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Table of Contents: September 2017

Villoutreix and colleagues report a new approach to data fusion in studies of developmental dynamics and use it to reconstruct multivariable dynamics of a patterning cascade in the early Drosophila embryo. The image shows an optical cross-section of the embryo during the 3rd hour of development. Villoutreix et al.

Image Credit: Bomyi Lim

Editorials

Ten simple rules for structuring papers

Brett Mensh, Konrad Kording

Ten simple rules for developing a mentor–mentee expectations document

Kristyn S. Masters, Pamela K. Kreeger

Ten simple rules for successfully completing a graduate degree in Latin America

Ernesto Ruelas Inzunza, Gabriela I. Salazar-Rivera, Magdiel Láinez, María Guadalupe Ruiz-Gómez, Carlo A. Domínguez-Eusebio, Griselda Cristóbal-Sánchez, Issaac A. Teodosio Faustino, Edel Pérez-López, Meagan L. Campbell, Marcus Vinicius Merfa, Ivonne Tatiana Latorre Beltrán, Fernanda Armas, Claudio Mota-Vargas

How can computation advance microbiome research?

Ruth Nussinov, Jason A. Papin

Education

The eBioKit, a stand-alone educational platform for bioinformatics

Rafael Hernández-de-Diego, Etienne P. de Villiers, Tomas Klingström, Hadrien Gourlé, Ana Conesa, Erik Bongcam-Rudloff

Research Articles

Multi-layer network utilizing rewarded spike time dependent plasticity to learn a foraging task

Pavel Sanda, Steven Skorheim, Maxim Bazhenov

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect

Chiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans Victor Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina

Exploiting ecology in drug pulse sequences in favour of population reduction

Marianne Bauer, Isabella R. Graf, Vudtiwat Ngampruetikorn, Greg J. Stephens, Erwin Frey

Interactions between the tumor and the blood systemic response of breast cancer patients

Vanessa Dumeaux, Bjørn Fjukstad, Hans E. Fjosne, Jan-Ole Frantzen, Marit Muri Holmen, Enno Rodegerdts, Ellen Schlichting, Anne-Lise Børresen-Dale, Lars Ailo Bongo, Eiliv Lund, Michael Hallett

Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence

Michiel van Boven, Jan van de Kassteele, Marjolein J. Korndewal, Christiaan H. van Dorp, Mirjam Kretzschmar, Fiona van der Klis, Hester E. de Melker, Ann C. Vossen, Debbie van Baarle

Correlated receptor transport processes buffer single-cell heterogeneity

Stefan M. Kallenberger, Anne L. Unger, Stefan Legewie, Konstantinos Lymperopoulos, Ursula Klingmüller, Roland Eils, Dirk-Peter Herten

Predictive representations can link model-based reinforcement learning to model-free mechanisms

Evan M. Russek, Ida Momennejad, Matthew M. Botvinick, Samuel J. Gershman, Nathaniel D. Daw

Force encoding in muscle spindles during stretch of passive muscle

Kyle P. Blum, Boris Lamotte D’Incamps, Daniel Zytnicki, Lena H. Ting

Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem

Cai Wingfield, Li Su, Xunying Liu, Chao Zhang, Phil Woodland, Andrew Thwaites, Elisabeth Fonteneau, William D. Marslen-Wilson

Altering neuronal excitability to preserve network connectivity in a computational model of Alzheimer's disease

Willem de Haan, Elisabeth C. W. van Straaten, Alida A. Gouw, Cornelis J. Stam

Phase changes in neuronal postsynaptic spiking due to short term plasticity

Mark D. McDonnell, Bruce P. Graham

Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer

Shyam Kumar Sudhakar, Sungho Hong, Ivan Raikov, Rodrigo Publio, Claus Lang, Thomas Close, Daqing Guo, Mario Negrello, Erik De Schutter

The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs

Jean-Louis Dinh, Etienne Farcot, Charlie Hodgman

C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis

Kaido Lepik, Tarmo Annilo, Viktorija Kukuškina, eQTLGen Consortium, Kai Kisand, Zoltán Kutalik, Pärt Peterson, Hedi Peterson

Synthesizing developmental trajectories

Paul Villoutreix, Joakim Andén, Bomyi Lim, Hang Lu, Ioannis G. Kevrekidis, Amit Singer, Stanislav Y. Shvartsman

Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

Alexey A. Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal

Reconstructing promoter activity from Lux bioluminescent reporters

Mudassar Iqbal, Neil Doherty, Anna M. L. Page, Saara N. A. Qazi, Ishan Ajmera, Peter A. Lund, Theodore Kypraios, David J. Scott, Philip J. Hill, Dov J. Stekel

Probing eukaryotic cell mechanics via mesoscopic simulations

Kirill Lykov, Yasaman Nematbakhsh, Menglin Shang, Chwee Teck Lim, Igor V. Pivkin

Quantifying the effects of antiangiogenic and chemotherapy drug combinations on drug delivery and treatment efficacy

Sirin Yonucu, Defne Yιlmaz, Colin Phipps, Mehmet Burcin Unlu, Mohammad Kohandel

Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies

Burcu Tepekule, Hildegard Uecker, Isabel Derungs, Antoine Frenoy, Sebastian Bonhoeffer

Stochastic principles governing alternative splicing of RNA

Jianfei Hu, Eli Boritz, William Wylie, Daniel C. Douek

Analysis of the relationship between coexpression domains and chromatin 3D organization

María E. Soler-Oliva, José A. Guerrero-Martínez, Valentina Bachetti, José C. Reyes

Projecting social contact matrices in 152 countries using contact surveys and demographic data

Kiesha Prem, Alex R. Cook, Mark Jit

Cost-efficient vaccination protocols for network epidemiology

Petter Holme, Nelly Litvak

Exploring the inhibition mechanism of adenylyl cyclase type 5 by n-terminal myristoylated Gαi1

Siri Camee van Keulen, Ursula Rothlisberger

Mobility can promote the evolution of cooperation via emergent self-assortment dynamics

Jaideep Joshi, Iain D Couzin, Simon A Levin, Vishwesha Guttal

Population FBA predicts metabolic phenotypes in yeast

Piyush Labhsetwar, Marcelo C. R. Melo, John A. Cole, Zaida Luthey-Schulten

Two passive mechanical conditions modulate power generation by the outer hair cells

Yanju Liu, Sheryl M. Gracewski, Jong-Hoon Nam

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity

Kevin D. Murray, Christfried Webers, Cheng Soon Ong, Justin Borevitz, Norman Warthmann

DeepPep: Deep proteome inference from peptide profiles

Minseung Kim, Ameen Eetemadi, Ilias Tagkopoulos

Estimating short-term synaptic plasticity from pre- and postsynaptic spiking

Abed Ghanbari, Aleksey Malyshev, Maxim Volgushev, Ian H. Stevenson

A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms

Pietro Balbi, Paolo Massobrio, Jeanette Hellgren Kotaleski

A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells

Richard B. Greaves, Sabine Dietmann, Austin Smith, Susan Stepney, Julianne D. Halley