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Table of Contents

August 2021

Cover

A mosaic image of an anopheles mosquito was created by representing each pixel of the template with a deep ultraviolet microscopy image of an individual red blood cell. The red blood cell images were drawn from a pool containing healthy cells and P.falciparum-infected cells. Red blood cell images were adjusted in their mean intensity values to reflect template pixel intensities. Lebel et al 2021

Image Credit: The template anopheles mosquito image was modified from a BioRender.com icon (Anopheles mosquito, 2020). The mosaic was created using custom software written by Paul Lebel and is being shared under the creative commons license (CC BY 4.0).

Editorials

Ten simple rules for teaching applied programming in an authentic and immersive online environment

Frances Hooley, Peter J. Freeman, Angela C. Davies

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

Benjamin Moore, Patricia Carvajal-López, Paballo Abel Chauke, Marco Cristancho, Victoria Dominguez Del Angel, Selene L. Fernandez-Valverde, Amel Ghouila, Piraveen Gopalasingam, Fatma Zahra Guerfali, Alice Matimba, Sarah L. Morgan, Guilherme Oliveira, Verena Ras, Alejandro Reyes, Javier De Las Rivas, Nicola Mulder

Ten simple rules for creating reusable pathway models for computational analysis and visualization

Kristina Hanspers, Martina Kutmon, Susan L. Coort, Daniela Digles, Lauren J. Dupuis, Friederike Ehrhart, Finterly Hu, Elisson N. Lopes, Marvin Martens, Nhung Pham, Woosub Shin, Denise N. Slenter, Andra Waagmeester, Egon L. Willighagen, Laurent A. Winckers, Chris T. Evelo, Alexander R. Pico

Ten simple rules for conducting a mendelian randomization study

Sarah A. Gagliano Taliun, David M. Evans

Ten simple rules for aspiring graduate students

Andrea I. Luppi, Charlotte Coco Newton, Lynde Folsom, Elisa Galliano, Rafael Romero-Garcia

Ten simple rules for Global North researchers to stop perpetuating helicopter research in the Global South

Danny Haelewaters, Tina A. Hofmann, Adriana L. Romero-Olivares

Review

Review of machine learning methods for RNA secondary structure prediction

Qi Zhao, Zheng Zhao, Xiaoya Fan, Zhengwei Yuan, Qian Mao, Yudong Yao

Research Articles

PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions

Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W. Ritchie, Marie-Dominique Devignes

Using machine learning and big data to explore the drug resistance landscape in HIV

Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué, Olivier Gascuel, On behalf of the UK HIV Drug Resistance Database

Critical behaviour of the stochastic Wilson-Cowan model

Antonio de Candia, Alessandro Sarracino, Ilenia Apicella, Lucilla de Arcangelis

High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING

Wesley M. Marin, Ravi Dandekar, Danillo G. Augusto, Tasneem Yusufali, Bianca Heyn, Jan Hofmann, Vinzenz Lange, Jürgen Sauter, Paul J. Norman, Jill A. Hollenbach

Identification of structures for ion channel kinetic models

Kathryn E. Mangold, Wei Wang, Eric K. Johnson, Druv Bhagavan, Jonathan D. Moreno, Jeanne M. Nerbonne, Jonathan R. Silva

A modular approach for modeling the cell cycle based on functional response curves

Jolan De Boeck, Jan Rombouts, Lendert Gelens

Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread

John R. Giles, Derek A. T. Cummings, Bryan T. Grenfell, Andrew J. Tatem, Elisabeth zu Erbach-Schoenberg, CJE Metcalf, Amy Wesolowski

An uncertainty-based model of the effects of fixation on choice

Zhi-Wei Li, Wei Ji Ma

Wing structure and neural encoding jointly determine sensing strategies in insect flight

Alison I. Weber, Thomas L. Daniel, Bingni W. Brunton

Dendritic normalisation improves learning in sparsely connected artificial neural networks

Alex D. Bird, Peter Jedlicka, Hermann Cuntz

Models of heterogeneous dopamine signaling in an insect learning and memory center

Linnie Jiang, Ashok Litwin-Kumar

A multi-approach and multi-scale platform to model CD4+ T cells responding to infections

Kenneth Y. Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar

The unbiased estimation of the fraction of variance explained by a model

Dean A. Pospisil, Wyeth Bair

Topology-preserving smoothing of retinotopic maps

Yanshuai Tu, Duyan Ta, Zhong-Lin Lu, Yalin Wang

Evaluation and comparison of multi-omics data integration methods for cancer subtyping

Ran Duan, Lin Gao, Yong Gao, Yuxuan Hu, Han Xu, Mingfeng Huang, Kuo Song, Hongda Wang, Yongqiang Dong, Chaoqun Jiang, Chenxing Zhang, Songwei Jia

Relating simulation studies by provenance—Developing a family of Wnt signaling models

Kai Budde, Jacob Smith, Pia Wilsdorf, Fiete Haack, Adelinde M. Uhrmacher

A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes

Karoline Horgmo Jæger, Andrew G. Edwards, Wayne R. Giles, Aslak Tveito

Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic

Ritabrata Dutta, Susana N. Gomes, Dante Kalise, Lorenzo Pacchiardi

Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space

Daisuke Imoto, Nen Saito, Akihiko Nakajima, Gen Honda, Motohiko Ishida, Toyoko Sugita, Sayaka Ishihara, Koko Katagiri, Chika Okimura, Yoshiaki Iwadate, Satoshi Sawai

Improving the understanding of cytoneme-mediated morphogen gradients by in silico modeling

Adrián Aguirre-Tamaral, Isabel Guerrero

A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers

Frances L. Heredia, Abiel Roche-Lima, Elsie I. Parés-Matos

IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA

Zhonghe Shao, Ting Wang, Meng Zhang, Zhou Jiang, Shuiping Huang, Ping Zeng

A large-scale brain network mechanism for increased seizure propensity in Alzheimer’s disease

Luke Tait, Marinho A. Lopes, George Stothart, John Baker, Nina Kazanina, Jiaxiang Zhang, Marc Goodfellow

Using de novo assembly to identify structural variation of eight complex immune system gene regions

Jia-Yuan Zhang, Hannah Roberts, David S. C. Flores, Antony J. Cutler, Andrew C. Brown, Justin P. Whalley, Olga Mielczarek, David Buck, Helen Lockstone, Barbara Xella, Karen Oliver, Craig Corton, Emma Betteridge, Rachael Bashford-Rogers, Julian C. Knight, John A. Todd, Gavin Band

Computational identification and experimental characterization of preferred downstream positions in human core promoters

René Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bucher, Tamar Juven-Gershon

Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining

Paul Lebel, Rebekah Dial, Venkata N. P. Vemuri, Valentina Garcia, Joseph DeRisi, Rafael Gómez-Sjöberg

Bistability in fatty-acid oxidation resulting from substrate inhibition

Fentaw Abegaz, Anne-Claire M. F. Martines, Marcel A. Vieira-Lara, Melany Rios-Morales, Dirk-Jan Reijngoud, Ernst C. Wit, Barbara M. Bakker

Interspike interval correlations in neuron models with adaptation and correlated noise

Lukas Ramlow, Benjamin Lindner

A multi-objective genetic algorithm to find active modules in multiplex biological networks

Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, Anaïs Baudot

Mitigating COVID-19 outbreaks in workplaces and schools by hybrid telecommuting

Simon Mauras, Vincent Cohen-Addad, Guillaume Duboc, Max Dupré la Tour, Paolo Frasca, Claire Mathieu, Lulla Opatowski, Laurent Viennot

Unveiling functions of the visual cortex using task-specific deep neural networks

Kshitij Dwivedi, Michael F. Bonner, Radoslaw Martin Cichy, Gemma Roig

Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows

Daniel Schindler, Ted Moldenhawer, Maike Stange, Valentino Lepro, Carsten Beta, Matthias Holschneider, Wilhelm Huisinga

Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations

Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gómez-Sjöberg

SiGMoiD: A super-statistical generative model for binary data

Xiaochuan Zhao, Germán Plata, Purushottam D. Dixit

The evolutionary history of topological variations in the CPA/AT transporters

Govindarajan Sudha, Claudio Bassot, John Lamb, Nanjiang Shu, Yan Huang, Arne Elofsson

A hidden Markov model reliably characterizes ketamine-induced spectral dynamics in macaque local field potentials and human electroencephalograms

Indie C. Garwood, Sourish Chakravarty, Jacob Donoghue, Meredith Mahnke, Pegah Kahali, Shubham Chamadia, Oluwaseun Akeju, Earl K. Miller, Emery N. Brown

Optimal closed-loop deep brain stimulation using multiple independently controlled contacts

Gihan Weerasinghe, Benoit Duchet, Christian Bick, Rafal Bogacz

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

Xianggen Liu, Yunan Luo, Pengyong Li, Sen Song, Jian Peng

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants

Natália Teruel, Olivier Mailhot, Rafael J. Najmanovich

Estimating the conditional probability of developing human papilloma virus related oropharyngeal cancer by combining machine learning and inverse Bayesian modelling

Prerna Tewari, Eugene Kashdan, Cathal Walsh, Cara M. Martin, Andrew C. Parnell, John J. O’Leary

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks

Multiscale representations of community structures in attractor neural networks

Tatsuya Haga, Tomoki Fukai

Quantifying dose-, strain-, and tissue-specific kinetics of parainfluenza virus infection

Lubna Pinky, Crystal W. Burke, Charles J. Russell, Amber M. Smith

Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions

Jason Liu, Daniel J. Spakowicz, Garrett I. Ash, Rebecca Hoyd, Rohan Ahluwalia, Andrew Zhang, Shaoke Lou, Donghoon Lee, Jing Zhang, Carolyn Presley, Ann Greene, Matthew Stults-Kolehmainen, Laura M. Nally, Julien S. Baker, Lisa M. Fucito, Stuart A. Weinzimer, Andrew V. Papachristos, Mark Gerstein

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach

Nikolas Dovrolis, Katerina Kassela, Konstantinos Konstantinidis, Adamantia Kouvela, Stavroula Veletza, Ioannis Karakasiliotis

The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus

Sam R. Hill, Reidun Twarock, Eric C. Dykeman

DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions

Vincent Rocher, Matthieu Genais, Elissar Nassereddine, Raphael Mourad

A probabilistic model for the ultradian timing of REM sleep in mice

Sung-Ho Park, Justin Baik, Jiso Hong, Hanna Antila, Benjamin Kurland, Shinjae Chung, Franz Weber

The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes

Sharon Guerstein, Victoria Romeo-Aznar, Ma’ayan Dekel, Oren Miron, Nadav Davidovitch, Rami Puzis, Shai Pilosof

Neurally-constrained modeling of human gaze strategies in a change blindness task

Akshay Jagatap, Simran Purokayastha, Hritik Jain, Devarajan Sridharan

Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence

Simon M. Lichtinger, Adiran Garaizar, Rosana Collepardo-Guevara, Aleks Reinhardt

Ankyrin repeats in context with human population variation

Javier S. Utgés, Maxim I. Tsenkov, Noah J. M. Dietrich, Stuart A. MacGowan, Geoffrey J. Barton

The role of memory in non-genetic inheritance and its impact on cancer treatment resistance

Tyler Cassidy, Daniel Nichol, Mark Robertson-Tessi, Morgan Craig, Alexander R. A. Anderson

Targeted pandemic containment through identifying local contact network bottlenecks

Shenghao Yang, Priyabrata Senapati, Di Wang, Chris T. Bauch, Kimon Fountoulakis

AIM: A network model of attention in auditory cortex

Kenny F. Chou, Kamal Sen

Corrections

Correction: Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape

David R. J. Pleydell, Samuel Soubeyrand, Sylvie Dallot, Gérard Labonne, Joël Chadœuf, Emmanuel Jacquot, Gaël Thébaud

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Correction: Personalized glucose forecasting for type 2 diabetes using data assimilation

David J. Albers, Matthew Levine, Bruce Gluckman, Henry Ginsberg, George Hripcsak, Lena Mamykina

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Correction: Quantification of nematic cell polarity in three-dimensional tissues

André Scholich, Simon Syga, Hernán Morales-Navarrete, Fabián Segovia-Miranda, Hidenori Nonaka, Kirstin Meyer, Walter de Back, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial, Frank Jülicher, Benjamin M. Friedrich

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