May 2020

Nuclear Magnetic Resonance (NMR) spectroscopy is indispensable in elucidating the three dimensional structures of molecules. Measured in parts per million, chemical shifts (CS) yielded by NMR describe how the resonances of atomic nuclei differ from those of known references. Such perturbations of nuclear resonance emerge from high-order structure, and knowledge of the latter is critically important to identifying molecular determinants of diseases and developing treatments. Through the directive-based OpenACC API, Wright et al. have accelerated the well-established CS prediction software PPM_One, enabling its use on bleeding-edge GPU architectures and broadening its application to large biomolecules such as the HIV-1 capsid.

Image Credit: Alex Bryer and Juan R. Perilla

Editorials

Ten Simple Rules for a successful remote postdoc

Kevin R. Burgio, Caitlin McDonough MacKenzie, Stephanie B. Borrelle, S. K. Morgan Ernest, Jacquelyn L. Gill, Kurt E. Ingeman, Amy Teffer, Ethan P. White

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007809

Ten simple rules for running a successful women-in-STEM organization on an academic campus

Deborah D. Rupert, Alexandra C. Nowlan, Oliver H. Tam, Molly Gale Hammell

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007754

Ten simple rules to run a successful BioHackathon

Leyla Garcia, Erick Antezana, Alexander Garcia, Evan Bolton, Rafael Jimenez, Pjotr Prins, Juan M. Banda, Toshiaki Katayama

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007808

Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles

Alastair M. Kilpatrick, Audra Anjum, Lonnie Welch

PLOS Computational Biology: published May 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007868

Improving reproducibility in computational biology research

Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David Nickerson, Anand Rampadarath

PLOS Computational Biology: published May 19, 2020 | https://doi.org/10.1371/journal.pcbi.1007881

Ten simple rules for making training materials FAIR

Leyla Garcia, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez del Angel, Michel Dumontier, Kim T. Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L. Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W. G. van Gelder, Patricia M. Palagi

PLOS Computational Biology: published May 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007854

Education

Ad hoc efforts for advancing data science education

Orianna DeMasi, Alexandra Paxton, Kevin Koy

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007695

Review

Better together: Elements of successful scientific software development in a distributed collaborative community

Julia Koehler Leman, Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W. Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland Dunbrack, Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007507

Research Articles

Inference on dengue epidemics with Bayesian regime switching models

Jue Tao Lim, Borame Sue Dickens, Sun Haoyang, Ng Lee Ching, Alex R. Cook

PLOS Computational Biology: published May 1, 2020 | https://doi.org/10.1371/journal.pcbi.1007839

When two are better than one: Modeling the mechanisms of antibody mixtures

Tal Einav, Jesse D. Bloom

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007830

Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis

Amanda Brucker, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz, Tzu-Pin Lu, Jung-Ying Tzeng

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007797

Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry

Andrew J. Bernoff, Michael Culshaw-Maurer, Rebecca A. Everett, Maryann E. Hohn, W. Christopher Strickland, Jasper Weinburd

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007820

An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver

James A. Hay, Amanda Minter, Kylie E. C. Ainslie, Justin Lessler, Bingyi Yang, Derek A. T. Cummings, Adam J. Kucharski, Steven Riley

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007840

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease

Christine A. Tataru, Maude M. David

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007859

Conservation laws by virtue of scale symmetries in neural systems

Erik D. Fagerholm, W. M. C. Foulkes, Yasir Gallero-Salas, Fritjof Helmchen, Karl J. Friston, Rosalyn J. Moran, Robert Leech

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007865

The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth

Juami Hermine Mariama van Gils, Erik van Dijk, Alessia Peduzzo, Alexander Hofmann, Nicola Vettore, Marie P. Schützmann, Georg Groth, Halima Mouhib, Daniel E. Otzen, Alexander K. Buell, Sanne Abeln

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007767

Robustness and parameter geography in post-translational modification systems

Kee-Myoung Nam, Benjamin M. Gyori, Silviana V. Amethyst, Daniel J. Bates, Jeremy Gunawardena

PLOS Computational Biology: published May 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007573

Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures

Elan Shatoff, Ralf Bundschuh

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007852

Path integration in large-scale space and with novel geometries: Comparing vector addition and encoding-error models

Sevan K. Harootonian, Robert C. Wilson, Lukáš Hejtmánek, Eli M. Ziskin, Arne D. Ekstrom

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007489

Randomly connected networks generate emergent selectivity and predict decoding properties of large populations of neurons

Audrey Sederberg, Ilya Nemenman

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007875

Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities

Leonardo Pacciani-Mori, Andrea Giometto, Samir Suweis, Amos Maritan

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007896

Self-organization in brain tumors: How cell morphology and cell density influence glioma pattern formation

Sara Jamous, Andrea Comba, Pedro R. Lowenstein, Sebastien Motsch

PLOS Computational Biology: published May 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007611

Mechanistic modeling of light-induced chemotactic infiltration of bacteria into leaf stomata

Mohsen Ranjbaran, Mina Solhtalab, Ashim K. Datta

PLOS Computational Biology: published May 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007841

Autonomous emergence of connectivity assemblies via spike triplet interactions

Lisandro Montangie, Christoph Miehl, Julijana Gjorgjieva

PLOS Computational Biology: published May 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007835

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer

Magali Richard, Clémentine Decamps, Florent Chuffart, Elisabeth Brambilla, Sophie Rousseaux, Saadi Khochbin, Daniel Jost

PLOS Computational Biology: published May 11, 2020 | https://doi.org/10.1371/journal.pcbi.1007869

Standard multiscale entropy reflects neural dynamics at mismatched temporal scales: What’s signal irregularity got to do with it?

Julian Q. Kosciessa, Niels A. Kloosterman, Douglas D. Garrett

PLOS Computational Biology: published May 11, 2020 | https://doi.org/10.1371/journal.pcbi.1007885

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type

Alan Le Goallec, Braden T. Tierney, Jacob M. Luber, Evan M. Cofer, Aleksandar D. Kostic, Chirag J. Patel

PLOS Computational Biology: published May 11, 2020 | https://doi.org/10.1371/journal.pcbi.1007895

Calibration of individual-based models to epidemiological data: A systematic review

C. Marijn Hazelbag, Jonathan Dushoff, Emanuel M. Dominic, Zinhle E. Mthombothi, Wim Delva

PLOS Computational Biology: published May 11, 2020 | https://doi.org/10.1371/journal.pcbi.1007893

Scale free topology as an effective feedback system

Alexander Rivkind, Hallel Schreier, Naama Brenner, Omri Barak

PLOS Computational Biology: published May 11, 2020 | https://doi.org/10.1371/journal.pcbi.1007825

StanDep: Capturing transcriptomic variability improves context-specific metabolic models

Chintan J. Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O’Rourke, Nathan E. Lewis

PLOS Computational Biology: published May 12, 2020 | https://doi.org/10.1371/journal.pcbi.1007764

Differentiation of Cytopathic Effects (CPE) induced by influenza virus infection using deep Convolutional Neural Networks (CNN)

Ting-En Wang, Tai-Ling Chao, Hsin-Tsuen Tsai, Pi-Han Lin, Yen-Lung Tsai, Sui-Yuan Chang

PLOS Computational Biology: published May 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007883

Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC

Eric Wright, Mauricio H. Ferrato, Alexander J. Bryer, Robert Searles, Juan R. Perilla, Sunita Chandrasekaran

PLOS Computational Biology: published May 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007877

Towards a data-driven characterization of behavioral changes induced by the seasonal flu

Nicolò Gozzi, Daniela Perrotta, Daniela Paolotti, Nicola Perra

PLOS Computational Biology: published May 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007879

Shape-preserving elastic solid models of macromolecules

Guang Song

PLOS Computational Biology: published May 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007855

Complex interactions can create persistent fluctuations in high-diversity ecosystems

Felix Roy, Matthieu Barbier, Giulio Biroli, Guy Bunin

PLOS Computational Biology: published May 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007827

Mutation severity spectrum of rare alleles in the human genome is predictive of disease type

Jimin Pei, Lisa N. Kinch, Zbyszek Otwinowski, Nick V. Grishin

PLOS Computational Biology: published May 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007775

The Affective Ising Model: A computational account of human affect dynamics

Tim Loossens, Merijn Mestdagh, Egon Dejonckheere, Peter Kuppens, Francis Tuerlinckx, Stijn Verdonck

PLOS Computational Biology: published May 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007860

Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity

Joseph Farris, Barbara Calhoun, Md. Suhail Alam, Shaun Lee, Kasturi Haldar

PLOS Computational Biology: published May 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007871

Learning clinical networks from medical records based on information estimates in mixed-type data

Vincent Cabeli, Louis Verny, Nadir Sella, Guido Uguzzoni, Marc Verny, Hervé Isambert

PLOS Computational Biology: published May 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007866

iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation

Kai Zheng, Zhu-Hong You, Jian-Qiang Li, Lei Wang, Zhen-Hao Guo, Yu-An Huang

PLOS Computational Biology: published May 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007872

Estimating a novel stochastic model for within-field disease dynamics of banana bunchy top virus via approximate Bayesian computation

Abhishek Varghese, Christopher Drovandi, Antonietta Mira, Kerrie Mengersen

PLOS Computational Biology: published May 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007878

Stimulus-choice (mis)alignment in primate area MT

Yuan Zhao, Jacob L. Yates, Aaron J. Levi, Alexander C. Huk, Il Memming Park

PLOS Computational Biology: published May 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007614

Bayesian regression explains how human participants handle parameter uncertainty

Jannes Jegminat, Maya A. Jastrzębowska, Matthew V. Pachai, Michael H. Herzog, Jean-Pascal Pfister

PLOS Computational Biology: published May 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007886

Dynamical network analysis reveals key microRNAs in progressive stages of lung cancer

Chao Kong, Yu-Xiang Yao, Zhi-Tong Bing, Bing-Hui Guo, Liang Huang, Zi-Gang Huang, Ying-Cheng Lai

PLOS Computational Biology: published May 19, 2020 | https://doi.org/10.1371/journal.pcbi.1007793

A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination

Timothy Wessler, Louis R. Joslyn, H. Jacob Borish, Hannah P. Gideon, JoAnne L. Flynn, Denise E. Kirschner, Jennifer J. Linderman

PLOS Computational Biology: published May 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007280

Modelling the dynamics of tuberculosis lesions in a virtual lung: Role of the bronchial tree in endogenous reinfection

Martí Català, Jordi Bechini, Montserrat Tenesa, Ricardo Pérez, Mariano Moya, Cristina Vilaplana, Joaquim Valls, Sergio Alonso, Daniel López, Pere-Joan Cardona, Clara Prats

PLOS Computational Biology: published May 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007772

GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm

Lei Wang, Zhu-Hong You, Yang-Ming Li, Kai Zheng, Yu-An Huang

PLOS Computational Biology: published May 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007568

Sequence-based prediction of protein binding mode landscapes

Attila Horvath, Marton Miskei, Viktor Ambrus, Michele Vendruscolo, Monika Fuxreiter

PLOS Computational Biology: published May 26, 2020 | https://doi.org/10.1371/journal.pcbi.1007864

Predicting host taxonomic information from viral genomes: A comparison of feature representations

Francesca Young, Simon Rogers, David L. Robertson

PLOS Computational Biology: published May 26, 2020 | https://doi.org/10.1371/journal.pcbi.1007894

Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA

Arumay Pal, Yaakov Levy

PLOS Computational Biology: published May 26, 2020 | https://doi.org/10.1371/journal.pcbi.1007867

Cover

Chemical shifts of large macromolecular assemblies.

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