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Table of Contents: August 2017

Microbiome data exhibit rich temporal and phylogenetic structure especially following perturbations. The leaves of the central phylogenetic tree correspond to individual bacterial species, while the lines that radiate out from it represent their abundances over time. Color gives a sense of phylogenetic relationships, while the heights of bars at the base of these lines corresponds to the coefficients of a tree-aware discriminant analysis (treeDA) applied to a study of a perturbation of the human gut microbiome. Fukuyama et al.

Image Credit: Fukuyama et al.

Editorials

Ten simple rules for getting the most out of a summer laboratory internship

Toby P. Aicher, Dániel L. Barabási, Benjamin D. Harris, Ajay Nadig, Kaitlin L. Williams

Ten simple rules to initiate and run a postdoctoral association

Chiara Bruckmann, Endre Sebestyén

Education

The application of project-based learning in bioinformatics training

Laura R. Emery, Sarah L. Morgan

Research Articles

Mouth-clicks used by blind expert human echolocators – signal description and model based signal synthesis

Lore Thaler, Galen M. Reich, Xinyu Zhang, Dinghe Wang, Graeme E. Smith, Zeng Tao, Raja Syamsul Azmir Bin. Raja Abdullah, Mikhail Cherniakov, Christopher J. Baker, Daniel Kish, Michail Antoniou

HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes

Idan Alter, Loren Gragert, Stephanie Fingerson, Martin Maiers, Yoram Louzoun

A method of determining where to target surveillance efforts in heterogeneous epidemiological systems

Alexander J. Mastin, Frank van den Bosch, Timothy R. Gottwald, Vasthi Alonso Chavez, Stephen R. Parnell

Noise correlations in the human brain and their impact on pattern classification

Vikranth R. Bejjanki, Rava Azeredo da Silveira, Jonathan D. Cohen, Nicholas B. Turk-Browne

Robust averaging protects decisions from noise in neural computations

Vickie Li, Santiago Herce Castañón, Joshua A. Solomon, Hildward Vandormael, Christopher Summerfield

From homeostasis to behavior: Balanced activity in an exploration of embodied dynamic environmental-neural interaction

Peter John Hellyer, Claudia Clopath, Angie A. Kehagia, Federico E. Turkheimer, Robert Leech

Data driven flexible backbone protein design

Mark G. F. Sun, Philip M. Kim

Spread of hospital-acquired infections: A comparison of healthcare networks

Narimane Nekkab, Pascal Astagneau, Laura Temime, Pascal Crépey

Histologic and biochemical alterations predict pulmonary mechanical dysfunction in aging mice with chronic lung inflammation

Christopher B. Massa, Angela M. Groves, Smita U. Jaggernauth, Debra L. Laskin, Andrew J. Gow

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity

Michal Bassani-Sternberg, Chloé Chong, Philippe Guillaume, Marthe Solleder, HuiSong Pak, Philippe O. Gannon, Lana E. Kandalaft, George Coukos, David Gfeller

Temperature manipulation of neuronal dynamics in a forebrain motor control nucleus

Matías A. Goldin, Gabriel B. Mindlin

Host population structure impedes reversion to drug sensitivity after discontinuation of treatment

Jonas I. Liechti, Gabriel E. Leventhal, Sebastian Bonhoeffer

Spatial dynamics of synthetic microbial mutualists and their parasites

Daniel R. Amor, Raúl Montañez, Salva Duran-Nebreda, Ricard Solé

Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock

Wesley M. Botello-Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jerome J. Lacroix, Jijun Hao, Yun Luo

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb

Remo Monti, Iros Barozzi, Marco Osterwalder, Elizabeth Lee, Momoe Kato, Tyler H. Garvin, Ingrid Plajzer-Frick, Catherine S. Pickle, Jennifer A. Akiyama, Veena Afzal, Niko Beerenwinkel, Diane E. Dickel, Axel Visel, Len A. Pennacchio

Neuron’s eye view: Inferring features of complex stimuli from neural responses

Xin Chen, Jeffrey M. Beck, John M. Pearson

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A. Relman, Susan P. Holmes

Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach

Elsje Pienaar, Jansy Sarathy, Brendan Prideaux, Jillian Dietzold, Véronique Dartois, Denise E. Kirschner, Jennifer J. Linderman

An optimal strategy for epilepsy surgery: Disruption of the rich-club?

Marinho A. Lopes, Mark P. Richardson, Eugenio Abela, Christian Rummel, Kaspar Schindler, Marc Goodfellow, John R. Terry

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

Maike K. Aurich, Ronan M. T. Fleming, Ines Thiele

Confirmation bias in human reinforcement learning: Evidence from counterfactual feedback processing

Stefano Palminteri, Germain Lefebvre, Emma J. Kilford, Sarah-Jayne Blakemore

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio

A stochastic-field description of finite-size spiking neural networks

Grégory Dumont, Alexandre Payeur, André Longtin

Multi-scale approaches for high-speed imaging and analysis of large neural populations

Johannes Friedrich, Weijian Yang, Daniel Soudry, Yu Mu, Misha B. Ahrens, Rafael Yuste, Darcy S. Peterka, Liam Paninski

Measuring distance through dense weighted networks: The case of hospital-associated pathogens

Tjibbe Donker, Timo Smieszek, Katherine L. Henderson, Alan P. Johnson, A. Sarah Walker, Julie V. Robotham

Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype

Eilon Sharon, Hao Shi, Sandhya Kharbanda, Winston Koh, Lance R. Martin, Kiran K. Khush, Hannah Valantine, Jonathan K. Pritchard, Iwijn De Vlaminck

Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network

Jinyuan Yan, Maxime Deforet, Kerry E. Boyle, Rayees Rahman, Raymond Liang, Chinweike Okegbe, Lars E. P. Dietrich, Weigang Qiu, Joao B. Xavier

The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades

Eduardo A. Aponte, Dario Schöbi, Klaas E. Stephan, Jakob Heinzle

Rearrangement moves on rooted phylogenetic networks

Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi, Celine Scornavacca