PLOS Computational Biology

2005 - 2025

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Volume 19, issue 12, 2023

multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results pp. 1-27

Aastha Khatiwada, Ayse Selen Yilmaz, Bethany J Wolf, Maciej Pietrzak and Dongjun Chung

Using mixture density networks to emulate a stochastic within-host model of Francisella tularensis infection pp. 1-15

Jonathan Carruthers and Thomas Finnie

The influence of saccades on yaw gaze stabilization in fly flight pp. 1-15

Brock A Davis and Jean-Michel Mongeau

From dawn till dusk: Time-adaptive bayesian optimization for neurostimulation pp. 1-24

John E Fleming, Ines Pont Sanchis, Oscar Lemmens, Angus Denison-Smith, Timothy O West, Timothy Denison and Hayriye Cagnan

PyRates—A code-generation tool for modeling dynamical systems in biology and beyond pp. 1-24

Richard Gast, Thomas R Knösche and Ann Kennedy

resevol: An R package for spatially explicit models of pesticide resistance given evolving pest genomes pp. 1-12

A Bradley Duthie, Rosie Mangan, C Rose McKeon, Matthew C Tinsley and Luc F Bussière

RMDGCN: Prediction of RNA methylation and disease associations based on graph convolutional network with attention mechanism pp. 1-21

Lian Liu, Yumeng Zhou and Xiujuan Lei

Major depressive disorder and bistability in an HPA-CNS toggle switch pp. 1-19

Ben Ron Mizrachi, Avichai Tendler, Omer Karin, Tomer Milo, Dafna Haran, Avi Mayo and Uri Alon

Ten simple rules for humane data science pp. 1-7

Hassan Masum and Philip E Bourne

Learning massive interpretable gene regulatory networks of the human brain by merging Bayesian networks pp. 1-25

Niko Bernaola, Mario Michiels, Pedro Larrañaga and Concha Bielza

4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction pp. 1-20

Zihao Wang, Songhao Luo, Zhenquan Zhang, Tianshou Zhou and Jiajun Zhang

Transcript assembly and annotations: Bias and adjustment pp. 1-20

Qimin Zhang and Mingfu Shao

Statistical prediction of microbial metabolic traits from genomes pp. 1-35

Zeqian Li, Ahmed Selim and Seppe Kuehn

Sparsity in an artificial neural network predicts beauty: Towards a model of processing-based aesthetics pp. 1-16

Nicolas M Dibot, Sonia Tieo, Tamra C Mendelson, William Puech and Julien P Renoult

Recurrence risk stratification of hepatocellular carcinomas based on immune gene expression and features extracted from pathological images pp. 1-14

Tao Ding, Xiao Li, Jiu Mo, Gregory Alexander and Jialu Li

Metric information in cognitive maps: Euclidean embedding of non-Euclidean environments pp. 1-14

Tristan Baumann and Hanspeter A Mallot

Ten simple rules for writing a PLOS Computational Biology quick tips article pp. 1-6

Patricia M Palagi, Russell Schwartz, Scott Markel and B F Francis Ouellette

Estimating neuronal firing density: A quantitative analysis of firing rate map algorithms pp. 1-38

Roddy M Grieves

Volume 19, issue 11, 2023

The mechanism of MinD stability modulation by MinE in Min protein dynamics pp. 1-27

William C Carlquist and Eric N Cytrynbaum

Tuning social interactions’ strength drives collective response to light intensity in schooling fish pp. 1-27

Tingting Xue, Xu Li, GuoZheng Lin, Ramón Escobedo, Zhangang Han, Xiaosong Chen, Clément Sire and Guy Theraulaz

External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration pp. 1-27

Chiara Dazzi, Julia Mehl, Mounir Benamar, Holger Gerhardt, Petra Knaus, Georg N Duda and Sara Checa

Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany pp. 1-27

Elisabeth K Brockhaus, Daniel Wolffram, Tanja Stadler, Michael Osthege, Tanmay Mitra, Jonas M Littek, Ekaterina Krymova, Anna J Klesen, Jana S Huisman, Stefan Heyder, Laura M Helleckes, Matthias an der Heiden, Sebastian Funk, Sam Abbott and Johannes Bracher

GENERALIST: A latent space based generative model for protein sequence families pp. 1-15

Hoda Akl, Brooke Emison, Xiaochuan Zhao, Arup Mondal, Alberto Perez and Purushottam D Dixit

Assessing the importance of demographic risk factors across two waves of SARS-CoV-2 using fine-scale case data pp. 1-18

Anthony J Wood, Aeron R Sanchez, Paul R Bessell, Rebecca Wightman and Rowland R Kao

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale pp. 1-26

Tyler W H Backman, Christina Schenk, Tijana Radivojevic, David Ando, Jahnavi Singh, Jeffrey J Czajka, Zak Costello, Jay D Keasling, Yinjie Tang, Elena Akhmatskaya and Hector Garcia Martin

Interaction between decision-making and motor learning when selecting reach targets in the presence of bias and noise pp. 1-26

Tianyao Zhu, Jason P Gallivan, Daniel M Wolpert and J Randall Flanagan

Ten simple rules for students navigating summer research experiences for undergraduates (REU) programs: From application to program completion pp. 1-13

Maria Manzanares, Courtney Peña, Kayla C Kobak and Miranda B Stratton

Exploring strategy differences between humans and monkeys with recurrent neural networks pp. 1-29

Ben Tsuda, Barry J Richmond and Terrence J Sejnowski

Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data pp. 1-21

Javier Kipen and Joakim Jaldén

Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation pp. 1-32

Sarvesh Nikumbh and Boris Lenhard

Modeling the diverse effects of divisive normalization on noise correlations pp. 1-31

Oren Weiss, Hayley A Bounds, Hillel Adesnik and Ruben Coen-Cagli

Attention-based deep clustering method for scRNA-seq cell type identification pp. 1-19

Shenghao Li, Hui Guo, Simai Zhang, Yizhou Li and Menglong Li

Adaptive oscillators support Bayesian prediction in temporal processing pp. 1-25

Keith B Doelling, Luc H Arnal and M Florencia Assaneo

A data-driven semi-parametric model of SARS-CoV-2 transmission in the United States pp. 1-17

John M Drake, Andreas Handel, Éric Marty, Eamon B O’Dea, Tierney O’Sullivan, Giovanni Righi and Andrew T Tredennick

Learning efficient representations of environmental priors in working memory pp. 1-28

Tahra L Eissa and Zachary P Kilpatrick

On convolutional neural networks for selection inference: Revealing the effect of preprocessing on model learning and the capacity to discover novel patterns pp. 1-20

Ryan M Cecil and Lauren A Sugden

Addressing erroneous scale assumptions in microbe and gene set enrichment analysis pp. 1-16

Kyle C McGovern, Michelle Pistner Nixon and Justin D Silverman

Volume 19, issue 10, 2023

Combining the dynamic model and deep neural networks to identify the intensity of interventions during COVID-19 pandemic pp. 1-23

Mengqi He, Sanyi Tang and Yanni Xiao

Temperature sensitive contact modes allosterically gate TRPV3 pp. 1-23

Daniel Burns, Vincenzo Venditti and Davit A Potoyan

Circadian distribution of epileptiform discharges in epilepsy: Candidate mechanisms of variability pp. 1-19

Isabella Marinelli, Jamie J Walker, Udaya Seneviratne, Wendyl D’Souza, Mark J Cook, Clare Anderson, Andrew P Bagshaw, Stafford L Lightman, Wessel Woldman and John R Terry

Lévy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers pp. 1-19

Andrea Falcón-Cortés, Denis Boyer, Maximino Aldana and Gabriel Ramos-Fernández

Rapid runtime learning by curating small datasets of high-quality items obtained from memory pp. 1-32

Joseph Scott German, Guofeng Cui, Chenliang Xu and Robert A Jacobs

Modeling functional cell types in spike train data pp. 1-22

Daniel N Zdeblick, Eric T Shea-Brown, Daniela M Witten and Michael A Buice

Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data pp. 1-22

Lorenzo Posani, Francesca Rizzato, Rémi Monasson and Simona Cocco

A 2D model to study how secondary growth affects the self-supporting behaviour of climbing plants pp. 1-21

Giacomo Vecchiato, Tom Hattermann, Michele Palladino, Fabio Tedone, Patrick Heuret, Nick P Rowe and Pierangelo Marcati

Deep convolutional and conditional neural networks for large-scale genomic data generation pp. 1-21

Burak Yelmen, Aurélien Decelle, Leila Lea Boulos, Antoine Szatkownik, Cyril Furtlehner, Guillaume Charpiat and Flora Jay

Phi fluctuates with surprisal: An empirical pre-study for the synthesis of the free energy principle and integrated information theory pp. 1-30

Christoffer Lundbak Olesen, Peter Thestrup Waade, Larissa Albantakis and Christoph Mathys

Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies pp. 1-35

Yilin Gao and Fengzhu Sun

Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease pp. 1-16

Jaime Cascante-Vega, Marta Galanti, Katharina Schley, Sen Pei and Jeffrey Shaman

Establishing brain states in neuroimaging data pp. 1-16

Zalina Dezhina, Jonathan Smallwood, Ting Xu, Federico E Turkheimer, Rosalyn J Moran, Karl J Friston, Robert Leech and Erik D Fagerholm

Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization pp. 1-17

Fanni Ojala, Mohamad R Abdul Sater, Loren G Miller, James A McKinnell, Mary K Hayden, Susan S Huang, Yonatan H Grad and Pekka Marttinen

Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms pp. 1-45

Larissa Albantakis, Leonardo Barbosa, Graham Findlay, Matteo Grasso, Andrew M Haun, William Marshall, William G P Mayner, Alireza Zaeemzadeh, Melanie Boly, Bjørn E Juel, Shuntaro Sasai, Keiko Fujii, Isaac David, Jeremiah Hendren, Jonathan P Lang and Giulio Tononi

Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker pp. 1-26

Oliver J Meacock and William M Durham

Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning pp. 1-26

Philipp D Lösel, Coline Monchanin, Renaud Lebrun, Alejandra Jayme, Jacob J Relle, Jean-Marc Devaud, Vincent Heuveline and Mathieu Lihoreau

Rational social distancing policy during epidemics with limited healthcare capacity pp. 1-24

Simon K Schnyder, John J Molina, Ryoichi Yamamoto and Matthew S Turner

Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment pp. 1-18

Aymara Sancho-Araiz, Zinnia P Parra-Guillen, Jean Bragard, Sergio Ardanza, Victor Mangas-Sanjuan and Iñaki F Trocóniz

Distilling identifiable and interpretable dynamic models from biological data pp. 1-27

Gemma Massonis, Alejandro F Villaverde and Julio R Banga

Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis pp. 1-29

Steven A LaBelle, A Marsh Poulson Iv, Steve A Maas, Adam Rauff, Gerard A Ateshian and Jeffrey A Weiss

Recognition and reconstruction of cell differentiation patterns with deep learning pp. 1-29

Robin Dirk, Jonas L Fischer, Simon Schardt, Markus J Ankenbrand and Sabine C Fischer

Objects guide human gaze behavior in dynamic real-world scenes pp. 1-39

Nicolas Roth, Martin Rolfs, Olaf Hellwich and Klaus Obermayer

Volume 19, issue 9, 2023

Error-independent effect of sensory uncertainty on motor learning when both feedforward and feedback control processes are engaged pp. 1-45

Christopher L Hewitson, David M Kaplan and Matthew J Crossley

An automated interface for sedimentation velocity analysis in SEDFIT pp. 1-17

Peter Schuck, Samuel C To and Huaying Zhao

Simulation-based inference for efficient identification of generative models in computational connectomics pp. 1-28

Jan Boelts, Philipp Harth, Richard Gao, Daniel Udvary, Felipe Yáñez, Daniel Baum, Hans-Christian Hege, Marcel Oberlaender and Jakob H Macke

Mixtures of strategies underlie rodent behavior during reversal learning pp. 1-28

Nhat Minh Le, Murat Yildirim, Yizhi Wang, Hiroki Sugihara, Mehrdad Jazayeri and Mriganka Sur

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease pp. 1-20

Ziheng Duan, Yi Dai, Ahyeon Hwang, Cheyu Lee, Kaichi Xie, Chutong Xiao, Min Xu, Matthew J Girgenti and Jing Zhang

The inhibitory control of traveling waves in cortical networks pp. 1-32

Grishma Palkar, Jian-young Wu and Bard Ermentrout

Self-loops in evolutionary graph theory: Friends or foes? pp. 1-32

Nikhil Sharma, Sedigheh Yagoobi and Arne Traulsen

Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model pp. 1-31

Shuaijie Zhang, Fan Yang, Lijie Wang, Shucheng Si, Jianmei Zhang and Fuzhong Xue

Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models pp. 1-31

Matthew J Simpson and Oliver J Maclaren

Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony pp. 1-19

Seirana Hashemi, Zahra Razaghi-Moghadam and Zoran Nikoloski

Beyond ℓ1 sparse coding in V1 pp. 1-21

Ilias Rentzeperis, Luca Calatroni, Laurent U Perrinet and Dario Prandi

Identifying a developmental transition in honey bees using gene expression data pp. 1-22

Bryan C Daniels, Ying Wang, Robert E Page and Gro V Amdam

Human-environment feedback and the consistency of proenvironmental behavior pp. 1-22

Claire Ecotière, Sylvain Billiard, Jean-Baptiste André, Pierre Collet, Régis Ferrière and Sylvie Méléard

Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England pp. 1-22

James D Munday, Sam Abbott, Sophie Meakin and Sebastian Funk

Ten simple rules for interpreting and evaluating a meta-analysis pp. 1-13

Rebecca B Carlson, Jennifer R Martin and Robert D Beckett

iCVS—Inferring Cardio-Vascular hidden States from physiological signals available at the bedside pp. 1-29

Neta Ravid Tannenbaum, Omer Gottesman, Azadeh Assadi, Mjaye Mazwi, Uri Shalit and Danny Eytan

A role for cortical interneurons as adversarial discriminators pp. 1-26

Ari S Benjamin and Konrad P Kording

Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data pp. 1-26

Simon Boutry, Raphaël Helaers, Tom Lenaerts and Miikka Vikkula

Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches pp. 1-24

Zheng Jiang, Yue-Yue Shen and Rong Liu

Measuring uncertainty in human visual segmentation pp. 1-24

Jonathan Vacher, Claire Launay, Pascal Mamassian and Ruben Coen-Cagli

Fixation dynamics on hypergraphs pp. 1-24

Ruodan Liu and Naoki Masuda

Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding pp. 1-27

Billy Tchounke, Leopoldo Sanchez, Joseph Martin Bell and David Cros

What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases pp. 1-27

Francis Banville, Dominique Gravel and Timothée Poisot

Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels pp. 1-27

Erik Nordquist, Guohui Zhang, Shrishti Barethiya, Nathan Ji, Kelli M White, Lu Han, Zhiguang Jia, Jingyi Shi, Jianmin Cui and Jianhan Chen

Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models pp. 1-36

Christian Tönsing, Bernhard Steiert, Jens Timmer and Clemens Kreutz

Uncovering specific mechanisms across cell types in dynamical models pp. 1-18

Adrian L Hauber, Marcus Rosenblatt and Jens Timmer

Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics pp. 1-18

Serena Aneli, Piero Fariselli, Elena Chierto, Carla Bini, Carlo Robino and Giovanni Birolo

Volume 19, issue 8, 2023

Switching state-space modeling of neural signal dynamics pp. 1-41

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

Disentangling Abstraction from Statistical Pattern Matching in Human and Machine Learning pp. 1-21

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

iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction pp. 1-22

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

Structural identifiability of biomolecular controller motifs with and without flow measurements as model output pp. 1-33

Eivind S Haus, Tormod Drengstig and Kristian Thorsen

Inferring gene regulatory networks using transcriptional profiles as dynamical attractors pp. 1-31

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

Hybrid predictive coding: Inferring, fast and slow pp. 1-31

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

Redundant representations are required to disambiguate simultaneously presented complex stimuli pp. 1-31

W Jeffrey Johnston and David J Freedman

Enhancing reinforcement learning models by including direct and indirect pathways improves performance on striatal dependent tasks pp. 1-31

Kim T Blackwell and Kenji Doya

Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration pp. 1-31

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

E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction pp. 1-19

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

An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space pp. 1-23

Bastian Volker Helmut Hornung and Nicolas Terrapon

Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model pp. 1-23

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

In-silico and in-vitro morphometric analysis of intestinal organoids pp. 1-23

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

Neural network models for influenza forecasting with associated uncertainty using Web search activity trends pp. 1-23

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

Scoring epidemiological forecasts on transformed scales pp. 1-23

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

Receptive field sizes and neuronal encoding bandwidth are constrained by axonal conduction delays pp. 1-25

Tim C Hladnik and Jan Grewe

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 pp. 1-25

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

The specious art of single-cell genomics pp. 1-20

Tara Chari and Lior Pachter

Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network pp. 1-20

Wenxing Hu, Lixin Guan and Mengshan Li

Mathematical models of developmental vascular remodelling: A review pp. 1-28

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

Efficient sampling-based Bayesian Active Learning for synaptic characterization pp. 1-28

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

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models pp. 1-28

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

Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool pp. 1-14

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

Ten simple rules for writing a technical book pp. 1-6

Jess Haberman and Greg Wilson

Geometry of population activity in spiking networks with low-rank structure pp. 1-34

Ljubica Cimeša, Lazar Ciric and Srdjan Ostojic

A new method for the analysis of access period experiments, illustrated with whitefly-borne cassava mosaic begomovirus pp. 1-15

Ruairí Donnelly and Christopher A Gilligan

Ensemble inference of unobserved infections in networks using partial observations pp. 1-18

Renquan Zhang, Jilei Tai and Sen Pei

Synaptic weights that correlate with presynaptic selectivity increase decoding performance pp. 1-18

Júlia V Gallinaro, Benjamin Scholl and Claudia Clopath

Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance pp. 1-18

Johann F Jadebeck, Wolfgang Wiechert and Katharina Nöh

Curated single cell multimodal landmark datasets for R/Bioconductor pp. 1-24

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

Functional and spatial rewiring principles jointly regulate context-sensitive computation pp. 1-24

Jia Li, Ilias Rentzeperis and Cees van Leeuwen

STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring pp. 1-24

Azka Javaid and Hildreth Robert Frost

From time-series transcriptomics to gene regulatory networks: A review on inference methods pp. 1-26

Malvina Marku and Vera Pancaldi

Ten simple rules for a mom-friendly Academia pp. 1-12

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

Automatic extraction of actin networks in plants pp. 1-29

Jordan Hembrow, Michael J Deeks and David M Richards

Volume 19, issue 7, 2023

Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection pp. 1-21

Alain J Mbebi and Zoran Nikoloski

The interplay between age structure and cultural transmission pp. 1-21

Anne Kandler, Laurel Fogarty and Folgert Karsdorp

Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach pp. 1-22

Christian Blau, Linnea Yvonnesdotter and Erik Lindahl

Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants pp. 1-22

Ahmed Taha, Mauricio Patón, David R Penas, Julio R Banga and Jorge Rodríguez

Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment pp. 1-33

Roger Vargas, Liam Abbott, Daniel Bower, Nicole Frahm, Mike Shaffer and Wen-Han Yu

Sequential mutations in exponentially growing populations pp. 1-32

Michael D Nicholson, David Cheek and Tibor Antal

RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure pp. 1-19

Elena Rivas

Mapping the semi-nested community structure of 3D chromosome contact networks pp. 1-23

Dolores Bernenko, Sang Hoon Lee, Per Stenberg and Ludvig Lizana

Indirect reciprocity with stochastic and dual reputation updates pp. 1-25

Yohsuke Murase and Christian Hilbe

Network feature-based phenotyping of leaf venation robustly reconstructs the latent space pp. 1-17

Kohei Iwamasa and Koji Noshita

LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity pp. 1-17

Juan Xie, Hyeongseon Jeon, Gang Xin, Qin Ma and Dongjun Chung

Monte Carlo samplers for efficient network inference pp. 1-20

Zeliha Kilic, Max Schweiger, Camille Moyer and Steve Pressé

Continuous action with a neurobiologically inspired computational approach reveals the dynamics of selection history pp. 1-20

Mukesh Makwana, Fan Zhang, Dietmar Heinke and Joo-Hyun Song

LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses pp. 1-16

Alexei J Drummond, Kylie Chen, Fábio K Mendes and Dong Xie

Biological complexity facilitates tuning of the neuronal parameter space pp. 1-24

Marius Schneider, Alexander D Bird, Albert Gidon, Jochen Triesch, Peter Jedlicka and Hermann Cuntz

A multi-scale clutch model for adhesion complex mechanics pp. 1-26

Chiara Venturini and Pablo Sáez

Unified tumor growth mechanisms from multimodel inference and dataset integration pp. 1-39

Samantha P Beik, Leonard A Harris, Michael A Kochen, Julien Sage, Vito Quaranta and Carlos F Lopez

Mechanisms of sensorimotor adaptation in a hierarchical state feedback control model of speech pp. 1-39

Kwang S Kim, Jessica L Gaines, Benjamin Parrell, Vikram Ramanarayanan, Srikantan S Nagarajan and John F Houde

Modality independent or modality specific? Common computations underlie confidence judgements in visual and auditory decisions pp. 1-39

Rebecca K West, William J Harrison, Natasha Matthews, Jason B Mattingley and David K Sewell

SpikeShip: A method for fast, unsupervised discovery of high-dimensional neural spiking patterns pp. 1-29

Boris Sotomayor-Gómez, Francesco P Battaglia and Martin Vinck

Volume 19, issue 6, 2023

Adaptive dynamics of memory-one strategies in the repeated donation game pp. 1-31

Philip LaPorte, Christian Hilbe and Martin A Nowak

Humans decompose tasks by trading off utility and computational cost pp. 1-31

Carlos G Correa, Mark K Ho, Frederick Callaway, Nathaniel D Daw and Thomas L Griffiths

Grouping promotes both partnership and rivalry with long memory in direct reciprocity pp. 1-23

Yohsuke Murase and Seung Ki Baek

BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo pp. 1-19

Hongliang Li and Bin Liu

Supervised learning and model analysis with compositional data pp. 1-19

Shimeng Huang, Elisabeth Ailer, Niki Kilbertus and Niklas Pfister

Distinguishing between different percolation regimes in noisy dynamic networks with an application to epileptic seizures pp. 1-22

Xiaojing Zhu, Heather Shappell, Mark A Kramer, Catherine J Chu and Eric D Kolaczyk

Stochastic simulations of self-organized elastogenesis in the developing lung pp. 1-16

Xiru Fan, Cristian Valenzuela, Weijing Zhao, Zi Chen, Dong Wang and Steven J Mentzer

Recall DNA methylation levels at low coverage sites using a CNN model in WGBS pp. 1-14

Ximei Luo, Yansu Wang, Quan Zou and Lei Xu

Estimating fine age structure and time trends in human contact patterns from coarse contact data: The Bayesian rate consistency model pp. 1-30

Shozen Dan, Yu Chen, Yining Chen, Melodie Monod, Veronika K Jaeger, Samir Bhatt, André Karch, Oliver Ratmann and on behalf of the Machine Learning & Global Health network

Patient groups in Rheumatoid arthritis identified by deep learning respond differently to biologic or targeted synthetic DMARDs pp. 1-17

Maria Kalweit, Andrea M Burden, Joschka Boedecker, Thomas Hügle and Theresa Burkard

HAT: Hypergraph analysis toolbox pp. 1-7

Joshua Pickard, Can Chen, Rahmy Salman, Cooper Stansbury, Sion Kim, Amit Surana, Anthony Bloch and Indika Rajapakse

Learning from the past: A short term forecast method for the COVID-19 incidence curve pp. 1-20

Jean-David Morel, Jean-Michel Morel and Luis Alvarez

Environmental dynamics shape perceptual decision bias pp. 1-20

Julie A Charlton, Wiktor F Młynarski, Yoon H Bai, Ann M Hermundstad and Robbe L T Goris

Knowledge graph embedding for profiling the interaction between transcription factors and their target genes pp. 1-20

Yang-Han Wu, Yu-An Huang, Jian-Qiang Li, Zhu-Hong You, Peng-Wei Hu, Lun Hu, Victor C M Leung and Zhi-Hua Du

Nonlinear eco-evolutionary games with global environmental fluctuations and local environmental feedbacks pp. 1-20

Yishen Jiang, Xin Wang, Longzhao Liu, Ming Wei, Jingwu Zhao, Zhiming Zheng and Shaoting Tang

Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth pp. 1-26

Hugo Dourado, Wolfram Liebermeister, Oliver Ebenhöh and Martin J Lercher

The biomechanics of chewing and suckling in the infant: A potential mechanism for physiologic metopic suture closure pp. 1-26

Pranav N Haravu, Miguel Gonzalez, Shelby L Nathan, Callum F Ross, Olga Panagiotopoulou and Russell R Reid

HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph pp. 1-27

Joshua Daniel Rubin, Nicola Alexandra Vogel, Shyam Gopalakrishnan, Peter Wad Sackett and Gabriel Renaud

A mutation-level covariate model for mutational signatures pp. 1-10

Itay Kahane, Mark D M Leiserson and Roded Sharan

Analysis of high-dimensional metabolomics data with complex temporal dynamics using RM-ASCA+ pp. 1-18

Balázs Erdős, Johan A Westerhuis, Michiel E Adriaens, Shauna D O’Donovan, Ren Xie, Cécile M Singh-Povel, Age K Smilde and Ilja C W Arts

Teaching students to R3eason, not merely to solve problem sets: The role of philosophy and visual data communication in accessible data science education pp. 1-12

Ilinca I Ciubotariu and Gundula Bosch

Volume 19, issue 5, 2023

Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths pp. 1-31

Jean-Michel Arbona, Hadi Kabalane, Jeremy Barbier, Arach Goldar, Olivier Hyrien and Benjamin Audit

Matrix prior for data transfer between single cell data types in latent Dirichlet allocation pp. 1-19

Alan Min, Timothy Durham, Louis Gevirtzman and William Stafford Noble

Tight basis cycle representatives for persistent homology of large biological data sets pp. 1-23

Manu Aggarwal and Vipul Periwal

A unitary mechanism underlies adaptation to both local and global environmental statistics in time perception pp. 1-23

Tianhe Wang, Yingrui Luo, Richard B Ivry, Jonathan S Tsay, Ernst Pöppel and Yan Bao

An approximate diffusion process for environmental stochasticity in infectious disease transmission modelling pp. 1-21

Sanmitra Ghosh, Paul J Birrell and Daniela De Angelis

Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression pp. 1-22

Kexin Huang, Yun Zhang, Haoran Gong, Zhengzheng Qiao, Tiangang Wang, Weiling Zhao, Liyu Huang and Xiaobo Zhou

Targeting operational regimes of interest in recurrent neural networks pp. 1-25

Pierre Ekelmans, Nataliya Kraynyukova and Tatjana Tchumatchenko

Canonical Response Parameterization: Quantifying the structure of responses to single-pulse intracranial electrical brain stimulation pp. 1-25

Kai J Miller, Klaus-Robert Müller, Gabriela Ojeda Valencia, Harvey Huang, Nicholas M Gregg, Gregory A Worrell and Dora Hermes

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning pp. 1-20

Olga Mineeva, Daniel Danciu, Bernhard Schölkopf, Ruth E Ley, Gunnar Rätsch and Nicholas D Youngblut

Predicting anti-cancer drug combination responses with a temporal cell state network model pp. 1-20

Deepraj Sarmah, Wesley O Meredith, Ian K Weber, Madison R Price and Marc R Birtwistle

Enabling interpretable machine learning for biological data with reliability scores pp. 1-24

K D Ahlquist, Lauren A Sugden and Sohini Ramachandran

Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier pp. 1-26

Matthew Beauregard Smith, Zack Booth Simpson and Edward M Marcotte

Data-driven segmentation of cortical calcium dynamics pp. 1-36

Sydney C Weiser, Brian R Mullen, Desiderio Ascencio and James B Ackman

Random walk informed heterogeneity detection reveals how the lymph node conduit network influences T cells collective exploration behavior pp. 1-18

Solène Song, Malek Senoussi, Paul Escande and Paul Villoutreix

Identifying prognostic subgroups of luminal-A breast cancer using deep autoencoders and gene expressions pp. 1-18

Seunghyun Wang and Doheon Lee

Four guiding principles for effective trainee-led STEM community engagement through high school outreach pp. 1-13

Stefanie Luecke, Allison Schiffman, Apeksha Singh, Helen Huang, Barbara Shannon and Catera L Wilder

Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data pp. 1-29

David Augustin, Ben Lambert, Ken Wang, Antje-Christine Walz, Martin Robinson and David Gavaghan

Volume 19, issue 4, 2023

Efficient coding of natural scenes improves neural system identification pp. 1-29

Yongrong Qiu, David A Klindt, Klaudia P Szatko, Dominic Gonschorek, Larissa Hoefling, Timm Schubert, Laura Busse, Matthias Bethge and Thomas Euler

Calibrating agent-based models to tumor images using representation learning pp. 1-13

Colin G Cess and Stacey D Finley

Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data pp. 1-18

Krystian Zieliński, Sebastian Pukszta, Małgorzata Mickiewicz, Marta Kotlarz, Piotr Wygocki, Marcin Zieleń, Dominika Drzewiecka, Damian Drzyzga, Anna Kloska and Joanna Jakóbkiewicz-Banecka

Recurrent predictive coding models for associative memory employing covariance learning pp. 1-27

Mufeng Tang, Tommaso Salvatori, Beren Millidge, Yuhang Song, Thomas Lukasiewicz and Rafal Bogacz

Minor variations in multicellular life cycles have major effects on adaptation pp. 1-24

Hanna Isaksson, Åke Brännström and Eric Libby

Gate-based quantum computing for protein design pp. 1-20

Mohammad Hassan Khatami, Udson C Mendes, Nathan Wiebe and Philip M Kim

Shape-driven deep neural networks for fast acquisition of aortic 3D pressure and velocity flow fields pp. 1-20

Endrit Pajaziti, Javier Montalt-Tordera, Claudio Capelli, Raphaël Sivera, Emilie Sauvage, Michael Quail, Silvia Schievano and Vivek Muthurangu

Fidelity of hyperbolic space for Bayesian phylogenetic inference pp. 1-20

Matthew Macaulay, Aaron Darling and Mathieu Fourment

Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference pp. 1-28

Aidan B Estelle, August George, Elisar J Barbar and Daniel M Zuckerman

Establishing effective cross-disciplinary collaboration: Combining simple rules for reproducible computational research, a good data management plan, and good research practice pp. 1-6

Bogna Stawarczyk and Małgorzata Roos

Bridging the gap between mechanistic biological models and machine learning surrogates pp. 1-16

Ioana M Gherman, Zahraa S Abdallah, Wei Pang, Thomas E Gorochowski, Claire S Grierson and Lucia Marucci

Rare-event sampling analysis uncovers the fitness landscape of the genetic code pp. 1-14

Yuji Omachi, Nen Saito and Chikara Furusawa

Fusing an agent-based model of mosquito population dynamics with a statistical reconstruction of spatio-temporal abundance patterns pp. 1-21

Sean M Cavany, Guido España, Alun L Lloyd, Gonzalo M Vazquez-Prokopec, Helvio Astete, Lance A Waller, Uriel Kitron, Thomas W Scott, Amy C Morrison, Robert C Reiner and T Alex Perkins

Multi-view clustering by CPS-merge analysis with application to multimodal single-cell data pp. 1-21

Lixiang Zhang, Lin Lin and Jia Li

High rifampicin peak plasma concentrations accelerate the slow phase of bacterial decline in tuberculosis patients: Evidence for heteroresistance pp. 1-23

Antal Martinecz, Martin J Boeree, Andreas H Diacon, Rodney Dawson, Colin Hemez, Rob E Aarnoutse and Pia Abel zur Wiesch

Model certainty in cellular network-driven processes with missing data pp. 1-31

Michael W Irvin, Arvind Ramanathan and Carlos F Lopez

Volume 19, issue 3, 2023

Predicting functional effects of ion channel variants using new phenotypic machine learning methods pp. 1-16

Christian Malte Boßelmann, Ulrike B S Hedrich, Holger Lerche and Nico Pfeifer

Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity pp. 1-38

Máté László Telek and Elisenda Feliu

Ten simple rules for serving as an editor pp. 1-7

Cameron Mura and Philip E Bourne

A new method for the joint estimation of instantaneous reproductive number and serial interval during epidemics pp. 1-25

Chenxi Dai, Dongsheng Zhou, Bo Gao and Kaifa Wang

Ten simple rules for socially responsible science pp. 1-17

Alon Zivony, Rasha Kardosh, Liadh Timmins and Niv Reggev

One model fits all: Combining inference and simulation of gene regulatory networks pp. 1-28

Elias Ventre, Ulysse Herbach, Thibault Espinasse, Gérard Benoit and Olivier Gandrillon

Global nonlinear approach for mapping parameters of neural mass models pp. 1-28

Dominic M Dunstan, Mark P Richardson, Eugenio Abela, Ozgur E Akman and Marc Goodfellow

BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach pp. 1-28

Mahmood Kalemati, Mojtaba Zamani Emani and Somayyeh Koohi

OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer pp. 1-31

Anni S Halkola, Kaisa Joki, Tuomas Mirtti, Marko M Mäkelä, Tero Aittokallio and Teemu D Laajala

Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates pp. 1-19

Christoffer Norn and Ingemar André

CustOmics: A versatile deep-learning based strategy for multi-omics integration pp. 1-19

Hakim Benkirane, Yoann Pradat, Stefan Michiels and Paul-Henry Cournède

MGAE-DC: Predicting the synergistic effects of drug combinations through multi-channel graph autoencoders pp. 1-19

Peng Zhang and Shikui Tu

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins pp. 1-19

Carlos A Gandarilla-Pérez, Sergio Pinilla, Anne-Florence Bitbol and Martin Weigt

Inferring protein fitness landscapes from laboratory evolution experiments pp. 1-21

Sameer D’Costa, Emily C Hinds, Chase R Freschlin, Hyebin Song and Philip A Romero

Macroscopic resting state model predicts theta burst stimulation response: A randomized trial pp. 1-21

Neda Kaboodvand, Behzad Iravani, Martijn P van den Heuvel, Jonas Persson and Robert Boden

Modelling daily weight variation in honey bee hives pp. 1-22

Karina Arias-Calluari, Theotime Colin, Tanya Latty, Mary Myerscough and Eduardo G Altmann

Inferring feature importance with uncertainties with application to large genotype data pp. 1-22

Pål Vegard Johnsen, Inga Strümke, Mette Langaas, Andrew Thomas DeWan and Signe Riemer-Sørensen

A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya pp. 1-13

Ruth Nanjala, Festus Nyasimi, Daniel Masiga and Caleb Kipkurui Kibet

Coding of object location by heterogeneous neural populations with spatially dependent correlations in weakly electric fish pp. 1-29

Myriah Haggard and Maurice J Chacron

The effect of non-linear signal in classification problems using gene expression pp. 1-12

Benjamin J Heil, Jake Crawford and Casey S Greene

Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression pp. 1-24

Christophe Le Priol, Chloé-Agathe Azencott and Xavier Gidrol

Validation framework for epidemiological models with application to COVID-19 models pp. 1-24

Kimberly A Dautel, Ephraim Agyingi and Pras Pathmanathan

A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer pp. 1-26

Delora Baptista, Pedro G Ferreira and Miguel Rocha

Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning pp. 1-27

Bercem Dutagaci, Bingbing Duan, Chenxi Qiu, Craig D Kaplan and Michael Feig

Robust deep learning object recognition models rely on low frequency information in natural images pp. 1-15

Zhe Li, Josue Ortega Caro, Evgenia Rusak, Wieland Brendel, Matthias Bethge, Fabio Anselmi, Ankit B Patel, Andreas S Tolias and Xaq Pitkow

Ten (not so) simple rules for clinical trial data-sharing pp. 1-10

Claude Pellen, Anne Le Louarn, Gilliosa Spurrier-Bernard, Evelyne Decullier, Jean-Marie Chrétien, Eric Rosenthal, Gérard Le Goff, David Moher, John P A Ioannidis and Florian Naudet

Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load pp. 1-18

Paul Manuel Müller and Christian Meisel

Hindcasts and forecasts of suicide mortality in US: A modeling study pp. 1-18

Sasikiran Kandula, Mark Olfson, Madelyn S Gould, Katherine M Keyes and Jeffrey Shaman

Volume 19, issue 2, 2023

iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures pp. 1-20

Joris J R Louwen, Satria A Kautsar, Sven van der Burg, Marnix H Medema and Justin J J van der Hooft

Temporal progression along discrete coding states during decision-making in the mouse gustatory cortex pp. 1-28

Liam Lang, Giancarlo La Camera and Alfredo Fontanini

Neural adaptation and fractional dynamics as a window to underlying neural excitability pp. 1-17

Brian Nils Lundstrom and Thomas J Richner

LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics pp. 1-29

Giulio Ruffini, Giada Damiani, Diego Lozano-Soldevilla, Nikolas Deco, Fernando E Rosas, Narsis A Kiani, Adrián Ponce-Alvarez, Morten L Kringelbach, Robin Carhart-Harris and Gustavo Deco

A linear discriminant analysis model of imbalanced associative learning in the mushroom body compartment pp. 1-13

David Lipshutz, Aneesh Kashalikar, Shiva Farashahi and Dmitri B Chklovskii

Forecasting upper respiratory tract infection burden using high-dimensional time series data and forecast combinations pp. 1-14

Jue Tao Lim, Kelvin Bryan Tan, John Abisheganaden and Borame L Dickens

Criticality in probabilistic models of spreading dynamics in brain networks: Epileptic seizures pp. 1-41

S Amin Moosavi and Wilson Truccolo

Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs pp. 1-23

Rion Brattig Correia, Alain Barrat and Luis M Rocha

Evolutionary dynamics of hyperbolic language pp. 1-23

Madison S Krieger

Non-destructive classification of unlabeled cells: Combining an automated benchtop magnetic resonance scanner and artificial intelligence pp. 1-31

Philipp Fey, Daniel Ludwig Weber, Jannik Stebani, Philipp Mörchel, Peter Jakob, Jan Hansmann, Karl-Heinz Hiller and Daniel Haddad

Unsupervised learning reveals interpretable latent representations for translucency perception pp. 1-31

Chenxi Liao, Masataka Sawayama and Bei Xiao

AI reveals insights into link between CD33 and cognitive impairment in Alzheimer’s Disease pp. 1-24

Tamara Raschka, Meemansa Sood, Bruce Schultz, Aybuge Altay, Christian Ebeling and Holger Fröhlich

Simulation-based inference for non-parametric statistical comparison of biomolecule dynamics pp. 1-24

Hippolyte Verdier, François Laurent, Alhassan Cassé, Christian L Vestergaard, Christian G Specht and Jean-Baptiste Masson

Functional duality in group criticality via ambiguous interactions pp. 1-24

Takayuki Niizato, Hisashi Murakami and Takuya Musha

Volume 19, issue 1, 2023

Interspecific comparison of gene expression profiles using machine learning pp. 1-20

Artem S Kasianov, Anna V Klepikova, Alexey V Mayorov, Gleb S Buzanov, Maria D Logacheva and Aleksey A Penin

A dual graph neural network for drug–drug interactions prediction based on molecular structure and interactions pp. 1-20

Mei Ma and Xiujuan Lei

Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis pp. 1-28

Caleb M Phillips, Ernesto A B F Lima, Manasa Gadde, Angela M Jarrett, Marissa Nichole Rylander and Thomas E Yankeelov

Skilled motor control of an inverted pendulum implies low entropy of states but high entropy of actions pp. 1-28

Nicola Catenacci Volpi, Martin Greaves, Dari Trendafilov, Christoph Salge, Giovanni Pezzulo and Daniel Polani

Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics pp. 1-30

Oshane O Thomas, Hongyu Shen, Ryan L Raaum, William E H Harcourt-Smith, John D Polk and Mark Hasegawa-Johnson

Ecological landscapes guide the assembly of optimal microbial communities pp. 1-33

Ashish B George and Kirill S Korolev

Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit pp. 1-23

Yibo Zhao, Nikoleta Vavouraki, Ruth C Lovering, Valentina Escott-Price, Kirsten Harvey, Patrick A Lewis and Claudia Manzoni

Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks pp. 1-19

Polina Lakrisenko, Paul Stapor, Stephan Grein, Łukasz Paszkowski, Dilan Pathirana, Fabian Fröhlich, Glenn Terje Lines, Daniel Weindl and Jan Hasenauer

Surround suppression in mouse auditory cortex underlies auditory edge detection pp. 1-19

Omri David Gilday, Benedikt Praegel, Ido Maor, Tav Cohen, Israel Nelken and Adi Mizrahi

Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia pp. 1-31

Edoardo Pinzuti, Patricia Wollstadt, Oliver Tüscher and Michael Wibral

Ten simple rules for implementing open and reproducible research practices after attending a training course pp. 1-11

Verena Heise, Constance Holman, Hung Lo, Ekaterini Maria Lyras, Mark Christopher Adkins, Maria Raisa Jessica Aquino, Konstantinos I Bougioukas, Katherine O Bray, Martyna Gajos, Xuanzong Guo, Corinna Hartling, Rodrigo Huerta-Gutierrez, Miroslava Jindrová, Joanne P M Kenney, Adrianna P Kępińska, Laura Kneller, Elena Lopez-Rodriguez, Felix Mühlensiepen, Angela Richards, Gareth Richards, Maximilian Siebert, James A Smith, Natalie Smith, Nicolai Stransky, Sirpa Tarvainen, Daniela Sofia Valdes, Kayleigh L Warrington, Nina-Maria Wilpert, Disa Witkowska, Mirela Zaneva, Jeanette Zanker and Tracey L Weissgerber

Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability pp. 1-29

Ryan J Murphy, Gency Gunasingh, Nikolas K Haass and Matthew J Simpson

Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates pp. 1-29

Alexander P Browning and Matthew J Simpson

Ten simple rules for defining a computational biology project pp. 1-4

William Stafford Noble

Environmental uncertainty and the advantage of impulsive choice strategies pp. 1-34

Diana C Burk and Bruno B Averbeck

One dimensional approximations of neuronal dynamics reveal computational strategy pp. 1-27

Connor Brennan, Adeeti Aggarwal, Rui Pei, David Sussillo and Alex Proekt

Bayesian reconstruction of memories stored in neural networks from their connectivity pp. 1-27

Sebastian Goldt, Florent Krzakala, Lenka Zdeborová and Nicolas Brunel

Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons pp. 1-26

Yann Roussel, Csaba Verasztó, Dimitri Rodarie, Tanguy Damart, Michael Reimann, Srikanth Ramaswamy, Henry Markram and Daniel Keller

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks pp. 1-26

Souvik Seal, Qunhua Li, Elle Butler Basner, Laura M Saba and Katerina Kechris

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering pp. 1-26

Theresa Ullmann, Stefanie Peschel, Philipp Finger, Christian L Müller and Anne-Laure Boulesteix

Improving the validity of neuroimaging decoding tests of invariant and configural neural representation pp. 1-44

Fabian A Soto and Sanjay Narasiwodeyar

Relating local connectivity and global dynamics in recurrent excitatory-inhibitory networks pp. 1-46

Yuxiu Shao and Srdjan Ostojic