PLOS Computational Biology

2005 - 2025

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Volume 20, issue 12, 2024

Uncovering population contributions to the extracellular potential in the mouse visual system using Laminar Population Analysis pp. 1-39

Atle E Rimehaug, Anders M Dale, Anton Arkhipov and Gaute T Einevoll

A multi-scale study of thalamic state-dependent responsiveness pp. 1-24

Jorin Overwiening, Federico Tesler, Domenico Guarino and Alain Destexhe

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors pp. 1-24

Henri Schmidt and Benjamin J Raphael

Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction pp. 1-44

Akash Bahai, Chee Keong Kwoh, Yuguang Mu and Yinghui Li

A framework for modelling desert locust population dynamics and large-scale dispersal pp. 1-27

Renata Retkute, William Thurston, Keith Cressman and Christopher A Gilligan

Mechanical network equivalence between the katydid and mammalian inner ears pp. 1-17

Emine Celiker, Charlie Woodrow, Òscar Guadayol, Leonidas-Romanos Davranoglou, Christian M Schlepütz, Beth Mortimer, Graham K Taylor, Stuart Humphries and Fernando Montealegre-Z

Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity pp. 1-17

Alexandre Guet-McCreight, Frank Mazza, Thomas D Prevot, Etienne Sibille and Etay Hay

Marked point process variational autoencoder with applications to unsorted spiking activities pp. 1-31

Ryohei Shibue and Tomoharu Iwata

Mathematical basis and toolchain for hierarchical optimization of biochemical networks pp. 1-31

Nisha Ann Viswan, Alexandre Tribut, Manvel Gasparyan, Ovidiu Radulescu and Upinder S Bhalla

Neuro-cognitive multilevel causal modeling: A framework that bridges the explanatory gap between neuronal activity and cognition pp. 1-32

Moritz Grosse-Wentrup, Akshey Kumar, Anja Meunier and Manuel Zimmer

Hands-on training about data clustering with orange data mining toolbox pp. 1-9

Janez Demšar and Blaž Zupan

Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework pp. 1-43

Máté Mohácsi, Márk Patrik Török, Sára Sáray, Luca Tar, Gábor Farkas and Szabolcs Káli

Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling pp. 1-29

Jiyoung Kang and Hae-Jeong Park

ClustAll: An R package for patient stratification in complex diseases pp. 1-11

Asier Ortega-Legarreta, Sara Palomino-Echeverria, Estefania Huergo, Vincenzo Lagani, Narsis A Kiani, Pierre-Emmanuel Rautou, Nuria Planell Picola, Jesper Tegner and David Gomez-Cabrero

Parallel development of object recognition in newborn chicks and deep neural networks pp. 1-37

Lalit Pandey, Donsuk Lee, Samantha M W Wood and Justin N Wood

Evolution of cooperation in multichannel games on multiplex networks pp. 1-26

Amit Basak and Supratim Sengupta

Extracting interpretable signatures of whole-brain dynamics through systematic comparison pp. 1-46

Annie G Bryant, Kevin Aquino, Linden Parkes, Alex Fornito and Ben D Fulcher

Optimisation strategies for directed evolution without sequencing pp. 1-18

Jessica James, Sebastian Towers, Jakob Foerster and Harrison Steel

Randomness as a driver of inactivity in social groups pp. 1-10

Abel Bernadou and Raphaël Jeanson

Estimating the time-varying effective reproduction number via Cycle Threshold-based Transformer pp. 1-25

Xin-Yu Zhang, Lan-Lan Yu, Wei-Yi Wang, Gui-Quan Sun, Jian-Cheng Lv, Tao Zhou and Quan-Hui Liu

Preserving friendships in school contacts: An algorithm to construct synthetic temporal networks for epidemic modelling pp. 1-20

Lucille Calmon, Elisabetta Colosi, Giulia Bassignana, Alain Barrat and Vittoria Colizza

Properties of winning Iterated Prisoner’s Dilemma strategies pp. 1-19

Nikoleta E Glynatsi, Vincent Knight and Marc Harper

Adapting to time: Why nature may have evolved a diverse set of neurons pp. 1-19

Karim G Habashy, Benjamin D Evans, Dan F M Goodman and Jeffrey S Bowers

Machine learning mathematical models for incidence estimation during pandemics pp. 1-19

Oscar Fajardo-Fontiveros, Mattia Mattei, Giulio Burgio, Clara Granell, Sergio Gómez, Alex Arenas, Marta Sales-Pardo and Roger Guimerà

The Burr distribution as a model for the delay between key events in an individual’s infection history pp. 1-22

Nyall Jamieson, Christiana Charalambous, David M Schultz and Ian Hall

Mapping genes for human face shape: Exploration of univariate phenotyping strategies pp. 1-22

Meng Yuan, Seppe Goovaerts, Michiel Vanneste, Harold Matthews, Hanne Hoskens, Stephen Richmond, Ophir D Klein, Richard A Spritz, Benedikt Hallgrimsson, Susan Walsh, Mark D Shriver, John R Shaffer, Seth M Weinberg, Hilde Peeters and Peter Claes

Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform pp. 1-22

Xavier Escriba-Montagut, Yannick Marcon, Augusto Anguita-Ruiz, Demetris Avraam, Jose Urquiza, Andrei S Morgan, Rebecca C Wilson, Paul Burton and Juan R Gonzalez

Estimating the distribution of parameters in differential equations with repeated cross-sectional data pp. 1-22

Hyeontae Jo, Sung Woong Cho and Hyung Ju Hwang

scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum pp. 1-21

Yuqian Liu, Yan Chen, Huanwen Wu, Xuanping Zhang, Yuqi Wang, Xin Yi, Zhiyong Liang and Jiayin Wang

Volume 20, issue 11, 2024

Eleven quick tips for properly handling tabular data pp. 1-10

Marla I Hertz and Ashley S McNeill

The evolutionary cost of homophily: Social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens pp. 1-18

Shuanger Li, Davorka Gulisija and Oana Carja

Co-contraction embodies uncertainty: An optimal feedforward strategy for robust motor control pp. 1-27

Bastien Berret, Dorian Verdel, Etienne Burdet and Frédéric Jean

Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics pp. 1-24

Alexandria M Jensen, Peter DeWitt, Brianne M Bettcher, Julia Wrobel, Katerina Kechris and Debashis Ghosh

Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits pp. 1-25

Vitaly V Ganusov, Afsal Kolloli and Selvakumar Subbian

Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion pp. 1-25

Aaron R Allred, Caroline R Austin, Lanna Klausing, Nicholas Boggess and Torin K Clark

Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function pp. 1-17

Yuanchen Zhao, Otto X Cordero and Mikhail Tikhonov

MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm pp. 1-17

Chao Wang and Quan Zou

Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models pp. 1-17

Wyatt G Madden, Wei Jin, Benjamin Lopman, Andreas Zufle, Benjamin Dalziel, C Jessica E. Metcalf, Bryan T Grenfell and Max S Y Lau

An inductive bias for slowly changing features in human reinforcement learning pp. 1-30

Noa L Hedrich, Eric Schulz, Sam Hall-McMaster and Nicolas W Schuck

A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates pp. 1-30

Baike She, Rebecca Lee Smith, Ian Pytlarz, Shreyas Sundaram and Philip E Paré

Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations pp. 1-33

Aylin Bircan, Nurdan Kuru, Onur Dereli, Berkay Selçuk and Ogün Adebali

A new look at TFPI inhibition of factor X activation pp. 1-21

Fabian Santiago, Amandeep Kaur, Shannon Bride, Dougald Monroe, Karin Leiderman and Suzanne Sindi

Approximate planning in spatial search pp. 1-21

Marta Kryven, Suhyoun Yu, Max Kleiman-Weiner, Tomer Ullman and Joshua Tenenbaum

scGRN-Entropy: Inferring cell differentiation trajectories using single-cell data and gene regulation network-based transfer entropy pp. 1-21

Rui Sun, Wenjie Cao, ShengXuan Li, Jian Jiang, Yazhou Shi and Bengong Zhang

Socially driven negative feedback regulates activity and energy use in ant colonies pp. 1-19

Maurizio Porfiri, Nicole Abaid and Simon Garnier

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning pp. 1-23

Robert van Dijk, John Arevalo, Mehrtash Babadi, Anne E Carpenter and Shantanu Singh

A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors pp. 1-23

Alireza Rezvani-Sharif, Hadi Lioe, Steven K Dower, Matthias Pelzing, Con Panousis, Dalton J E Harvie and Ineke L Muir

Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing pp. 1-23

Sven B Gould, Jonas Magiera, Carolina García García and Parth K Raval

GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies pp. 1-23

Lin Lin, Rachel L Spreng, Kelly E Seaton, S Moses Dennison, Lindsay C Dahora, Daniel J Schuster, Sheetal Sawant, Peter B Gilbert, Youyi Fong, Neville Kisalu, Andrew J Pollard, Georgia D Tomaras and Jia Li

Teaching deep networks to see shape: Lessons from a simplified visual world pp. 1-32

Christian Jarvers and Heiko Neumann

Volume 20, issue 10, 2024

Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals pp. 1-20

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 and Edwin K Silverman

IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation pp. 1-20

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

The optimal spatially-dependent control measures to effectively and economically eliminate emerging infectious diseases pp. 1-28

Fan Xia, Yanni Xiao and Junling Ma

EEG microstate transition cost correlates with task demands pp. 1-17

Giacomo Barzon, Ettore Ambrosini, Antonino Vallesi and Samir Suweis

Integrating information from historical data into mechanistic models for influenza forecasting pp. 1-17

Alessio Andronico, Juliette Paireau and Simon Cauchemez

A Computational Framework for Understanding the Impact of Prior Experiences on Pain Perception and Neuropathic Pain pp. 1-25

Malin Ramne and Jon Sensinger

Regularizing hyperparameters of interacting neural signals in the mouse cortex reflect states of arousal pp. 1-25

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

A flexible generative algorithm for growing in silico placentas pp. 1-45

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

Bayesian polynomial neural networks and polynomial neural ordinary differential equations pp. 1-38

Colby Fronk, Jaewoong Yun, Prashant Singh and Linda Petzold

Best practices for estimating and reporting epidemiological delay distributions of infectious diseases pp. 1-21

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 and Sam Abbott

PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites pp. 1-21

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

Enhancing insights in sexually transmitted infection mapping: Syphilis in Forsyth County, North Carolina, a case study pp. 1-19

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

Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson’s disease pp. 1-32

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 and Joshua G A Cashaback

Mcadet: A feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection pp. 1-39

Saishi Cui, Sina Nassiri and Issa Zakeri

Compression-based inference of network motif sets pp. 1-29

Alexis Bénichou, Jean-Baptiste Masson and Christian L Vestergaard

Why aphid virus retention needs more attention: Modelling aphid behaviour and virus manipulation in non-persistent plant virus transmission pp. 1-29

Elin K Falla and Nik J Cunniffe

Gene signatures for cancer research: A 25-year retrospective and future avenues pp. 1-10

Wei Liu, Huaqin He and Davide Chicco

Learning probability distributions of sensory inputs with Monte Carlo predictive coding pp. 1-34

Gaspard Oliviers, Rafal Bogacz and Alexander Meulemans

Computational joint action: Dynamical models to understand the development of joint coordination pp. 1-27

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

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history pp. 1-27

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

Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data pp. 1-24

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

Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer pp. 1-24

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

Volume 20, issue 9, 2024

Ten quick tips for ensuring machine learning model validity pp. 1-12

Wilson Wen Bin Goh, Mohammad Neamul Kabir, Sehwan Yoo and Limsoon Wong

Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting pp. 1-11

Anis Ur Rahman, Gleb Tikhonov, Jari Oksanen, Tuomas Rossi and Otso Ovaskainen

A Physics-Informed Neural Network approach for compartmental epidemiological models pp. 1-29

Caterina Millevoi, Damiano Pasetto and Massimiliano Ferronato

Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases pp. 1-18

Joseph Shingleton, David Mustard, Steven Dyke, Hannah Williams, Emma Bennett and Thomas Finnie

Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments pp. 1-24

Janice Yang, Neil J Daily, Taylor K Pullinger, Tetsuro Wakatsuki and Eric A Sobie

Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model pp. 1-24

Yanpeng Yang, Yanyi Zheng, Quan Zou, Jian Li and Hailin Feng

SEMbap: Bow-free covariance search and data de-correlation pp. 1-24

Mario Grassi and Barbara Tarantino

GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments pp. 1-28

Cecile Le Sueur, Magnus Rattray and Mikhail Savitski

Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency pp. 1-20

Eslam Abousamra, Marlin Figgins and Trevor Bedford

Construct prognostic models of multiple myeloma with pathway information incorporated pp. 1-20

Shuo Wang, ShanJin Wang, Wei Pan, YuYang Yi and Junyan Lu

Impact of phylogeny on the inference of functional sectors from protein sequence data pp. 1-25

Nicola Dietler, Alia Abbara, Subham Choudhury and Anne-Florence Bitbol

Learning to integrate parts for whole through correlated neural variability pp. 1-25

Zhichao Zhu, Yang Qi, Wenlian Lu and Jianfeng Feng

Bayesian clustering with uncertain data pp. 1-17

Kath Nicholls, Paul D W Kirk and Chris Wallace

Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies pp. 1-17

Adrian J Green, Lisa Truong, Preethi Thunga, Connor Leong, Melody Hancock, Robyn L Tanguay and David M Reif

A hierarchy of metabolite exchanges in metabolic models of microbial species and communities pp. 1-21

Ylva Katarina Wedmark, Jon Olav Vik and Ove Øyås

HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures pp. 1-22

Olav N L Aga, Morten Brun, Kazeem A Dauda, Ramon Diaz-Uriarte, Konstantinos Giannakis and Iain G Johnston

Calibrating dimension reduction hyperparameters in the presence of noise pp. 1-19

Justin Lin and Julia Fukuyama

HELP: A computational framework for labelling and predicting human common and context-specific essential genes pp. 1-23

Ilaria Granata, Lucia Maddalena, Mario Manzo, Mario Rosario Guarracino and Maurizio Giordano

The primacy model and the structure of olfactory space pp. 1-23

Hamza Giaffar, Sergey Shuvaev, Dmitry Rinberg and Alexei A Koulakov

Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data pp. 1-23

Michiel Stock, Wim Van Criekinge, Dimitri Boeckaerts, Steff Taelman, Maxime Van Haeverbeke, Pieter Dewulf and Bernard De Baets

Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter pp. 1-23

Jolanda Malamud, Sinan Guloksuz, Ruud van Winkel, Philippe Delespaul, Marc A F De Hert, Catherine Derom, Evert Thiery, Nele Jacobs, Bart P F Rutten and Quentin J M Huys

The role of training variability for model-based and model-free learning of an arbitrary visuomotor mapping pp. 1-43

Carlos A Velázquez-Vargas, Nathaniel D Daw and Jordan A Taylor

Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803 pp. 1-32

Tobias Pfennig, Elena Kullmann, Tomáš Zavřel, Andreas Nakielski, Oliver Ebenhöh, Jan Červený, Gábor Bernát and Anna Barbara Matuszyńska

Ten simple rules for successfully carrying out funded research projects pp. 1-9

Diego A Forero, Walter H Curioso and Wei Wang

Finding the rhythm: Humans exploit nonlinear intrinsic dynamics of compliant systems in periodic interaction tasks pp. 1-31

Annika Schmidt, Marion Forano, Arne Sachtler, Davide Calzolari, Bernhard M Weber, David W Franklin and Alin Albu-Schäffer

Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing pp. 1-31

Breanne Sparta, Timothy Hamilton, Gunalan Natesan, Samuel D Aragones and Eric J Deeds

Volume 20, issue 8, 2024

Attentional selection and communication through coherence: Scope and limitations pp. 1-23

Priscilla E Greenwood and Lawrence M Ward

COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms pp. 1-23

Teemu J Rintala and Vittorio Fortino

iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites pp. 1-23

Lin Yuan, Ling Zhao, Jinling Lai, Yufeng Jiang, Qinhu Zhang, Zhen Shen, Chun-Hou Zheng and Huang De-Shuang

Understanding patient-derived tumor organoid growth through an integrated imaging and mathematical modeling framework pp. 1-26

Einar Bjarki Gunnarsson, Seungil Kim, Brandon Choi, J Karl Schmid, Karn Kaura, Heinz-Josef Lenz, Shannon M Mumenthaler and Jasmine Foo

A general model unifying the adaptive, transient and sustained properties of ON and OFF auditory neural responses pp. 1-32

Ulysse Rançon, Timothée Masquelier and Benoit R Cottereau

Interacting particle models on the impact of spatially heterogeneous human behavioral factors on dynamics of infectious diseases pp. 1-32

Yunfeng Xiong, Chuntian Wang and Yuan Zhang

Signatures of hierarchical temporal processing in the mouse visual system pp. 1-31

Lucas Rudelt, Daniel González Marx, F Paul Spitzner, Benjamin Cramer, Johannes Zierenberg and Viola Priesemann

Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands pp. 1-21

Catherine M Byrne, Ana Citlali Márquez, Bing Cai, Daniel Coombs and Soren Gantt

Upper bounds for integrated information pp. 1-21

Alireza Zaeemzadeh and Giulio Tononi

Bird song comparison using deep learning trained from avian perceptual judgments pp. 1-21

Lies Zandberg, Veronica Morfi, Julia M George, David F Clayton, Dan Stowell and Robert F Lachlan

Diffusion model predicts the geometry of actin cytoskeleton from cell morphology pp. 1-22

Honghan Li, Shiyou Liu, Shinji Deguchi and Daiki Matsunaga

scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization pp. 1-22

Yuqing Qian, Quan Zou, Mengyuan Zhao, Yi Liu, Fei Guo and Yijie Ding

Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention pp. 1-22

Keyvan Mahjoory, Andreas Bahmer and Molly J Henry

The rules of multiplayer cooperation in networks of communities pp. 1-22

Diogo L Pires and Mark Broom

Rhythmidia: A modern tool for circadian period analysis of filamentous fungi pp. 1-16

Alex T Keeley, Jeffrey M Lotthammer and Jacqueline F Pelham

scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data pp. 1-28

Fengdi Zhao, Xin Ma, Bing Yao, Qing Lu and Li Chen

Influence of surprise on reinforcement learning in younger and older adults pp. 1-25

Christoph Koch, Ondrej Zika, Rasmus Bruckner and Nicolas W Schuck

Reliable estimation of tree branch lengths using deep neural networks pp. 1-25

Anton Suvorov and Daniel R Schrider

Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions pp. 1-25

Efrat Cohen-Davidi and Isana Veksler-Lublinsky

Ten simple rules for successfully managing EU research grants pp. 1-11

David G Pina

Volume 20, issue 7, 2024

Identifying cell states in single-cell RNA-seq data at statistically maximal resolution pp. 1-21

Pascal Grobecker, Thomas Sakoparnig and Erik van Nimwegen

Probabilistic neural transfer function estimation with Bayesian system identification pp. 1-21

Nan Wu, Isabel Valera, Fabian Sinz, Alexander Ecker, Thomas Euler and Yongrong Qiu

Generating information-dense promoter sequences with optimal string packing pp. 1-22

Virgile Andreani, Eric J South and Mary J Dunlop

When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty pp. 1-19

Nathan J Doyle, Fergus Cumming, Robin N Thompson and Michael J Tildesley

Quantifying massively parallel microbial growth with spatially mediated interactions pp. 1-23

Florian Borse, Dovydas Kičiatovas, Teemu Kuosmanen, Mabel Vidal, Guillermo Cabrera-Vives, Johannes Cairns, Jonas Warringer and Ville Mustonen

Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers pp. 1-23

David R Penas, Meysam Hashemi, Viktor K Jirsa and Julio R Banga

Identifying topologically associating domains using differential kernels pp. 1-23

Luka Maisuradze, Megan C King, Ivan V Surovtsev, Simon G J Mochrie, Mark D Shattuck and Corey S O’Hern

Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations pp. 1-23

Yingjun Ma and Yuanyuan Ma

Jointly efficient encoding and decoding in neural populations pp. 1-32

Simone Blanco Malerba, Aurora Micheli, Michael Woodford and Rava Azeredo da Silveira

FedGMMAT: Federated generalized linear mixed model association tests pp. 1-28

Wentao Li, Han Chen, Xiaoqian Jiang and Arif Harmanci

Nonlinear fusion is optimal for a wide class of multisensory tasks pp. 1-20

Marcus Ghosh, Gabriel Béna, Volker Bormuth and Dan F M Goodman

scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics pp. 1-25

Gustavo Magaña-López, Laurence Calzone, Andrei Zinovyev and Loïc Paulevé

Detection of disease-specific signatures in B cell repertoires of lymphomas using machine learning pp. 1-17

Paul Schmidt-Barbo, Gabriel Kalweit, Mehdi Naouar, Lisa Paschold, Edith Willscher, Christoph Schultheiß, Bruno Märkl, Stefan Dirnhofer, Alexandar Tzankov, Mascha Binder and Maria Kalweit

Competitive advantages of T-even phage lysis inhibition in response to secondary infection pp. 1-17

Ulrik Hvid and Namiko Mitarai

Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong pp. 1-17

Yiu-Chung Lau, Songwei Shan, Dong Wang, Dongxuan Chen, Zhanwei Du, Eric H Y Lau, Daihai He, Linwei Tian, Peng Wu, Benjamin J Cowling and Sheikh Taslim Ali

Nine quick tips for open meta-analyses pp. 1-14

David Moreau and Kristina Wiebels

Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission pp. 1-27

Elias Rosenblatt, Jonathan D Cook, Graziella V DiRenzo, Evan H Campbell Grant, Fernando Arce, Kim M Pepin, F Javiera Rudolph, Michael C Runge, Susan Shriner, Daniel P Walsh and Brittany A Mosher

A low-dimensional approximation of optimal confidence pp. 1-27

Pierre Le Denmat, Tom Verguts and Kobe Desender

NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies pp. 1-36

Thomas Couppey, Louis Regnacq, Roland Giraud, Olivier Romain, Yannick Bornat and Florian Kolbl

Fixation times on directed graphs pp. 1-15

David A Brewster, Martin A Nowak and Josef Tkadlec

Modeling soybean growth: A mixed model approach pp. 1-26

Maud Delattre, Yusuke Toda, Jessica Tressou and Hiroyoshi Iwata

Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis pp. 1-37

Harry Saxton, Xu Xu, Torsten Schenkel, Richard H Clayton and Ian Halliday

An integrative approach to protein sequence design through multiobjective optimization pp. 1-37

Lu Hong and Tanja Kortemme

BCI Toolbox: An open-source python package for the Bayesian causal inference model pp. 1-12

Haocheng Zhu, Ulrik Beierholm and Ladan Shams

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile pp. 1-12

Patrick Bryant and Frank Noé

Volume 20, issue 6, 2024

Strong association between genomic 3D structure and CRISPR cleavage efficiency pp. 1-24

Shaked Bergman and Tamir Tuller

Threshold-awareness in adaptive cancer therapy pp. 1-26

MingYi Wang, Jacob G Scott and Alexander Vladimirsky

Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club pp. 1-10

Roberto Efraín Díaz and Stephanie A Wankowicz

mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics pp. 1-19

Kris Sankaran and Pratheepa Jeganathan

Machine learning prediction of malaria vaccine efficacy based on antibody profiles pp. 1-23

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

An algorithm to build synthetic temporal contact networks based on close-proximity interactions data pp. 1-23

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

Ten simple rules for implementing electronic lab notebooks (ELNs) pp. 1-9

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

Ten simple rules for computational biologists collaborating with wet lab researchers pp. 1-9

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 and Izaskun Mallona

Beliefs, compulsive behavior and reduced confidence in control pp. 1-33

Lionel Rigoux, Klaas E Stephan and Frederike H Petzschner

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 pp. 1-21

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

GEM-based computational modeling for exploring metabolic interactions in a microbial community pp. 1-21

Soraya Mirzaei and Mojtaba Tefagh

Zero-shot denoising of microscopy images recorded at high-resolution limits pp. 1-22

Sebastian Salwig, Jakob Drefs and Jörg Lücke

Beyond homogeneity: Assessing the validity of the Michaelis–Menten rate law in spatially heterogeneous environments pp. 1-22

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

Older adults select different but not simpler strategies than younger adults in risky choice pp. 1-16

Florian Bolenz and Thorsten Pachur

ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning pp. 1-16

Youcheng Li, Leann Lac, Qian Liu and Pingzhao Hu

Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments pp. 1-28

Jeremy VanderDoes, Claire Marceaux, Kenta Yokote, Marie-Liesse Asselin-Labat, Gregory Rice and Jack D Hywood

Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection pp. 1-28

Ellie Mainou, Ruy M Ribeiro and Jessica M Conway

Synergistic information supports modality integration and flexible learning in neural networks solving multiple tasks pp. 1-28

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

Infection patterns in simple and complex contagion processes on networks pp. 1-20

Diego Andrés Contreras, Giulia Cencetti and Alain Barrat

Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways pp. 1-20

Leopold Zehetner, Diana Széliová, Barbara Kraus, Juan A Hernandez Bort and Jürgen Zanghellini

Volume 20, issue 5, 2024

Graph topological transformations in space-filling cell aggregates pp. 1-24

Tanmoy Sarkar and Matej Krajnc

Interpretable online network dictionary learning for inferring long-range chromatin interactions pp. 1-24

Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim and Olgica Milenkovic

Astrocytes as a mechanism for contextually-guided network dynamics and function pp. 1-24

Lulu Gong, Fabio Pasqualetti, Thomas Papouin and ShiNung Ching

Adaptive modeling and inference of higher-order coordination in neuronal assemblies: A dynamic greedy estimation approach pp. 1-27

Shoutik Mukherjee and Behtash Babadi

Brain2GAN: Feature-disentangled neural encoding and decoding of visual perception in the primate brain pp. 1-27

Thirza Dado, Paolo Papale, Antonio Lozano, Lynn Le, Feng Wang, Marcel van Gerven, Pieter Roelfsema, Yağmur Güçlütürk and Umut Güçlü

Data–driven modelling makes quantitative predictions regarding bacteria surface motility pp. 1-27

Daniel L Barton, Yow-Ren Chang, William Ducker and Jure Dobnikar

Estimating mutation rates under heterogeneous stress responses pp. 1-27

Lucy Lansch-Justen, Meriem El Karoui and Helen K Alexander

PESSA: A web tool for pathway enrichment score-based survival analysis in cancer pp. 1-13

Hong Yang, Ying Shi, Anqi Lin, Chang Qi, Zaoqu Liu, Quan Cheng, Kai Miao, Jian Zhang and Peng Luo

MGSurvE: A framework to optimize trap placement for genetic surveillance of mosquito populations pp. 1-13

Héctor M Sánchez C., David L Smith and John M Marshall

FAIR-USE4OS: Guidelines for creating impactful open-source software pp. 1-8

Raphael Sonabend, Hugo Gruson, Leo Wolansky, Agnes Kiragga and Daniel S Katz

Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization pp. 1-32

Benjamin Antin, Masato Sadahiro, Marta Gajowa, Marcus A Triplett, Hillel Adesnik and Liam Paninski

Temporal dynamics of short-term neural adaptation across human visual cortex pp. 1-31

Amber Marijn Brands, Sasha Devore, Orrin Devinsky, Werner Doyle, Adeen Flinker, Daniel Friedman, Patricia Dugan, Jonathan Winawer and Iris Isabelle Anna Groen

Mathematical modeling of the evolution of resistance and aggressiveness of high-grade serous ovarian cancer from patient CA-125 time series pp. 1-23

Kanyarat Jitmana, Jason I Griffiths, Sian Fereday, Anna DeFazio, David Bowtell, for Australian Ovarian Cancer Study and Frederick R Adler

Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration pp. 1-23

James Ryu, Amin Nejatbakhsh, Mahdi Torkashvand, Sahana Gangadharan, Maedeh Seyedolmohadesin, Jinmahn Kim, Liam Paninski and Vivek Venkatachalam

A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships pp. 1-23

Alexander Kroll, Sahasra Ranjan and Martin J Lercher

Estimating receptive fields of simple and complex cells in early visual cortex: A convolutional neural network model with parameterized rectification pp. 1-35

Philippe Nguyen, Jinani Sooriyaarachchi, Qianyu Huang and Curtis L Baker

Modeling oxygen transport in the brain: An efficient coarse-grid approach to capture perivascular gradients in the parenchyma pp. 1-30

David Pastor-Alonso, Maxime Berg, Franck Boyer, Natalie Fomin-Thunemann, Michel Quintard, Yohan Davit and Sylvie Lorthois

Dissecting Bayes: Using influence measures to test normative use of probability density information derived from a sample pp. 1-30

Keiji Ota and Laurence T Maloney

Modeling spatial evolution of multi-drug resistance under drug environmental gradients pp. 1-30

Tomas Ferreira Amaro Freire, Zhijian Hu, Kevin B Wood and Erida Gjini

Marmosets mutually compensate for differences in rhythms when coordinating vigilance pp. 1-26

Nikhil Phaniraj, Rahel K Brügger and Judith M Burkart

Differential disruptions in population coding along the dorsal-ventral axis of CA1 in the APP/PS1 mouse model of Aβ pathology pp. 1-37

Udaysankar Chockanathan and Krishnan Padmanabhan

The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance pp. 1-34

Charles Mullon, Jorge Peña and Laurent Lehmann

Foraging in a non-foraging task: Fitness maximization explains human risk preference dynamics under changing environment pp. 1-34

Yasuhiro Mochizuki, Norihiro Harasawa, Mayank Aggarwal, Chong Chen and Haruaki Fukuda

The impact of health inequity on spatial variation of COVID-19 transmission in England pp. 1-15

Thomas Rawson, Wes Hinsley, Raphael Sonabend, Elizaveta Semenova, Anne Cori and Neil M Ferguson

How well do models of visual cortex generalize to out of distribution samples? pp. 1-29

Yifei Ren and Pouya Bashivan

Surprise-minimization as a solution to the structural credit assignment problem pp. 1-29

Franz Wurm, Benjamin Ernst and Marco Steinhauser

Clustering and visualization of single-cell RNA-seq data using path metrics pp. 1-19

Andriana Manousidaki, Anna Little and Yuying Xie

Leveraging conformal prediction to annotate enzyme function space with limited false positives pp. 1-21

Kerr Ding, Jiaqi Luo and Yunan Luo

A systematic analysis of regression models for protein engineering pp. 1-22

Richard Michael, Jacob Kæstel-Hansen, Peter Mørch Groth, Simon Bartels, Jesper Salomon, Pengfei Tian, Nikos S Hatzakis and Wouter Boomsma

Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model pp. 1-22

Alexander Massey, Corentin Boennec, Claudia Ximena Restrepo-Ortiz, Christophe Blanchet, Samuel Alizon and Mircea T Sofonea

Topological state-space estimation of functional human brain networks pp. 1-33

Moo K Chung, Shih-Gu Huang, Ian C Carroll, Vince D Calhoun and H Hill Goldsmith

Artificial neural networks for model identification and parameter estimation in computational cognitive models pp. 1-33

Milena Rmus, Ti-Fen Pan, Liyu Xia and Anne G E Collins

Challenges of COVID-19 Case Forecasting in the US, 2020–2021 pp. 1-25

Velma K Lopez, Estee Y Cramer, Robert Pagano, John M Drake, Eamon B O’Dea, Madeline Adee, Turgay Ayer, Jagpreet Chhatwal, Ozden O Dalgic, Mary A Ladd, Benjamin P Linas, Peter P Mueller, Jade Xiao, Johannes Bracher, Alvaro J Castro Rivadeneira, Aaron Gerding, Tilmann Gneiting, Yuxin Huang, Dasuni Jayawardena, Abdul H Kanji, Khoa Le, Anja Mühlemann, Jarad Niemi, Evan L Ray, Ariane Stark, Yijin Wang, Nutcha Wattanachit, Martha W Zorn, Sen Pei, Jeffrey Shaman, Teresa K Yamana, Samuel R Tarasewicz, Daniel J Wilson, Sid Baccam, Heidi Gurung, Steve Stage, Brad Suchoski, Lei Gao, Zhiling Gu, Myungjin Kim, Xinyi Li, Guannan Wang, Lily Wang, Yueying Wang, Shan Yu, Lauren Gardner, Sonia Jindal, Maximilian Marshall, Kristen Nixon, Juan Dent, Alison L Hill, Joshua Kaminsky, Elizabeth C Lee, Joseph C Lemaitre, Justin Lessler, Claire P Smith, Shaun Truelove, Matt Kinsey, Luke C Mullany, Kaitlin Rainwater-Lovett, Lauren Shin, Katharine Tallaksen, Shelby Wilson, Dean Karlen, Lauren Castro, Geoffrey Fairchild, Isaac Michaud, Dave Osthus, Jiang Bian, Wei Cao, Zhifeng Gao, Juan Lavista Ferres, Chaozhuo Li, Tie-Yan Liu, Xing Xie, Shun Zhang, Shun Zheng, Matteo Chinazzi, Jessica T Davis, Kunpeng Mu, Ana Pastore y Piontti, Alessandro Vespignani, Xinyue Xiong, Robert Walraven, Jinghui Chen, Quanquan Gu, Lingxiao Wang, Pan Xu, Weitong Zhang, Difan Zou, Graham Casey Gibson, Daniel Sheldon, Ajitesh Srivastava, Aniruddha Adiga, Benjamin Hurt, Gursharn Kaur, Bryan Lewis, Madhav Marathe, Akhil Sai Peddireddy, Przemyslaw Porebski, Srinivasan Venkatramanan, Lijing Wang, Pragati V Prasad, Jo W Walker, Alexander E Webber, Rachel B Slayton, Matthew Biggerstaff, Nicholas G Reich and Michael A Johansson

Scuphr: A probabilistic framework for cell lineage tree reconstruction pp. 1-25

Hazal Koptagel, Seong-Hwan Jun, Joanna Hård and Jens Lagergren

Machine-learning and mechanistic modeling of metastatic breast cancer after neoadjuvant treatment pp. 1-20

Sebastien Benzekry, Michalis Mastri, Chiara Nicolò and John M L Ebos

Inferring fungal growth rates from optical density data pp. 1-20

Tara Hameed, Natasha Motsi, Elaine Bignell and Reiko J Tanaka

Transferable deep generative modeling of intrinsically disordered protein conformations pp. 1-28

Giacomo Janson and Michael Feig

Volume 20, issue 4, 2024

Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity pp. 1-25

Irena Balzekas, Joshua Trzasko, Grace Yu, Thomas J Richner, Filip Mivalt, Vladimir Sladky, Nicholas M Gregg, Jamie Van Gompel, Kai Miller, Paul E Croarkin, Vaclav Kremen and Gregory A Worrell

Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains pp. 1-25

Christian Donner, Julian Bartram, Philipp Hornauer, Taehoon Kim, Damian Roqueiro, Andreas Hierlemann, Guillaume Obozinski and Manuel Schröter

Modeling single cell trajectory using forward-backward stochastic differential equations pp. 1-25

Kevin Zhang, Junhao Zhu, Dehan Kong and Zhaolei Zhang

Encoding surprise by retinal ganglion cells pp. 1-20

Danica Despotović, Corentin Joffrois, Olivier Marre and Matthew Chalk

Optimizing strategies for slowing the spread of invasive species pp. 1-20

Adam Lampert

Partial label learning for automated classification of single-cell transcriptomic profiles pp. 1-28

Malek Senoussi, Thierry Artieres and Paul Villoutreix

Wagers for work: Decomposing the costs of cognitive effort pp. 1-28

Sarah L Master, Clayton E Curtis and Peter Dayan

Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error pp. 1-14

Robert Challen, Anastasia Chatzilena, George Qian, Glenda Oben, Rachel Kwiatkowska, Catherine Hyams, Adam Finn, Krasimira Tsaneva-Atanasova and Leon Danon

Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations pp. 1-16

Jong Hyuk Byun, Hye Seon Jeon, Hwi-yeol Yun and Jae Kyoung Kim

MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface pp. 1-30

Adam Husar, Mariam Ordyan, Guadalupe C Garcia, Joel G Yancey, Ali S Saglam, James R Faeder, Thomas M Bartol, Mary B Kennedy and Terrence J Sejnowski

Non-invasive assessment of stroke volume and cardiovascular parameters based on peripheral pressure waveform pp. 1-21

Kamil Wołos, Leszek Pstras, Malgorzata Debowska, Wojciech Dabrowski, Dorota Siwicka-Gieroba and Jan Poleszczuk

DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction pp. 1-22

Hui Liu, Feng Wang, Jian Yu, Yong Pan, Chaoju Gong, Liang Zhang and Lin Zhang

What does the mean mean? A simple test for neuroscience pp. 1-32

Alejandro Tlaie, Katharine Shapcott, Thijs L van der Plas, James Rowland, Robert Lees, Joshua Keeling, Adam Packer, Paul Tiesinga, Marieke L Schölvinck and Martha N Havenith

Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates pp. 1-32

Adrian Lison, Sam Abbott, Jana Huisman and Tanja Stadler

Human decision making balances reward maximization and policy compression pp. 1-32

Lucy Lai and Samuel J Gershman

Predictive coding networks for temporal prediction pp. 1-31

Beren Millidge, Mufeng Tang, Mahyar Osanlouy, Nicol S Harper and Rafal Bogacz

Mathematical analysis of left ventricular elastance with respect to afterload change during ejection phase pp. 1-31

Shiro Kato, Yukiko Himeno and Akira Amano

Informing policy via dynamic models: Cholera in Haiti pp. 1-31

Jesse Wheeler, AnnaElaine Rosengart, Zhuoxun Jiang, Kevin Tan, Noah Treutle and Edward L Ionides

Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models pp. 1-19

Judith A Bouman, Anthony Hauser, Simon L Grimm, Martin Wohlfender, Samir Bhatt, Elizaveta Semenova, Andrew Gelman, Christian L Althaus and Julien Riou

Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation pp. 1-19

Tianhe Wang, Guy Avraham, Jonathan S Tsay, Sabrina J Abram and Richard B Ivry

Ten simple rules for leading a successful undergraduate-intensive research lab pp. 1-8

Hickman Kje and Geoffrey Zahn

StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling pp. 1-29

Luca Giudice, Ahmed Mohamed and Tarja Malm

Dopamine encoding of novelty facilitates efficient uncertainty-driven exploration pp. 1-27

Yuhao Wang, Armin Lak, Sanjay G Manohar and Rafal Bogacz

Learning spatio-temporal patterns with Neural Cellular Automata pp. 1-27

Alex D Richardson, Tibor Antal, Richard A Blythe and Linus J Schumacher

HGCLAMIR: Hypergraph contrastive learning with attention mechanism and integrated multi-view representation for predicting miRNA-disease associations pp. 1-24

Dong Ouyang, Yong Liang, Jinfeng Wang, Le Li, Ning Ai, Junning Feng, Shanghui Lu, Shuilin Liao, Xiaoying Liu and Shengli Xie

Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model pp. 1-26

Rui Meng and Kristofer E Bouchard

Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error pp. 1-26

H Robert Frost

Volume 20, issue 3, 2024

Ten simple rules to leverage large language models for getting grants pp. 1-7

Elizabeth Seckel, Brandi Y Stephens and Fatima Rodriguez

Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers pp. 1-20

Kosaku Kitagawa, Kwang Su Kim, Masashi Iwamoto, Sanae Hayashi, Hyeongki Park, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Shinji Nakaoka, Kazuyuki Aihara, Alan S Perelson, Lena Allweiss, Maura Dandri, Koichi Watashi, Yasuhito Tanaka and Shingo Iwami

Ten simple rules for pushing boundaries of inclusion at academic events pp. 1-22

Siobhan Mackenzie Hall, Daniel Kochin, Carmel Carne, Patricia Herterich, Kristen Lenay Lewers, Mohamed Abdelhack, Arun Ramasubramanian, Juno Felecia Michael Alphonse, Visotheary Ung, Sara El-Gebali, Christopher Brian Currin, Esther Plomp, Rachel Thompson and Malvika Sharan

A multiscale computational framework for the development of spines in molluscan shells pp. 1-21

Derek E Moulton, Nathanaël Aubert-Kato, Axel A Almet and Atsuko Sato

Bayesian inference is facilitated by modular neural networks with different time scales pp. 1-21

Kohei Ichikawa and Kunihiko Kaneko

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration pp. 1-33

Cecilia Wieder, Juliette Cooke, Clement Frainay, Nathalie Poupin, Russell Bowler, Fabien Jourdan, Katerina J Kechris, Rachel PJ Lai and Timothy Ebbels

AI-Aristotle: A physics-informed framework for systems biology gray-box identification pp. 1-33

Nazanin Ahmadi Daryakenari, Mario De Florio, Khemraj Shukla and George Em Karniadakis

Bias in the arrival of variation can dominate over natural selection in Richard Dawkins’s biomorphs pp. 1-31

Nora S Martin, Chico Q Camargo and Ard A Louis

kCSD-python, reliable current source density estimation with quality control pp. 1-23

Chaitanya Chintaluri, Marta Bejtka, Władysław Średniawa, Michał Czerwiński, Jakub M Dzik, Joanna Jędrzejewska-Szmek and Daniel K Wójcik

Enrichment on steps, not genes, improves inference of differentially expressed pathways pp. 1-23

Nicholas Markarian, Kimberly M Van Auken, Dustin Ebert and Paul W Sternberg

Learning environment-specific learning rates pp. 1-23

Jonas Simoens, Tom Verguts and Senne Braem

Evolutionary graph theory beyond pairwise interactions: Higher-order network motifs shape times to fixation in structured populations pp. 1-19

Yang Ping Kuo and Oana Carja

Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating pp. 1-12

Jakub Svoboda, Soham Joshi, Josef Tkadlec and Krishnendu Chatterjee

Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data pp. 1-29

Chenyu Wu, Einar Bjarki Gunnarsson, Even Moa Myklebust, Alvaro Köhn-Luque, Dagim Shiferaw Tadele, Jorrit Martijn Enserink, Arnoldo Frigessi, Jasmine Foo and Kevin Leder

Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1 pp. 1-27

Tyler Cassidy, Kathryn E Stephenson, Dan H Barouch and Alan S Perelson

Raising awareness of uncertain choices in empirical data analysis: A teaching concept toward replicable research practices pp. 1-10

Maximilian M Mandl, Sabine Hoffmann, Sebastian Bieringer, Anna E Jacob, Marie Kraft, Simon Lemster and Anne-Laure Boulesteix

Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation pp. 1-18

Nadin Haase, Wolf Holtkamp, Simon Christ, Dag Heinemann, Marina V Rodnina and Sophia Rudorf

Bayesian inference of relative fitness on high-throughput pooled competition assays pp. 1-18

Manuel Razo-Mejia, Madhav Mani and Dmitri Petrov

Cortical cell assemblies and their underlying connectivity: An in silico study pp. 1-26

András Ecker, Daniela Egas Santander, Sirio Bolaños-Puchet, James B Isbister and Michael W Reimann

Mathematical models of Plasmodium vivax transmission: A scoping review pp. 1-26

Md Nurul Anwar, Lauren Smith, Angela Devine, Somya Mehra, Camelia R Walker, Elizabeth Ivory, Eamon Conway, Ivo Mueller, James M McCaw, Jennifer A Flegg and Roslyn I Hickson

Volume 20, issue 2, 2024

The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion pp. 1-33

Martijn A de Jong, Esmée Adegeest, Noémie M L P Bérenger-Currias, Maria Mircea, Roeland M H Merks and Stefan Semrau

The successor representation subserves hierarchical abstraction for goal-directed behavior pp. 1-41

Sven Wientjes and Clay B Holroyd

EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks pp. 1-22

Francesco Pinotti, José Lourenço, Sunetra Gupta, Suman Das Gupta, Joerg Henning, Damer Blake, Fiona Tomley, Tony Barnett, Dirk Pfeiffer, Md Ahasanul Hoque and Guillaume Fournié

Accounting for isoform expression increases power to identify genetic regulation of gene expression pp. 1-22

Nathan LaPierre and Harold Pimentel

Robust expansion of phylogeny for fast-growing genome sequence data pp. 1-22

Yongtao Ye, Marcus H Shum, Joseph L Tsui, Guangchuang Yu, David K Smith, Huachen Zhu, Joseph T Wu, Yi Guan and Tommy Tsan-Yuk Lam

A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization pp. 1-22

Lily Monnier and Paul-Henry Cournède

Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology pp. 1-19

Daniele Dall’Olio, Eric Sträng, Amin T Turki, Jesse M Tettero, Martje Barbus, Renate Schulze-Rath, Javier Martinez Elicegui, Tommaso Matteuzzi, Alessandra Merlotti, Luciana Carota, Claudia Sala, Matteo G Della Porta, Enrico Giampieri, Jesús María Hernández-Rivas, Lars Bullinger, Gastone Castellani and with the HARMONY Healthcare Alliance Consortium

Quantifying the clusterness and trajectoriness of single-cell RNA-seq data pp. 1-19

Hong Seo Lim and Peng Qiu

Trained recurrent neural networks develop phase-locked limit cycles in a working memory task pp. 1-23

Matthijs Pals, Jakob H Macke and Omri Barak

Shared input and recurrency in neural networks for metabolically efficient information transmission pp. 1-23

Tomas Barta and Lubomir Kostal

Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity pp. 1-23

Pan Li and Jae Kyoung Kim

A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites pp. 1-32

Moritz Groden, Hannah M Moessinger, Barbara Schaffran, Javier DeFelipe, Ruth Benavides-Piccione, Hermann Cuntz and Peter Jedlicka

Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae) pp. 1-20

Sarah Percival, Joyce G Onyenedum, Daniel H Chitwood and Aman Y Husbands

Attractor neural networks with double well synapses pp. 1-25

Yu Feng and Nicolas Brunel

Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex pp. 1-30

Linxing Preston Jiang and Rajesh P N Rao

A beta-Poisson model for infectious disease transmission pp. 1-18

Joe Hilton and Ian Hall

Connectivity Matrix Seriation via Relaxation pp. 1-18

Alexander Borst

The geometric evolution of aortic dissections: Predicting surgical success using fluctuations in integrated Gaussian curvature pp. 1-27

Kameel Khabaz, Karen Yuan, Joseph Pugar, David Jiang, Seth Sankary, Sanjeev Dhara, Junsung Kim, Janet Kang, Nhung Nguyen, Kathleen Cao, Newell Washburn, Nicole Bohr, Cheong Jun Lee, Gordon Kindlmann, Ross Milner and Luka Pocivavsek

Generating synthetic population for simulating the spatiotemporal dynamics of epidemics pp. 1-26

Kemin Zhu, Ling Yin, Kang Liu, Junli Liu, Yepeng Shi, Xuan Li, Hongyang Zou and Huibin Du

Sleep deprivation detected by voice analysis pp. 1-24

Etienne Thoret, Thomas Andrillon, Caroline Gauriau, Damien Léger and Daniel Pressnitzer

Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians pp. 1-24

Li-Dunn Chen, Michael A Caprio, Devin M Chen, Andrew J Kouba and Carrie K Kouba

STGIC: A graph and image convolution-based method for spatial transcriptomic clustering pp. 1-24

Chen Zhang, Junhui Gao, Hong-Yu Chen, Lingxin Kong, Guangshuo Cao, Xiangyu Guo, Wei Liu, Bin Ren and Dong-Qing Wei

HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics pp. 1-11

Margaritis Voliotis, Ali Abbara, Julia K Prague, Johannes D Veldhuis, Waljit S Dhillo and Krasimira Tsaneva-Atanasova

magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing pp. 1-13

Zhenxing Guo, Daoyu Duan, Wen Tang, Julia Zhu, William S Bush, Liangliang Zhang, Xiaofeng Zhu, Fulai Jin and Hao Feng

Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference pp. 1-29

Nicholas Tolley, Pedro L C Rodrigues, Alexandre Gramfort and Stephanie R Jones

Volume 20, issue 1, 2024

Joint representation of molecular networks from multiple species improves gene classification pp. 1-20

Christopher A Mancuso, Kayla A Johnson, Renming Liu and Arjun Krishnan

Revealing and reshaping attractor dynamics in large networks of cortical neurons pp. 1-20

Chen Beer and Omri Barak

Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer pp. 1-25

Chin-Hsuan Sophie Lin, Trang Thuy Do, Lee Unsworth and Marta I Garrido

Controlling target brain regions by optimal selection of input nodes pp. 1-30

Karan Kabbur Hanumanthappa Manjunatha, Giorgia Baron, Danilo Benozzo, Erica Silvestri, Maurizio Corbetta, Alessandro Chiuso, Alessandra Bertoldo, Samir Suweis and Michele Allegra

Ten simple rules for establishing an experimental lab pp. 1-6

Marcus Kaiser

Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior pp. 1-22

Yoav Ger, Eliya Nachmani, Lior Wolf and Nitzan Shahar

Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex pp. 1-21

Sebastian Idesis, Sebastián Geli, Joshua Faskowitz, Jakub Vohryzek, Yonatan Sanz Perl, Florian Pieper, Edgar Galindo-Leon, Andreas K Engel and Gustavo Deco

Landscape quantifies the intermediate state and transition dynamics in ecological networks pp. 1-23

Jinchao Lv, Jin Wang and Chunhe Li

Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces pp. 1-19

Enrique R Sebastian, Julio Esparza and Liset M. de la Prida

PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning pp. 1-31

Anand Ramachandran, Steven S Lumetta and Deming Chen

A genome-wide comprehensive analysis of nucleosome positioning in yeast pp. 1-32

Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina and Arach Goldar

MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks pp. 1-18

Sebastian Himbert, Dorian Gaboo, Emre Brookes, John F Nagle and Maikel C Rheinstädter

Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand pp. 1-15

Michael J Plank, Leighton Watson and Oliver J Maclaren

Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis pp. 1-15

Yong-Jin Huang, Chun-Wei Chang and Chih-hao Hsieh

Inferring country-specific import risk of diseases from the world air transportation network pp. 1-26

Pascal P Klamser, Adrian Zachariae, Benjamin F Maier, Olga Baranov, Clara Jongen, Frank Schlosser and Dirk Brockmann

Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions pp. 1-26

Paul J N Brodersen, Hannah Alfonsa, Lukas B Krone, Cristina Blanco-Duque, Angus S Fisk, Sarah J Flaherty, Mathilde C C Guillaumin, Yi-Ge Huang, Martin C Kahn, Laura E McKillop, Linus Milinski, Lewis Taylor, Christopher W Thomas, Tomoko Yamagata, Russell G Foster, Vladyslav V Vyazovskiy and Colin J Akerman

Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells pp. 1-24

Paul F Lang, David R Penas, Julio R Banga, Daniel Weindl and Bela Novak

Explaining the flaws in human random generation as local sampling with momentum pp. 1-24

Lucas Castillo, Pablo León-Villagrá, Nick Chater and Adam Sanborn

Transformations of sensory information in the brain suggest changing criteria for optimality pp. 1-24

Tyler S Manning, Emma Alexander, Bruce G Cumming, Gregory C DeAngelis, Xin Huang and Emily A Cooper

A neural network model for the evolution of learning in changing environments pp. 1-24

Magdalena Kozielska and Franz J Weissing