PLOS Computational Biology

2005 - 2025

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Volume 18, issue 12, 2022

Monitoring real-time transmission heterogeneity from incidence data pp. 1-24

Yunjun Zhang, Tom Britton and Xiaohua Zhou

Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins pp. 1-36

Jakub W Wojciechowski, Emirhan Tekoglu, Marlena Gąsior-Głogowska, Virginie Coustou, Natalia Szulc, Monika Szefczyk, Marta Kopaczyńska, Sven J Saupe and Witold Dyrka

A phylogenetic approach to inferring the order in which mutations arise during cancer progression pp. 1-31

Yuan Gao, Jeff Gaither, Julia Chifman and Laura Kubatko

Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images pp. 1-23

Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita and Yasuhiro Matsunaga

Input correlations impede suppression of chaos and learning in balanced firing-rate networks pp. 1-23

Rainer Engelken, Alessandro Ingrosso, Ramin Khajeh, Sven Goedeke and L F Abbott

A fast lasso-based method for inferring higher-order interactions pp. 1-23

Kieran Elmes, Astra Heywood, Zhiyi Huang and Alex Gavryushkin

Model-based prioritization for acquiring protection pp. 1-23

Sarah M Tashjian, Toby Wise and Dean Mobbs

Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden pp. 1-17

Fanny Bergström, Felix Günther, Michael Höhle and Tom Britton

The effects of base rate neglect on sequential belief updating and real-world beliefs pp. 1-37

Brandon K Ashinoff, Justin Buck, Michael Woodford and Guillermo Horga

Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction pp. 1-26

Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu and Yang Zhang

Bayesian inference of multi-point macromolecular architecture mixtures at nanometre resolution pp. 1-34

Peter A Embacher, Tsvetelina E Germanova, Emanuele Roscioli, Andrew D McAinsh and Nigel J Burroughs

Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments pp. 1-15

Yulia Fridman, Zihan Wang, Sergei Maslov and Akshit Goyal

Ten quick tips for sequence-based prediction of protein properties using machine learning pp. 1-15

Qingzhen Hou, Katharina Waury, Dea Gogishvili and K Anton Feenstra

Ten simple rules for failing successfully in academia pp. 1-10

Stefan Gaillard, Tara van Viegen, Michele Veldsman, Melanie I Stefan and Veronika Cheplygina

Ten simple rules for creating a sense of belonging in your research group pp. 1-10

Nidia Ruedas-Gracia, Crystal M Botham, Amber R Moore and Courtney Peña

Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods pp. 1-18

Marion F S Fischer, James E Crowe and Jens Meiler

scDSSC: Deep Sparse Subspace Clustering for scRNA-seq Data pp. 1-18

HaiYun Wang, JianPing Zhao, ChunHou Zheng and YanSen Su

tension: A Python package for FORCE learning pp. 1-12

Lu Bin Liu, Attila Losonczy and Zhenrui Liao

Ten simple rules for empowering women in STEM pp. 1-19

Patricia Guevara-Ramírez, Viviana A Ruiz-Pozo, Santiago Cadena-Ullauri, Gabriela Salazar-Navas, Ana Acosta Bedón, J Faustino V-Vázquez and Ana Karina Zambrano

ToMExO: A probabilistic tree-structured model for cancer progression pp. 1-22

Mohammadreza Mohaghegh Neyshabouri and Jens Lagergren

Eleven quick tips for data cleaning and feature engineering pp. 1-21

Davide Chicco, Luca Oneto and Erica Tavazzi

Allosteric regulation in STAT3 interdomains is mediated by a rigid core: SH2 domain regulation by CCD in D170A variant pp. 1-21

Tingting Zhao, Nischal Karki, Brian D Zoltowski and Devin A Matthews

Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework pp. 1-33

Yansong Wang, Zilong Hou, Yuning Yang, Ka-chun Wong and Xiangtao Li

Recalibrating probabilistic forecasts of epidemics pp. 1-16

Aaron Rumack, Ryan J Tibshirani and Roni Rosenfeld

Ten simple rules for launching an academic research career pp. 1-6

Jason A Papin, Jessica Keim-Malpass and Sana Syed

Interacting active surfaces: A model for three-dimensional cell aggregates pp. 1-25

Alejandro Torres-Sánchez, Max Kerr Winter and Guillaume Salbreux

Comparing T cell receptor repertoires using optimal transport pp. 1-28

Branden J Olson, Stefan A Schattgen, Paul G Thomas, Philip Bradley and Frederick A Matsen Iv

Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation pp. 1-28

Olivier Mailhot, Vincent Frappier, François Major and Rafael J Najmanovich

Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data pp. 1-20

Nana Wei, Yating Nie, Lin Liu, Xiaoqi Zheng and Hua-Jun Wu

Volume 18, issue 11, 2022

Inferring parameters of cancer evolution in chronic lymphocytic leukemia pp. 1-32

Nathan D Lee and Ivana Bozic

The geometry of representational drift in natural and artificial neural networks pp. 1-41

Kyle Aitken, Marina Garrett, Shawn Olsen and Stefan Mihalas

Sampling effects and measurement overlap can bias the inference of neuronal avalanches pp. 1-21

Joao Pinheiro Neto, F Paul Spitzner and Viola Priesemann

Inference of B cell clonal families using heavy/light chain pairing information pp. 1-33

Duncan K Ralph and Frederick A Matsen Iv

Computationally efficient mechanism discovery for cell invasion with uncertainty quantification pp. 1-35

Daniel J VandenHeuvel, Christopher Drovandi and Matthew J Simpson

Look twice: A generalist computational model predicts return fixations across tasks and species pp. 1-38

Mengmi Zhang, Marcelo Armendariz, Will Xiao, Olivia Rose, Katarina Bendtz, Margaret Livingstone, Carlos Ponce and Gabriel Kreiman

Effective resistance against pandemics: Mobility network sparsification for high-fidelity epidemic simulations pp. 1-17

Alexander Mercier, Samuel Scarpino and Cristopher Moore

Tracking human skill learning with a hierarchical Bayesian sequence model pp. 1-28

Noémi Éltető, Dezső Nemeth, Karolina Janacsek and Peter Dayan

Brain-wide connectome inferences using functional connectivity MultiVariate Pattern Analyses (fc-MVPA) pp. 1-28

Alfonso Nieto-Castanon

Inferring a spatial code of cell-cell interactions across a whole animal body pp. 1-28

Erick Armingol, Abbas Ghaddar, Chintan J Joshi, Hratch Baghdassarian, Isaac Shamie, Jason Chan, Hsuan-Lin Her, Samuel Berhanu, Anushka Dar, Fabiola Rodriguez-Armstrong, Olivia Yang, Eyleen J O’Rourke and Nathan E Lewis

Probabilistic program inference in network-based epidemiological simulations pp. 1-40

Niklas Smedemark-Margulies, Robin Walters, Heiko Zimmermann, Lucas Laird, Christian van der Loo, Neela Kaushik, Rajmonda Caceres and Jan-Willem van de Meent

Efficient inference and identifiability analysis for differential equation models with random parameters pp. 1-26

Alexander P Browning, Christopher Drovandi, Ian W Turner, Adrianne L Jenner and Matthew J Simpson

Deep reinforcement learning for optimal experimental design in biology pp. 1-24

Neythen J Treloar, Nathan Braniff, Brian Ingalls and Chris P Barnes

Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease pp. 1-24

Massimo Cavallaro, Juliana Coelho, Derren Ready, Valerie Decraene, Theresa Lamagni, Noel D McCarthy, Dan Todkill and Matt J Keeling

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications pp. 1-24

Connor Chato, Yi Feng, Yuhua Ruan, Hui Xing, Joshua Herbeck, Marcia Kalish and Art F Y Poon

Statistical perspective on functional and causal neural connectomics: The Time-Aware PC algorithm pp. 1-27

Rahul Biswas and Eli Shlizerman

Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners pp. 1-27

Himangi Srivastava, Michael J Lippincott, Jordan Currie, Robert Canfield, Maggie P Y Lam and Edward Lau

Ten simple rules for running a summer research program pp. 1-10

Joseph C Ayoob and Juan S Ramírez-Lugo

Social dilemmas of sociality due to beneficial and costly contagion pp. 1-29

Daniel B Cooney, Dylan H Morris, Simon A Levin, Daniel I Rubenstein and Pawel Romanczuk

A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion pp. 1-29

Nikita Sivakumar, Helen V Warner, Shayn M Peirce and Matthew J Lazzara

Ten simple rules to cultivate belonging in collaborative data science research teams pp. 1-12

Kaitlyn M Gaynor, Therese Azevedo, Clarissa Boyajian, Julien Brun, Amber E Budden, Allie Cole, Samantha Csik, Joe DeCesaro, Halina Do-Linh, Joan Dudney, Carmen Galaz García, Scout Leonard, Nicholas J Lyon, Althea Marks, Julia Parish, Alexandra A Phillips, Courtney Scarborough, Joshua Smith, Marcus Thompson, Camila Vargas Poulsen and Caitlin R Fong

Ten simple rules for funding scientific open source software pp. 1-12

Carly Strasser, Kate Hertweck, Josh Greenberg, Dario Taraborelli and Elizabeth Vu

SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more pp. 1-12

Hasan Balci, Ugur Dogrusoz, Yusuf Ziya Ozgul and Perman Atayev

Volume 18, issue 10, 2022

Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins pp. 1-22

Javier A Romero, Paulina Putko, Mateusz Urbańczyk, Krzysztof Kazimierczuk and Anna Zawadzka-Kazimierczuk

Disentangling choice value and choice conflict in sequential decisions under risk pp. 1-22

Laura Fontanesi, Amitai Shenhav and Sebastian Gluth

Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin pp. 1-19

Annie M Westerlund, Akshay Sridhar, Leo Dahl, Alma Andersson, Anna-Yaroslava Bodnar and Lucie Delemotte

Parameterized syncmer schemes improve long-read mapping pp. 1-19

Abhinav Dutta, David Pellow and Ron Shamir

Efficient Bayesian inference for stochastic agent-based models pp. 1-28

Andreas Christ Sølvsten Jørgensen, Atiyo Ghosh, Marc Sturrock and Vahid Shahrezaei

Structured random receptive fields enable informative sensory encodings pp. 1-28

Biraj Pandey, Marius Pachitariu, Bingni W Brunton and Kameron Decker Harris

Emergent multilevel selection in a simple spatial model of the evolution of altruism pp. 1-28

Rutger Hermsen

A deep learning approach to real-time HIV outbreak detection using genetic data pp. 1-20

Michael D Kupperman, Thomas Leitner and Ruian Ke

An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA pp. 1-20

Gerardo Chowell, Sushma Dahal, Amna Tariq, Kimberlyn Roosa, James M Hyman and Ruiyan Luo

MetaLP: An integrative linear programming method for protein inference in metaproteomics pp. 1-20

Shichao Feng, Hong-Long Ji, Huan Wang, Bailu Zhang, Ryan Sterzenbach, Chongle Pan and Xuan Guo

Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond pp. 1-20

Kody A Waldstein, Jirong Yi, Myung Cho, Raghu Mudumbai, Xiaodong Wu, Steven M Varga and Weiyu Xu

Bayesian parameter estimation for dynamical models in systems biology pp. 1-48

Nathaniel J Linden, Boris Kramer and Padmini Rangamani

Magnitude-sensitive reaction times reveal non-linear time costs in multi-alternative decision-making pp. 1-17

James A R Marshall, Andreagiovanni Reina, Célia Hay, Audrey Dussutour and Angelo Pirrone

Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains pp. 1-17

Sabrin Hilau, Sophia Katz, Tanya Wasserman, Ruth Hershberg and Yonatan Savir

Altered expression response upon repeated gene repression in single yeast cells pp. 1-17

Lea Schuh, Igor Kukhtevich, Poonam Bheda, Melanie Schulz, Maria Bordukova, Robert Schneider and Carsten Marr

The value of confidence: Confidence prediction errors drive value-based learning in the absence of external feedback pp. 1-25

Lena Esther Ptasczynski, Isa Steinecker, Philipp Sterzer and Matthias Guggenmos

Hippocampal and medial prefrontal cortices encode structural task representations following progressive and interleaved training schedules pp. 1-30

Sam C Berens and Chris M Bird

Multiple bumps can enhance robustness to noise in continuous attractor networks pp. 1-38

Raymond Wang and Louis Kang

Random-effects meta-analysis of effect sizes as a unified framework for gene set analysis pp. 1-16

Mohammad A Makrooni, Dónal O’Shea, Paul Geeleher and Cathal Seoighe

Deep mendelian randomization: Investigating the causal knowledge of genomic deep learning models pp. 1-14

Stephen Malina, Daniel Cizin and David A Knowles

HAL-X: Scalable hierarchical clustering for rapid and tunable single-cell analysis pp. 1-18

James Anibal, Alexandre G Day, Erol Bahadiroglu, Liam O’Neil, Long Phan, Alec Peltekian, Amir Erez, Mariana Kaplan, Grégoire Altan-Bonnet and Pankaj Mehta

Fast and interpretable consensus clustering via minipatch learning pp. 1-18

Luqin Gan and Genevera I Allen

Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men pp. 1-15

Sara Andresen, Suraj Balakrishna, Catrina Mugglin, Axel J Schmidt, Dominique L Braun, Alex Marzel, Thanh Doco Lecompte, Katharine EA Darling, Jan A Roth, Patrick Schmid, Enos Bernasconi, Huldrych F Günthard, Andri Rauch, Roger D Kouyos, Luisa Salazar-Vizcaya and the Swiss HIV Cohort Study

Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis pp. 1-34

Chen Jia, Abhyudai Singh and Ramon Grima

Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans pp. 1-27

Yuxiang Wu, Shang Wu, Xin Wang, Chengtian Lang, Quanshi Zhang, Quan Wen and Tianqi Xu

EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number pp. 1-27

Oswaldo Gressani, Jacco Wallinga, Christian L Althaus, Niel Hens and Christel Faes

Chaos in synthetic microbial communities pp. 1-24

Behzad D Karkaria, Angelika Manhart, Alex J H Fedorec and Chris P Barnes

Stochastic dynamics of Type-I interferon responses pp. 1-24

Benjamin D Maier, Luis U Aguilera, Sven Sahle, Pascal Mutz, Priyata Kalra, Christopher Dächert, Ralf Bartenschlager, Marco Binder and Ursula Kummer

Reaction-diffusion models in weighted and directed connectomes pp. 1-39

Oliver Schmitt, Christian Nitzsche, Peter Eipert, Vishnu Prathapan, Marc-Thorsten Hütt and Claus C Hilgetag

Ten simple rules for creating and sustaining antiracist graduate programs pp. 1-11

Edgar Perez-Lopez, Larisa Gavrilova, Janice Disla, Melissa Goodlad, Dalena Ngo, Arabi Seshappan, Farhana Sharmin, Jesus Cisneros, Christopher T Kello and Asmeret Asefaw Berhe

Ten simple rules for successfully supporting first-generation/low-income (FLI) students in STEM pp. 1-8

Courtney Peña, Nidia Ruedas-Gracia, Jennifer R Cohen, Ngoc Tran and Miranda B Stratton

Volume 18, issue 9, 2022

Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection pp. 1-31

Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco and Petr Šulc

Robust inference of population size histories from genomic sequencing data pp. 1-32

Gautam Upadhya and Matthias Steinrücken

Utility of constraints reflecting system stability on analyses for biological models pp. 1-32

Yoshiaki Kariya, Masashi Honma, Keita Tokuda, Akihiko Konagaya and Hiroshi Suzuki

Investigating differential abundance methods in microbiome data: A benchmark study pp. 1-32

Marco Cappellato, Giacomo Baruzzo and Barbara Di Camillo

A normative model of peripersonal space encoding as performing impact prediction pp. 1-23

Zdenek Straka, Jean-Paul Noel and Matej Hoffmann

Optimizing laboratory-based surveillance networks for monitoring multi-genotype or multi-serotype infections pp. 1-23

Qu Cheng, Philip A Collender, Alexandra K Heaney, Aidan McLoughlin, Yang Yang, Yuzi Zhang, Jennifer R Head, Rohini Dasan, Song Liang, Qiang Lv, Yaqiong Liu, Changhong Yang, Howard H Chang, Lance A Waller, Jon Zelner, Joseph A Lewnard and Justin V Remais

Optimal anti-amyloid-beta therapy for Alzheimer’s disease via a personalized mathematical model pp. 1-19

Wenrui Hao, Suzanne Lenhart and Jeffrey R Petrella

An expert judgment model to predict early stages of the COVID-19 pandemic in the United States pp. 1-19

Thomas McAndrew and Nicholas G Reich

Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays pp. 1-19

Luke Ternes, Jia-Ren Lin, Yu-An Chen, Joe W Gray and Young Hwan Chang

ceRNAR: An R package for identification and analysis of ceRNA-miRNA triplets pp. 1-22

Yi-Wen Hsiao, Lin Wang and Tzu-Pin Lu

Fast and accurate Ab Initio Protein structure prediction using deep learning potentials pp. 1-22

Robin Pearce, Yang Li, Gilbert S Omenn and Yang Zhang

A quantitative modelling approach for DNA repair on a population scale pp. 1-21

Leo Zeitler, Cyril Denby Wilkes, Arach Goldar and Julie Soutourina

Interaction between games give rise to the evolution of moral norms of cooperation pp. 1-35

Mohammad Salahshour

Generalism drives abundance: A computational causal discovery approach pp. 1-16

Chuliang Song, Benno I Simmons, Marie-Josée Fortin and Andrew Gonzalez

Strange attractor of a narwhal (Monodon monoceros) pp. 1-16

Evgeny A Podolskiy and Mads Peter Heide-Jørgensen

Bayesian estimation of community size and overlap from random subsamples pp. 1-16

Erik K Johnson and Daniel B Larremore

PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization pp. 1-16

Wenhui Yan, Wending Tang, Lihua Wang, Yannan Bin and Junfeng Xia

Comparing and linking machine learning and semi-mechanistic models for the predictability of endemic measles dynamics pp. 1-14

Max S Y Lau, Alex Becker, Wyatt Madden, Lance A Waller, C Jessica E Metcalf and Bryan T Grenfell

Systems-level identification of key transcription factors in immune cell specification pp. 1-30

Cong Liu, Kyla Omilusik, Clara Toma, Nadia S Kurd, John T Chang, Ananda W Goldrath and Wei Wang

MouseNet: A biologically constrained convolutional neural network model for the mouse visual cortex pp. 1-30

Jianghong Shi, Bryan Tripp, Eric Shea-Brown, Stefan Mihalas and Michael A. Buice

Testing microbiome associations with survival times at both the community and individual taxon levels pp. 1-17

Yingtian Hu, Yunxiao Li, Glen A Satten and Yi-Juan Hu

Extracting individual characteristics from population data reveals a negative social effect during honeybee defence pp. 1-20

Tatjana Petrov, Matej Hajnal, Julia Klein, David Šafránek and Morgane Nouvian

EpiBeds: Data informed modelling of the COVID-19 hospital burden in England pp. 1-20

Christopher E Overton, Lorenzo Pellis, Helena B Stage, Francesca Scarabel, Joshua Burton, Christophe Fraser, Ian Hall, Thomas A House, Chris Jewell, Anel Nurtay, Filippo Pagani and Katrina A Lythgoe

What lies underneath: Precise classification of brain states using time-dependent topological structure of dynamics pp. 1-20

Fernando Soler-Toscano, Javier A Galadí, Anira Escrichs, Yonatan Sanz Perl, Ane López-González, Jacobo D Sitt, Jitka Annen, Olivia Gosseries, Aurore Thibaut, Rajanikant Panda, Francisco J Esteban, Steven Laureys, Morten L Kringelbach, José A Langa and Gustavo Deco

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes pp. 1-20

Lin Zhang, Likai Chen, Xiaoqian (Annie) Yu, Claire Duvallet, Siavash Isazadeh, Chengzhen Dai, Shinkyu Park, Katya Frois-Moniz, Fabio Duarte, Carlo Ratti, Eric J Alm and Fangqiong Ling

A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis pp. 1-28

Michela Carlotta Massi, Lorenzo Dominoni, Francesca Ieva and Giovanni Fiorito

A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data pp. 1-28

Ran Su, Haitang Yang, Leyi Wei, Siqi Chen and Quan Zou

A hierarchical process model links behavioral aging and lifespan in C. elegans pp. 1-28

Natasha Oswal, Olivier M F Martin, Sofia Stroustrup, Monika Anna Matusiak Bruckner and Nicholas Stroustrup

Comparing human and model-based forecasts of COVID-19 in Germany and Poland pp. 1-24

Nikos I Bosse, Sam Abbott, Johannes Bracher, Habakuk Hain, Billy J Quilty, Mark Jit, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Edwin van Leeuwen, Anne Cori and Sebastian Funk

Optimal control methods for nonlinear parameter estimation in biophysical neuron models pp. 1-24

Nirag Kadakia

Using Fluorescence Recovery After Photobleaching data to uncover filament dynamics pp. 1-24

J C Dallon, Cécile Leduc, Christopher P Grant, Emily J Evans, Sandrine Etienne-Manneville and Stéphanie Portet

Patterns of asymmetry and energy cost generated from predictive simulations of hemiparetic gait pp. 1-26

Russell T Johnson, Nicholas A Bianco and James M Finley

Ambiguity drives higher-order Pavlovian learning pp. 1-36

Tomislav D Zbozinek, Omar D Perez, Toby Wise, Michael Fanselow and Dean Mobbs

Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets pp. 1-27

Melissa A Iacovidou, Priscille Barreaux, Simon E F Spencer, Matthew B Thomas, Erin E Gorsich and Kat S Rock

Towards reliable quantification of cell state velocities pp. 1-27

Valérie Marot-Lassauzaie, Brigitte Joanne Bouman, Fearghal Declan Donaghy, Yasmin Demerdash, Marieke Alida Gertruda Essers and Laleh Haghverdi

Graph-based algorithms for Laplace transformed coalescence time distributions pp. 1-13

Gertjan Bisschop

Volume 18, issue 8, 2022

Spatiotemporal dynamics of human high gamma discriminate naturalistic behavioral states pp. 1-24

Abdulwahab Alasfour, Paolo Gabriel, Xi Jiang, Isaac Shamie, Lucia Melloni, Thomas Thesen, Patricia Dugan, Daniel Friedman, Werner Doyle, Orin Devinsky, David Gonda, Shifteh Sattar, Sonya Wang, Eric Halgren and Vikash Gilja

Terminal heterocyst differentiation in the Anabaena patA mutant as a result of post-transcriptional modifications and molecular leakage pp. 1-26

Pau Casanova-Ferrer, Saúl Ares and Javier Muñoz-García

Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics pp. 1-26

Marie Chion, Christine Carapito and Frédéric Bertrand

Nine quick tips for pathway enrichment analysis pp. 1-15

Davide Chicco and Giuseppe Agapito

VGsim: Scalable viral genealogy simulator for global pandemic pp. 1-15

Vladimir Shchur, Vadim Spirin, Dmitry Sirotkin, Evgeni Burovski, Nicola De Maio and Russell Corbett-Detig

Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm pp. 1-27

Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei and Alice C McHardy

How growers make decisions impacts plant disease control pp. 1-27

Rachel E Murray-Watson, Frédéric M Hamelin and Nik J Cunniffe

Adaptive search space pruning in complex strategic problems pp. 1-27

Ofra Amir, Liron Tyomkin and Yuval Hart

Novel feature selection methods for construction of accurate epigenetic clocks pp. 1-18

Adam Li, Amber Mueller, Brad English, Anthony Arena, Daniel Vera, Alice E Kane and David A Sinclair

Ten simple rules for reporting information on species interactions pp. 1-10

Cristina A Kita, Guillermo Florez-Montero, Sebastián Montoya-Bustamante, Renata L Muylaert, Natalya Zapata-Mesa and Marco A R Mello

Ten simple rules for a successful EU Marie Skłodowska-Curie Actions Postdoctoral (MSCA) fellowship application pp. 1-8

Philipp Baumert, Francesco Cenni and Mikhail L Antonkine

Understanding the structure of cognitive noise pp. 1-11

Jian-Qiao Zhu, Pablo León-Villagrá, Nick Chater and Adam N Sanborn

A framework for macroscopic phase-resetting curves for generalised spiking neural networks pp. 1-31

Grégory Dumont, Alberto Pérez-Cervera and Boris Gutkin

The pursuit of happiness: A reinforcement learning perspective on habituation and comparisons pp. 1-32

Rachit Dubey, Thomas L Griffiths and Peter Dayan

Ten simple rules for organizing a special session at a scientific conference pp. 1-9

Davide Chicco and Philip E Bourne

TreeKnit: Inferring ancestral reassortment graphs of influenza viruses pp. 1-19

Pierre Barrat-Charlaix, Timothy G Vaughan and Richard A Neher

Subunit promotion energies for channel opening in heterotetrameric olfactory CNG channels pp. 1-22

Jana Schirmeyer, Thomas Eick, Eckhard Schulz, Sabine Hummert, Christian Sattler, Ralf Schmauder and Klaus Benndorf

Cross-fitted instrument: A blueprint for one-sample Mendelian randomization pp. 1-21

William R P Denault, Jon Bohlin, Christian M Page, Stephen Burgess and Astanand Jugessur

The impact of sparsity in low-rank recurrent neural networks pp. 1-21

Elizabeth Herbert and Srdjan Ostojic

Avoiding costly mistakes in groups: The evolution of error management in collective decision making pp. 1-21

Alan N Tump, Max Wolf, Pawel Romanczuk and Ralf H J M Kurvers

Constructive connectomics: How neuronal axons get from here to there using gene-expression maps derived from their family trees pp. 1-33

Stan Kerstjens, Gabriela Michel and Rodney J Douglas

SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2 pp. 1-16

Richard A Stein and Hassane S Mchaourab

A simple model of the attentional blink and its modulation by mental training pp. 1-14

Nadav Amir, Naftali Tishby and Israel Nelken

Archetypal Analysis for population genetics pp. 1-17

Julia Gimbernat-Mayol, Albert Dominguez Mantes, Carlos D Bustamante, Daniel Mas Montserrat and Alexander G Ioannidis

Ten quick tips for biomarker discovery and validation analyses using machine learning pp. 1-17

Ramon Diaz-Uriarte, Elisa Gómez de Lope, Rosalba Giugno, Holger Fröhlich, Petr V Nazarov, Isabel A Nepomuceno-Chamorro, Armin Rauschenberger and Enrico Glaab

iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank pp. 1-17

Wenxiang Zhang, Jialu Hou and Bin Liu

Volume 18, issue 7, 2022

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses pp. 1-17

Wendi Bacon, Alexandra Holinski, Marina Pujol, Meredith Wilmott, Sarah L Morgan and on behalf of the European Molecular Biology Laboratory—European Bioinformatics Institute Training Team

Graphia: A platform for the graph-based visualisation and analysis of high dimensional data pp. 1-17

Tom C Freeman, Sebastian Horsewell, Anirudh Patir, Josh Harling-Lee, Tim Regan, Barbara B Shih, James Prendergast, David A Hume and Tim Angus

The accuracy of absolute differential abundance analysis from relative count data pp. 1-25

Kimberly E Roche and Sayan Mukherjee

Physiological characterization of electrodermal activity enables scalable near real-time autonomic nervous system activation inference pp. 1-28

Rafiul Amin and Rose T Faghih

Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models pp. 1-28

Fabian Fröhlich and Peter K Sorger

ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients pp. 1-20

Bodhayan Prasad, Cathy McGeough, Amanda Eakin, Tan Ahmed, Dawn Small, Philip Gardiner, Adrian Pendleton, Gary Wright, Anthony J Bjourson, David S Gibson and Priyank Shukla

Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study pp. 1-20

Joseph Chadi Lemaitre, Damiano Pasetto, Mario Zanon, Enrico Bertuzzo, Lorenzo Mari, Stefano Miccoli, Renato Casagrandi, Marino Gatto and Andrea Rinaldo

To what extent naringenin binding and membrane depolarization shape mitoBK channel gating—A machine learning approach pp. 1-20

Monika Richter-Laskowska, Paulina Trybek, Piotr Bednarczyk and Agata Wawrzkiewicz-Jałowiecka

Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design pp. 1-16

Jennifer Brennan, Lalit Jain, Sofia Garman, Ann E Donnelly, Erik Scott Wright and Kevin Jamieson

Suboptimal human inference can invert the bias-variance trade-off for decisions with asymmetric evidence pp. 1-30

Tahra L Eissa, Joshua I Gold, Krešimir Josić and Zachary P Kilpatrick

nAdder: A scale-space approach for the 3D analysis of neuronal traces pp. 1-22

Minh Son Phan, Katherine Matho, Emmanuel Beaurepaire, Jean Livet and Anatole Chessel

Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2 pp. 1-22

Jose M Jimenez-Guardeño, Ana Maria Ortega-Prieto, Borja Menendez Moreno, Thomas J A Maguire, Adam Richardson, Juan Ignacio Diaz-Hernandez, Javier Diez Perez, Mark Zuckerman, Albert Mercadal Playa, Carlos Cordero Deline, Michael H Malim and Rocio Teresa Martinez-Nunez

A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission pp. 1-21

Fabian Santiago and Suzanne Sindi

AC-PCoA: Adjustment for confounding factors using principal coordinate analysis pp. 1-21

Yu Wang, Fengzhu Sun, Wei Lin and Shuqin Zhang

Pooling strategies in V1 can account for the functional and structural diversity across species pp. 1-21

Victor Boutin, Angelo Franciosini, Frédéric Chavane and Laurent U Perrinet

Gaze-dependent evidence accumulation predicts multi-alternative risky choice behaviour pp. 1-33

Felix Molter, Armin W Thomas, Scott A Huettel, Hauke R Heekeren and Peter N C Mohr

Suprathreshold perceptual decisions constrain models of confidence pp. 1-31

Shannon M Locke, Michael S Landy and Pascal Mamassian

Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions pp. 1-23

Saleh Fayaz, Mohammad Amin Fakharian and Ali Ghazizadeh

Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data pp. 1-23

Long Liu, Qingyu Meng, Cherry Weng, Qing Lu, Tong Wang and Yalu Wen

A Bayesian method for identifying associations between response variables and bacterial community composition pp. 1-19

Adrian Verster, Nicholas Petronella, Judy Green, Fernando Matias and Stephen P J Brooks

Ten simple rules for designing and running a computing minor for bio/chem students pp. 1-11

Rochelle-Jan Reyes, Nina Hosmane, Shasta Ihorn, Milo Johnson, Anagha Kulkarni, Jennifer Nelson, Michael Savvides, Duc Ta, Ilmi Yoon and Pleuni S Pennings

Ten simple rules to host an inclusive conference pp. 1-13

Rocío Joo, Andrea Sánchez-Tapia, Sara Mortara, Yanina Bellini Saibene, Heather Turner, Dorothea Hug Peter, Natalia Soledad Morandeira, Matt Bannert, Batool Almazrouq, Elizabeth Hare, Laura Ación, Juan Pablo Narváez-Gómez, Marcela Alfaro Córdoba, Federico Marini, Rita Giordano, Silvia Canelón, Anicet Ebou, Adithi R Upadhya, Joselyn Chávez and Janani Ravi

Asymmetric and adaptive reward coding via normalized reinforcement learning pp. 1-15

Kenway Louie

The spectrum of covariance matrices of randomly connected recurrent neuronal networks with linear dynamics pp. 1-27

Yu Hu and Haim Sompolinsky

Dimensionality reduction of longitudinal ’omics data using modern tensor factorizations pp. 1-18

Uria Mor, Yotam Cohen, Rafael Valdés-Mas, Denise Kviatcovsky, Eran Elinav and Haim Avron

The computational relationship between reinforcement learning, social inference, and paranoia pp. 1-26

Joseph M Barnby, Mitul A Mehta and Michael Moutoussis

Volume 18, issue 6, 2022

sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics pp. 1-12

Nadezhda M Belonogova, Gulnara R Svishcheva, Anatoly V Kirichenko, Irina V Zorkoltseva, Yakov A Tsepilov and Tatiana I Axenovich

Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling pp. 1-29

Niklas Kolbe, Lorenz Hexemer, Lukas-Malte Bammert, Alexander Loewer, Mária Lukáčová-Medvid’ová and Stefan Legewie

Characterizing superspreading potential of infectious disease: Decomposition of individual transmissibility pp. 1-29

Shi Zhao, Marc K C Chong, Sukhyun Ryu, Zihao Guo, Mu He, Boqiang Chen, Salihu S Musa, Jingxuan Wang, Yushan Wu, Daihai He and Maggie H Wang

SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data pp. 1-18

Christos Maniatis, Catalina A Vallejos and Guido Sanguinetti

Strain design optimization using reinforcement learning pp. 1-18

Maryam Sabzevari, Sandor Szedmak, Merja Penttilä, Paula Jouhten and Juho Rousu

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation pp. 1-18

Raphael R Eguchi, Christian A Choe and Po-Ssu Huang

Pulmonary drug delivery and retention: A computational study to identify plausible parameters based on a coupled airway-mucus flow model pp. 1-15

Aranyak Chakravarty, Mahesh V Panchagnula, Alladi Mohan and Neelesh A Patankar

Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology pp. 1-15

Laurynas Kalesinskas, Sanjana Gupta and Purvesh Khatri

Modeling cortical synaptic effects of anesthesia and their cholinergic reversal pp. 1-34

Bolaji P Eniwaye, Victoria Booth, Anthony G Hudetz and Michal Zochowski

Metastable spiking networks in the replica-mean-field limit pp. 1-36

Luyan Yu and Thibaud O Taillefumier

Addressing delayed case reporting in infectious disease forecast modeling pp. 1-26

Lauren J Beesley, Dave Osthus and Sara Y Del Valle

Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design pp. 1-26

Jeremy Grignard, Véronique Lamamy, Eva Vermersch, Philippe Delagrange, Jean-Philippe Stephan, Thierry Dorval and François Fages

Priority-based transformations of stimulus representation in visual working memory pp. 1-24

Quan Wan, Jorge A Menendez and Bradley R Postle

A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale pp. 1-24

Vítor Vieira, Jorge Ferreira and Miguel Rocha

Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue pp. 1-24

Sang-Woo Lee and Yoshihiro Morishita

Interpretable pairwise distillations for generative protein sequence models pp. 1-20

Christoph Feinauer, Barthelemy Meynard-Piganeau and Carlo Lucibello

Explainable detection of adverse drug reaction with imbalanced data distribution pp. 1-17

Jin Wang, Liang-Chih Yu and Xuejie Zhang

Characterizing collaborative transcription regulation with a graph-based deep learning approach pp. 1-25

Zhenhao Zhang, Fan Feng and Jie Liu

Efficient Bayesian inference for mechanistic modelling with high-throughput data pp. 1-25

Simon Martina Perez, Heba Sailem and Ruth E Baker

Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data pp. 1-25

Jair Andrade and Jim Duggan

An approximate stochastic optimal control framework to simulate nonlinear neuro-musculoskeletal models in the presence of noise pp. 1-30

Tom Van Wouwe, Lena H Ting and Friedl De Groote

Differential methods for assessing sensitivity in biological models pp. 1-30

Rachel Mester, Alfonso Landeros, Chris Rackauckas and Kenneth Lange

Ten simple rules for succeeding as an underrepresented STEM undergraduate pp. 1-14

Melanie Duc Bo Massey, Suchinta Arif, Shanukie Embuldeniya, Karma Nanglu and Joseph Bielawski

Ten simple rules for improving communication among scientists pp. 1-14

Carla Bautista, Narjes Alfuraiji, Anna Drangowska-Way, Karishma Gangwani, Alida de Flamingh and Philip E Bourne

Ten simple rules for good research practice pp. 1-14

Simon Schwab, Perrine Janiaud, Michael Dayan, Valentin Amrhein, Radoslaw Panczak, Patricia M Palagi, Lars G Hemkens, Meike Ramon, Nicolas Rothen, Stephen Senn, Eva Furrer and Leonhard Held

Tracking the contribution of inductive bias to individualised internal models pp. 1-35

Balázs Török, David G Nagy, Mariann Kiss, Karolina Janacsek, Dezső Németh and Gergő Orbán

Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of ‘stripe’ formation in human data pp. 1-33

Pratik Mullick, Sylvain Fontaine, Cécile Appert-Rolland, Anne-Hélène Olivier, William H Warren and Julien Pettré

Towards a more general understanding of the algorithmic utility of recurrent connections pp. 1-33

Brett W Larsen and Shaul Druckmann

Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks pp. 1-21

Timon Wittenstein, Nava Leibovich and Andreas Hilfinger

A weighted constraint satisfaction approach to human goal-directed decision making pp. 1-23

Yuxuan Li and James L McClelland

Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies pp. 1-23

Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak and Thierry Mora

HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data pp. 1-19

Qing Xie, Chenggong Han, Victor Jin and Shili Lin

A method for the inference of cytokine interaction networks pp. 1-31

Joanneke E Jansen, Dominik Aschenbrenner, Holm H Uhlig, Mark C Coles and Eamonn A Gaffney

Epidemic management and control through risk-dependent individual contact interventions pp. 1-32

Tapio Schneider, Oliver R A Dunbar, Jinlong Wu, Lucas Böttcher, Dmitry Burov, Alfredo Garbuno-Inigo, Gregory L Wagner, Sen Pei, Chiara Daraio, Raffaele Ferrari and Jeffrey Shaman

Volume 18, issue 5, 2022

Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers pp. 1-12

Luis Fernando Montaño-Gutierrez, Nahuel Manzanaro Moreno, Iseabail L Farquhar, Yu Huo, Lucia Bandiera and Peter S Swain

BOSO: A novel feature selection algorithm for linear regression with high-dimensional data pp. 1-29

Luis V Valcárcel, Edurne San José-Enériz, Xabier Cendoya, Ángel Rubio, Xabier Agirre, Felipe Prósper and Francisco J Planes

Predicting knee adduction moment response to gait retraining with minimal clinical data pp. 1-15

Nataliya Rokhmanova, Katherine J Kuchenbecker, Peter B Shull, Reed Ferber and Eni Halilaj

Enhancing long-term forecasting: Learning from COVID-19 models pp. 1-15

Hazhir Rahmandad, Ran Xu and Navid Ghaffarzadegan

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences pp. 1-27

Andonis Gerardos, Nicola Dietler and Anne-Florence Bitbol

Analyzing nested experimental designs—A user-friendly resampling method to determine experimental significance pp. 1-26

Rishikesh U Kulkarni, Catherine L Wang and Carolyn R Bertozzi

Anomalous diffusion and asymmetric tempering memory in neutrophil chemotaxis pp. 1-26

Peter Dieterich, Otto Lindemann, Mats Leif Moskopp, Sebastien Tauzin, Anna Huttenlocher, Rainer Klages, Aleksei Chechkin and Albrecht Schwab

Uncertainty–guided learning with scaled prediction errors in the basal ganglia pp. 1-24

Moritz Möller, Sanjay Manohar and Rafal Bogacz

CBEA: Competitive balances for taxonomic enrichment analysis pp. 1-24

Quang P Nguyen, Anne G Hoen and H Robert Frost

Linear viscoelastic properties of the vertex model for epithelial tissues pp. 1-24

Sijie Tong, Navreeta K Singh, Rastko Sknepnek and Andrej Košmrlj

Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics pp. 1-16

Christopher I Jarvis, Amy Gimma, Flavio Finger, Tim P Morris, Jennifer A Thompson, Olivier le Polain de Waroux, W John Edmunds, Sebastian Funk and Thibaut Jombart

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota pp. 1-30

Alice J Sommer, Annette Peters, Martina Rommel, Josef Cyrys, Harald Grallert, Dirk Haller, Christian L Müller and Marie-Abèle C Bind

Designing optimal allocations for cancer screening using queuing network models pp. 1-30

Justin Dean, Evan Goldberg and Franziska Michor

A topological data analytic approach for discovering biophysical signatures in protein dynamics pp. 1-42

Wai Shing Tang, Gabriel Monteiro da Silva, Henry Kirveslahti, Erin Skeens, Bibo Feng, Timothy Sudijono, Kevin K Yang, Sayan Mukherjee, Brenda Rubenstein and Lorin Crawford

Conflict and competition between model-based and model-free control pp. 1-22

Yuqing Lei and Alec Solway

Performance-gated deliberation: A context-adapted strategy in which urgency is opportunity cost pp. 1-33

Maximilian Puelma Touzel, Paul Cisek and Guillaume Lajoie

Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap) pp. 1-32

Reyhaneh Abbasi, Peter Balazs, Maria Adelaide Marconi, Doris Nicolakis, Sarah M Zala and Dustin J Penn

Observing others give & take: A computational account of bystanders’ feelings and actions pp. 1-23

Bastien Blain, Joseph Marks, Philipp Czech and Tali Sharot

Gene regulation by a protein translation factor at the single-cell level pp. 1-19

Roswitha Dolcemascolo, Lucas Goiriz, Roser Montagud-Martínez and Guillermo Rodrigo

Volume 18, issue 4, 2022

Ten simple rules to ruin a collaborative environment pp. 1-11

Carolyn J Lawrence-Dill, Robyn L Allscheid, Albert Boaitey, Todd Bauman, Edward S Buckler Iv, Jennifer L Clarke, Christopher Cullis, Jack Dekkers, Cassandra J Dorius, Shawn F Dorius, David Ertl, Matthew Homann, Guiping Hu, Mary Losch, Eric Lyons, Brenda Murdoch, Zahra-Katy Navabi, Somashekhar Punnuri, Fahad Rafiq, James M Reecy, Patrick S Schnable, Nicole M Scott, Moira Sheehan, Xavier Sirault, Margaret Staton, Christopher K Tuggle, Alison Van Eenennaam and Rachael Voas

Cell type-specific mechanisms of information transfer in data-driven biophysical models of hippocampal CA3 principal neurons pp. 1-29

Daniele Linaro, Matthew J Levy and David L Hunt

Application of modular response analysis to medium- to large-size biological systems pp. 1-18

Meriem Mekedem, Patrice Ravel and Jacques Colinge

Ten simple rules for building a successful science start-up pp. 1-10

Tobias Reichmuth and Collin Y Ewald

SUITOR: Selecting the number of mutational signatures through cross-validation pp. 1-27

Donghyuk Lee, Difei Wang, Xiaohong R Yang, Jianxin Shi, Maria Teresa Landi and Bin Zhu

Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors pp. 1-27

Nicolas Sundqvist, Nina Grankvist, Jeramie Watrous, Jain Mohit, Roland Nilsson and Gunnar Cedersund

Microbiome-based disease prediction with multimodal variational information bottlenecks pp. 1-27

Filippo Grazioli, Raman Siarheyeu, Israa Alqassem, Andreas Henschel, Giampaolo Pileggi and Andrea Meiser

Phylogenetic analysis of migration, differentiation, and class switching in B cells pp. 1-24

Kenneth B Hoehn, Oliver G Pybus and Steven H Kleinstein

Using topic modeling to detect cellular crosstalk in scRNA-seq pp. 1-20

Alexandrina Pancheva, Helen Wheadon, Simon Rogers and Thomas D Otto

Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention pp. 1-20

Bryan T Mayer, Allan C deCamp, Yunda Huang, Joshua T Schiffer, Raphael Gottardo, Peter B Gilbert and Daniel B Reeves

RNA folding using quantum computers pp. 1-17

Dillion M Fox, Christopher M MacDermaid, Andrea M A Schreij, Magdalena Zwierzyna and Ross C Walker

Ten simple rules for using entrepreneurship skills to improve research careers and culture pp. 1-7

Matt Bawn, David Dent and Philip E Bourne

Alpha blocking and 1/fβ spectral scaling in resting EEG can be accounted for by a sum of damped alpha band oscillatory processes pp. 1-30

Rick Evertz, Damien G Hicks and David T J Liley

Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets pp. 1-33

Anuradha Kar, Manuel Petit, Yassin Refahi, Guillaume Cerutti, Christophe Godin and Jan Traas

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants pp. 1-22

Nicholas J Ose, Brandon M Butler, Avishek Kumar, I Can Kazan, Maxwell Sanderford, Sudhir Kumar and S Banu Ozkan

Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa pp. 1-22

Renato Giliberti, Sara Cavaliere, Italia Elisa Mauriello, Danilo Ercolini and Edoardo Pasolli

Optimizing interneuron circuits for compartment-specific feedback inhibition pp. 1-21

Joram Keijser and Henning Sprekeler

Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs pp. 1-21

Vinita Periwal, Stefan Bassler, Sergej Andrejev, Natalia Gabrielli, Kaustubh Raosaheb Patil, Athanasios Typas and Kiran Raosaheb Patil

Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states pp. 1-19

Amanda L Peiffer, Julie M Garlick, Stephen T Joy, Anna K Mapp and Charles L Brooks

Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders pp. 1-31

Yuge Wang and Hongyu Zhao

Chaotic and stochastic dynamics of epileptiform-like activities in sclerotic hippocampus resected from patients with pharmacoresistant epilepsy pp. 1-31

Noemi S Araújo, Selvin Z Reyes-Garcia, João A F Brogin, Douglas D Bueno, Esper A Cavalheiro, Carla A Scorza and Jean Faber

Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit pp. 1-9

Gautam Munglani, Hannes Vogler and Ueli Grossniklaus

Ten simple rules for getting started with statistics in graduate school pp. 1-9

Rachel A Zitomer, Jessica Karr, Mark Kerstens, Lindsey Perry, Kayla Ruth, Lindsay Adrean, Suzanne Austin, Jamie Cornelius, Jonathan Dachenhaus, Jonathan Dinkins, Alan Harrington, Hankyu Kim, Terrah Owens, Claire Revekant, Vanessa Schroeder, Chelsea Sink, Jonathon J Valente, Ethan Woodis and James W Rivers

Volume 18, issue 3, 2022

A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data pp. 1-16

Snehalika Lall, Sumanta Ray and Sanghamitra Bandyopadhyay

Constructing benchmark test sets for biological sequence analysis using independent set algorithms pp. 1-14

Samantha Petti and Sean R Eddy

Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms pp. 1-14

Noortje G Godijk, Martin C J Bootsma, Henri C van Werkhoven, Valentijn A Schweitzer, Sabine C de Greeff, Annelot F Schoffelen and Marc J M Bonten

Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data pp. 1-14

Pablo M De Salazar, Fred Lu, James A Hay, Diana Gómez-Barroso, Pablo Fernández-Navarro, Elena V Martínez, Jenaro Astray-Mochales, Rocío Amillategui, Ana García-Fulgueiras, Maria D Chirlaque, Alonso Sánchez-Migallón, Amparo Larrauri, María J Sierra, Marc Lipsitch, Fernando Simón, Mauricio Santillana and Miguel A Hernán

Estimating genetic variance contributed by a quantitative trait locus: A random model approach pp. 1-30

Shibo Wang, Fangjie Xie and Shizhong Xu

Pooled testing of traced contacts under superspreading dynamics pp. 1-17

Stratis Tsirtsis, Abir De, Lars Lorch and Manuel Gomez-Rodriguez

Ten quick tips for deep learning in biology pp. 1-20

Benjamin D Lee, Anthony Gitter, Casey S Greene, Sebastian Raschka, Finlay Maguire, Alexander J Titus, Michael D Kessler, Alexandra J Lee, Marc G Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J Fertig, Alexandr A Kalinin, Brandon Signal, Benjamin J Lengerich, Timothy J Triche and Simina M Boca

Transcriptome diversity is a systematic source of variation in RNA-sequencing data pp. 1-20

Pablo E García-Nieto, Ban Wang and Hunter B Fraser

Oscillator decomposition of infant fNIRS data pp. 1-31

Takeru Matsuda, Fumitaka Homae, Hama Watanabe, Gentaro Taga and Fumiyasu Komaki

Cortical oscillations support sampling-based computations in spiking neural networks pp. 1-41

Agnes Korcsak-Gorzo, Michael G Müller, Andreas Baumbach, Luziwei Leng, Oliver J Breitwieser, Sacha J van Albada, Walter Senn, Karlheinz Meier, Robert Legenstein and Mihai A Petrovici

Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches pp. 1-21

Timos Papadopoulos and Emilia Vynnycky

How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments pp. 1-21

Immanuel Meyer, Bnaya Steinmetz and Nadav M Shnerb

The role of cell geometry and cell-cell communication in gradient sensing pp. 1-22

Jonathan Fiorentino and Antonio Scialdone

Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level pp. 1-22

Anđela Davidović, Remy Chait, Gregory Batt and Jakob Ruess

Performance of early warning signals for disease re-emergence: A case study on COVID-19 data pp. 1-22

Daniele Proverbio, Françoise Kemp, Stefano Magni and Jorge Gonçalves

Survival analysis of pathway activity as a prognostic determinant in breast cancer pp. 1-13

Gustavo S Jeuken, Nicholas P Tobin and Lukas Käll

Encoding time in neural dynamic regimes with distinct computational tradeoffs pp. 1-29

Shanglin Zhou, Sotiris C Masmanidis and Dean V Buonomano

Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation pp. 1-29

Yingjing Feng, Caroline H Roney, Jason D Bayer, Steven A Niederer, Mélèze Hocini and Edward J Vigmond

Ten simple rules for principled simulation modelling pp. 1-8

Laurel Fogarty, Madeleine Ammar, Thomas Holding, Adam Powell and Anne Kandler

Task-induced neural covariability as a signature of approximate Bayesian learning and inference pp. 1-39

Richard D Lange and Ralf M Haefner

Bayesian calibration, process modeling and uncertainty quantification in biotechnology pp. 1-46

Laura Marie Helleckes, Michael Osthege, Wolfgang Wiechert, Eric von Lieres and Marco Oldiges

Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition pp. 1-24

Shin-ichi Koda and Shinji Saito

Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness pp. 1-26

Daniel J Lugar and Ganesh Sriram

Automatic wound detection and size estimation using deep learning algorithms pp. 1-26

Héctor Carrión, Mohammad Jafari, Michelle Dawn Bagood, Hsin-ya Yang, Roslyn Rivkah Isseroff and Marcella Gomez

Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins pp. 1-27

Lei Wang, Jiangguo Zhang, Dali Wang and Chen Song

Bayesian inference of ancestral recombination graphs pp. 1-15

Ali Mahmoudi, Jere Koskela, Jerome Kelleher, Yao-ban Chan and David Balding

Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2 pp. 1-15

Leonardo Souto Ferreira, Otavio Canton, Rafael Lopes Paixão da Silva, Silas Poloni, Vítor Sudbrack, Marcelo Eduardo Borges, Caroline Franco, Flavia Maria Darcie Marquitti, José Cássio de Moraes, Maria Amélia de Sousa Mascena Veras, Roberto André Kraenkel and Renato Mendes Coutinho

The ability to classify patients based on gene-expression data varies by algorithm and performance metric pp. 1-34

Stephen R Piccolo, Avery Mecham, Nathan P Golightly, Jérémie L Johnson and Dustin B Miller

SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included pp. 1-18

Jianle Sun, Ruiqi Lyu, Luojia Deng, Qianwen Li, Yang Zhao and Yue Zhang

Volume 18, issue 2, 2022

Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts pp. 1-35

Robert C Mines, Tomasz Lipniacki and Xiling Shen

Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates pp. 1-38

Alessandra Løchen, James E Truscott and Nicholas J Croucher

Evaluating supervised and unsupervised background noise correction in human gut microbiome data pp. 1-25

Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin and Nandita R Garud

Ten simple rules for initial data analysis pp. 1-7

Mark Baillie, Saskia le Cessie, Carsten Oliver Schmidt, Lara Lusa, Marianne Huebner and for the Topic Group “Initial Data Analysis” of the STRATOS Initiative

Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics pp. 1-28

Leonie van Steijn, Inge M N Wortel, Clément Sire, Loïc Dupré, Guy Theraulaz and Roeland M H Merks

Inference of trajectory presence by tree dimension and subset specificity by subtree cover pp. 1-20

Lovemore Tenha and Mingzhou Song

Near-term forecasting of companion animal tick paralysis incidence: An iterative ensemble model pp. 1-20

Nicholas J Clark, Tatiana Proboste, Guyan Weerasinghe and Ricardo J Soares Magalhães

Hidden Markov Modeling with HMMTeacher pp. 1-9

Camilo Fuentes-Beals, Alejandro Valdés-Jiménez and Gonzalo Riadi

Learning as filtering: Implications for spike-based plasticity pp. 1-23

Jannes Jegminat, Simone Carlo Surace and Jean-Pascal Pfister

Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster pp. 1-19

Katherine E Overman, Daniel M Choi, Kawai Leung, Joshua W Shaevitz and Gordon J Berman

A computationally tractable birth-death model that combines phylogenetic and epidemiological data pp. 1-22

Alexander Eugene Zarebski, Louis du Plessis, Kris Varun Parag and Oliver George Pybus

Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus pp. 1-22

Siyu Wang, Stephanie M Reeve, Graham T Holt, Adegoke A Ojewole, Marcel S Frenkel, Pablo Gainza, Santosh Keshipeddy, Vance G Fowler, Dennis L Wright and Bruce R Donald

High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication pp. 1-22

Nithya Ramakrishnan, Sibi Raj B Pillai and Ranjith Padinhateeri

Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights pp. 1-21

Ramin Khajeh, Francesco Fumarola and Abbott Lf

Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19 pp. 1-21

Xian Yang, Shuo Wang, Yuting Xing, Ling Li, Richard Yi Da Xu, Karl J Friston and Yike Guo

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic pp. 1-21

Yuen Ler Chow, Shantanu Singh, Anne E Carpenter and Gregory P Way

Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning pp. 1-21

Indriani P Astono, James S Welsh, Christopher W Rowe and Phillip Jobling

There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk pp. 1-11

Jon Zelner, Nina B Masters, Ramya Naraharisetti, Sanyu A Mojola, Merlin Chowkwanyun and Ryan Malosh

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support pp. 1-12

M Eric Irrgang, Caroline Davis and Peter M Kasson

Combination and competition between path integration and landmark navigation in the estimation of heading direction pp. 1-26

Sevan K Harootonian, Arne D Ekstrom and Robert C Wilson

In silico prediction of HIV-1-host molecular interactions and their directionality pp. 1-26

Haiting Chai, Quan Gu, Joseph Hughes and David L Robertson

RNA-Seq is not required to determine stable reference genes for qPCR normalization pp. 1-24

Nirmal Kumar Sampathkumar, Venkat Krishnan Sundaram, Prakroothi S Danthi, Rasha Barakat, Shiden Solomon, Mrityunjoy Mondal, Ivo Carre, Tatiana El Jalkh, Aïda Padilla-Ferrer, Julien Grenier, Charbel Massaad and Jacqueline C Mitchell

Meta-control of social learning strategies pp. 1-27

Anil Yaman, Nicolas Bredeche, Onur Çaylak, Joel Z Leibo and Sang Wan Lee

Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network pp. 1-27

R Krishnakumaran, Mohammed Raees and Supratim Ray

Classical mathematical models for prediction of response to chemotherapy and immunotherapy pp. 1-18

Narmin Ghaffari Laleh, Chiara Maria Lavinia Loeffler, Julia Grajek, Kateřina Staňková, Alexander T Pearson, Hannah Sophie Muti, Christian Trautwein, Heiko Enderling, Jan Poleszczuk and Jakob Nikolas Kather

Volume 18, issue 1, 2022

A lexical approach for identifying behavioural action sequences pp. 1-29

Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Olivier Mirat and Claire Wyart

The evolutionary maintenance of Lévy flight foraging pp. 1-26

Winston Campeau, Andrew M Simons and Brett Stevens

Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach pp. 1-26

Chen Jia, Abhyudai Singh and Ramon Grima

Formation, collective motion, and merging of macroscopic bacterial aggregates pp. 1-24

George Courcoubetis, Manasi S Gangan, Sean Lim, Xiaokan Guo, Stephan Haas and James Q Boedicker

Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach pp. 1-24

Marcell Miski, Bence Márk Keömley-Horváth, Dorina Rákóczi Megyeriné, Attila Csikász-Nagy and Zoltán Gáspári

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data pp. 1-18

Raga Krishnakumar and Anne M Ruffing

Identification of periodic attractors in Boolean networks using a priori information pp. 1-27

Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp and Tatsuya Akutsu

Interpretable machine learning for high-dimensional trajectories of aging health pp. 1-30

Spencer Farrell, Arnold Mitnitski, Kenneth Rockwood and Andrew D Rutenberg

Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships pp. 1-30

Nina Kudryashova, Theoklitos Amvrosiadis, Nathalie Dupuy, Nathalie Rochefort and Arno Onken

An initial ‘snapshot’ of sensory information biases the likelihood and speed of subsequent changes of mind pp. 1-16

William Turner, Daniel Feuerriegel, Robert Hester and Stefan Bode

Discovering adaptation-capable biological network structures using control-theoretic approaches pp. 1-28

Priyan Bhattacharya, Karthik Raman and Arun K Tangirala

Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution pp. 1-20

Tadamune Kaneko and Macoto Kikuchi

CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach pp. 1-17

Mengting Niu, Quan Zou and Chen Lin

Efficient ReML inference in variance component mixed models using a Min-Max algorithm pp. 1-19

Fabien Laporte, Alain Charcosset and Tristan Mary-Huard

Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection pp. 1-19

Alasdair D F Clarke, Amelia R Hunt and Anna E Hughes

Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables pp. 1-23

Arno Strouwen, Bart M Nicolaï and Peter Goos

Analytical kinetic model of native tandem promoters in E. coli pp. 1-23

Vatsala Chauhan, Mohamed N M Bahrudeen, Cristina S D Palma, Ines S C Baptista, Bilena L B Almeida, Suchintak Dash, Vinodh Kandavalli and Andre S Ribeiro

Optimism and pessimism in optimised replay pp. 1-32

Georgy Antonov, Christopher Gagne, Eran Eldar and Peter Dayan

Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods pp. 1-21

Richard Jiang, Prashant Singh, Fredrik Wrede, Andreas Hellander and Linda Petzold

Fast and accurate influenza forecasting in the United States with Inferno pp. 1-22

Dave Osthus

Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy pp. 1-22

Alexander B Brummer, Xin Yang, Eric Ma, Margarita Gutova, Christine E Brown and Russell C Rockne

Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data pp. 1-22

Qi Jiang, Shuo Zhang and Lin Wan