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Table of Contents

May 2019

Cover

A Raspberry Pi being set up prior to deployment.
Issue Image

One of the great benefits of the Pi is that its GPIO (General Purpose Input Output) pins can be used to both read and control many peripherals. In this set-up, we see an HD camera, buzzer, a two-line LCD screen and connection to an audio output. This device is being prototyped prior to various read sensors (temperature, humidity, Rf receiver and light level sensors) being added.

Image Credit: Fletcher and Mura.

Editorials

Ten simple rules for carrying out and writing meta-analyses

Diego A. Forero, Sandra Lopez-Leon, Yeimy González-Giraldo, Pantelis G. Bagos

PLOS Computational Biology: published May 16, 2019 | https://doi.org/10.1371/journal.pcbi.1006922

Wisdom of crowds in computational biology

Jason A. Papin, Feilim Mac Gabhann

PLOS Computational Biology: published May 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007032

Education Articles

Ten quick tips for biocuration

Y. Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C. Munoz-Torres, Drashtti V. Vasant, Eleanor Williams, Melissa Haendel

PLOS Computational Biology: published May 2, 2019 | https://doi.org/10.1371/journal.pcbi.1006906

Ten quick tips for using a Raspberry Pi

Anthony C. Fletcher, Cameron Mura

PLOS Computational Biology: published May 2, 2019 | https://doi.org/10.1371/journal.pcbi.1006959

A quick guide for using Microsoft OneNote as an electronic laboratory notebook

Santiago Guerrero, Andrés López-Cortés, Jennyfer M. García-Cárdenas, Pablo Saa, Alberto Indacochea, Isaac Armendáriz-Castillo, Ana Karina Zambrano, Verónica Yumiceba, Andy Pérez-Villa, Patricia Guevara-Ramírez, Oswaldo Moscoso-Zea, Joel Paredes, Paola E. Leone, César Paz-y-Miño

PLOS Computational Biology: published May 9, 2019 | https://doi.org/10.1371/journal.pcbi.1006918

Establishing a computational biology flipped classroom

Phillip Compeau

PLOS Computational Biology: published May 23, 2019 | https://doi.org/10.1371/journal.pcbi.1006764

Perspectives

The statistics of epidemic transitions

John M. Drake, Tobias S. Brett, Shiyang Chen, Bogdan I. Epureanu, Matthew J. Ferrari, Éric Marty, Paige B. Miller, Eamon B. O’Dea, Suzanne M. O’Regan, Andrew W. Park, Pejman Rohani

PLOS Computational Biology: published May 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006917

Securing the future of research computing in the biosciences

Joanna Leng, Massa Shoura, Tom C. B. McLeish, Alan N. Real, Mariann Hardey, James McCafferty, Neil A. Ranson, Sarah A. Harris

PLOS Computational Biology: published May 16, 2019 | https://doi.org/10.1371/journal.pcbi.1006958

Research Articles

Dynamic balance between vesicle transport and microtubule growth enables neurite outgrowth

Arjun Singh Yadaw, Mustafa M. Siddiq, Vera Rabinovich, Rosa Tolentino, Jens Hansen, Ravi Iyengar

PLOS Computational Biology: published May 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006877

Uncovering functional signature in neural systems via random matrix theory

Assaf Almog, M. Renate Buijink, Ori Roethler, Stephan Michel, Johanna H. Meijer, Jos H. T. Rohling, Diego Garlaschelli

PLOS Computational Biology: published May 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006934

Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design

Daniel A. Cannon, Lu Shan, Qun Du, Lena Shirinian, Keith W. Rickert, Kim L. Rosenthal, Martin Korade III, Lilian E. van Vlerken-Ysla, Andrew Buchanan, Tristan J. Vaughan, Melissa M. Damschroder, Bojana Popovic

PLOS Computational Biology: published May 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006980

Balance of mechanical forces drives endothelial gap formation and may facilitate cancer and immune-cell extravasation

Jorge Escribano, Michelle B. Chen, Emad Moeendarbary, Xuan Cao, Vivek Shenoy, Jose Manuel Garcia-Aznar, Roger D. Kamm, Fabian Spill

PLOS Computational Biology: published May 2, 2019 | https://doi.org/10.1371/journal.pcbi.1006395

Identification of avian flapping motion from non-volant winged dinosaurs based on modal effective mass analysis

Yaser Saffar Talori, Jing-Shan Zhao, Yun-Fei Liu, Wen-Xiu Lu, Zhi-Heng Li, Jingmai Kathleen O'Connor

PLOS Computational Biology: published May 2, 2019 | https://doi.org/10.1371/journal.pcbi.1006846

Modeling of the axon plasma membrane structure and its effects on protein diffusion

Yihao Zhang, Anastasios V. Tzingounis, George Lykotrafitis

PLOS Computational Biology: published May 2, 2019 | https://doi.org/10.1371/journal.pcbi.1007003

How Dendrites Affect Online Recognition Memory

Xundong Wu, Gabriel C. Mel, D. J. Strouse, Bartlett W. Mel

PLOS Computational Biology: published May 3, 2019 | https://doi.org/10.1371/journal.pcbi.1006892

A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli

Anne Grimbs, David F. Klosik, Stefan Bornholdt, Marc-Thorsten Hütt

PLOS Computational Biology: published May 3, 2019 | https://doi.org/10.1371/journal.pcbi.1006962

Amplitude cancellation influences the association between frequency components in the neural drive to muscle and the rectified EMG signal

Jakob Lund Dideriksen, Dario Farina

PLOS Computational Biology: published May 3, 2019 | https://doi.org/10.1371/journal.pcbi.1006985

Enchained growth and cluster dislocation: A possible mechanism for microbiota homeostasis

Florence Bansept, Kathrin Schumann-Moor, Médéric Diard, Wolf-Dietrich Hardt, Emma Slack, Claude Loverdo

PLOS Computational Biology: published May 3, 2019 | https://doi.org/10.1371/journal.pcbi.1006986

Quasiperiodic rhythms of the inferior olive

Mario Negrello, Pascal Warnaar, Vincenzo Romano, Cullen B. Owens, Sander Lindeman, Elisabetta Iavarone, Jochen K. Spanke, Laurens W. J. Bosman, Chris I. De Zeeuw

PLOS Computational Biology: published May 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006475

A dynamic network model of temporal receptive fields in primary auditory cortex

Monzilur Rahman, Ben D. B. Willmore, Andrew J. King, Nicol S. Harper

PLOS Computational Biology: published May 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006618

Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares

Yuning Hao, Ming Yan, Blake R. Heath, Yu L. Lei, Yuying Xie

PLOS Computational Biology: published May 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006976

Reward-driven changes in striatal pathway competition shape evidence evaluation in decision-making

Kyle Dunovan, Catalina Vich, Matthew Clapp, Timothy Verstynen, Jonathan Rubin

PLOS Computational Biology: published May 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006998

EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches

Chi-Chou Liao, Liang-Jwu Chen, Shuen-Fang Lo, Chi-Wei Chen, Yen-Wei Chu

PLOS Computational Biology: published May 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006942

A neuromechanistic model for rhythmic beat generation

Amitabha Bose, Áine Byrne, John Rinzel

PLOS Computational Biology: published May 9, 2019 | https://doi.org/10.1371/journal.pcbi.1006450

An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis

Niki Karagianni, Ksanthi Kranidioti, Nikolaos Fikas, Maria Tsochatzidou, Panagiotis Chouvardas, Maria C. Denis, George Kollias, Christoforos Nikolaou

PLOS Computational Biology: published May 9, 2019 | https://doi.org/10.1371/journal.pcbi.1006933

Macroscopic phase resetting-curves determine oscillatory coherence and signal transfer in inter-coupled neural circuits

Grégory Dumont, Boris Gutkin

PLOS Computational Biology: published May 9, 2019 | https://doi.org/10.1371/journal.pcbi.1007019

Beyond Bouma's window: How to explain global aspects of crowding?

Adrien Doerig, Alban Bornet, Ruth Rosenholtz, Gregory Francis, Aaron M. Clarke, Michael H. Herzog

PLOS Computational Biology: published May 10, 2019 | https://doi.org/10.1371/journal.pcbi.1006580

Pathway-specific protein domains are predictive for human diseases

Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee, Insuk Lee

PLOS Computational Biology: published May 10, 2019 | https://doi.org/10.1371/journal.pcbi.1007052

DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images

Victor Kulikov, Syuan-Ming Guo, Matthew Stone, Allen Goodman, Anne Carpenter, Mark Bathe, Victor Lempitsky

PLOS Computational Biology: published May 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007012

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Vikash Pandey, Noushin Hadadi, Vassily Hatzimanikatis

PLOS Computational Biology: published May 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007036

The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern

Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C. P. Holstege, K. Anton Feenstra, Patrick Kemmeren

PLOS Computational Biology: published May 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007061

Interacting cells driving the evolution of multicellular life cycles

Yuanxiao Gao, Arne Traulsen, Yuriy Pichugin

PLOS Computational Biology: published May 14, 2019 | https://doi.org/10.1371/journal.pcbi.1006987

Human representation of multimodal distributions as clusters of samples

Jingwei Sun, Jian Li, Hang Zhang

PLOS Computational Biology: published May 14, 2019 | https://doi.org/10.1371/journal.pcbi.1007047

Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG

Natalie Schaworonkow, Vadim V. Nikulin

PLOS Computational Biology: published May 14, 2019 | https://doi.org/10.1371/journal.pcbi.1007055

Beyond core object recognition: Recurrent processes account for object recognition under occlusion

Karim Rajaei, Yalda Mohsenzadeh, Reza Ebrahimpour, Seyed-Mahdi Khaligh-Razavi

PLOS Computational Biology: published May 15, 2019 | https://doi.org/10.1371/journal.pcbi.1007001

DigChem: Identification of disease-gene-chemical relationships from Medline abstracts

Jeongkyun Kim, Jung-jae Kim, Hyunju Lee

PLOS Computational Biology: published May 15, 2019 | https://doi.org/10.1371/journal.pcbi.1007022

Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons

Elisabetta Iavarone, Jane Yi, Ying Shi, Bas-Jan Zandt, Christian O’Reilly, Werner Van Geit, Christian Rössert, Henry Markram, Sean L. Hill

PLOS Computational Biology: published May 16, 2019 | https://doi.org/10.1371/journal.pcbi.1006753

Amplifying the redistribution of somato-dendritic inhibition by the interplay of three interneuron types

Loreen Hertäg, Henning Sprekeler

PLOS Computational Biology: published May 16, 2019 | https://doi.org/10.1371/journal.pcbi.1006999

Evolution of major histocompatibility complex gene copy number

Piotr Bentkowski, Jacek Radwan

PLOS Computational Biology: published May 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007015

Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer

Alina Malyutina, Muntasir Mamun Majumder, Wenyu Wang, Alberto Pessia, Caroline A. Heckman, Jing Tang

PLOS Computational Biology: published May 20, 2019 | https://doi.org/10.1371/journal.pcbi.1006752

Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions

Matti Javanainen, Giray Enkavi, Ramon Guixà-Gonzaléz, Waldemar Kulig, Hector Martinez-Seara, Ilya Levental, Ilpo Vattulainen

PLOS Computational Biology: published May 20, 2019 | https://doi.org/10.1371/journal.pcbi.1007033

Detecting interaction networks in the human microbiome with conditional Granger causality

Kumar Mainali, Sharon Bewick, Briana Vecchio-Pagan, David Karig, William F. Fagan

PLOS Computational Biology: published May 20, 2019 | https://doi.org/10.1371/journal.pcbi.1007037

Host contact dynamics shapes richness and dominance of pathogen strains

Francesco Pinotti, Éric Fleury, Didier Guillemot, Pierre-Yves Böelle, Chiara Poletto

PLOS Computational Biology: published May 21, 2019 | https://doi.org/10.1371/journal.pcbi.1006530

Noise-precision tradeoff in predicting combinations of mutations and drugs

Avichai Tendler, Anat Zimmer, Avi Mayo, Uri Alon

PLOS Computational Biology: published May 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006956

Efficient algorithms to discover alterations with complementary functional association in cancer

Rebecca Sarto Basso, Dorit S. Hochbaum, Fabio Vandin

PLOS Computational Biology: published May 23, 2019 | https://doi.org/10.1371/journal.pcbi.1006802

Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes

Anupama Sharma, Shakti N. Menon, V. Sasidevan, Sitabhra Sinha

PLOS Computational Biology: published May 23, 2019 | https://doi.org/10.1371/journal.pcbi.1006977

Forecasting national and regional influenza-like illness for the USA

Michal Ben-Nun, Pete Riley, James Turtle, David P. Bacon, Steven Riley

PLOS Computational Biology: published May 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007013

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data

Ajeet K. Sharma, Pietro Sormanni, Nabeel Ahmed, Prajwal Ciryam, Ulrike A. Friedrich, Günter Kramer, Edward P. O’Brien

PLOS Computational Biology: published May 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007070

Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias

Ming Bo Cai, Nicolas W. Schuck, Jonathan W. Pillow, Yael Niv

PLOS Computational Biology: published May 24, 2019 | https://doi.org/10.1371/journal.pcbi.1006299

Modeling visual performance differences ‘around’ the visual field: A computational observer approach

Eline R. Kupers, Marisa Carrasco, Jonathan Winawer

PLOS Computational Biology: published May 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007063

Leveraging genetic interactions for adverse drug-drug interaction prediction

Sheng Qian, Siqi Liang, Haiyuan Yu

PLOS Computational Biology: published May 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007068

Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features

David A. Knowles, Gina Bouchard, Sylvia Plevritis

PLOS Computational Biology: published May 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006743

Comprehensively benchmarking applications for detecting copy number variation

Le Zhang, Wanyu Bai, Na Yuan, Zhenglin Du

PLOS Computational Biology: published May 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007069

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  1. Correction: Comprehensively benchmarking applications for detecting copy number variation

Modeling enamel matrix secretion in mammalian teeth

Teemu J. Häkkinen, S. Susanna Sova, Ian J. Corfe, Leo Tjäderhane, Antti Hannukainen, Jukka Jernvall

PLOS Computational Biology: published May 29, 2019 | https://doi.org/10.1371/journal.pcbi.1007058

Close proximity interactions support transmission of ESBL-K. pneumoniae but not ESBL-E. coli in healthcare settings

Audrey Duval, Thomas Obadia, Pierre-Yves Boëlle, Eric Fleury, Jean-Louis Herrmann, Didier Guillemot, Laura Temime, Lulla Opatowski, the i-Bird Study group

PLOS Computational Biology: published May 30, 2019 | https://doi.org/10.1371/journal.pcbi.1006496

Parameter estimation and identifiability in a neural population model for electro-cortical activity

Agus Hartoyo, Peter J. Cadusch, David T. J. Liley, Damien G. Hicks

PLOS Computational Biology: published May 30, 2019 | https://doi.org/10.1371/journal.pcbi.1006694

Differential sustained and transient temporal processing across visual streams

Anthony Stigliani, Brianna Jeska, Kalanit Grill-Spector

PLOS Computational Biology: published May 30, 2019 | https://doi.org/10.1371/journal.pcbi.1007011

Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification

Shilo Ohayon, Arik Girsault, Maisa Nasser, Shai Shen-Orr, Amit Meller

PLOS Computational Biology: published May 30, 2019 | https://doi.org/10.1371/journal.pcbi.1007067

State-aware detection of sensory stimuli in the cortex of the awake mouse

Audrey J. Sederberg, Aurélie Pala, He J. V. Zheng, Biyu J. He, Garrett B. Stanley

PLOS Computational Biology: published May 31, 2019 | https://doi.org/10.1371/journal.pcbi.1006716

Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

Alessandro Pandini, Howard Schulman, Shahid Khan

PLOS Computational Biology: published May 31, 2019 | https://doi.org/10.1371/journal.pcbi.1006796

Properties of cardiac conduction in a cell-based computational model

Karoline Horgmo Jæger, Andrew G. Edwards, Andrew McCulloch, Aslak Tveito

PLOS Computational Biology: published May 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007042

Perturbing low dimensional activity manifolds in spiking neuronal networks

Emil Wärnberg, Arvind Kumar

PLOS Computational Biology: published May 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007074

Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability

Gergely Boza, Sarah F. Worsley, Douglas W. Yu, István Scheuring

PLOS Computational Biology: published May 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007109

Corrections

Correction: Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

Yarden Golan, Raphael Alhadeff, Fabian Glaser, Assaf Ganoth, Arieh Warshel, Yehuda G. Assaraf

PLOS Computational Biology: published May 1, 2019 | https://doi.org/10.1371/journal.pcbi.1007021

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  1. Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

Correction: The role of the encapsulated cargo in microcompartment assembly

The PLOS Computational Biology Staff

PLOS Computational Biology: published May 2, 2019 | https://doi.org/10.1371/journal.pcbi.1006901

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  1. The role of the encapsulated cargo in microcompartment assembly

Correction: How pupil responses track value-based decision-making during and after reinforcement learning

Joanne C. Van Slooten, Sara Jahfari, Tomas Knapen, Jan Theeuwes

PLOS Computational Biology: published May 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007031

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  1. How pupil responses track value-based decision-making during and after reinforcement learning

Notice of Republication: Ten simple rules for organizing a webinar series

The PLOS Computational Biology Staff

PLOS Computational Biology: published May 8, 2019 | https://doi.org/10.1371/journal.pcbi.1007048

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  1. Ten simple rules for organizing a webinar series

Correction: Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models

The PLOS Computational Biology Staff

PLOS Computational Biology: published May 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007062

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  1. Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models

Formal Comment

Comment on "A comprehensive overview and evaluation of circular RNA detection tools"

Chia-Ying Chen, Trees-Juen Chuang

PLOS Computational Biology: published May 31, 2019 | https://doi.org/10.1371/journal.pcbi.1006158

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  1. A comprehensive overview and evaluation of circular RNA detection tools
  2. Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang