Table of Contents: October 2012

Integrating metabolic networks at the cellular scale into physiologically based pharmacokinetic models at the organism level allows the mechanistic description of drug action, pathogenesis, or adverse events across multiple layers of biological organization. Such multiscale approaches therefore provide the opportunity for novel rational approaches in medical diagnostics and pharmaceutical drug development. The figure illustrates a schematic overview of the approach used in Krauss et al.

Image Credit: Stephan Schaller, Markus Krauss, and Lars Kuepfer.

Research Articles

Predictive Dynamics of Human Pain Perception

Guillermo A. Cecchi, Lejian Huang, Javeria Ali Hashmi, Marwan Baliki, María V. Centeno, Irina Rish, A. Vania Apkarian

How Recent History Affects Perception: The Normative Approach and Its Heuristic Approximation

Ofri Raviv, Merav Ahissar, Yonatan Loewenstein

Next-Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency

Maria Ximena Sosa, I. K. Ashok Sivakumar, Samantha Maragh, Vamsi Veeramachaneni, Ramesh Hariharan, Minothi Parulekar, Karin M. Fredrikson, Timothy T. Harkins, Jeffrey Lin, Andrew B. Feldman, Pramila Tata, Georg B. Ehret, Aravinda Chakravarti

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

Steven W. Kembel, Martin Wu, Jonathan A. Eisen, Jessica L. Green

Emergence of the Mitochondrial Reticulum from Fission and Fusion Dynamics

Valerii M. Sukhorukov, Daniel Dikov, Andreas S. Reichert, Michael Meyer-Hermann

Integrating Cellular Metabolism into a Multiscale Whole-Body Model

Markus Krauss, Stephan Schaller, Steffen Borchers, Rolf Findeisen, Jörg Lippert, Lars Kuepfer

Multiple Spike Time Patterns Occur at Bifurcation Points of Membrane Potential Dynamics

J. Vincent Toups, Jean-Marc Fellous, Peter J. Thomas, Terrence J. Sejnowski, Paul H. Tiesinga

Osteoprotegerin in Bone Metastases: Mathematical Solution to the Puzzle

Marc D. Ryser, Yiding Qu, Svetlana V. Komarova

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor, Jiri Damborsky

Spatially Pooled Contrast Responses Predict Neural and Perceptual Similarity of Naturalistic Image Categories

Iris I. A. Groen, Sennay Ghebreab, Victor A. F. Lamme, H. Steven Scholte

The Dynamics of Naturally Acquired Immunity to Plasmodium falciparum Infection

Mykola Pinkevych, Janka Petravic, Kiprotich Chelimo, James W. Kazura, Ann M. Moormann, Miles P. Davenport

Estimating the Hidden Burden of Bovine Tuberculosis in Great Britain

Andrew J. K. Conlan, Trevelyan J. McKinley, Katerina Karolemeas, Ellen Brooks Pollock, Anthony V. Goodchild, Andrew P. Mitchell, Colin P. D. Birch, Richard S. Clifton-Hadley, James L. N. Wood

Linkers of Cell Polarity and Cell Cycle Regulation in the Fission Yeast Protein Interaction Network

Federico Vaggi, James Dodgson, Archana Bajpai, Anatole Chessel, Ferenc Jordán, Masamitsu Sato, Rafael Edgardo Carazo-Salas, Attila Csikász-Nagy

The Laminar Cortex Model: A New Continuum Cortex Model Incorporating Laminar Architecture

Jiaxin Du, Viktor Vegh, David C. Reutens

Membrane-Elasticity Model of Coatless Vesicle Budding Induced by ESCRT Complexes

Bartosz Różycki, Evzen Boura, James H. Hurley, Gerhard Hummer

A Structural Systems Biology Approach for Quantifying the Systemic Consequences of Missense Mutations in Proteins

Tammy M. K. Cheng, Lucas Goehring, Linda Jeffery, Yu-En Lu, Jacqueline Hayles, Béla Novák, Paul A. Bates

Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation

Elsa W. Birch, Nicholas A. Ruggero, Markus W. Covert

Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations

Noah S. Bieler, Tuomas P. J. Knowles, Daan Frenkel, Robert Vácha

Discovering Relations Between Mind, Brain, and Mental Disorders Using Topic Mapping

Russell A. Poldrack, Jeanette A. Mumford, Tom Schonberg, Donald Kalar, Bishal Barman, Tal Yarkoni

Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task

Hang Zhang, Camille Morvan, Louis-Alexandre Etezad-Heydari, Laurence T. Maloney

Functional Modules, Structural Topology, and Optimal Activity in Metabolic Networks

Osbaldo Resendis-Antonio, Magdalena Hernández, Yolanda Mora, Sergio Encarnación

Modeling Dynamic Regulatory Processes in Stroke

Jason E. McDermott, Kenneth Jarman, Ronald Taylor, Mary Lancaster, Harish Shankaran, Keri B. Vartanian, Susan L. Stevens, Mary P. Stenzel-Poore, Antonio Sanfilippo

Prediction and Dissection of Widely-Varying Association Rate Constants of Actin-Binding Proteins

Xiaodong Pang, Kenneth H. Zhou, Sanbo Qin, Huan-Xiang Zhou

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

Vladimir Vacic, Phineus R. L. Markwick, Christopher J. Oldfield, Xiaoyue Zhao, Chad Haynes, Vladimir N. Uversky, Lilia M. Iakoucheva

Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors

Samuel Murail, Rebecca J. Howard, Torben Broemstrup, Edward J. Bertaccini, R. Adron Harris, James R. Trudell, Erik Lindahl

Random Field Model Reveals Structure of the Protein Recombinational Landscape

Philip A. Romero, Frances H. Arnold

A Model of Reward- and Effort-Based Optimal Decision Making and Motor Control

Lionel Rigoux, Emmanuel Guigon