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Table of Contents

March 2016

Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Churakov et al.

Image Credit: Churakov et al.

Message from ISCB

ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing

Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine Orengo, Bruno Gaeta, Scott Markel, Alfonso Valencia

Perspectives

Understanding Genotype-Phenotype Effects in Cancer via Network Approaches

Yoo-Ah Kim, Dong-Yeon Cho, Teresa M. Przytycka

Systems Approaches to the Eukaryotic Stress Response

Christine Vogel

Review

NMR Methods to Study Dynamic Allostery

Sarina Grutsch, Sven Brüschweiler, Martin Tollinger

Research Articles

Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes

Jeffrey J. Sutherland, Robert A. Jolly, Keith M. Goldstein, James L. Stevens

Deep Learning for Population Genetic Inference

Sara Sheehan, Yun S. Song

Modeling the Excess Cell Surface Stored in a Complex Morphology of Bleb-Like Protrusions

Maryna Kapustina, Denis Tsygankov, Jia Zhao, Timothy Wessler, Xiaofeng Yang, Alex Chen, Nathan Roach, Timothy C. Elston, Qi Wang, Ken Jacobson, M. Gregory Forest

Impaired Air Conditioning within the Nasal Cavity in Flat-Faced Homo

Takeshi Nishimura, Futoshi Mori, Sho Hanida, Kiyoshi Kumahata, Shigeru Ishikawa, Kaouthar Samarat, Takako Miyabe-Nishiwaki, Misato Hayashi, Masaki Tomonaga, Juri Suzuki, Tetsuro Matsuzawa, Teruo Matsuzawa

Cellular Growth Arrest and Persistence from Enzyme Saturation

J. Christian J. Ray, Michelle L. Wickersheim, Ameya P. Jalihal, Yusuf O. Adeshina, Tim F. Cooper, Gábor Balázsi

Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases

Nikita Chopra, Thomas E. Wales, Raji E. Joseph, Scott E. Boyken, John R. Engen, Robert L. Jernigan, Amy H. Andreotti

Evolutionary Conserved Positions Define Protein Conformational Diversity

Tadeo E. Saldaño, Alexander M. Monzon, Gustavo Parisi, Sebastian Fernandez-Alberti

Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis

Prakash Chandra Rathi, Alexander Fulton, Karl-Erich Jaeger, Holger Gohlke

Inhibition as a Binary Switch for Excitatory Plasticity in Pyramidal Neurons

Katharina A. Wilmes, Henning Sprekeler, Susanne Schreiber

Noise Expands the Response Range of the Bacillus subtilis Competence Circuit

Andrew Mugler, Mark Kittisopikul, Luke Hayden, Jintao Liu, Chris H. Wiggins, Gürol M. Süel, Aleksandra M. Walczak

Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses

Nicolas Dérian, Bertrand Bellier, Hang Phuong Pham, Eliza Tsitoura, Dorothea Kazazi, Christophe Huret, Penelope Mavromara, David Klatzmann, Adrien Six

Quantitative Analysis of Axonal Branch Dynamics in the Developing Nervous System

Kelsey Chalmers, Elizabeth M. Kita, Ethan K. Scott, Geoffrey J. Goodhill

A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry

Bonnie Nijhof, Anna Castells-Nobau, Louis Wolf, Jolanda M. Scheffer-de Gooyert, Ignacio Monedero, Laura Torroja, Lluis Coromina, Jeroen A. W. M. van der Laak, Annette Schenck

Feedback, Lineages and Self-Organizing Morphogenesis

Sameeran Kunche, Huaming Yan, Anne L. Calof, John S. Lowengrub, Arthur D. Lander

Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search

G. Matthew Fricke, Kenneth A. Letendre, Melanie E. Moses, Judy L. Cannon

Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome

Matthieu Gilson, Ruben Moreno-Bote, Adrián Ponce-Alvarez, Petra Ritter, Gustavo Deco

The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB

Dominique Cadosch, Pia Abel zur Wiesch, Roger Kouyos, Sebastian Bonhoeffer

Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces

Cristiano De Michele, Paolo De Los Rios, Giuseppe Foffi, Francesco Piazza

Causal Inference for Spatial Constancy across Saccades

Jeroen Atsma, Femke Maij, Mathieu Koppen, David E. Irwin, W. Pieter Medendorp

Distinguishing Antimicrobial Models with Different Resistance Mechanisms via Population Pharmacodynamic Modeling

Matthieu Jacobs, Nicolas Grégoire, William Couet, Jurgen B. Bulitta

Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection

Andreas Milias-Argeitis, Ana Paula Oliveira, Luca Gerosa, Laura Falter, Uwe Sauer, John Lygeros

Motor Demands Constrain Cognitive Rule Structures

Anne Gabrielle Eva Collins, Michael Joshua Frank

Dynamic Modelling Reveals ‘Hotspots’ on the Pathway to Enzyme-Substrate Complex Formation

Shane E. Gordon, Daniel K. Weber, Matthew T. Downton, John Wagner, Matthew A. Perugini

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

Andrej Kuritzin, Tabea Kischka, Jürgen Schmitz, Gennady Churakov

Integrating Transgenic Vector Manipulation with Clinical Interventions to Manage Vector-Borne Diseases

Kenichi W. Okamoto, Fred Gould, Alun L. Lloyd

SMOG 2: A Versatile Software Package for Generating Structure-Based Models

Jeffrey K. Noel, Mariana Levi, Mohit Raghunathan, Heiko Lammert, Ryan L. Hayes, José N. Onuchic, Paul C. Whitford

Stability of Ensemble Models Predicts Productivity of Enzymatic Systems

Matthew K. Theisen, Jimmy G. Lafontaine Rivera, James C. Liao

Pathway-Based Genomics Prediction using Generalized Elastic Net

Artem Sokolov, Daniel E. Carlin, Evan O. Paull, Robert Baertsch, Joshua M. Stuart

Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies

Nils Giordano, Francis Mairet, Jean-Luc Gouzé, Johannes Geiselmann, Hidde de Jong

BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data

Lies Boelen, Patrick K. O’Neill, Kathryn J. Quigley, Catherine J. Reynolds, Bernard Maillere, John H. Robinson, Ganjana Lertmemongkolchai, Daniel M. Altmann, Rosemary J. Boyton, Becca Asquith

Annealed Importance Sampling for Neural Mass Models

Will Penny, Biswa Sengupta

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

André Schultz, Amina A. Qutub

Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability

Sam F. Greenbury, Steffen Schaper, Sebastian E. Ahnert, Ard A. Louis

Power-Law Dynamics of Membrane Conductances Increase Spiking Diversity in a Hodgkin-Huxley Model

Wondimu Teka, David Stockton, Fidel Santamaria

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

Ramya Raviram, Pedro P. Rocha, Christian L. Müller, Emily R. Miraldi, Sana Badri, Yi Fu, Emily Swanzey, Charlotte Proudhon, Valentina Snetkova, Richard Bonneau, Jane A. Skok

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

Michael D. Karcher, Julia A. Palacios, Trevor Bedford, Marc A. Suchard, Vladimir N. Minin