August 2023

Acute lymphoblastic leukaemia (ALL) is a blood cancer which mainly affects children and adolescents. Therapy fails for approximately 20% of patients who suffer relapse. We use methods from topological data analysis, which quantifies shapes in data, to analyse pre-treatment ALL datasets with known outcomes. We combine these analyses with machine learning to identify significant shape characteristics in the data (notably, isolated data islands and empty spaces between them) and show that they predict risk of relapse with high accuracy. We also confirm the predictive power of CD10, CD20, CD38 and CD45 as biomarkers for ALL diagnosis. Chulián et al 2023

Image Credit: Salvador Chulián, salvador.chulian@uca.es

Editorial

The blossoming of methods and software in computational biology

Feilim Mac Gabhann, Virginia E. Pitzer, Jason A. Papin

PLOS Computational Biology: published August 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011390

Education Articles

Ten simple rules for writing a technical book

Jess Haberman, Greg Wilson

PLOS Computational Biology: published August 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011305

Ten quick tips for harnessing the power of ChatGPT in computational biology

Tiago Lubiana, Rafael Lopes, Pedro Medeiros, Juan Carlo Silva, Andre Nicolau Aquime Goncalves, Vinicius Maracaja-Coutinho, Helder I. Nakaya

PLOS Computational Biology: published August 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011319

Ten simple rules for a mom-friendly Academia

Esther Sebastián-González, Eva Graciá, Alejandra Morán-Ordóñez, Irene Pérez-Ibarra, Ana Sanz-Aguilar, Mar Sobral

PLOS Computational Biology: published August 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011284

Perspective

The specious art of single-cell genomics

Tara Chari, Lior Pachter

PLOS Computational Biology: published August 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011288

Reviews

Mathematical models of developmental vascular remodelling: A review

Jessica R. Crawshaw, Jennifer A. Flegg, Miguel O. Bernabeu, James M. Osborne

PLOS Computational Biology: published August 3, 2023 | https://doi.org/10.1371/journal.pcbi.1011130

From time-series transcriptomics to gene regulatory networks: A review on inference methods

Malvina Marku, Vera Pancaldi

PLOS Computational Biology: published August 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011254

Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook

Sizhe Qiu, Aidong Yang, Hong Zeng

PLOS Computational Biology: published August 24, 2023 | https://doi.org/10.1371/journal.pcbi.1011391

Research Articles

Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes

Kevin Sawade, Andreas Marx, Christine Peter, Oleksandra Kukharenko

PLOS Computational Biology: published August 1, 2023 | https://doi.org/10.1371/journal.pcbi.1010531

Hybrid predictive coding: Inferring, fast and slow

Alexander Tscshantz, Beren Millidge, Anil K. Seth, Christopher L. Buckley

PLOS Computational Biology: published August 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011280

Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics

Atesmachew Hailegiorgis, Yuji Ishida, Nicholson Collier, Michio Imamura, Zhenzhen Shi, Vladimir Reinharz, Masataka Tsuge, Danny Barash, Nobuhiko Hiraga, Hiroshi Yokomichi, Chise Tateno, Jonathan Ozik, Susan L. Uprichard, Kazuaki Chayama, Harel Dahari

PLOS Computational Biology: published August 3, 2023 | https://doi.org/10.1371/journal.pcbi.1011309

Modeling the role of the thalamus in resting-state functional connectivity: Nature or structure

Jesús Cabrera-Álvarez, Nina Doorn, Fernando Maestú, Gianluca Susi

PLOS Computational Biology: published August 3, 2023 | https://doi.org/10.1371/journal.pcbi.1011007

Species-specific wiring of cortical circuits for small-world networks in the primary visual cortex

Seungdae Baek, Youngjin Park, Se-Bum Paik

PLOS Computational Biology: published August 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011343

A triple distinction of cerebellar function for oculomotor learning and fatigue compensation

Jana Masselink, Alexis Cheviet, Caroline Froment-Tilikete, Denis Pélisson, Markus Lappe

PLOS Computational Biology: published August 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011322

The σ^B alternative sigma factor circuit modulates noise to generate different types of pulsing dynamics

Torkel E. Loman, James C. W. Locke

PLOS Computational Biology: published August 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011265

Evolutionary dynamics on sequential temporal networks

Anzhi Sheng, Aming Li, Long Wang

PLOS Computational Biology: published August 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011333

Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution

Joeri van Strien, Felix Evers, Madhurya Lutikurti, Stijn L. Berendsen, Alejandro Garanto, Geert-Jan van Gemert, Alfredo Cabrera-Orefice, Richard J. Rodenburg, Ulrich Brandt, Taco W. A. Kooij, Martijn A. Huynen

PLOS Computational Biology: published August 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011090

Effective mechanical potential of cell–cell interaction explains three-dimensional morphologies during early embryogenesis

Hiroshi Koyama, Hisashi Okumura, Atsushi M. Ito, Kazuyuki Nakamura, Tetsuhisa Otani, Kagayaki Kato, Toshihiko Fujimori

PLOS Computational Biology: published August 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011306

Synaptic weights that correlate with presynaptic selectivity increase decoding performance

Júlia V. Gallinaro, Benjamin Scholl, Claudia Clopath

PLOS Computational Biology: published August 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011362

Modeling the kinetics of the neutralizing antibody response against SARS-CoV-2 variants after several administrations of Bnt162b2

Quentin Clairon, Mélanie Prague, Delphine Planas, Timothée Bruel, Laurent Hocqueloux, Thierry Prazuck, Olivier Schwartz, Rodolphe Thiébaut, Jérémie Guedj

PLOS Computational Biology: published August 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011282

Geometry of population activity in spiking networks with low-rank structure

Ljubica Cimeša, Lazar Ciric, Srdjan Ostojic

PLOS Computational Biology: published August 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011315

Ensemble inference of unobserved infections in networks using partial observations

Renquan Zhang, Jilei Tai, Sen Pei

PLOS Computational Biology: published August 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011355

Simulating the effect of ankle plantarflexion and inversion-eversion exoskeleton torques on center of mass kinematics during walking

Nicholas A. Bianco, Steven H. Collins, Karen Liu, Scott L. Delp

PLOS Computational Biology: published August 7, 2023 | https://doi.org/10.1371/journal.pcbi.1010712

Spatial organisation of the mesoscale connectome: A feature influencing synchrony and metastability of network dynamics

Michael Mackay, Siyu Huo, Marcus Kaiser

PLOS Computational Biology: published August 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011349

Investigating the ability of astrocytes to drive neural network synchrony

Gregory Handy, Alla Borisyuk

PLOS Computational Biology: published August 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011290

Impact of variants of concern on SARS-CoV-2 viral dynamics in non-human primates

Aurélien Marc, Romain Marlin, Flora Donati, Mélanie Prague, Marion Kerioui, Cécile Hérate, Marie Alexandre, Nathalie Dereuddre-bosquet, Julie Bertrand, Vanessa Contreras, Sylvie Behillil, Pauline Maisonnasse, Sylvie Van Der Werf, Roger Le Grand, Jérémie Guedj

PLOS Computational Biology: published August 9, 2023 | https://doi.org/10.1371/journal.pcbi.1010721

The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions

Diego Tec-Campos, Camila Posadas, Juan D. Tibocha-Bonilla, Deepan Thiruppathy, Nathan Glonek, Cristal Zuñiga, Alejandro Zepeda, Karsten Zengler

PLOS Computational Biology: published August 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011371

Redundant representations are required to disambiguate simultaneously presented complex stimuli

W. Jeffrey Johnston, David J. Freedman

PLOS Computational Biology: published August 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011327

Call detail record aggregation methodology impacts infectious disease models informed by human mobility

Hamish Gibbs, Anwar Musah, Omar Seidu, William Ampofo, Franklin Asiedu-Bekoe, Jonathan Gray, Wole A. Adewole, James Cheshire, Michael Marks, Rosalind M. Eggo

PLOS Computational Biology: published August 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011368

A new method for the analysis of access period experiments, illustrated with whitefly-borne cassava mosaic begomovirus

Ruairí Donnelly, Christopher A. Gilligan

PLOS Computational Biology: published August 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011291

Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration

Caetano Souto-Maior, Yazmin L. Serrano Negron, Susan T. Harbison

PLOS Computational Biology: published August 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011389

SARS-CoV-2 infection perturbs enhancer mediated transcriptional regulation of key pathways

Yahel Yedidya, Daniel Davis, Yotam Drier

PLOS Computational Biology: published August 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011397

Influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics within human airway epithelium

Benjamin Raach, Nils Bundgaard, Marika J. Haase, Jörn Starruß, Rocio Sotillo, Megan L. Stanifer, Frederik Graw

PLOS Computational Biology: published August 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011356

VarSCAT: A computational tool for sequence context annotations of genomic variants

Ning Wang, Sofia Khan, Laura L. Elo

PLOS Computational Biology: published August 11, 2023 | https://doi.org/10.1371/journal.pcbi.1010727

Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy

Christina Y. Lee, Jenna Diegel, Michael T. France, Jacques Ravel, Kelly B. Arnold

PLOS Computational Biology: published August 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011295

Functional and spatial rewiring principles jointly regulate context-sensitive computation

Jia Li, Ilias Rentzeperis, Cees van Leeuwen

PLOS Computational Biology: published August 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011325

Intrinsic motivation for choice varies with individual risk attitudes and the controllability of the environment

Jérôme Munuera, Marta Ribes Agost, David Bendetowicz, Adrien Kerebel, Valérian Chambon, Brian Lau

PLOS Computational Biology: published August 11, 2023 | https://doi.org/10.1371/journal.pcbi.1010551

Receptive field sizes and neuronal encoding bandwidth are constrained by axonal conduction delays

Tim C. Hladnik, Jan Grewe

PLOS Computational Biology: published August 11, 2023 | https://doi.org/10.1371/journal.pcbi.1010871

Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance

Johann F. Jadebeck, Wolfgang Wiechert, Katharina Nöh

PLOS Computational Biology: published August 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011378

Collaborative nowcasting of COVID-19 hospitalization incidences in Germany

Daniel Wolffram, Sam Abbott, Matthias an der Heiden, Sebastian Funk, Felix Günther, Davide Hailer, Stefan Heyder, Thomas Hotz, Jan van de Kassteele, Helmut Küchenhoff, Sören Müller-Hansen, Diellë Syliqi, Alexander Ullrich, Maximilian Weigert, Melanie Schienle, Johannes Bracher

PLOS Computational Biology: published August 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011394

Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals

Akhilesh Nandan, Aneta Koseska

PLOS Computational Biology: published August 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011388

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

William T. Scott Jr., Sara Benito-Vaquerizo, Johannes Zimmermann, Djordje Bajić, Almut Heinken, Maria Suarez-Diez, Peter J. Schaap

PLOS Computational Biology: published August 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011363

Prediction of opioid-related outcomes in a medicaid surgical population: Evidence to guide postoperative opiate therapy and monitoring

Oualid El Hajouji, Ran S. Sun, Alban Zammit, Keith Humphreys, Steven M. Asch, Ian Carroll, Catherine M. Curtin, Tina Hernandez-Boussard

PLOS Computational Biology: published August 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011376

In-silico and in-vitro morphometric analysis of intestinal organoids

Sandra Montes-Olivas, Danny Legge, Abbie Lund, Alexander G. Fletcher, Ann C. Williams, Lucia Marucci, Martin Homer

PLOS Computational Biology: published August 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011386

The shape of cancer relapse: Topological data analysis predicts recurrence in paediatric acute lymphoblastic leukaemia

Salvador Chulián, Bernadette J. Stolz, Álvaro Martínez-Rubio, Cristina Blázquez Goñi, Juan F. Rodríguez Gutiérrez, Teresa Caballero Velázquez, Águeda Molinos Quintana, Manuel Ramírez Orellana, Ana Castillo Robleda, José Luis Fuster Soler, Alfredo Minguela Puras, María V. Martínez Sánchez, María Rosa, Víctor M. Pérez-García, Helen M. Byrne

PLOS Computational Biology: published August 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011329

Deconvolution of cancer cell states by the XDec-SM method

Oscar D. Murillo, Varduhi Petrosyan, Emily L. LaPlante, Lacey E. Dobrolecki, Michael T. Lewis, Aleksandar Milosavljevic

PLOS Computational Biology: published August 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011365

A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance

Peter Czuppon, Troy Day, Florence Débarre, François Blanquart

PLOS Computational Biology: published August 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011364

A physiologically based pharmacokinetic model to optimize the dosage regimen and withdrawal time of cefquinome in pigs

Kun Mi, Lei Sun, Yixuan Hou, Xin Cai, Kaixiang Zhou, Wenjin Ma, Xiangyue Xu, Yuanhu Pan, Zhenli Liu, Lingli Huang

PLOS Computational Biology: published August 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011331

An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space

Bastian Volker Helmut Hornung, Nicolas Terrapon

PLOS Computational Biology: published August 16, 2023 | https://doi.org/10.1371/journal.pcbi.1010881

Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning

Li Xie, Lei Xie

PLOS Computational Biology: published August 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010974

Enhancing reinforcement learning models by including direct and indirect pathways improves performance on striatal dependent tasks

Kim T. Blackwell, Kenji Doya

PLOS Computational Biology: published August 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011385

Efficient sampling-based Bayesian Active Learning for synaptic characterization

Camille Gontier, Simone Carlo Surace, Igor Delvendahl, Martin Müller, Jean-Pascal Pfister

PLOS Computational Biology: published August 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011342

Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding

Isaline Guex, Christian Mazza, Manupriyam Dubey, Maxime Batsch, Renyi Li, Jan Roelof van der Meer

PLOS Computational Biology: published August 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011402

Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses

Connor J. Moore, Christopher P. Holstege, Jason A. Papin

PLOS Computational Biology: published August 21, 2023 | https://doi.org/10.1371/journal.pcbi.1010927

A subcomponent-guided deep learning method for interpretable cancer drug response prediction

Xuan Liu, Wen Zhang

PLOS Computational Biology: published August 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011382

When does humoral memory enhance infection?

Ariel Nikas, Hasan Ahmed, Mia R. Moore, Veronika I. Zarnitsyna, Rustom Antia

PLOS Computational Biology: published August 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011377

STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring

Azka Javaid, Hildreth Robert Frost

PLOS Computational Biology: published August 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011413

Inferring gene regulatory networks using transcriptional profiles as dynamical attractors

Ruihao Li, Jordan C. Rozum, Morgan M. Quail, Mohammad N. Qasim, Suzanne S. Sindi, Clarissa J. Nobile, Réka Albert, Aaron D. Hernday

PLOS Computational Biology: published August 22, 2023 | https://doi.org/10.1371/journal.pcbi.1010991

Mathematical modeling indicates that regulatory inhibition of CD8⁺ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load

Jonathan W. Cody, Amy L. Ellis-Connell, Shelby L. O’Connor, Elsje Pienaar

PLOS Computational Biology: published August 24, 2023 | https://doi.org/10.1371/journal.pcbi.1011425

Curated single cell multimodal landmark datasets for R/Bioconductor

Kelly B. Eckenrode, Dario Righelli, Marcel Ramos, Ricard Argelaguet, Christophe Vanderaa, Ludwig Geistlinger, Aedin C. Culhane, Laurent Gatto, Vincent Carey, Martin Morgan, Davide Risso, Levi Waldron

PLOS Computational Biology: published August 25, 2023 | https://doi.org/10.1371/journal.pcbi.1011324

Rapid memory encoding in a recurrent network model with behavioral time scale synaptic plasticity

Pan Ye Li, Alex Roxin

PLOS Computational Biology: published August 25, 2023 | https://doi.org/10.1371/journal.pcbi.1011139

Disentangling Abstraction from Statistical Pattern Matching in Human and Machine Learning

Sreejan Kumar, Ishita Dasgupta, Nathaniel D. Daw, Jonathan. D. Cohen, Thomas L. Griffiths

PLOS Computational Biology: published August 25, 2023 | https://doi.org/10.1371/journal.pcbi.1011316

TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary structure(s) of RNA targets

Atara Neugroschl, Irina E. Catrina

PLOS Computational Biology: published August 25, 2023 | https://doi.org/10.1371/journal.pcbi.1011418

Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network

Wenxing Hu, Lixin Guan, Mengshan Li

PLOS Computational Biology: published August 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011370

Accelerating Bayesian inference of dependency between mixed-type biological traits

Zhenyu Zhang, Akihiko Nishimura, Nídia S. Trovão, Joshua L. Cherry, Andrew J. Holbrook, Xiang Ji, Philippe Lemey, Marc A. Suchard

PLOS Computational Biology: published August 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011419

Switching state-space modeling of neural signal dynamics

Mingjian He, Proloy Das, Gladia Hotan, Patrick L. Purdon

PLOS Computational Biology: published August 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011395

Neural network models for influenza forecasting with associated uncertainty using Web search activity trends

Michael Morris, Peter Hayes, Ingemar J. Cox, Vasileios Lampos

PLOS Computational Biology: published August 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011392

Structural identifiability of biomolecular controller motifs with and without flow measurements as model output

Eivind S. Haus, Tormod Drengstig, Kristian Thorsen

PLOS Computational Biology: published August 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011398

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models

Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina Sakharova, Manja Marz, Alejandro Reyes Muñoz, Martin Hölzer, Robert D. Finn

PLOS Computational Biology: published August 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011422

Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool

Rebecca K. Nash, Samir Bhatt, Anne Cori, Pierre Nouvellet

PLOS Computational Biology: published August 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011439

Scoring epidemiological forecasts on transformed scales

Nikos I. Bosse, Sam Abbott, Anne Cori, Edwin van Leeuwen, Johannes Bracher, Sebastian Funk

PLOS Computational Biology: published August 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011393

Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model

Shawn A. Means, Mathias W. Roesler, Amy S. Garrett, Leo Cheng, Alys R. Clark

PLOS Computational Biology: published August 30, 2023 | https://doi.org/10.1371/journal.pcbi.1011359

Modulation of antigen discrimination by duration of immune contacts in a kinetic proofreading model of T cell activation with extreme statistics

Jonathan Morgan, Alan E. Lindsay

PLOS Computational Biology: published August 30, 2023 | https://doi.org/10.1371/journal.pcbi.1011216

Automatic extraction of actin networks in plants

Jordan Hembrow, Michael J. Deeks, David M. Richards

PLOS Computational Biology: published August 30, 2023 | https://doi.org/10.1371/journal.pcbi.1011407

iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction

Lin Yuan, Jiawang Zhao, Zhen Shen, Qinhu Zhang, Yushui Geng, Chun-Hou Zheng, De-Shuang Huang

PLOS Computational Biology: published August 31, 2023 | https://doi.org/10.1371/journal.pcbi.1011344

Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family

Olivier Dennler, François Coste, Samuel Blanquart, Catherine Belleannée, Nathalie Théret

PLOS Computational Biology: published August 31, 2023 | https://doi.org/10.1371/journal.pcbi.1011404

E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction

Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, Debswapna Bhattacharya

PLOS Computational Biology: published August 31, 2023 | https://doi.org/10.1371/journal.pcbi.1011435

Methods

serosim: An R package for simulating serological data arising from vaccination, epidemiological and antibody kinetics processes

Arthur Menezes, Saki Takahashi, Isobel Routledge, C. Jessica E. Metcalf, Andrea L. Graham, James A. Hay

PLOS Computational Biology: published August 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011384

Software

BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus

Agnete T. Lundgaard, Frédéric Burdet, Troels Siggaard, David Westergaard, Danai Vagiaki, Lisa Cantwell, Timo Röder, Dorte Vistisen, Thomas Sparsø, Giuseppe N. Giordano, Mark Ibberson, Karina Banasik, Søren Brunak

PLOS Computational Biology: published August 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011403

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Topological data analysis predicts recurrence in paediatric acute lymphoblastic leukaemia

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