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Table of Contents

December 2015

Plesiosaurs maintained the same basic four-flipper body plan across their 135 million year history, yet there is no modern-day swimmer with a similar flipper arrangement. Numerous proposals have been made about the motions of their flippers during swimming. This computer-generated image shows the 3D model of Meyerasaurus victor that was used to study plesiosaur swimming. Thousands of different periodic motions of the flippers were tried using computer simulation. Numerical optimization determined that the fastest swimming motion uses the front flippers in an underwater flight stroke, and that the back flippers could not substantially contribute to forward motion. Turk et al.

Image Credit: Shiqiu Liu

Review

Locust Collective Motion and Its Modeling

Gil Ariel, Amir Ayali

Research Articles

The Effect of Farmers’ Decisions on Pest Control with Bt Crops: A Billion Dollar Game of Strategy

Alice E. Milne, James R. Bell, William D. Hutchison, Frank van den Bosch, Paul D. Mitchell, David Crowder, Stephen Parnell, Andrew P. Whitmore

Complete Firing-Rate Response of Neurons with Complex Intrinsic Dynamics

Maximilian Puelma Touzel, Fred Wolf

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set

Matthew Hall, Mark Woolhouse, Andrew Rambaut

Where’s the Noise? Key Features of Spontaneous Activity and Neural Variability Arise through Learning in a Deterministic Network

Christoph Hartmann, Andreea Lazar, Bernhard Nessler, Jochen Triesch

Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction

Tatjana Braun, Julia Koehler Leman, Oliver F. Lange

Clustered Desynchronization from High-Frequency Deep Brain Stimulation

Dan Wilson, Jeff Moehlis

Capabilities and Limitations of Tissue Size Control through Passive Mechanical Forces

Jochen Kursawe, Pavel A. Brodskiy, Jeremiah J. Zartman, Ruth E. Baker, Alexander G. Fletcher

Formation and Maintenance of Robust Long-Term Information Storage in the Presence of Synaptic Turnover

Michael Fauth, Florentin Wörgötter, Christian Tetzlaff

Multistability in Large Scale Models of Brain Activity

Mathieu Golos, Viktor Jirsa, Emmanuel Daucé

Modeling the Slow CD4+ T Cell Decline in HIV-Infected Individuals

Sunpeng Wang, Patricia Hottz, Mauro Schechter, Libin Rong

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis

Wei Zhang, Jae-Woong Chang, Lilong Lin, Kay Minn, Baolin Wu, Jeremy Chien, Jeongsik Yong, Hui Zheng, Rui Kuang

Elastohydrodynamics and Kinetics of Protein Patterning in the Immunological Synapse

Andreas Carlson, L. Mahadevan

Distinctive Behaviors of Druggable Proteins in Cellular Networks

Costas Mitsopoulos, Amanda C. Schierz, Paul Workman, Bissan Al-Lazikani

The Role of Symmetric Stem Cell Divisions in Tissue Homeostasis

Jienian Yang, Maksim V. Plikus, Natalia L. Komarova

Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks

Henrik Ronellenfitsch, Jana Lasser, Douglas C. Daly, Eleni Katifori

How Obstacles Perturb Population Fronts and Alter Their Genetic Structure

Wolfram Möbius, Andrew W. Murray, David R. Nelson

Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population

Taina T. Immonen, Jessica M. Conway, Ethan O. Romero-Severson, Alan S. Perelson, Thomas Leitner

Sources of Variability in a Synthetic Gene Oscillator

Alan Veliz-Cuba, Andrew J. Hirning, Adam A. Atanas, Faiza Hussain, Flavia Vancia, Krešimir Josić, Matthew R. Bennett

Cultured Cortical Neurons Can Perform Blind Source Separation According to the Free-Energy Principle

Takuya Isomura, Kiyoshi Kotani, Yasuhiko Jimbo

Defectors Can Create Conditions That Rescue Cooperation

Adam James Waite, Caroline Cannistra, Wenying Shou

Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

R. Gonzalo Parra, Rocío Espada, Nina Verstraete, Diego U. Ferreiro

Coherent Motion of Monolayer Sheets under Confinement and Its Pathological Implications

S S Soumya, Animesh Gupta, Andrea Cugno, Luca Deseri, Kaushik Dayal, Dibyendu Das, Shamik Sen, Mandar M. Inamdar

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

James Kaminski, Molly K. Gibson, Eric A. Franzosa, Nicola Segata, Gautam Dantas, Curtis Huttenhower

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer

Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan

Computer Simulations Imply Forelimb-Dominated Underwater Flight in Plesiosaurs

Shiqiu Liu, Adam S. Smith, Yuting Gu, Jie Tan, C. Karen Liu, Greg Turk

The Essential Complexity of Auditory Receptive Fields

Ivar L. Thorson, Jean Liénard, Stephen V. David

Dynamic Network Drivers of Seizure Generation, Propagation and Termination in Human Neocortical Epilepsy

Ankit N. Khambhati, Kathryn A. Davis, Brian S. Oommen, Stephanie H. Chen, Timothy H. Lucas, Brian Litt, Danielle S. Bassett

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

Zhichao Miao, Eric Westhof

Modeling Fatty Acid Transfer from Artery to Cardiomyocyte

Theo Arts, Robert S. Reneman, James B. Bassingthwaighte, Ger J. van der Vusse

Operational Principles for the Dynamics of the In Vitro ParA-ParB System

Lavisha Jindal, Eldon Emberly

Computing the Local Field Potential (LFP) from Integrate-and-Fire Network Models

Alberto Mazzoni, Henrik Lindén, Hermann Cuntz, Anders Lansner, Stefano Panzeri, Gaute T. Einevoll

MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures

Fabiana A. Caetano, Brennan S. Dirk, Joshua H. K. Tam, P. Craig Cavanagh, Maria Goiko, Stephen S. G. Ferguson, Stephen H. Pasternak, Jimmy D. Dikeakos, John R. de Bruyn, Bryan Heit

The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects

Piotr J. Kamola, Yuko Nakano, Tomoko Takahashi, Paul A. Wilson, Kumiko Ui-Tei

Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics

Akli Ben Imeddourene, Ahmad Elbahnsi, Marc Guéroult, Christophe Oguey, Nicolas Foloppe, Brigitte Hartmann

Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations

Frances Hutchings, Cheol E. Han, Simon S. Keller, Bernd Weber, Peter N. Taylor, Marcus Kaiser

Model-Based Evaluation of Spontaneous Tumor Regression in Pilocytic Astrocytoma

Thomas Buder, Andreas Deutsch, Barbara Klink, Anja Voss-Böhme

Text Mining for Protein Docking

Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser

Morphological and Stress Vulnerability Indices for Human Coronary Plaques and Their Correlations with Cap Thickness and Lipid Percent: An IVUS-Based Fluid-Structure Interaction Multi-patient Study

Liang Wang, Jie Zheng, Akiko Maehara, Chun Yang, Kristen L. Billiar, Zheyang Wu, Richard Bach, David Muccigrosso, Gary S. Mintz, Dalin Tang

Biases in Visual, Auditory, and Audiovisual Perception of Space

Brian Odegaard, David R. Wozny, Ladan Shams

Protein Connectivity in Chemotaxis Receptor Complexes

Stephan Eismann, Robert G. Endres

Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation

Brenda N. Vo, Christopher C. Drovandi, Anthony N. Pettitt, Graeme J. Pettet

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

István Bartha, Antonio Rausell, Paul J. McLaren, Pejman Mohammadi, Manuel Tardaguila, Nimisha Chaturvedi, Jacques Fellay, Amalio Telenti

MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells

Richard Moore, Hsu Kiang Ooi, Taek Kang, Leonidas Bleris, Lan Ma

Gene Expression Switching of Receptor Subunits in Human Brain Development

Ossnat Bar-Shira, Ronnie Maor, Gal Chechik

Computational Identification of Mechanistic Factors That Determine the Timing and Intensity of the Inflammatory Response

Sridevi Nagaraja, Jaques Reifman, Alexander Y. Mitrophanov

A Functional Cartography of Cognitive Systems

Marcelo G. Mattar, Michael W. Cole, Sharon L. Thompson-Schill, Danielle S. Bassett

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner

Cerebellar Nuclear Neurons Use Time and Rate Coding to Transmit Purkinje Neuron Pauses

Shyam Kumar Sudhakar, Benjamin Torben-Nielsen, Erik De Schutter

Wham: Identifying Structural Variants of Biological Consequence

Zev N. Kronenberg, Edward J. Osborne, Kelsey R. Cone, Brett J. Kennedy, Eric T. Domyan, Michael D. Shapiro, Nels C. Elde, Mark Yandell

Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality

Shree Hari Gautam, Thanh T. Hoang, Kylie McClanahan, Stephen K. Grady, Woodrow L. Shew

Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules

Gregory R. Johnson, Jieyue Li, Aabid Shariff, Gustavo K. Rohde, Robert F. Murphy