Current Issue | PLOS Computational Biology

Through a combination of computational modeling and behavioral experiments, we demonstrate how the process of generating objects—actively reconstructing the most plausible object representation from noisy visual input—guides attention towards specific features or locations within an image (known functions of top-down attention), thereby enhancing the system's robustness to various types of noise and corruption. We found that this generative attention mechanism could explain, not only the time that it took people to recognize challenging objects, but also the types of recognition errors made by people (seeing an object as one thing when it was really another). Ahn et al

Image Credit: Seoyoung Ahn

Education Articles

Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club

Roberto Efraín Díaz, Stephanie A. Wankowicz

PLOS Computational Biology: published June 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012166

Eight quick tips for including chromosome X in genome-wide association studies

Justin Bellavance, Linda Wang, Sarah A. Gagliano Taliun

PLOS Computational Biology: published June 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012160

Ten simple rules for computational biologists collaborating with wet lab researchers

Mark D. Robinson, Peiying Cai, Martin Emons, Reto Gerber, Pierre-Luc Germain, Samuel Gunz, Siyuan Luo, Giulia Moro, Emanuel Sonder, Anthony Sonrel, Jiayi Wang, David Wissel, Izaskun Mallona

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012174

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows

Genís Bayarri, Pau Andrio, Josep Lluís Gelpí, Adam Hospital, Modesto Orozco

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012173

Ten simple rules for implementing electronic lab notebooks (ELNs)

Justine Vandendorpe, Beatrix Adam, Jeanne Wilbrandt, Birte Lindstädt, Konrad U. Förstner

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012170

Ten simple rules to make computable knowledge shareable and reusable

Marisa L. Conte, Peter Boisvert, Philip Barrison, Farid Seifi, Zach Landis-Lewis, Allen Flynn, Charles P. Friedman

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012179

Cracking AlphaFold2: Leveraging the power of artificial intelligence in undergraduate biochemistry curriculums

Devon J. Boland, Nicola M. Ayres

PLOS Computational Biology: published June 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012123

Ten “simple” rules for non-Indigenous researchers engaging Indigenous communities in Arctic research

Joy M. O’Brien, Nathan Blais, Carmen Butler, Natalie White, Ash Bustead, Collin Figler, McKenna Wells, George Anderson, Anna Yuhas, Jessica Gilman Ernakovich

PLOS Computational Biology: published June 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012093

Ten simple rules for successful and sustainable African research collaborations

Roseline Dzekem Dine, Lamis Yahia Mohamed Elkheir, Morufu Olalekan Raimi, Micheal Alemayehu, Salem Youssef Mohamed, Justice Kwadwo Turzin, Femi Qudus Arogundade, Elizabeth Akinyi Ochola, Alex Mukungu Nasiyo, Raziah Quallatein Mwawanga, Yahaya Abubakar Yabo

PLOS Computational Biology: published June 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012197

Perspective

Ten simple rules for implementing a successful field season

Lindsey R. Perry, Rebecca L. Kelble, Valerie N. Brewer, Cara E. Christensen, Mark E. Kerstens, Terrah M. Owens, Megan A. Sampognaro, Dorothy L. Zahor, Rachel A. Zitomer, Suzanne H. Austin, Jamie M. Cornelius, Jonathan B. Dinkins, Sarah J. K. Frey, Cecelia E. Frisinger, Stephanie M. LeQuier, Carl G. Lundblad, Jamie Oskowski, Hallie R. Perlman, William J. Price, Richard Rich, Kayla A. Ruth, Vanessa M. Schroeder, Shawn B. Szabo, James W. Rivers

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012189

Research Articles

Synergistic information supports modality integration and flexible learning in neural networks solving multiple tasks

Alexandra M. Proca, Fernando E. Rosas, Andrea I. Luppi, Daniel Bor, Matthew Crosby, Pedro A. M. Mediano

PLOS Computational Biology: published June 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012178

Data-driven learning of structure augments quantitative prediction of biological responses

Yuanchi Ha, Helena R. Ma, Feilun Wu, Andrea Weiss, Katherine Duncker, Helen Z. Xu, Jia Lu, Max Golovsky, Daniel Reker, Lingchong You

PLOS Computational Biology: published June 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012185

Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data

Xiaoman Xie, Saurabh Sinha

PLOS Computational Biology: published June 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012103

A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems

Lu Zhang, Gang Xue, Xiaolin Zhou, Jiandong Huang, Zhiyuan Li

PLOS Computational Biology: published June 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011882

Beyond homogeneity: Assessing the validity of the Michaelis–Menten rate law in spatially heterogeneous environments

Seolah Shin, Seok Joo Chae, Seunggyu Lee, Jae Kyoung Kim

PLOS Computational Biology: published June 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012205

Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression

Pavel Sanda, Jaroslav Hlinka, Monica van den Berg, Antonin Skoch, Maxim Bazhenov, Georgios A. Keliris, Giri P. Krishnan

PLOS Computational Biology: published June 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012099

Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection

Ellie Mainou, Ruy M. Ribeiro, Jessica M. Conway

PLOS Computational Biology: published June 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012129

Machine learning prediction of malaria vaccine efficacy based on antibody profiles

Jacqueline Wistuba-Hamprecht, Bernhard Reuter, Rolf Fendel, Stephen L. Hoffman, Joseph J. Campo, Philip L. Felgner, Peter G. Kremsner, Benjamin Mordmüller, Nico Pfeifer

PLOS Computational Biology: published June 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012131

Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors

Christina M. P. Ray, Huilin Yang, Jamie B. Spangler, Feilim Mac Gabhann

PLOS Computational Biology: published June 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012157

Strong association between genomic 3D structure and CRISPR cleavage efficiency

Shaked Bergman, Tamir Tuller

PLOS Computational Biology: published June 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012214

Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics

Roberth Anthony Rojas Chávez, Mohammad Fili, Changze Han, Syed A. Rahman, Isaiah G. L. Bicar, Sullivan Gregory, Annika Helverson, Guiping Hu, Benjamin W. Darbro, Jishnu Das, Grant D. Brown, Hillel Haim

PLOS Computational Biology: published June 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012215

Infection patterns in simple and complex contagion processes on networks

Diego Andrés Contreras, Giulia Cencetti, Alain Barrat

PLOS Computational Biology: published June 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012206

Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies

Xiangting Li, Tom Chou

PLOS Computational Biology: published June 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012183

Older adults select different but not simpler strategies than younger adults in risky choice

Florian Bolenz, Thorsten Pachur

PLOS Computational Biology: published June 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012204

Regulatory properties of transcription factors with diverse mechanistic function

Md Zulfikar Ali, Sunil Guharajan, Vinuselvi Parisutham, Robert C. Brewster

PLOS Computational Biology: published June 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012194

Zero-shot denoising of microscopy images recorded at high-resolution limits

Sebastian Salwig, Jakob Drefs, Jörg Lücke

PLOS Computational Biology: published June 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012192

Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites

Nikolaos M. Dimitriou, Salvador Flores-Torres, Maria Kyriakidou, Joseph Matthew Kinsella, Georgios D. Mitsis

PLOS Computational Biology: published June 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012112

The influence of cross-border mobility on the COVID-19 epidemic in Nordic countries

Mikhail Shubin, Hilde Kjelgaard Brustad, Jørgen Eriksson Midtbø, Felix Günther, Laura Alessandretti, Tapio Ala-Nissila, Gianpaolo Scalia Tomba, Mikko Kivelä, Louis Yat Hin Chan, Lasse Leskelä

PLOS Computational Biology: published June 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012182

Conductance-based dendrites perform Bayes-optimal cue integration

Jakob Jordan, João Sacramento, Willem A. M. Wybo, Mihai A. Petrovici, Walter Senn

PLOS Computational Biology: published June 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012047

Revisiting the invasion paradox: Resistance-richness relationship is driven by augmentation and displacement trends

Yu Zhu, Babak Momeni

PLOS Computational Biology: published June 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012193

The attentive reconstruction of objects facilitates robust object recognition

Seoyoung Ahn, Hossein Adeli, Gregory J. Zelinsky

PLOS Computational Biology: published June 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012159

An algorithm to build synthetic temporal contact networks based on close-proximity interactions data

Audrey Duval, Quentin J. Leclerc, Didier Guillemot, Laura Temime, Lulla Opatowski

PLOS Computational Biology: published June 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012227

Combined translational and rotational perturbations of standing balance reveal contributions of reduced reciprocal inhibition to balance impairments in children with cerebral palsy

Jente Willaert, Kaat Desloovere, Anja Van Campenhout, Lena H. Ting, Friedl De Groote

PLOS Computational Biology: published June 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012209

Threshold-awareness in adaptive cancer therapy

MingYi Wang, Jacob G. Scott, Alexander Vladimirsky

PLOS Computational Biology: published June 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012165

Missing data in amortized simulation-based neural posterior estimation

Zijian Wang, Jan Hasenauer, Yannik Schälte

PLOS Computational Biology: published June 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012184

Computational design of Periplasmic binding protein biosensors guided by molecular dynamics

Jack M. O’Shea, Peter Doerner, Annis Richardson, Christopher W. Wood

PLOS Computational Biology: published June 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012212

A dynamic foot model for predictive simulations of human gait reveals causal relations between foot structure and whole-body mechanics

Lars D’Hondt, Friedl De Groote, Maarten Afschrift

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012219

Beliefs, compulsive behavior and reduced confidence in control

Lionel Rigoux, Klaas E. Stephan, Frederike H. Petzschner

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012207

ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii

Lakshmipuram S. Swapna, Grant C. Stevens, Aline Sardinha-Silva, Lucas Zhongming Hu, Verena Brand, Daniel D. Fusca, Cuihong Wan, Xuejian Xiong, Jon P. Boyle, Michael E. Grigg, Andrew Emili, John Parkinson

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012208

GEM-based computational modeling for exploring metabolic interactions in a microbial community

Soraya Mirzaei, Mojtaba Tefagh

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012233

Knotted artifacts in predicted 3D RNA structures

Bartosz A. Gren, Maciej Antczak, Tomasz Zok, Joanna I. Sulkowska, Marta Szachniuk

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011959

Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data

Tina Yao, Endrit Pajaziti, Michael Quail, Silvia Schievano, Jennifer Steeden, Vivek Muthurangu

PLOS Computational Biology: published June 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012231

Correction

Correction: Seasonal influenza: Modelling approaches to capture immunity propagation

Edward M. Hill, Stavros Petrou, Simon de Lusignan, Ivelina Yonova, Matt J. Keeling

PLOS Computational Biology: published June 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012213

Software

Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline

Joshua M. Mitchell, Yuanye Chi, Maheshwor Thapa, Zhiqiang Pang, Jianguo Xia, Shuzhao Li

PLOS Computational Biology: published June 6, 2024 | https://doi.org/10.1371/journal.pcbi.1011912

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June 2024

Cover

Object reconstruction as top-down attentional feedback

Education Articles

Perspective

Research Articles

Correction

Related Articles

Methods

Software

This page is brought to you by Brian Golding (Golding@McMaster.CA) and is copied locally here to speed your access. To go to the original page (should you find something interesting or should you wish to follow links) click on

Current Issue of PLoSBiology