro Laio, Cristian Micheletti

Comments: 7 pages, 3 figures, 1 table

Subjects: Biomolecules (q-bio.BM)

[39] arXiv:q-bio/0510039 [pdf, other]

Title: Biological nonlocality and the mind-brain interaction problem: comments on a new empirical approach

Fred Thaheld

Comments: 21 pages

Journal-ref: BioSystems 70 (2003) 35-41

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

[40] arXiv:q-bio/0510040 [pdf, other]

Title: The role of inhibitory feedback for information processing in thalamocortical circuits

Joerg Mayer, Heinz Georg Schuster, Jens Christian Claussen (University Kiel)

Comments: 16 pages, 15eps figures included. To appear in Physical Review E

Journal-ref: Phys. Rev. E 73, 031908 (2006)

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

[41] arXiv:q-bio/0510041 [pdf, other]

Title: A New Form-Factor Method for the Analysis of Tissue Fluorescence

V. Gavryushin

Comments: 13 pages, 7 figures, submitted to "Journal of Medical Physics", 2005. As the supplemental material, 4 animation files illustrating the reconstruction procedures and properties of fluorophores spectra, by the proposed line-shape model. To view them with comments, - use link: this http URL

Subjects: Biomolecules (q-bio.BM)

[42] arXiv:q-bio/0510042 [pdf, other]

Title: Impact of Tandem Repeats on the Scaling of Nucleotide Sequences

Radhakrishnan Nagarajan, Meenakshi Upreti

Comments: 14 Pages, 3 Figures

Subjects: Genomics (q-bio.GN); Statistical Mechanics (cond-mat.stat-mech)

[43] arXiv:q-bio/0510043 [pdf, other]

Title: How do proteins search for their specific sites on coiled or globular DNA

Tao Hu, A.Yu.Grosberg, B.I.Shklovskii

Comments: 16 pages, 5 figures

Journal-ref: Biophysical Journal, v. 90, p. 2731-2744, 2006

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

[44] arXiv:q-bio/0510044 [pdf, other]

Title: Long-range dependencies in heart rate signals- revisited

Danuta Makowiec, Rafal Galaska, Aleksandra Dudkowska, Andrzej Rynkiewicz, Marcin Zwierz

Comments: 24 pages

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

[45] arXiv:q-bio/0510045 [pdf, other]

Title: Dominant Pathways in Protein Folding

P.Faccioli, M.Sega, F.Pederiva, H.Orland

Comments: Final version, accepted for publication in Phys. Rev. Lett

Journal-ref: Phys.Rev.Lett. 97 (2006) 108101

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft); High Energy Physics - Phenomenology (hep-ph)

[46] arXiv:q-bio/0510046 [pdf, other]

Title: Speed of synchronization in complex networks of neural oscillators Analytic results based on Random Matrix Theory

Marc Timme, Theo Geisel, Fred Wolf

Comments: 17 pages, 12 figures, submitted to Chaos

Journal-ref: Chaos 16, 015108 (2006)

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

[47] arXiv:q-bio/0510047 [pdf, other]

Title: An Algorithm for Missing Value Estimation for DNA Microarray Data

Shmuel Friedland, Mostafa Kaveh, Amir Niknejad, Hossein Zare

Subjects: Genomics (q-bio.GN); Numerical Analysis (math.NA)

[48] arXiv:q-bio/0510048 [pdf, other]

Title: Solvent and mutation effects on the nucleation of amyloid $\beta$-protein folding

Luis Cruz, Brigita Urbanc, Jose M. Borreguero, Noel D. Lazo, David B. Teplow, H. Eugene Stanley

Comments: 3 figures, 2 tables

Subjects: Biomolecules (q-bio.BM)

[49] arXiv:q-bio/0510049 [pdf, other]

Title: Stretching short biopolymers by fields and forces

Yuko Hori, Ashok Prasad, Jane' Kondev

Comments: 10 pages, 7 figures

Journal-ref: PHYSICAL REVIEW E 75, 041904 (2007)

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

[50] arXiv:q-bio/0510050 [pdf, other]

Title: Continuum Description of the Cytoskeleton: Ring Formation in the Cell Cortex

Alexander Zumdieck, Marco Cosentino Lagomarsino, Catalin Tanase, Karsten Kruse, Bela Mulder, Marileen Dogterom, Frank J"ulicher

Comments: 5 pages, 4 figures

Subjects: Subcellular Processes (q-bio.SC)