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Table of Contents: April 2010

Electronic noses (eNoses) are typically tuned to identify particular odorants, ranging from "cocaine" to "spoiled milk". In contrast, here an eNose was tuned to the perceptual axis of odorant pleasantness, i.e., an axis ranging from very pleasant (e.g., rose) to very unpleasant (e.g., skunk). This allowed the eNose to then smell novel odorants it never encountered before, yet still generate odor pleasantness estimates in high agreement with human assessments regardless of the subject's cultural background. This suggests an innate component of odorant pleasantness that is tightly linked to molecular structure (see Haddad et al., doi:10.1371/journal.pcbi.1000740).

Image Credit: Genia Brodsky and Noam Sobel (The Weizmann Institute)

Perspective

PLoS Computational Biology Conference Postcards from PSB 2010

Ruchira S. Datta, Matthew W. Lux, Philip E. Bourne

Research Articles

Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions

Dirk Helbing, Attila Szolnoki, Matjaž Perc, György Szabó

How Informative Are Spatial CA3 Representations Established by the Dentate Gyrus?

Erika Cerasti, Alessandro Treves

Robustness under Functional Constraint: The Genetic Network for Temporal Expression in Drosophila Neurogenesis

Akihiko Nakajima, Takako Isshiki, Kunihiko Kaneko, Shuji Ishihara

Learning “graph-mer” Motifs that Predict Gene Expression Trajectories in Development

Xuejing Li, Casandra Panea, Chris H. Wiggins, Valerie Reinke, Christina Leslie

Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study

Jussi Aittoniemi, Heidi de Wet, Frances M. Ashcroft, Mark S. P. Sansom

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

Daniel Ting, Guoli Wang, Maxim Shapovalov, Rajib Mitra, Michael I. Jordan, Roland L. Dunbrack Jr

A Critical Quantity for Noise Attenuation in Feedback Systems

Liming Wang, Jack Xin, Qing Nie

The Brain's Router: A Cortical Network Model of Serial Processing in the Primate Brain

Ariel Zylberberg, Diego Fernández Slezak, Pieter R. Roelfsema, Stanislas Dehaene, Mariano Sigman

Accurately Measuring Recombination between Closely Related HIV-1 Genomes

Timothy E. Schlub, Redmond P. Smyth, Andrew J. Grimm, Johnson Mak, Miles P. Davenport

A New Approach for Determining Phase Response Curves Reveals that Purkinje Cells Can Act as Perfect Integrators

Elena Phoka, Hermann Cuntz, Arnd Roth, Michael Häusser

Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences

Vinal V. Lakhani, Feng Ding, Nikolay V. Dokholyan

A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression

Kenzie D. MacIsaac, Kinyui A. Lo, William Gordon, Shmulik Motola, Tali Mazor, Ernest Fraenkel

Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex

Lucy J. Colwell, Michael P. Brenner, Katharina Ribbeck

Efficient Physical Embedding of Topologically Complex Information Processing Networks in Brains and Computer Circuits

Danielle S. Bassett, Daniel L. Greenfield, Andreas Meyer-Lindenberg, Daniel R. Weinberger, Simon W. Moore, Edward T. Bullmore

A Reaction-Diffusion Model of Human Brain Development

Julien Lefèvre, Jean-François Mangin

Structural Characteristics of Novel Protein Folds

Narcis Fernandez-Fuentes, Joseph M. Dybas, Andras Fiser

Coordinate Dependence of Variability Analysis

Dagmar Sternad, Se-Woong Park, Hermann Müller, Neville Hogan

Accurate Distinction of Pathogenic from Benign CNVs in Mental Retardation

Jayne Y. Hehir-Kwa, Nienke Wieskamp, Caleb Webber, Rolph Pfundt, Han G. Brunner, Christian Gilissen, Bert B. A. de Vries, Chris P. Ponting, Joris A. Veltman

Ion Channel Density Regulates Switches between Regular and Fast Spiking in Soma but Not in Axons

Hugo Zeberg, Clas Blomberg, Peter Århem

Simulating Microdosimetry in a Virtual Hepatic Lobule

John Wambaugh, Imran Shah

Independent Component Analysis in Spiking Neurons

Cristina Savin, Prashant Joshi, Jochen Triesch

Global Entrainment of Transcriptional Systems to Periodic Inputs

Giovanni Russo, Mario di Bernardo, Eduardo D. Sontag

Predicting Odor Pleasantness with an Electronic Nose

Rafi Haddad, Abebe Medhanie, Yehudah Roth, David Harel, Noam Sobel

Flow-Based Cytometric Analysis of Cell Cycle via Simulated Cell Populations

M. Rowan Brown, Huw D. Summers, Paul Rees, Paul J. Smith, Sally C. Chappell, Rachel J. Errington

Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets

Manikandan Narayanan, Adrian Vetta, Eric E. Schadt, Jun Zhu

Prediction of Co-Receptor Usage of HIV-1 from Genotype

J. Nikolaj Dybowski, Dominik Heider, Daniel Hoffmann

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

Sridhar Ranganathan, Patrick F. Suthers, Costas D. Maranas

A Multi-Variant, Viral Dynamic Model of Genotype 1 HCV to Assess the in vivo Evolution of Protease-Inhibitor Resistant Variants

Bambang S. Adiwijaya, Eva Herrmann, Brian Hare, Tara Kieffer, Chao Lin, Ann D. Kwong, Varun Garg, John C. R. Randle, Christoph Sarrazin, Stefan Zeuzem, Paul R. Caron

Dynamics and Control of Diseases in Networks with Community Structure

Marcel Salathé, James H. Jones

New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach

Enrico Petretto, Leonardo Bottolo, Sarah R. Langley, Matthias Heinig, Chris McDermott-Roe, Rizwan Sarwar, Michal Pravenec, Norbert Hübner, Timothy J. Aitman, Stuart A. Cook, Sylvia Richardson

Signatures of Arithmetic Simplicity in Metabolic Network Architecture

William J. Riehl, Paul L. Krapivsky, Sidney Redner, Daniel Segrè

The Origins of Time-Delay in Template Biopolymerization Processes

Luis Mier-y-Terán-Romero, Mary Silber, Vassily Hatzimanikatis

Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling

Petras J. Kundrotas, Ilya A. Vakser

Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes

Aleksej Zelezniak, Tune H. Pers, Simão Soares, Mary Elizabeth Patti, Kiran Raosaheb Patil

Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis

Younghee Lee, Xinan Yang, Yong Huang, Hanli Fan, Qingbei Zhang, Youngfei Wu, Jianrong Li, Rifat Hasina, Chao Cheng, Mark W. Lingen, Mark B. Gerstein, Ralph R. Weichselbaum, H. Rosie Xing, Yves A. Lussier

A Stevedore's Protein Knot

Daniel Bölinger, Joanna I. Sułkowska, Hsiao-Ping Hsu, Leonid A. Mirny, Mehran Kardar, José N. Onuchic, Peter Virnau

Why Genes Evolve Faster on Secondary Chromosomes in Bacteria

Vaughn S. Cooper, Samuel H. Vohr, Sarah C. Wrocklage, Philip J. Hatcher