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Table of Contents: October 2018

Redox reactions define the energetic constraints within which life exists. However, measurements of reduction potentials are scarce and current prediction methods fall short of desired accuracy and coverage. We harness quantum chemistry to enable the high-throughput prediction of reduction potentials with unparalleled accuracy. We calculate the reduction potentials of all redox pairs that can be generated using known biochemical compounds. This high-resolution dataset reveals global trends in metabolism - including the differences between and within oxidoreductase groups - and optimality principles that explain the redox potential of NAD(P). The cover figure depicts the predicted reversibility of the reaction converting shikimate to 3-dehydroshikimate.

Image Credit: Benjamin Sanchez-Lengeling

Editorials

Ten simple rules for scientists: Improving your writing productivity

Todd C. Peterson, Sofie R. Kleppner, Crystal M. Botham

Ten simple rules when considering retirement

Philip E. Bourne

Education Articles

Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor

Richard A. Erickson, Michael N. Fienen, S. Grace McCalla, Emily L. Weiser, Melvin L. Bower, Jonathan M. Knudson, Greg Thain

Ten quick tips for getting the most scientific value out of numerical data

Lars Ole Schwen, Sabrina Rueschenbaum

Perspective

What to know before forecasting the flu

Prithwish Chakraborty, Bryan Lewis, Stephen Eubank, John S. Brownstein, Madhav Marathe, Naren Ramakrishnan

Research Articles

Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine

Francisco Y. Cai, Thomas Fussell, Sarah Cobey, Marc Lipsitch

Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data

Fabian A. Soto, Lauren E. Vucovich, F. Gregory Ashby

Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing

Michael F. Staddon, Dapeng Bi, A. Pasha Tabatabai, Visar Ajeti, Michael P. Murrell, Shiladitya Banerjee

Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design

Andreas Handel, Yan Li, Brian McKay, Kasia A. Pawelek, Veronika Zarnitsyna, Rustom Antia

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays

Sahar Gelfman, Quanli Wang, Yi-Fan Lu, Diana Hall, Christopher D. Bostick, Ryan Dhindsa, Matt Halvorsen, K. Melodi McSweeney, Ellese Cotterill, Tom Edinburgh, Michael A. Beaumont, Wayne N. Frankel, Slavé Petrovski, Andrew S. Allen, Michael J. Boland, David B. Goldstein, Stephen J. Eglen

A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons

Andreas Solbrå, Aslak Wigdahl Bergersen, Jonas van den Brink, Anders Malthe-Sørenssen, Gaute T. Einevoll, Geir Halnes

Noise propagation in an integrated model of bacterial gene expression and growth

Istvan T. Kleijn, Laurens H. J. Krah, Rutger Hermsen

Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals

Iksoo Huh, Isabel Mendizabal, Taesung Park, Soojin V. Yi

Interactive reservoir computing for chunking information streams

Toshitake Asabuki, Naoki Hiratani, Tomoki Fukai

In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability

Vasileios Vavourakis, Triantafyllos Stylianopoulos, Peter A. Wijeratne

Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function

Robin Moss, Frank B. Sachse, Eloy G. Moreno-Galindo, Ricardo A. Navarro-Polanco, Martin Tristani-Firouzi, Gunnar Seemann

Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells

Ernest C. Y. Ho, Juan Nicolas Malagón, Abha Ahuja, Rama Singh, Ellen Larsen

Seizure pathways: A model-based investigation

Philippa J. Karoly, Levin Kuhlmann, Daniel Soudry, David B. Grayden, Mark J. Cook, Dean R. Freestone

Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern

Huy Tran, Jonathan Desponds, Carmina Angelica Perez Romero, Mathieu Coppey, Cecile Fradin, Nathalie Dostatni, Aleksandra M. Walczak

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Joseph A. Lombardo, Matthew V. Macellaio, Bing Liu, Stephanie E. Palmer, Leslie C. Osborne

Internal but not external noise frees working memory resources

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Predicting B cell receptor substitution profiles using public repertoire data

Amrit Dhar, Kristian Davidsen, Frederick A. Matsen IV, Vladimir N. Minin

Genomic data integration systematically biases interactome mapping

Michael A. Skinnider, R. Greg Stacey, Leonard J. Foster

Data-driven brain network models differentiate variability across language tasks

Kanika Bansal, John D. Medaglia, Danielle S. Bassett, Jean M. Vettel, Sarah F. Muldoon

A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas

Maximilian Schmidt, Rembrandt Bakker, Kelly Shen, Gleb Bezgin, Markus Diesmann, Sacha Jennifer van Albada

Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques

Dominik Wodarz, Pamela J. Skinner, David N. Levy, Elizabeth Connick

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Hao Wang, Simonas Marcišauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Agren, Jens Nielsen, Eduard J. Kerkhoven

Predicting how and when hidden neurons skew measured synaptic interactions

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Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents

Sandra Giuliani, Arthur C. Silva, Joyce V. V. B. Borba, Pablo I. P. Ramos, Ross A. Paveley, Eugene N. Muratov, Carolina Horta Andrade, Nicholas Furnham

An agent-based model for drug-radiation interactions in the tumour microenvironment: Hypoxia-activated prodrug SN30000 in multicellular tumour spheroids

Xinjian Mao, Sarah McManaway, Jagdish K. Jaiswal, Priyanka B. Patel, William R. Wilson, Kevin O. Hicks, Gib Bogle

Quantum chemistry reveals thermodynamic principles of redox biochemistry

Adrian Jinich, Avi Flamholz, Haniu Ren, Sung-Jin Kim, Benjamin Sanchez-Lengeling, Charles A. R. Cotton, Elad Noor, Alán Aspuru-Guzik, Arren Bar-Even

Dilution and titration of cell-cycle regulators may control cell size in budding yeast

Frank S. Heldt, Reece Lunstone, John J. Tyson, Béla Novák

Modeling sensory-motor decisions in natural behavior

Ruohan Zhang, Shun Zhang, Matthew H. Tong, Yuchen Cui, Constantin A. Rothkopf, Dana H. Ballard, Mary M. Hayhoe

Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)

Ying-Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing-Ke Weng, Yi Wang

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data

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Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions

Scott W. Simpkins, Justin Nelson, Raamesh Deshpande, Sheena C. Li, Jeff S. Piotrowski, Erin H. Wilson, Abraham A. Gebre, Hamid Safizadeh, Reika Okamoto, Mami Yoshimura, Michael Costanzo, Yoko Yashiroda, Yoshikazu Ohya, Hiroyuki Osada, Minoru Yoshida, Charles Boone, Chad L. Myers

Modeling and subtleties of K-Ras and Calmodulin interaction

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Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase

Daniel S. Moore, Conor Brines, Heather Jewhurst, John P. Dalton, Irina G. Tikhonova

A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments

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Correction

Correction: Elucidation of molecular kinetic schemes from macroscopic traces using system identification

Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina

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