April 2022

Four antibody cocktails for HIV prevention.

Image Credit: Daniel B Reeves

Editorials

Ten simple rules for building a successful science start-up

Tobias Reichmuth, Collin Y. Ewald

PLOS Computational Biology: published April 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009982

Ten simple rules for using entrepreneurship skills to improve research careers and culture

Matt Bawn, David Dent, Philip E. Bourne

PLOS Computational Biology: published April 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009946

Ten simple rules for getting started with statistics in graduate school

Rachel A. Zitomer, Jessica Karr, Mark Kerstens, Lindsey Perry, Kayla Ruth, Lindsay Adrean, Suzanne Austin, Jamie Cornelius, Jonathan Dachenhaus, Jonathan Dinkins, Alan Harrington, Hankyu Kim, Terrah Owens, Claire Revekant, Vanessa Schroeder, Chelsea Sink, Jonathon J. Valente, Ethan Woodis, James W. Rivers

PLOS Computational Biology: published April 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010033

Perspective

Ten simple rules to ruin a collaborative environment

Carolyn J. Lawrence-Dill, Robyn L. Allscheid, Albert Boaitey, Todd Bauman, Edward S. Buckler IV, Jennifer L. Clarke, Christopher Cullis, Jack Dekkers, Cassandra J. Dorius, Shawn F. Dorius, David Ertl, Matthew Homann, Guiping Hu, Mary Losch, Eric Lyons, Brenda Murdoch, Zahra-Katy Navabi, Somashekhar Punnuri, Fahad Rafiq, James M. Reecy, Patrick S. Schnable, Nicole M. Scott, Moira Sheehan, Xavier Sirault, Margaret Staton, Christopher K. Tuggle, Alison Van Eenennaam, Rachael Voas

PLOS Computational Biology: published April 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009957

Review

Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets

Anuradha Kar, Manuel Petit, Yassin Refahi, Guillaume Cerutti, Christophe Godin, Jan Traas

PLOS Computational Biology: published April 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009879

Research Articles

Short-term and long-term epidemiological impacts of sustained vector control in various dengue endemic settings: A modelling study

Haoyang Sun, Joel Koo, Borame L. Dickens, Hannah E. Clapham, Alex R. Cook

PLOS Computational Biology: published April 1, 2022 | https://doi.org/10.1371/journal.pcbi.1009979

Modelling the interaction between stem cells derived cardiomyocytes patches and host myocardium to aid non-arrhythmic engineered heart tissue design

Damiano Fassina, Caroline M. Costa, Stefano Longobardi, Elias Karabelas, Gernot Plank, Sian E. Harding, Steven A. Niederer

PLOS Computational Biology: published April 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010030

Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders

Yuge Wang, Hongyu Zhao

PLOS Computational Biology: published April 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010025

The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities

Silvia Zaoli, Jacopo Grilli

PLOS Computational Biology: published April 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010043

Packaging contests between viral RNA molecules and kinetic selectivity

Inbal Mizrahi, Robijn Bruinsma, Joseph Rudnick

PLOS Computational Biology: published April 1, 2022 | https://doi.org/10.1371/journal.pcbi.1009913

SUITOR: Selecting the number of mutational signatures through cross-validation

Donghyuk Lee, Difei Wang, Xiaohong R. Yang, Jianxin Shi, Maria Teresa Landi, Bin Zhu

PLOS Computational Biology: published April 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009309

Understanding glioblastoma invasion using physically-guided neural networks with internal variables

Jacobo Ayensa-Jiménez, Mohamed H. Doweidar, Jose A. Sanz-Herrera, Manuel Doblare

PLOS Computational Biology: published April 4, 2022 | https://doi.org/10.1371/journal.pcbi.1010019

Understanding photosynthetic biofilm productivity and structure through 2D simulation

Bastien Polizzi, Andrea Fanesi, Filipa Lopes, Magali Ribot, Olivier Bernard

PLOS Computational Biology: published April 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009904

Meteorological factors and non-pharmaceutical interventions explain local differences in the spread of SARS-CoV-2 in Austria

Katharina Ledebur, Michaela Kaleta, Jiaying Chen, Simon D. Lindner, Caspar Matzhold, Florian Weidle, Christoph Wittmann, Katharina Habimana, Linda Kerschbaumer, Sophie Stumpfl, Georg Heiler, Martin Bicher, Nikolas Popper, Florian Bachner, Peter Klimek

PLOS Computational Biology: published April 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009973

Arousal state affects perceptual decision-making by modulating hierarchical sensory processing in a large-scale visual system model

Lynn K. A. Sörensen, Sander M. Bohté, Heleen A. Slagter, H. Steven Scholte

PLOS Computational Biology: published April 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009976

Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins

Stefano Pascarelli, Paola Laurino

PLOS Computational Biology: published April 4, 2022 | https://doi.org/10.1371/journal.pcbi.1010016

Moving in on human motor cortex. Characterizing the relationship between body parts with non-rigid population response fields

Wouter Schellekens, Carlijn Bakker, Nick F. Ramsey, Natalia Petridou

PLOS Computational Biology: published April 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009955

Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit

Gautam Munglani, Hannes Vogler, Ueli Grossniklaus

PLOS Computational Biology: published April 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009242

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita

PLOS Computational Biology: published April 5, 2022 | https://doi.org/10.1371/journal.pcbi.1009578

Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction

Xiang Liu, Huitao Feng, Jie Wu, Kelin Xia

PLOS Computational Biology: published April 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009943

Epigenetic cell memory: The gene’s inner chromatin modification circuit

Simone Bruno, Ruth J. Williams, Domitilla Del Vecchio

PLOS Computational Biology: published April 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009961

Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention

Bryan T. Mayer, Allan C. deCamp, Yunda Huang, Joshua T. Schiffer, Raphael Gottardo, Peter B. Gilbert, Daniel B. Reeves

PLOS Computational Biology: published April 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010003

Simulated actin reorganization mediated by motor proteins

Maria-Veronica Ciocanel, Aravind Chandrasekaran, Carli Mager, Qin Ni, Garegin A. Papoian, Adriana Dawes

PLOS Computational Biology: published April 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010026

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants

Nicholas J. Ose, Brandon M. Butler, Avishek Kumar, I. Can Kazan, Maxwell Sanderford, Sudhir Kumar, S. Banu Ozkan

PLOS Computational Biology: published April 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010006

Adaptive and optimized COVID-19 vaccination strategies across geographical regions and age groups

Jeta Molla, Alejandro Ponce de León Chávez, Takayuki Hiraoka, Tapio Ala-Nissila, Mikko Kivelä, Lasse Leskelä

PLOS Computational Biology: published April 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009974

A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections

Julia Jäger, Pintu Patra, Cecilia P. Sanchez, Michael Lanzer, Ulrich S. Schwarz

PLOS Computational Biology: published April 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009509

Deep learning for robust and flexible tracking in behavioral studies for C. elegans

Kathleen Bates, Kim N. Le, Hang Lu

PLOS Computational Biology: published April 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009942

Blind demixing methods for recovering dense neuronal morphology from barcode imaging data

Shuonan Chen, Jackson Loper, Pengcheng Zhou, Liam Paninski

PLOS Computational Biology: published April 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009991

Using topic modeling to detect cellular crosstalk in scRNA-seq

Alexandrina Pancheva, Helen Wheadon, Simon Rogers, Thomas D. Otto

PLOS Computational Biology: published April 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009975

Effective population size for culturally evolving traits

Dominik Deffner, Anne Kandler, Laurel Fogarty

PLOS Computational Biology: published April 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009430

Are transient protein-protein interactions more dispensable?

Mohamed Ali Ghadie, Yu Xia

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010013

Digital contact tracing and network theory to stop the spread of COVID-19 using big-data on human mobility geolocalization

Matteo Serafino, Higor S. Monteiro, Shaojun Luo, Saulo D. S. Reis, Carles Igual, Antonio S. Lima Neto, Matías Travizano, José S. Andrade Jr, Hernán A. Makse

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009865

Fundamental limits on inferring epidemic resurgence in real time using effective reproduction numbers

Kris V. Parag, Christl A. Donnelly

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010004

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity

Szilvia Barsi, Henrietta Papp, Alberto Valdeolivas, Dániel J. Tóth, Anett Kuczmog, Mónika Madai, László Hunyady, Péter Várnai, Julio Saez-Rodriguez, Ferenc Jakab, Bence Szalai

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010021

DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data

Lijun Cheng, Pratik Karkhanis, Birkan Gokbag, Yueze Liu, Lang Li

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1008885

Microbiome-based disease prediction with multimodal variational information bottlenecks

Filippo Grazioli, Raman Siarheyeu, Israa Alqassem, Andreas Henschel, Giampaolo Pileggi, Andrea Meiser

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010050

Validation-based model selection for ¹³C metabolic flux analysis with uncertain measurement errors

Nicolas Sundqvist, Nina Grankvist, Jeramie Watrous, Jain Mohit, Roland Nilsson, Gunnar Cedersund

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009999

Construction of disease-specific cytokine profiles by associating disease genes with immune responses

Tianyun Liu, Shiyin Wang, Michael Wornow, Russ B. Altman

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009497

Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments

Simone Di Leo, Stefano Marni, Carlos A. Plata, Tommaso P. Fraccia, Gregory P. Smith, Amos Maritan, Samir Suweis, Tommaso Bellini

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010051

RNA folding using quantum computers

Dillion M. Fox, Christopher M. MacDermaid, Andrea M. A. Schreij, Magdalena Zwierzyna, Ross C. Walker

PLOS Computational Biology: published April 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010032

Chaotic and stochastic dynamics of epileptiform-like activities in sclerotic hippocampus resected from patients with pharmacoresistant epilepsy

Noemi S. Araújo, Selvin Z. Reyes-Garcia, João A. F. Brogin, Douglas D. Bueno, Esper A. Cavalheiro, Carla A. Scorza, Jean Faber

PLOS Computational Biology: published April 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010027

A general framework for predicting the transcriptomic consequences of non-coding variation and small molecules

Moustafa Abdalla, Mohamed Abdalla

PLOS Computational Biology: published April 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010028

Dissecting recurrent waves of pertussis across the boroughs of London

Arash Saeidpour, Shweta Bansal, Pejman Rohani

PLOS Computational Biology: published April 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009898

Alpha blocking and 1/f^β spectral scaling in resting EEG can be accounted for by a sum of damped alpha band oscillatory processes

Rick Evertz, Damien G. Hicks, David T. J. Liley

PLOS Computational Biology: published April 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010012

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV

Simone Conti, Victor Ovchinnikov, Jonathan G. Faris, Arup K. Chakraborty, Martin Karplus, Kayla G. Sprenger

PLOS Computational Biology: published April 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009391

Predicting the functional impact of KCNQ1 variants with artificial neural networks

Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George Jr., Jens Meiler

PLOS Computational Biology: published April 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010038

All²: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons

Vivekananda Sarangi, Yeongjun Jang, Milovan Suvakov, Taejeong Bae, Liana Fasching, Shobana Sekar, Livia Tomasini, Jessica Mariani, Flora M. Vaccarino, Alexej Abyzov

PLOS Computational Biology: published April 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009487

Application of modular response analysis to medium- to large-size biological systems

Meriem Mekedem, Patrice Ravel, Jacques Colinge

PLOS Computational Biology: published April 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009312

BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts

William Poole, Ayush Pandey, Andrey Shur, Zoltan A. Tuza, Richard M. Murray

PLOS Computational Biology: published April 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009987

Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa

Renato Giliberti, Sara Cavaliere, Italia Elisa Mauriello, Danilo Ercolini, Edoardo Pasolli

PLOS Computational Biology: published April 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010066

Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states

Amanda L. Peiffer, Julie M. Garlick, Stephen T. Joy, Anna K. Mapp, Charles L. Brooks III

PLOS Computational Biology: published April 22, 2022 | https://doi.org/10.1371/journal.pcbi.1009977

Cell type-specific mechanisms of information transfer in data-driven biophysical models of hippocampal CA3 principal neurons

Daniele Linaro, Matthew J. Levy, David L. Hunt

PLOS Computational Biology: published April 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010071

Updating age-specific contact structures to match evolving demography in a dynamic mathematical model of tuberculosis vaccination

Chathika Krishan Weerasuriya, Rebecca Claire Harris, Christopher Finn McQuaid, Gabriela B. Gomez, Richard G. White

PLOS Computational Biology: published April 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010002

Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms

Hongyang Li, Ridvan Eksi, Daiyao Yi, Bradley Godfrey, Lisa R. Mathew, Christopher L. O’Connor, Markus Bitzer, Matthias Kretzler, Rajasree Menon, Yuanfang Guan

PLOS Computational Biology: published April 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010040

Phylogenetic analysis of migration, differentiation, and class switching in B cells

Kenneth B. Hoehn, Oliver G. Pybus, Steven H. Kleinstein

PLOS Computational Biology: published April 25, 2022 | https://doi.org/10.1371/journal.pcbi.1009885

Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection

Ryuichi Kumata, Shoya Iwanami, Katrina B. Mar, Yusuke Kakizoe, Naoko Misawa, Shinji Nakaoka, Yoshio Koyanagi, Alan S. Perelson, John W. Schoggins, Shingo Iwami, Kei Sato

PLOS Computational Biology: published April 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010053

Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs

Vinita Periwal, Stefan Bassler, Sergej Andrejev, Natalia Gabrielli, Kaustubh Raosaheb Patil, Athanasios Typas, Kiran Raosaheb Patil

PLOS Computational Biology: published April 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010029

Distinguishing excess mutations and increased cell death based on variant allele frequencies

Gergely Tibély, Dominik Schrempf, Imre Derényi, Gergely J. Szöllősi

PLOS Computational Biology: published April 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010048

Multiple nutrient transporters enable cells to mitigate a rate-affinity tradeoff

Luis Fernando Montaño-Gutierrez, Kevin Correia, Peter S. Swain

PLOS Computational Biology: published April 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010060

Calcium modeling of spine apparatus-containing human dendritic spines demonstrates an “all-or-nothing” communication switch between the spine head and dendrite

James Rosado, Viet Duc Bui, Carola A. Haas, Jürgen Beck, Gillian Queisser, Andreas Vlachos

PLOS Computational Biology: published April 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010069

Multi-targeting of K-Ras domains and mutations by peptide and small molecule inhibitors

Mansour Poorebrahim, Mohammad Foad Abazari, Leila Moradi, Behzad Shahbazi, Reza Mahmoudi, Hourieh Kalhor, Hassan Askari, Ladan Teimoori-Toolabi

PLOS Computational Biology: published April 26, 2022 | https://doi.org/10.1371/journal.pcbi.1009962

Mechanisms of ventricular arrhythmias elicited by coexistence of multiple electrophysiological remodeling in ischemia: A simulation study

Cuiping Liang, Qince Li, Kuanquan Wang, Yimei Du, Wei Wang, Henggui Zhang

PLOS Computational Biology: published April 27, 2022 | https://doi.org/10.1371/journal.pcbi.1009388

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Mixing perfect antibody cocktails for HIV

Editorials

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Research Articles

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