July 2009

Plants are very important in a bat's everyday life. They serve both as informative landmarks that a bat should use and as obstacles that it should avoid. An echolocating bat can use and avoid plants in complete darkness, using echolocation and relying on plant echoes. In this work the authors study the characteristics of plant echoes (see Yovel et al., 10.1371/journal.pcbi.1000429). They analyze the relation between the physical properties of a plant (e.g., its leaf size and density) and its echo, and examine the influence of the bat's sensory system on the echoes.

Image Credit: Dietmar Nill.

Message from ISCB

Getting Started in Text Mining: Part Two

Andrey Rzhetsky, Michael Seringhaus, Mark B. Gerstein

PLOS Computational Biology: published July 31, 2009 | https://doi.org/10.1371/journal.pcbi.1000411

Education

A Quick Guide to Organizing Computational Biology Projects

William Stafford Noble

PLOS Computational Biology: published July 31, 2009 | https://doi.org/10.1371/journal.pcbi.1000424

Review

Semantic Similarity in Biomedical Ontologies

Catia Pesquita, Daniel Faria, André O. Falcão, Phillip Lord, Francisco M. Couto

PLOS Computational Biology: published July 31, 2009 | https://doi.org/10.1371/journal.pcbi.1000443

Research Articles

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?

Xingyi Guo, Zhaolei Zhang, Mark B. Gerstein, Deyou Zheng

PLOS Computational Biology: published July 31, 2009 | https://doi.org/10.1371/journal.pcbi.1000449

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts

Jiao Li, Xiaoyan Zhu, Jake Yue Chen

PLOS Computational Biology: published July 31, 2009 | https://doi.org/10.1371/journal.pcbi.1000450

A Three Species Model to Simulate Application of Hyperbaric Oxygen Therapy to Chronic Wounds

Jennifer A. Flegg, Donald L. S. McElwain, Helen M. Byrne, Ian W. Turner

PLOS Computational Biology: published July 31, 2009 | https://doi.org/10.1371/journal.pcbi.1000451

Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome

Lun Yang, Jian Chen, Lin He

PLOS Computational Biology: published July 24, 2009 | https://doi.org/10.1371/journal.pcbi.1000441

Identification of a Topological Characteristic Responsible for the Biological Robustness of Regulatory Networks

Yangle Wu, Xiaomeng Zhang, Jianglei Yu, Qi Ouyang

PLOS Computational Biology: published July 24, 2009 | https://doi.org/10.1371/journal.pcbi.1000442

Power Efficiency of Outer Hair Cell Somatic Electromotility

Richard D. Rabbitt, Sarah Clifford, Kathryn D. Breneman, Brenda Farrell, William E. Brownell

PLOS Computational Biology: published July 24, 2009 | https://doi.org/10.1371/journal.pcbi.1000444

Topography of Extracellular Matrix Mediates Vascular Morphogenesis and Migration Speeds in Angiogenesis

Amy L. Bauer, Trachette L. Jackson, Yi Jiang

PLOS Computational Biology: published July 24, 2009 | https://doi.org/10.1371/journal.pcbi.1000445

Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors

Andrew J. Olaharski, Nina Gonzaludo, Hans Bitter, David Goldstein, Stephan Kirchner, Hirdesh Uppal, Kyle Kolaja

PLOS Computational Biology: published July 24, 2009 | https://doi.org/10.1371/journal.pcbi.1000446

Stem Cell Proliferation and Quiescence—Two Sides of the Same Coin

Ingmar Glauche, Kateri Moore, Lars Thielecke, Katrin Horn, Markus Loeffler, Ingo Roeder

PLOS Computational Biology: published July 24, 2009 | https://doi.org/10.1371/journal.pcbi.1000447

Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View

Yongping Pan, Ruth Nussinov

PLOS Computational Biology: published July 24, 2009 | https://doi.org/10.1371/journal.pcbi.1000448

The Natural Statistics of Audiovisual Speech

Chandramouli Chandrasekaran, Andrea Trubanova, Sébastien Stillittano, Alice Caplier, Asif A. Ghazanfar

PLOS Computational Biology: published July 17, 2009 | https://doi.org/10.1371/journal.pcbi.1000436

A Neural Computational Model of Incentive Salience

Jun Zhang, Kent C. Berridge, Amy J. Tindell, Kyle S. Smith, J. Wayne Aldridge

PLOS Computational Biology: published July 17, 2009 | https://doi.org/10.1371/journal.pcbi.1000437

Computational Analysis of Viscoelastic Properties of Crosslinked Actin Networks

Taeyoon Kim, Wonmuk Hwang, Hyungsuk Lee, Roger D. Kamm

PLOS Computational Biology: published July 17, 2009 | https://doi.org/10.1371/journal.pcbi.1000439

PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure

Marialuisa Pellegrini-Calace, Tim Maiwald, Janet M. Thornton

PLOS Computational Biology: published July 17, 2009 | https://doi.org/10.1371/journal.pcbi.1000440

Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation

Daniel Geberth, Marc-Thorsten Hütt

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000422

Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs

Flávio Codeço Coelho, Claudia T. Codeço

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000425

Movement Timing and Invariance Arise from Several Geometries

Daniel Bennequin, Ronit Fuchs, Alain Berthoz, Tamar Flash

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000426

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

Lucy R. Allen, Sergei V. Krivov, Emanuele Paci

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000428

Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels

Guido Gigante, Maurizio Mattia, Jochen Braun, Paolo Del Giudice

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000430

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants

Jiang Du, Robert D. Bjornson, Zhengdong D. Zhang, Yong Kong, Michael Snyder, Mark B. Gerstein

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000432

Relating Neuronal Firing Patterns to Functional Differentiation of Cerebral Cortex

Shigeru Shinomoto, Hideaki Kim, Takeaki Shimokawa, Nanae Matsuno, Shintaro Funahashi, Keisetsu Shima, Ichiro Fujita, Hiroshi Tamura, Taijiro Doi, Kenji Kawano, Naoko Inaba, Kikuro Fukushima, Sergei Kurkin, Kiyoshi Kurata, Masato Taira, Ken-Ichiro Tsutsui, Hidehiko Komatsu, Tadashi Ogawa, Kowa Koida, Jun Tanji, Keisuke Toyama

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000433

An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility

Susanne M. Rafelski, Jonathan B. Alberts, Garrett M. Odell

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000434

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

Olgun Guvench, Alexander D. MacKerell Jr

PLOS Computational Biology: published July 10, 2009 | https://doi.org/10.1371/journal.pcbi.1000435

Investigating the Conformational Stability of Prion Strains through a Kinetic Replication Model

Mattia Zampieri, Giuseppe Legname, Claudio Altafini

PLOS Computational Biology: published July 3, 2009 | https://doi.org/10.1371/journal.pcbi.1000420

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

Sarah L. Kinnings, Nina Liu, Nancy Buchmeier, Peter J. Tonge, Lei Xie, Philip E. Bourne

PLOS Computational Biology: published July 3, 2009 | https://doi.org/10.1371/journal.pcbi.1000423

Cover

**An echolocating bat (Myotis bechsteinii) avoiding collision with a plant while searching for a moth.**