Table of Contents: September 2016

A Drosophila epithelium expressing a GFP-tagged form of the morphogen Hedgehog (GFP:Hh, in green). The circles mark a photo-bleached area of the epithelium in a FRAP experiment aimed at determining the Hh effective diffusion coefficient. This coefficient, along with others, was used to parameterize the computational model of the growing eye disc that we developed. The model is based on regulatory interactions that have been experimentally determined and was used to explore how the signaling patterns during development affect the movement of the signaling wave sweeping across the tissue and impact on tissue growth. Fried et al.

Image Credit: Fried et al.

Research Articles

A Thalamocortical Neural Mass Model of the EEG during NREM Sleep and Its Response to Auditory Stimulation

Michael Schellenberger Costa, Arne Weigenand, Hong-Viet V. Ngo, Lisa Marshall, Jan Born, Thomas Martinetz, Jens Christian Claussen

Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration

Anu G. Nair, Upinder S. Bhalla, Jeanette Hellgren Kotaleski

Learning Reward Uncertainty in the Basal Ganglia

John G. Mikhael, Rafal Bogacz

Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection

Mark N. Read, Jacqueline Bailey, Jon Timmis, Tatyana Chtanova

Direct Correlation between Motile Behavior and Protein Abundance in Single Cells

Yann S. Dufour, Sébastien Gillet, Nicholas W. Frankel, Douglas B. Weibel, Thierry Emonet

Related Articles

  1. Correction: Direct Correlation between Motile Behavior and Protein Abundance in Single Cells

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes

Abibatou Mbodj, E. Hilary Gustafson, Lucia Ciglar, Guillaume Junion, Aitor Gonzalez, Charles Girardot, Laurent Perrin, Eileen E. M. Furlong, Denis Thieffry

Inhomogeneity Based Characterization of Distribution Patterns on the Plasma Membrane

Laura Paparelli, Nikky Corthout, Benjamin Pavie, Devin L. Wakefield, Ragna Sannerud, Tijana Jovanovic-Talisman, Wim Annaert, Sebastian Munck

The C. elegans Connectome Consists of Homogenous Circuits with Defined Functional Roles

Aharon Azulay, Eyal Itskovits, Alon Zaslaver

The Statistical Determinants of the Speed of Motor Learning

Kang He, You Liang, Farnaz Abdollahi, Moria Fisher Bittmann, Konrad Kording, Kunlin Wei

Stimulation-Based Control of Dynamic Brain Networks

Sarah Feldt Muldoon, Fabio Pasqualetti, Shi Gu, Matthew Cieslak, Scott T. Grafton, Jean M. Vettel, Danielle S. Bassett

Bipartite Community Structure of eQTLs

John Platig, Peter J. Castaldi, Dawn DeMeo, John Quackenbush

The Computational Properties of a Simplified Cortical Column Model

Nicholas Cain, Ramakrishnan Iyer, Christof Koch, Stefan Mihalas

Uncertainty-Dependent Extinction of Fear Memory in an Amygdala-mPFC Neural Circuit Model

Yuzhe Li, Ken Nakae, Shin Ishii, Honda Naoki

Processing Oscillatory Signals by Incoherent Feedforward Loops

Carolyn Zhang, Ryan Tsoi, Feilun Wu, Lingchong You

A Model of the Spatio-temporal Dynamics of Drosophila Eye Disc Development

Patrick Fried, Máximo Sánchez-Aragón, Daniel Aguilar-Hidalgo, Birgitta Lehtinen, Fernando Casares, Dagmar Iber

SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis

Maria Kogadeeva, Nicola Zamboni

A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains

Florian C. Rieger, Peter Virnau

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

Feixiong Cheng, James L. Murray, Junfei Zhao, Jinsong Sheng, Zhongming Zhao, Donald H. Rubin

A Computational Model of Hepatic Energy Metabolism: Understanding Zonated Damage and Steatosis in NAFLD

William B. Ashworth, Nathan A. Davies, I. David L. Bogle

Gamma Synchronization Influences Map Formation Time in a Topological Model of Spatial Learning

Edward Basso, Mamiko Arai, Yuri Dabaghian

M-Track: A New Software for Automated Detection of Grooming Trajectories in Mice

Sheldon L. Reeves, Kelsey E. Fleming, Lin Zhang, Annalisa Scimemi

Error Correction and the Structure of Inter-Trial Fluctuations in a Redundant Movement Task

Joby John, Jonathan B. Dingwell, Joseph P. Cusumano

Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement

Lars Lau Raket, Britta Grimme, Gregor Schöner, Christian Igel, Bo Markussen

In Silico Oncology: Quantification of the In Vivo Antitumor Efficacy of Cisplatin-Based Doublet Therapy in Non-Small Cell Lung Cancer (NSCLC) through a Multiscale Mechanistic Model

Eleni Kolokotroni, Dimitra Dionysiou, Christian Veith, Yoo-Jin Kim, Jörg Sabczynski, Astrid Franz, Aleksandar Grgic, Jan Palm, Rainer M. Bohle, Georgios Stamatakos

Forecasting Human African Trypanosomiasis Prevalences from Population Screening Data Using Continuous Time Models

Harwin de Vries, Albert P. M. Wagelmans, Epco Hasker, Crispin Lumbala, Pascal Lutumba, Sake J. de Vlas, Joris van de Klundert

Immersed Boundary Models for Quantifying Flow-Induced Mechanical Stimuli on Stem Cells Seeded on 3D Scaffolds in Perfusion Bioreactors

Yann Guyot, Bart Smeets, Tim Odenthal, Ramesh Subramani, Frank P. Luyten, Herman Ramon, Ioannis Papantoniou, Liesbet Geris

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline

Hao Chen, Mai Chan Lau, Michael Thomas Wong, Evan W. Newell, Michael Poidinger, Jinmiao Chen

Template-Based Modeling of Protein-RNA Interactions

Jinfang Zheng, Petras J. Kundrotas, Ilya A. Vakser, Shiyong Liu

Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics

Naveen K. Vaidya, Ruy M. Ribeiro, Alan S. Perelson, Anil Kumar

A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects

Jeanette Prinz, Ingo Vogt, Gianluca Adornetto, Mónica Campillos

Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction

Noam Auslander, Allon Wagner, Matthew Oberhardt, Eytan Ruppin

Decreases in Gap Junction Coupling Recovers Ca2+ and Insulin Secretion in Neonatal Diabetes Mellitus, Dependent on Beta Cell Heterogeneity and Noise

Aleena M. Notary, Matthew J. Westacott, Thomas H. Hraha, Marina Pozzoli, Richard K. P. Benninger

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

Nicola De Maio, Chieh-Hsi Wu, Daniel J Wilson

Exome Sequencing and Prediction of Long-Term Kidney Allograft Function

Laurent Mesnard, Thangamani Muthukumar, Maren Burbach, Carol Li, Huimin Shang, Darshana Dadhania, John R. Lee, Vijay K. Sharma, Jenny Xiang, Caroline Suberbielle, Maryvonnick Carmagnat, Nacera Ouali, Eric Rondeau, John J. Friedewald, Michael M. Abecassis, Manikkam Suthanthiran, Fabien Campagne

Adaptive Remodeling of Achilles Tendon: A Multi-scale Computational Model

Stuart R. Young, Bruce Gardiner, Arash Mehdizadeh, Jonas Rubenson, Brian Umberger, David W. Smith

Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation

Carlos S. N. Brito, Wulfram Gerstner

The Edge of Stability: Response Times and Delta Oscillations in Balanced Networks

Grant Gillary, Ernst Niebur

Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems

Alex D. Washburne, Joshua W. Burby, Daniel Lacker