Current Issue | PLOS Computational Biology

The Conditional Probabilistic Diffusion Model (CPDM) generates synthetic MRIs from multi-omic data through two pivotal phases: forward and backward diffusion. In forward diffusion, noise is progressively added to MRI images, ultimately degrading them to pure noise. In backward diffusion, the model iteratively refines the noisy images by removing the noise predicted by a cross-attention enhanced UNet module, guided by multi-omic features processed through Bayesian Tensor Factorization (BTF), to precisely reconstruct new MRIs. Chen et al

Image Credit: Lianghong Chen, Western University, 2024. Published under the Creative Commons Attribution License (CC BY 4.0).

Education

Ten simple rules to bridge ecology and palaeoecology by publishing outside palaeoecological journals

Nick Schafstall, Xavier Benito, Sandra O. Brugger, Althea L. Davies, Erle Ellis, Sergi Pla-Rabes, Alicja Bonk, M. Jane Bunting, Frank M. Chambers, Suzette G. A. Flantua, Tamara L. Fletcher, Caroline Greiser, Armand Hernández, Benjamin Gwinneth, Gerbrand Koren, Katarzyna Marcisz, Encarni Montoya, Adolfo Quesada-Román, Amila S. Ratnayake, Pierre Sabatier, John P. Smol, Nancy Y. Suárez-Mozo

PLOS Computational Biology: published October 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012487

Perspectives

Gene signatures for cancer research: A 25-year retrospective and future avenues

Wei Liu, Huaqin He, Davide Chicco

PLOS Computational Biology: published October 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012512

Best practices for estimating and reporting epidemiological delay distributions of infectious diseases

Kelly Charniga, Sang Woo Park, Andrei R. Akhmetzhanov, Anne Cori, Jonathan Dushoff, Sebastian Funk, Katelyn M. Gostic, Natalie M. Linton, Adrian Lison, Christopher E. Overton, Juliet R. C. Pulliam, Thomas Ward, Simon Cauchemez, Sam Abbott

PLOS Computational Biology: published October 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012520

Research Articles

Why aphid virus retention needs more attention: Modelling aphid behaviour and virus manipulation in non-persistent plant virus transmission

Elin K. Falla, Nik J. Cunniffe

PLOS Computational Biology: published October 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012479

Spatial distribution of poultry farms using point pattern modelling: A method to address livestock environmental impacts and disease transmission risks

Marie-Cécile Dupas, Francesco Pinotti, Chaitanya Joshi, Madhvi Joshi, Weerapong Thanapongtharm, Madhur Dhingra, Damer Blake, Fiona Tomley, Marius Gilbert, Guillaume Fournié

PLOS Computational Biology: published October 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011980

Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network

Bertram Klinger, Isabel Rausch, Anja Sieber, Helmut Kutz, Vanessa Kruse, Marieluise Kirchner, Philipp Mertins, Arnd Kieser, Nils Blüthgen, Dieter Kube

PLOS Computational Biology: published October 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012488

Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data

Safiye Celik, Jan-Christian Hütter, Sandra Melo Carlos, Nathan H. Lazar, Rahul Mohan, Conor Tillinghast, Tommaso Biancalani, Marta M. Fay, Berton A. Earnshaw, Imran S. Haque

PLOS Computational Biology: published October 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012463

Quantitative evaluation of DNA damage repair dynamics to elucidate predictors of autism vs. cancer in individuals with germline PTEN variants

Ruipeng Wei, Masahiro Hitomi, Tammy Sadler, Lamis Yehia, Daniela Calvetti, Jacob Scott, Charis Eng

PLOS Computational Biology: published October 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012449

Probing the link between vision and language in material perception using psychophysics and unsupervised learning

Chenxi Liao, Masataka Sawayama, Bei Xiao

PLOS Computational Biology: published October 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012481

Reverse-engineered models reveal differential membrane properties of autonomic and cutaneous unmyelinated fibers

Brandon J. Thio, Nathan D. Titus, Nicole A. Pelot, Warren M. Grill

PLOS Computational Biology: published October 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012475

The optimal spatially-dependent control measures to effectively and economically eliminate emerging infectious diseases

Fan Xia, Yanni Xiao, Junling Ma

PLOS Computational Biology: published October 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012498

A flexible generative algorithm for growing in silico placentas

Diana C. de Oliveira, Hani Cheikh Sleiman, Kelly Payette, Jana Hutter, Lisa Story, Joseph V. Hajnal, Daniel C. Alexander, Rebecca J. Shipley, Paddy J. Slator

PLOS Computational Biology: published October 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012470

Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer

Lianghong Chen, Zi Huai Huang, Yan Sun, Mike Domaratzki, Qian Liu, Pingzhao Hu

PLOS Computational Biology: published October 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012490

EEG microstate transition cost correlates with task demands

Giacomo Barzon, Ettore Ambrosini, Antonino Vallesi, Samir Suweis

PLOS Computational Biology: published October 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012521

Bayesian polynomial neural networks and polynomial neural ordinary differential equations

Colby Fronk, Jaewoong Yun, Prashant Singh, Linda Petzold

PLOS Computational Biology: published October 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012414

Successful cardiac resynchronization therapy reduces negative septal work in patient-specific models of dyssynchronous heart failure

Amanda Craine, Adarsh Krishnamurthy, Christopher T. Villongco, Kevin Vincent, David E. Krummen, Sanjiv M. Narayan, Roy C. P. Kerckhoffs, Jeffrey H. Omens, Francisco Contijoch, Andrew D. McCulloch

PLOS Computational Biology: published October 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012150

A diel multi-tissue genome-scale metabolic model of Vitis vinifera

Marta Sampaio, Miguel Rocha, Oscar Dias

PLOS Computational Biology: published October 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012506

De novo sensorimotor learning through reuse of movement components

George Gabriel, Faisal Mushtaq, J. Ryan Morehead

PLOS Computational Biology: published October 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012492

Bayesian inference of state feedback control parameters for f_o perturbation responses in cerebellar ataxia

Jessica L. Gaines, Kwang S. Kim, Ben Parrell, Vikram Ramanarayanan, Alvincé L. Pongos, Srikantan S. Nagarajan, John F. Houde

PLOS Computational Biology: published October 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011986

Dynamics of morphogen source formation in a growing tissue

Richard D. J. G. Ho, Kasumi Kishi, Maciej Majka, Anna Kicheva, Marcin Zagorski

PLOS Computational Biology: published October 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012508

Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson’s disease

Adam M. Roth, John H. Buggeln, Joanna E. Hoh, Jonathan M. Wood, Seth R. Sullivan, Truc T. Ngo, Jan A. Calalo, Rakshith Lokesh, Susanne M. Morton, Stephen Grill, John J. Jeka, Michael J. Carter, Joshua G. A. Cashaback

PLOS Computational Biology: published October 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012474

Human motor learning dynamics in high-dimensional tasks

Ankur Kamboj, Rajiv Ranganathan, Xiaobo Tan, Vaibhav Srivastava

PLOS Computational Biology: published October 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012455

Inference and design of antibody specificity: From experiments to models and back

Jorge Fernandez-de-Cossio-Diaz, Guido Uguzzoni, Kévin Ricard, Francesca Anselmi, Clément Nizak, Andrea Pagnani, Olivier Rivoire

PLOS Computational Biology: published October 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012522

Emergent order in epithelial sheets by interplay of cell divisions and cell fate regulation

Philip Greulich

PLOS Computational Biology: published October 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012465

A novel classification framework for genome-wide association study of whole brain MRI images using deep learning

Shaojun Yu, Junjie Wu, Yumeng Shao, Deqiang Qiu, Zhaohui S. Qin, for the Alzheimer’s Disease Neuroimaging Initiative

PLOS Computational Biology: published October 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012527

Regularizing hyperparameters of interacting neural signals in the mouse cortex reflect states of arousal

Dmitry R. Lyamzin, Andrea Alamia, Mohammad Abdolrahmani, Ryo Aoki, Andrea Benucci

PLOS Computational Biology: published October 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012478

Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters

Natchapon Srinak, Porntip Chiewchankaset, Saowalak Kalapanulak, Pornpan Panichnumsin, Treenut Saithong

PLOS Computational Biology: published October 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012533

Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals

Michele Gentili, Kimberly Glass, Enrico Maiorino, Brian D. Hobbs, Zhonghui Xu, Peter J. Castaldi, Michael H. Cho, Craig P. Hersh, Dandi Qiao, Jarrett D. Morrow, Vincent J. Carey, John Platig, Edwin K. Silverman

PLOS Computational Biology: published October 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011079

Understanding dual process cognition via the minimum description length principle

Ted Moskovitz, Kevin J. Miller, Maneesh Sahani, Matthew M. Botvinick

PLOS Computational Biology: published October 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012383

Mapping the physiological changes in sleep regulation across infancy and young childhood

Lachlan Webb, Andrew J. K. Phillips, James A. Roberts

PLOS Computational Biology: published October 21, 2024 | https://doi.org/10.1371/journal.pcbi.1012541

scCaT: An explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing

Xubin Zheng, Dian Meng, Duo Chen, Wan-Ki Wong, Ka-Ho To, Lei Zhu, JiaFei Wu, Yining Liang, Kwong-Sak Leung, Man-Hon Wong, Lixin Cheng

PLOS Computational Biology: published October 21, 2024 | https://doi.org/10.1371/journal.pcbi.1012083

Abrupt and spontaneous strategy switches emerge in simple regularised neural networks

Anika T. Löwe, Léo Touzo, Paul S. Muhle-Karbe, Andrew M. Saxe, Christopher Summerfield, Nicolas W. Schuck

PLOS Computational Biology: published October 21, 2024 | https://doi.org/10.1371/journal.pcbi.1012505

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery

Ulisses Rocha, Jonas Coelho Kasmanas, Rodolfo Toscan, Danilo S. Sanches, Stefania Magnusdottir, Joao Pedro Saraiva

PLOS Computational Biology: published October 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012530

PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites

Yun Zuo, Xingze Fang, Jiayong Wan, Wenying He, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng

PLOS Computational Biology: published October 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012544

Computational joint action: Dynamical models to understand the development of joint coordination

Cecilia De Vicariis, Vinil T. Chackochan, Laura Bandini, Eleonora Ravaschio, Vittorio Sanguineti

PLOS Computational Biology: published October 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011948

Distributed network flows generate localized category selectivity in human visual cortex

Carrisa V. Cocuzza, Ruben Sanchez-Romero, Takuya Ito, Ravi D. Mill, Brian P. Keane, Michael W. Cole

PLOS Computational Biology: published October 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012507

3-D Visualization of Atlantic salmon skin through Ultrasound and Photoacoustic Microscopy

Abhishek Ranjan, Jaya Kumari Swain, Balpreet Singh Ahluwalia, Frank Melandsø

PLOS Computational Biology: published October 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011709

On the identification of differentially-active transcription factors from ATAC-seq data

Felix Ezequiel Gerbaldo, Emanuel Sonder, Vincent Fischer, Selina Frei, Jiayi Wang, Katharina Gapp, Mark D. Robinson, Pierre-Luc Germain

PLOS Computational Biology: published October 23, 2024 | https://doi.org/10.1371/journal.pcbi.1011971

Modelling the impact of vaccination on COVID-19 in African countries

Dephney Mathebula, Abigail Amankwah, Kossi Amouzouvi, Kétévi Adiklè Assamagan, Somiealo Azote, Jesutofunmi Ayo Fajemisin, Jean Baptiste Fankam Fankame, Aluwani Guga, Moses Kamwela, Mulape Mutule Kanduza, Toivo Samuel Mabote, Francisco Fenias Macucule, Azwinndini Muronga, Ann Njeri, Michael Olusegun Oluwole, Cláudio Moisés Paulo

PLOS Computational Biology: published October 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012456

Just-in-time: Gaze guidance in natural behavior

Ashima Keshava, Farbod Nosrat Nezami, Henri Neumann, Krzysztof Izdebski, Thomas Schüler, Peter König

PLOS Computational Biology: published October 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012529

Tuning collective behaviour in zebrafish with genetic modification

Yushi Yang, Abdelwahab Kawafi, Qiao Tong, Erika Kague, Chrissy L. Hammond, C. Patrick Royall

PLOS Computational Biology: published October 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012034

IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation

Haolin Jiang, Yulian Xu, Yunguang Tong, Dong Zhang, Ruhong Zhou

PLOS Computational Biology: published October 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012293

Reinforcement learning when your life depends on it: A neuro-economic theory of learning

Jiamu Jiang, Emilie Foyard, Mark C. W. van Rossum

PLOS Computational Biology: published October 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012554

Non-genetic differences underlie variability in proliferation among esophageal epithelial clones

Raúl A. Reyes Hueros, Rodrigo A. Gier, Sydney M. Shaffer

PLOS Computational Biology: published October 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012360

Competitive plasticity to reduce the energetic costs of learning

Mark C. W. van Rossum, Aaron Pache

PLOS Computational Biology: published October 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012553

Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium

Olga A. Nev, Elena Zamaraeva, Romain De Oliveira, Ilia Ryzhkov, Lucian Duvenage, Wassim Abou-Jaoudé, Djomangan Adama Ouattara, Jennifer Claire Hoving, Ivana Gudelj, Alistair J. P. Brown

PLOS Computational Biology: published October 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012545

Integrating information from historical data into mechanistic models for influenza forecasting

Alessio Andronico, Juliette Paireau, Simon Cauchemez

PLOS Computational Biology: published October 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012523

Learning probability distributions of sensory inputs with Monte Carlo predictive coding

Gaspard Oliviers, Rafal Bogacz, Alexander Meulemans

PLOS Computational Biology: published October 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012532

Autistic traits foster effective curiosity-driven exploration

Francesco Poli, Maran Koolen, Carlos A. Velázquez-Vargas, Jessica Ramos-Sanchez, Marlene Meyer, Rogier B. Mars, Nanda Rommelse, Sabine Hunnius

PLOS Computational Biology: published October 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012453

Structural influences on synaptic plasticity: The role of presynaptic connectivity in the emergence of E/I co-tuning

Emmanouil Giannakakis, Oleg Vinogradov, Victor Buendía, Anna Levina

PLOS Computational Biology: published October 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012510

Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop

Lingxia Qiao, Michael Getz, Ben Gross, Brian Tenner, Jin Zhang, Padmini Rangamani

PLOS Computational Biology: published October 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012564

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history

Gabriel A. A. Silva, Avril M. Harder, Kenneth B. Kirksey, Samarth Mathur, Janna R. Willoughby

PLOS Computational Biology: published October 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012566

A Computational Framework for Understanding the Impact of Prior Experiences on Pain Perception and Neuropathic Pain

Malin Ramne, Jon Sensinger

PLOS Computational Biology: published October 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012097

Formal Comment

The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense

Jan Lause, Philipp Berens, Dmitry Kobak

PLOS Computational Biology: published October 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012403

Methods

Compression-based inference of network motif sets

Alexis Bénichou, Jean-Baptiste Masson, Christian L. Vestergaard

PLOS Computational Biology: published October 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012460

DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle

Yujie Zhang, Mark Mao, Robert Zhang, Yen-Te Liao, Vivian C. H. Wu

PLOS Computational Biology: published October 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012525

Mcadet: A feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection

Saishi Cui, Sina Nassiri, Issa Zakeri

PLOS Computational Biology: published October 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012560

Enhancing insights in sexually transmitted infection mapping: Syphilis in Forsyth County, North Carolina, a case study

Lani Fox, William C. Miller, Dionne Gesink, Irene Doherty, Marc Serre

PLOS Computational Biology: published October 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012464

TIBA: A web application for the visual analysis of temporal occurrences, interactions, and transitions of animal behavior

Nicolai Kraus, Michael Aichem, Karsten Klein, Etienne Lein, Alex Jordan, Falk Schreiber

PLOS Computational Biology: published October 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012425

October 2024

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CPDM: A Conditional Probabilistic Diffusion Model for Synthesizing Breast Cancer MRI from Integrated Multi-Omic Data Profiles

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