PLoS Computational Biology, Volume 19

Volume 19, Number 1, January 2023

Education Articles

• 
  Vishal H. Oza, Jordan H. Whitlock, Elizabeth J. Wilk, Angelina E. Uno-Antonison, Brandon M. Wilk, Manavalan Gajapathy, Timothy C. Howton, Austyn Trull, Lara Ianov, Elizabeth A. Worthey, Brittany N. Lasseigne:
  Ten simple rules for using public biological data for your research.
• 
  Davide Chicco, Rakesh Shiradkar:
  Ten quick tips for computational analysis of medical images.
• 
  Saskia D. Hiltemann, Helena Rasche, Simon L. Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel J. Blankenberg, Pratik D. Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J. Griffin, Coline Royaux, Yvan Le Bras, Subina P. Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi A. Bacon, Fotis E. Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A. Doyle, Beatriz Serrano-Solano, Anne Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, The Galaxy Team, Björn A. Grüning, Bérénice Batut:
  Galaxy Training: A powerful framework for teaching!

Perspective

• 
  William Stafford Noble:
  Ten simple rules for defining a computational biology project.

Review

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

Research Articles

• 
  Migle Gabrielaite, Marc Bennedbæk, Malthe Sebro Rasmussen, Virginia Kan, Hansjakob Furrer, Robert Flisiak, Marcelo Losso, Jens Dilling Lundgren, INSIGHT START Study Group, Rasmus L. Marvig:
  Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load.
• 
  Polina A. Lakrisenko, Paul Stapor, Stephan Grein, Lukasz Paszkowski, Dilan Pathirana, Fabian Fröhlich, Glenn Terje Lines, Daniel Weindl, Jan Hasenauer:
  Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks.
• 
  Frédéric Labbé, Qixin He, Qi Zhan, Kathryn E. Tiedje, Dionne C. Argyropoulos, Mun Hua Tan, Anita Ghansah, Karen P. Day, Mercedes Pascual:
  Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections.
• 
  Yann Roussel, Csaba Verasztó, Dimitri Rodarie, Tanguy Damart, Michael W. Reimann, Srikanth Ramaswamy, Henry Markram, Daniel X. Keller:
  Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons.
• 
  Connor Brennan, Adeeti Aggarwal, Rui Pei, David Sussillo, Alex Proekt:
  One dimensional approximations of neuronal dynamics reveal computational strategy.
• 
  Sebastian Sten, Henrik Podéus, Nicolas Sundqvist, Fredrik Elinder, Maria Engström, Gunnar Cedersund:
  A quantitative model for human neurovascular coupling with translated mechanisms from animals.
• 
  Souvik Seal, Qunhua Li, Elle Butler Basner, Laura M. Saba, Katerina J. Kechris:
  RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks.
• 
  Hongxuan Zhai, Julia Fukuyama:
  A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures.
• 
  Nicola Catenacci Volpi, Martin Greaves, Dari Trendafilov, Christoph Salge, Giovanni Pezzulo, Daniel Polani:
  Skilled motor control of an inverted pendulum implies low entropy of states but high entropy of actions.
• 
  Jason Asher, Annabelle Lemenuel-Diot, Matthew Clay, David P. Durham, Luis Mier-y-Teran-Romero, Carlos J. Arguello, Sébastien Jolivet, Diana Y. Wong, Klaus Kuhlbusch, Barry Clinch, Jean-Eric Charoin:
  Novel modelling approaches to predict the role of antivirals in reducing influenza transmission.
• 
  Lujun Shen, Jinqing Mo, Changsheng Yang, Yiquan Jiang, Liangru Ke, Dan Hou, Jingdong Yan, Tao Zhang, Weijun Fan:
  SurvivalPath:A R package for conducting personalized survival path mapping based on time-series survival data.
• 
  Junping Li, Lin Gao, Yusen Ye:
  HiSV: A control-free method for structural variation detection from Hi-C data.
• 
  Gian Luca Lancia, Mattia Eluchans, Marco D'Alessandro, Hugo J. Spiers, Giovanni Pezzulo:
  Humans account for cognitive costs when finding shortcuts: An information-theoretic analysis of navigation.
• 
  Theresa Ullmann, Stefanie Peschel, Philipp F. M. Baumann, Christian L. Müller, Anne-Laure Boulesteix:
  Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering.
• 
  Jiani Chen, Swan Tan, Vasanthi Avadhanula, Leonard Moise, Pedro A. Piedra, Anne S. De Groot, Justin Bahl:
  Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus.
• 
  Artem S. Kasianov, Anna V. Klepikova, Alexey V. Mayorov, Gleb S. Buzanov, Maria D. Logacheva, Aleksey A. Penin:
  Interspecific comparison of gene expression profiles using machine learning.
• 
  Ashish B. George, Kirill S. Korolev:
  Ecological landscapes guide the assembly of optimal microbial communities.
• 
  Noga Mosheiff, Bard Ermentrout, Chengcheng Huang:
  Chaotic dynamics in spatially distributed neuronal networks generate population-wide shared variability.
• 
  Ivan Lazarevich, Ilya Prokin, Boris Gutkin, Victor B. Kazantsev:
  Spikebench: An open benchmark for spike train time-series classification.
• 
  Ryan J. Murphy, Gency Gunasingh, Nikolas K. Haass, Matthew J. Simpson:
  Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability.
• 
  Kai Siedenburg, Jackson E. Graves, Daniel Pressnitzer:
  A unitary model of auditory frequency change perception.
• 
  Kahlan E. Newman, Syma Khalid:
  Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni.
• 
  Garima Singh, Mehmet A. Orman, Jacinta C. Conrad, Michael Nikolaou:
  Systematic design of pulse dosing to eradicate persister bacteria.
• 
  Adrianne L. Jenner, Wayne Kelly, Michael Dallaston, Robyn Araujo, Isobelle Parfitt, Dominic Steinitz, Pantea Pooladvand, Peter S. Kim, Samantha J. Wade, Kara L. Vine:
  Examining the efficacy of localised gemcitabine therapy for the treatment of pancreatic cancer using a hybrid agent-based model.
• 
  Tian Cai, Li Xie, Shuo Zhang, Muge Chen, Di He, Amitesh Badkul, Yang Liu, Hari Krishna Namballa, Michael Dorogan, Wayne W. Harding, Cameron Mura, Philip E. Bourne, Lei Xie:
  End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins.
• 
  Caleb M. Phillips, Ernesto A. B. F. Lima, Manasa Gadde, Angela M. Jarrett, Marissa Nichole Rylander, Thomas E. Yankeelov:
  Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis.
• 
  Timo Flesch, David G. Nagy, Andrew M. Saxe, Christopher Summerfield:
  Modelling continual learning in humans with Hebbian context gating and exponentially decaying task signals.
• 
  Yuki Sugiyama, Kohei Uno, Yusuke Matsui:
  Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments.
• 
  Omri David Gilday, Benedikt Praegel, Ido Maor, Tav Cohen, Israel Nelken, Adi Mizrahi:
  Surround suppression in mouse auditory cortex underlies auditory edge detection.
• 
  Oshane O. Thomas, Hongyu Shen, Ryan L. Raaum, William E. H. Harcourt-Smith, John D. Polk, Mark Hasegawa-Johnson:
  Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics.
• 
  Alexander P. Browning, Matthew J. Simpson:
  Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates.
• 
  Daipeng Chen, Zary Forghany, Xinxin Liu, Haijiang Wang, Roeland M. H. Merks, David A. Baker:
  A new model of Notch signalling: Control of Notch receptor cis-inhibition via Notch ligand dimers.
• 
  Carlos Gueto-Tettay, Di Tang, Lotta Happonen, Moritz Heusel, Hamed Khakzad, Johan Malmström, Lars Malmström:
  Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics.
• 
  Solveig Engebretsen, Alfonso Diz-Lois Palomares, Gunnar Rø, Anja Bråthen Kristoffersen, Jonas Christoffer Lindstrøm, Kenth Engø-Monsen, Meghana Kamineni, Louis Yat Hin Chan, Ørjan Dale, Jørgen Eriksson Midtbø, Kristian Lindalen Stenerud, Francesco Di Ruscio, Richard White, Arnoldo Frigessi, Birgitte Freiesleben de Blasio:
  A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting.
• 
  Gregory J. Kimmel, Richard J. Beck, Xiaoqing Yu, Thomas Veith, Samuel Bakhoum, Philipp M. Altrock, Noemi Andor:
  Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction.
• 
  Arash Mehrjou, Ashkan Soleymani, Amin Abyaneh, Samir Bhatt, Bernhard Schölkopf, Stefan Bauer:
  Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases.
• 
  Yuxiu Shao, Srdjan Ostojic:
  Relating local connectivity and global dynamics in recurrent excitatory-inhibitory networks.
• 
  Joel Roca-Martínez, Hrishikesh Dhondge, Michael Sattler, Wim F. Vranken:
  Deciphering the RRM-RNA recognition code: A computational analysis.
• 
  Eric C. Dykeman:
  Modelling ribosome kinetics and translational control on dynamic mRNA.
• 
  Fabian A. Soto, Sanjay Narasiwodeyar:
  Improving the validity of neuroimaging decoding tests of invariant and configural neural representation.
• 
  Cristoforo Simonetto, Ulrich Mansmann, Jan Christian Kaiser:
  Shape-specific characterization of colorectal adenoma growth and transition to cancer with stochastic cell-based models.
• 
  David J. Jörg, Doris H. Fuertinger, Peter Kotanko:
  Mechanisms of hemoglobin cycling in anemia patients treated with erythropoiesis-stimulating agents.
• 
  Malte Schilling, Holk Cruse:
  neuroWalknet, a controller for hexapod walking allowing for context dependent behavior.
• 
  Sören von Bülow, Mateusz Sikora, Florian E. C. Blanc, Roberto Covino, Gerhard Hummer:
  Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants.
• 
  Joonas P. Kosonen, Atte S. A. Eskelinen, Gustavo A. Orozco, Petteri Nieminen, Donald D. Anderson, Alan J. Grodzinsky, Rami K. Korhonen, Petri Tanska:
  Injury-related cell death and proteoglycan loss in articular cartilage: Numerical model combining necrosis, reactive oxygen species, and inflammatory cytokines.
• 
  Mei Ma, Xiujuan Lei:
  A dual graph neural network for drug-drug interactions prediction based on molecular structure and interactions.
• 
  Edoardo Pinzuti, Patricia Wollstadt, Oliver Tüscher, Michael Wibral:
  Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia.
• 
  Sebastian Goldt, Florent Krzakala, Lenka Zdeborová, Nicolas Brunel:
  Bayesian reconstruction of memories stored in neural networks from their connectivity.
• 
  Jacob D. O'Sullivan, J. Christopher D. Terry, Ramesh Wilson, Axel G. Rossberg:
  Community composition exceeds area as a predictor of long-term conservation value.
• 
  Diana Burk, Bruno B. Averbeck:
  Environmental uncertainty and the advantage of impulsive choice strategies.
• 
  Yibo Zhao, Nikoleta Vavouraki, Ruth C. Lovering, Valentina Escott-Price, Kirsten Harvey, Patrick A. Lewis, Claudia Manzoni:
  Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit.
• 
  Tareian A. Cazares, Faiz W. Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T. Bejjani, Joseph A. Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C. Kottyan, Artem Barski, Matthew T. Weirauch, V. B. Surya Prasath, Emily R. Miraldi:
  maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

Correction

• 
  Daniel Cresta, Donald C. Warren, Christian Quirouette, Amanda P. Smith, Lindey C. Lane, Amber M. Smith, Catherine A. A. Beauchemin:
  Correction: Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample's infection concentration.

Volume 19, Number 2, February 2023

Education

• 
  Roberto Marangoni, Vitoantonio Bevilacqua, Mario Cannataro, Bruno Hay Mele, Giancarlo Mauri, Anna Marabotti:
  An overview of bioinformatics courses delivered at the academic level in Italy: Reflections and recommendations from BITS.

Perspective

• 
  Liberata A. Mwita, William F. Mawalla, Frank R. Mtiiye, Daniel Kandonga, Jill Kent, Julie Makani, Raphael Zozimus Sangeda:
  Infrastructure for bioinformatics applications in Tanzania: Lessons from the Sickle Cell Programme.

Research Articles

• 
  Mojtaba Madadi Asl, Alireza Valizadeh, Peter A. Tass:
  Decoupling of interacting neuronal populations by time-shifted stimulation through spike-timing-dependent plasticity.
• 
  Hippolyte Verdier, François Laurent, Alhassan Cassé, Christian L. Vestergaard, Christian G. Specht, Jean-Baptiste Masson:
  Simulation-based inference for non-parametric statistical comparison of biomolecule dynamics.
• 
  Jérôme Tubiana, Lucia Adriana-Lifshits, Michael Nissan, Matan Gabay, Inbal Sher, Marina Sova, Haim J. Wolfson, Maayan Gal:
  Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions.
• 
  Francesca A. Lovell-Read, Stephen Parnell, Nik J. Cunniffe, Robin N. Thompson:
  Using 'sentinel' plants to improve early detection of invasive plant pathogens.
• 
  Giulio Ruffini, Giada Damiani, Diego Lozano-Soldevilla, Nikolas Deco, Fernando E. Rosas, Narsis A. Kiani, Adrián Ponce-Alvarez, Morten L. Kringelbach, Robin L. Carhart-Harris, Gustavo Deco:
  LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics.
• 
  Rossana Bettoni, Clare Hudson, Géraldine Williaume, Cathy Sirour, Hitoyoshi Yasuo, Sophie de Buyl, Geneviève Dupont:
  Model of neural induction in the ascidian embryo.
• 
  David Lipshutz, Aneesh Kashalikar, Shiva Farashahi, Dmitri B. Chklovskii:
  A linear discriminant analysis model of imbalanced associative learning in the mushroom body compartment.
• 
  Liam Lang, Giancarlo La Camera, Alfredo Fontanini:
  Temporal progression along discrete coding states during decision-making in the mouse gustatory cortex.
• 
  S. Amin Moosavi, Wilson Truccolo:
  Criticality in probabilistic models of spreading dynamics in brain networks: Epileptic seizures.
• 
  Jue Tao Lim, Kelvin Bryan Tan, John Arputhan Abisheganaden, Borame Sue Dickens:
  Forecasting upper respiratory tract infection burden using high-dimensional time series data and forecast combinations.
• 
  Chenxi Liao, Masataka Sawayama, Bei Xiao:
  Unsupervised learning reveals interpretable latent representations for translucency perception.
• 
  Irene Elices, Anirudh Kulkarni, Nicolas Escoubet, Léa-Laetitia Pontani, Alexis Michel Prevost, Romain Brette:
  An electrophysiological and kinematic model of Paramecium, the "swimming neuron".
• 
  Ke Li, James M. McCaw, Pengxing Cao:
  Enhanced viral infectivity and reduced interferon production are associated with high pathogenicity for influenza viruses.
• 
  Joris J. R. Louwen, Satria A. Kautsar, Sven van der Burg, Marnix H. Medema, Justin J. J. van der Hooft:
  iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures.
• 
  Gerald K. Cooray, Richard Rosch, Karl John Friston:
  Global dynamics of neural mass models.
• 
  Tamara Raschka, Meemansa Sood, Bruce Schultz, Aybuge Altay, Christian Ebeling, Holger Fröhlich:
  AI reveals insights into link between CD33 and cognitive impairment in Alzheimer's Disease.
• 
  Mohammad Dehghani-Habibabadi, Klaus Pawelzik:
  Synaptic self-organization of spatio-temporal pattern selectivity.
• 
  Francesca Callegari, Martina Brofiga, Paolo Massobrio:
  Modeling the three-dimensional connectivity of in vitro cortical ensembles coupled to Micro-Electrode Arrays.
• 
  Fengrong He, Ian H. Stevenson, Monty A. Escabí:
  Two stages of bandwidth scaling drives efficient neural coding of natural sounds.
• 
  Takayuki Niizato, Hisashi Murakami, Takuya Musha:
  Functional duality in group criticality via ambiguous interactions.
• 
  Julia Deichmann, Sara Bachmann, Marie-Anne Burckhardt, Marc Pfister, Gabor Szinnai, Hans-Michael Kaltenbach:
  New model of glucose-insulin regulation characterizes effects of physical activity and facilitates personalized treatment evaluation in children and adults with type 1 diabetes.
• 
  Karoline Horgmo Jæger, Ena Ivanovic, Jan P. Kucera, Aslak Tveito:
  Nano-scale solution of the Poisson-Nernst-Planck (PNP) equations in a fraction of two neighboring cells reveals the magnitude of intercellular electrochemical waves.
• 
  Bjarke Frost Nielsen, Chadi M. Saad-Roy, Yimei Li, Kim Sneppen, Lone Simonsen, Cécile Viboud, Simon A. Levin, Bryan T. Grenfell:
  Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2.
• 
  Brian Nils Lundstrom, Thomas J. Richner:
  Neural adaptation and fractional dynamics as a window to underlying neural excitability.
• 
  Matthew E. Berginski, Chinmaya U. Joisa, Brian T. Golitz, Shawn M. Gomez:
  Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types.
• 
  Maryl Lambros, Yehonatan Sella, Aviv Bergman:
  Phenotypic pliancy and the breakdown of epigenetic polycomb mechanisms.
• 
  Aaditya V. Rangan, Caroline C. McGrouther, Nivedita Bhadra, Stephanie Venn-Watson, Eric D. Jensen, Nicholas J. Schork:
  A time-series analysis of blood-based biomarkers within a 25-year longitudinal dolphin cohort.
• 
  Samuel Goldman, Maximino Aldana, Philippe Cluzel:
  Resonant learning in scale-free networks.
• 
  Philipp Fey, Daniel Ludwig Weber, Jannik Stebani, Philipp Mörchel, Peter Jakob, Jan Hansmann, Karl-Heinz Hiller, Daniel Haddad:
  Non-destructive classification of unlabeled cells: Combining an automated benchtop magnetic resonance scanner and artificial intelligence.
• 
  Yichen He, Christopher R. Cooney, Steve Maddock, Gavin H. Thomas:
  Using pose estimation to identify regions and points on natural history specimens.
• 
  Jake M. Ferguson, Andrea González-González, Johnathan A. Kaiser, Sara M. Winzer, Justin M. Anast, Ben Ridenhour, Tanya A. Miura, Christine E. Parent:
  Hidden variable models reveal the effects of infection from changes in host survival.
• 
  Rion Brattig Correia, Alain Barrat, Luis M. Rocha:
  Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs.
• 
  Madison S. Krieger:
  Evolutionary dynamics of hyperbolic language.
• 
  Rocky Diegmiller, Jasmin Imran Alsous, Duojia Li, Yukiko M. Yamashita, Stanislav Y. Shvartsman:
  Fusome topology and inheritance during insect gametogenesis.
• 
  John G. Holman, Winnie W. K. Lai, Paul Pichler, Daniel Saska, Leon Lagnado, Christopher L. Buckley:
  A behavioral and modeling study of control algorithms underlying the translational optomotor response in larval zebrafish with implications for neural circuit function.
• 
  Weicheng Qian, Kevin Gordon Stanley, Nathaniel David Osgood:
  Impacts of observation frequency on proximity contact data and modeled transmission dynamics.
• 
  David J. Haw, Matthew Biggerstaff, Pragati Prasad, Joseph Walker, Bryan T. Grenfell, Nimalan Arinaminpathy:
  Using real-time data to guide decision-making during an influenza pandemic: A modelling analysis.
• 
  Boya Yang, Jiaxu Li, Michael J. Haller, Desmond A. Schatz, Libin Rong:
  Modeling the progression of Type 2 diabetes with underlying obesity.
• 
  Inge M. N. Wortel, Johannes Textor:
  Interpreting T-cell search "strategies" in the light of evolution under constraints.
• 
  Luke Trinity, Ian Wark, Lance Lansing, Hosna Jabbari, Ulrike Stege:
  Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.

Volume 19, Number 3, March 2023

Education Articles

• 
  Ryan R. Wick, Louise M. Judd, Kathryn E. Holt:
  Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing.
• 
  Ruth Nanjala, Festus Nyasimi, Daniel Masiga, Caleb Kipkurui Kibet:
  A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya.
• 
  Cameron Mura, Philip E. Bourne:
  Ten simple rules for serving as an editor.
• 
  David Moreau, Kristina Wiebels:
  Ten simple rules for designing and conducting undergraduate replication projects.
• 
  Alon Zivony, Rasha Kardosh, Liadh Timmins, Niv Reggev:
  Ten simple rules for socially responsible science.

Perspective

• 
  Darya Pokutnaya, Bruce Childers, Alice E. Arcury-Quandt, Harry Hochheiser, Willem G. Van Panhuis:
  An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases.

Review

• 
  Claude Pellen, Anne Le Louarn, Gilliosa Spurrier-Bernard, Evelyne Decullier, Jean-Marie Chrétien, Eric Rosenthal, Gérard Le Goff, David Moher, John P. A. Ioannidis, Florian Naudet:
  Ten (not so) simple rules for clinical trial data-sharing.

Research Articles

• 
  Karina Arias-Calluari, Theotime Colin, Tanya Latty, Mary Myerscough, Eduardo G. Altmann:
  Modelling daily weight variation in honey bee hives.
• 
  Sameer D'Costa, Emily C. Hinds, Chase R. Freschlin, Hyebin Song, Philip A. Romero:
  Inferring protein fitness landscapes from laboratory evolution experiments.
• 
  Sean A. Rands, Christos C. Ioannou:
  Personality variation is eroded by simple social behaviours in collective foragers.
• 
  Myriah Haggard, Maurice J. Chacron:
  Coding of object location by heterogeneous neural populations with spatially dependent correlations in weakly electric fish.
• 
  Paul Manuel Müller, Christian Meisel:
  Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load.
• 
  Justas Birgiolas, Vergil Haynes, Padraig Gleeson, Richard C. Gerkin, Suzanne W. Dietrich, Sharon M. Crook:
  NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML.
• 
  Peng Zhang, Shikui Tu:
  MGAE-DC: Predicting the synergistic effects of drug combinations through multi-channel graph autoencoders.
• 
  Christian Malte Boßelmann, Ulrike B. S. Hedrich, Holger Lerche, Nico Pfeifer:
  Predicting functional effects of ion channel variants using new phenotypic machine learning methods.
• 
  Luciana Melina Luque, Carlos Manuel Carlevaro, Camilo Julio Llamoza Torres, Enrique Lomba:
  Physics-based tissue simulator to model multicellular systems: A study of liver regeneration and hepatocellular carcinoma recurrence.
• 
  Neda Kaboodvand, Behzad Iravani, Martijn P. van den Heuvel, Jonas Persson, Robert Boden:
  Macroscopic resting state model predicts theta burst stimulation response: A randomized trial.
• 
  Hakim Benkirane, Yoann Pradat, Stefan Michiels, Paul-Henry Cournède:
  CustOmics: A versatile deep-learning based strategy for multi-omics integration.
• 
  Matthias Mimault, Mariya Ptashnyk, Lionel X. Dupuy:
  Particle-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil.
• 
  Christophe Le Priol, Chloé-Agathe Azencott, Xavier Gidrol:
  Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression.
• 
  Marco Pensalfini, Adrian Buganza Tepole:
  Mechano-biological and bio-mechanical pathways in cutaneous wound healing.
• 
  Mira Barshai, Barak Engel, Idan Haim, Yaron Orenstein:
  G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data.
• 
  Anni S. Halkola, Kaisa Joki, Tuomas Mirtti, Marko M. Mäkelä, Tero Aittokallio, Teemu D. Laajala:
  OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer.
• 
  Magnus J. Haughey, Aleix Bassolas, Sandro Sousa, Ann-Marie Baker, Trevor A. Graham, Vincenzo Nicosia, Weini Huang:
  First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer.
• 
  Michael Lukowski, Andrew Prokhorenkov, Robert L. Grossman:
  Towards self-describing and FAIR bulk formats for biomedical data.
• 
  Sasikiran Kandula, Mark Olfson, Madelyn S. Gould, Katherine M. Keyes, Jeffrey Shaman:
  Hindcasts and forecasts of suicide mortality in US: A modeling study.
• 
  Yue Wu, Steven Mascaro, Mejbah Bhuiyan, Parveen Fathima, Ariel O. Mace, Mark P. Nicol, Peter C. Richmond, Lea-Ann Kirkham, Michael Dymock, David A. Foley, Charlie McLeod, Meredith L. Borland, Andrew Martin, Phoebe C. M. Williams, Julie A. Marsh, Thomas L. Snelling, Christopher C. Blyth:
  Predicting the causative pathogen among children with pneumonia using a causal Bayesian network.
• 
  Pål Vegard Johnsen, Inga Strümke, Mette Langaas, Andrew Thomas DeWan, Signe Riemer-Sørensen:
  Inferring feature importance with uncertainties with application to large genotype data.
• 
  Hui Peng, Limsoon Wong, Wilson Wen Bin Goh:
  ProInfer: An interpretable protein inference tool leveraging on biological networks.
• 
  Liangjie Sun, Yushan Qiu, Wai-Ki Ching, Pu Zhao, Quan Zou:
  PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progression.
• 
  Alicia Murga, Rahul Bale, Chung-Gang Li, Kazuhide Ito, Makoto Tsubokura:
  Large eddy simulation of droplet transport and deposition in the human respiratory tract to evaluate inhalation risk.
• 
  Dohoon Lee, Bonil Koo, Jeewon Yang, Sun Kim:
  Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments.
• 
  Lorenzo Cappello, Jaehee Kim, Julia A. Palacios:
  adaPop: Bayesian inference of dependent population dynamics in coalescent models.
• 
  Bercem Dutagaci, Bingbing Duan, Chenxi Qiu, Craig D. Kaplan, Michael Feig:
  Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning.
• 
  Jacqueline A. May, Zeny Feng, Sarah J. Adamowicz:
  A real data-driven simulation strategy to select an imputation method for mixed-type trait data.
• 
  Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, Andreas Dräger:
  New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells.
• 
  Sean B. King, Mona Singh:
  Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers.
• 
  Delora Baptista, Pedro G. Ferreira, Miguel Rocha:
  A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer.
• 
  Robert C. Glastad, Iain G. Johnston:
  Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions.
• 
  Eliram Nof, Saurabh Bhardwaj, Pantelis Koullapis, Ron Bessler, Stavros C. Kassinos, Josué Sznitman:
  In vitro-in silico correlation of three-dimensional turbulent flows in an idealized mouth-throat model.
• 
  Adam Ponzi, Salvador Dura-Bernal, Michele Migliore:
  Theta-gamma phase amplitude coupling in a hippocampal CA1 microcircuit.
• 
  Máté L. Telek, Elisenda Feliu:
  Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity.
• 
  Christoffer Norn, Ingemar André:
  Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates.
• 
  Ana Morán, Mathieu Lihoreau, Alfonso Pérez-Escudero, Jacques Gautrais:
  Modeling bee movement shows how a perceptual masking effect can influence flower discovery.
• 
  Dominic M. Dunstan, Mark P. Richardson, Eugenio Abela, Ozgur E. Akman, Marc Goodfellow:
  Global nonlinear approach for mapping parameters of neural mass models.
• 
  Simeon Adejumo, Tomonori Kikuchi, Kazuki Tsuji, Kana Maruyama-Onda, Ken Sugawara, Yoshikatsu Hayashi:
  A real-time feedback system stabilises the regulation of worker reproduction under various colony sizes.
• 
  Brennica Marlow, Georg Kuenze, Jens Meiler, Julia Koehler Leman:
  Docking cholesterol to integral membrane proteins with Rosetta.
• 
  Benjamin J. Heil, Jake Crawford, Casey S. Greene:
  The effect of non-linear signal in classification problems using gene expression.
• 
  Weiqi Lu, José N. Onuchic, Michele Di Pierro:
  An associative memory Hamiltonian model for DNA and nucleosomes.
• 
  Elias Ventre, Ulysse Herbach, Thibault Espinasse, Gérard Benoit, Olivier Gandrillon:
  One model fits all: Combining inference and simulation of gene regulatory networks.
• 
  Zhe Li, Josue Ortega Caro, Evgenia Rusak, Wieland Brendel, Matthias Bethge, Fabio Anselmi, Ankit B. Patel, Andreas S. Tolias, Xaq Pitkow:
  Robust deep learning object recognition models rely on low frequency information in natural images.
• 
  Joshua Adam Bull, Helen M. Byrne:
  Quantification of spatial and phenotypic heterogeneity in an agent-based model of tumour-macrophage interactions.
• 
  Arthur Bernard, Steffen Wischmann, Dario Floreano, Laurent Keller:
  The evolution of behavioral cues and signaling in displaced communication.
• 
  William T. Harvey, Vinny Davies, Rodney S. Daniels, Lynne Whittaker, Victoria Gregory, Alan J. Hay, Dirk Husmeier, John W. McCauley, Richard E. Reeve:
  A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses.
• 
  Nick P. Taylor, Nik J. Cunniffe:
  Modelling quantitative fungicide resistance and breakdown of resistant cultivars: Designing integrated disease management strategies for Septoria of winter wheat.
• 
  Kimberly A. Dautel, Ephraim Agyingi, Pras Pathmanathan:
  Validation framework for epidemiological models with application to COVID-19 models.
• 
  Karen E. Ross, Guolin Zhang, Cuneyt Akcora, Yu Lin, Bin Fang, John M. Koomen, Eric B. Haura, Mark Grimes:
  Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer.
• 
  Carlos A. Gandarilla-Pérez, Sergio Pinilla, Anne-Florence Bitbol, Martin Weigt:
  Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins.
• 
  Julian Herold, Eric Behle, Jakob Rosenbauer, Jacopo Ferruzzi, Alexander Schug:
  Development of a scoring function for comparing simulated and experimental tumor spheroids.
• 
  Chenxi Dai, Dongsheng Zhou, Bo Gao, Kaifa Wang:
  A new method for the joint estimation of instantaneous reproductive number and serial interval during epidemics.
• 
  Mahmood Kalemati, Mojtaba Zamani Emani, Somayyeh Koohi:
  BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach.
• 
  Alina Guo, Steven L. Salzberg, Aleksey V. Zimin:
  JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.
• 
  Maxx H. Tessmer, Stefan Stoll:
  chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling.
• 
  Stéphane Plaszczynski, Basile Grammaticos, Johan Pallud, Jean-Eric Campagne, Mathilde Badoual:
  Predicting regrowth of low-grade gliomas after radiotherapy.

Corrections

• 
  Wendi Bacon, Alexandra Holinski, Marina Pujol, Meredith Wilmott, Sarah L. Morgan:
  Correction: Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.
• 
  Samantha Petti, Sean R. Eddy:
  Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms.
• 
  Alasdair D. F. Clarke, Amelia R. Hunt, Anna E. Hughes:
  Correction: Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection.
• 
  Gustavo A. Orozco, Kalle Karjalainen, Eng Kuan Moo, Lauri Stenroth, Petri Tanska, Jaqueline Lourdes Rios, Teemu V. Tuomainen, Mikko J. Nissi, Hanna Isaksson, Walter Herzog, Rami K. Korhonen:
  Correction: A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait.

Volume 19, Number 4, April 2023

Education

• 
  Charlie Pilgrim, Paul Kent, Kasra Hosseini, Ed Chalstrey:
  Ten simple rules for working with other people's code.

Perspective

• 
  Bogna Stawarczyk, Malgorzata Roos:
  Establishing effective cross-disciplinary collaboration: Combining simple rules for reproducible computational research, a good data management plan, and good research practice.

Review

• 
  Ioana M. Gherman, Zahraa S. Abdallah, Wei Pang, Thomas E. Gorochowski, Claire S. Grierson, Lucia Marucci:
  Bridging the gap between mechanistic biological models and machine learning surrogates.

Research Articles

• 
  Cristiano Guttà, Christoph Morhard, Markus Rehm:
  Applying a GAN-based classifier to improve transcriptome-based prognostication in breast cancer.
• 
  Javier Baladron, Julien Vitay, Torsten Fietzek, Fred H. Hamker:
  The contribution of the basal ganglia and cerebellum to motor learning: A neuro-computational approach.
• 
  Shervin Safavi, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F. Ramirez-Villegas, Nikos K. Logothetis, Michel Besserve:
  Uncovering the organization of neural circuits with Generalized Phase Locking Analysis.
• 
  Carolin Zitzmann, Christopher Dächert, Bianca Schmid, Hilde van der Schaar, Martijn van Hemert, Alan S. Perelson, Frank J. M. van Kuppeveld, Ralf Bartenschlager, Marco Binder, Lars Kaderali:
  Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies.
• 
  Andrés Cumsille, Roberto E. Durán, Andrea Rodríguez-Delherbe, Vicente Saona-Urmeneta, Beatriz Cámara, Michael Seeger, Mauricio Araya, Nicolás A. Jara, Carlos Buil-Aranda:
  GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.
• 
  Benjamin James Lansdell, Konrad Paul Körding:
  Neural spiking for causal inference and learning.
• 
  Luis F. Garcia-Alles, Miguel Fuentes-Cabrera, Gilles Truan, David Reguera:
  Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements.
• 
  Reese A. Martin, Ann T. Tate:
  Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution.
• 
  Stephanie Khuu, Justin W. Fernandez, Geoffrey G. Handsfield:
  Delayed skeletal muscle repair following inflammatory damage in simulated agent-based models of muscle regeneration.
• 
  Tomer D. Mann, Eli Kopel, Eli Eisenberg, Erez Y. Levanon:
  Increased A-to-I RNA editing in atherosclerosis and cardiomyopathies.
• 
  Yuanhong Tang, Xingyu Zhang, Lingling An, Zhaofei Yu, Jian K. Liu:
  Diverse role of NMDA receptors for dendritic integration of neural dynamics.
• 
  Julia R. Rogers, Phillip L. Geissler:
  Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid-membrane contacts.
• 
  Frank Mazza, Alexandre Guet-McCreight, Taufik A. Valiante, John D. Griffiths, Etay Hay:
  In-silico EEG biomarkers of reduced inhibition in human cortical microcircuits in depression.
• 
  Paul Manz, Raoul-Martin Memmesheimer:
  Purely STDP-based assembly dynamics: Stability, learning, overlaps, drift and aging.
• 
  Anant B. Shinde, Sovesh Mohapatra, Gottfried Schlaug:
  Identifying the engagement of a brain network during a targeted tDCS-fMRI experiment using a machine learning approach.
• 
  Mohammad Hassan Khatami, Udson C. Mendes, Nathan Wiebe, Philip M. Kim:
  Gate-based quantum computing for protein design.
• 
  Pau Clusella, Gustavo Deco, Morten L. Kringelbach, Giulio Ruffini, Jordi García-Ojalvo:
  Complex spatiotemporal oscillations emerge from transverse instabilities in large-scale brain networks.
• 
  Brenda Lyn A. Gavina, Aurelio A. de los Reyes V., Mette S. Olufsen, Suzanne Lenhart, Johnny T. Ottesen:
  Toward an optimal contraception dosing strategy.
• 
  Bryan S. Hernandez, Patrick Vincent N. Lubenia, Matthew D. Johnston, Jae Kyoung Kim:
  A framework for deriving analytic steady states of biochemical reaction networks.
• 
  Antal Martinecz, Martin J. Boeree, Andreas H. Diacon, Rodney Dawson, Colin Hemez, Rob E. Aarnoutse, Pia Abel zur Wiesch:
  High rifampicin peak plasma concentrations accelerate the slow phase of bacterial decline in tuberculosis patients: Evidence for heteroresistance.
• 
  Vincent Arnaud, François Pellegrino, Sumir Keenan, Xavier St-Gelais, Nicolas Mathevon, Florence Levréro, Christophe Coupé:
  Improving the workflow to crack Small, Unbalanced, Noisy, but Genuine (SUNG) datasets in bioacoustics: The case of bonobo calls.
• 
  Mufeng Tang, Tommaso Salvatori, Beren Millidge, Yuhang Song, Thomas Lukasiewicz, Rafal Bogacz:
  Recurrent predictive coding models for associative memory employing covariance learning.
• 
  Magda Chafaï, Ariane Delrocq, Perrine Inquimbert, Ludivine Pidoux, Kevin Delanoe, Maurizio Toft, Frederic Brau, Eric Lingueglia, Romain Veltz, Emmanuel Deval:
  Dual contribution of ASIC1a channels in the spinal processing of pain information by deep projection neurons revealed by computational modeling.
• 
  Salim Ghannoum, Damiano Fantini, Muhammad Zahoor, Veronika Reiterer, Santosh Phuyal, Waldir Leoncio Netto, Øystein Sørensen, Arvind Iyer, Debarka Sengupta, Lina Prasmickaite, Gunhild Mari Mælandsmo, Alvaro Köhn-Luque, Hesso Farhan:
  A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression.
• 
  Xiangyun Qiu:
  Sequence similarity governs generalizability of de novo deep learning models for RNA secondary structure prediction.
• 
  Lixiang Zhang, Lin Lin, Jia Li:
  Multi-view clustering by CPS-merge analysis with application to multimodal single-cell data.
• 
  Moritz O. Buchholz, Alexandra Gastone Guilabert, Benjamin Ehret, Gregor F. P. Schuhknecht:
  How synaptic strength, short-term plasticity, and input synchrony contribute to neuronal spike output.
• 
  Yuji Omachi, Nen Saito, Chikara Furusawa:
  Rare-event sampling analysis uncovers the fitness landscape of the genetic code.
• 
  Jane A. Dwivedi-Yu, Zachary J. Oppler, Matthew W. Mitchell, Yun S. Song, Dustin Brisson:
  A fast machine-learning-guided primer design pipeline for selective whole genome amplification.
• 
  Natasa Puzovic, Tanvi Madaan, Julien Y. Dutheil:
  Being noisy in a crowd: Differential selective pressure on gene expression noise in model gene regulatory networks.
• 
  Colin G. Cess, Stacey D. Finley:
  Calibrating agent-based models to tumor images using representation learning.
• 
  Aidan B. Estelle, August George, Elisar J. Barbar, Daniel M. Zuckerman:
  Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference.
• 
  Zhihua Wu, Aike Guo:
  Bioinspired figure-ground discrimination via visual motion smoothing.
• 
  Timothy Qi, Benjamin G. Vincent, Yanguang Cao:
  A multispecies framework for modeling adaptive immunity and immunotherapy in cancer.
• 
  Aurel A. Lazar, Tingkai Liu, Chung-Heng Yeh:
  The functional logic of odor information processing in the Drosophila antennal lobe.
• 
  Zichen Wang, Parth Natekar, Challana Tea, Sharon Tamir, Hiroyuki Hakozaki, Johannes Schöneberg:
  MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data.
• 
  Hanna Isaksson, Åke Brännström, Eric Libby:
  Minor variations in multicellular life cycles have major effects on adaptation.
• 
  Tarun Kumar, Ramanathan Sethuraman, Sanga Mitra, Balaraman Ravindran, Manikandan Narayanan:
  MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication.
• 
  Yongrong Qiu, David A. Klindt, Klaudia P. Szatko, Dominic Gonschorek, Larissa Höfling, Timm Schubert, Laura Busse, Matthias Bethge, Thomas Euler:
  Efficient coding of natural scenes improves neural system identification.
• 
  Endrit Pajaziti, Javier Montalt-Tordera, Claudio Capelli, Raphaël Sivera, Emilie Sauvage, Michael Quail, Silvia Schievano, Vivek Muthurangu:
  Shape-driven deep neural networks for fast acquisition of aortic 3D pressure and velocity flow fields.
• 
  Natalia Ostrowska, Michael Feig, Joanna Trylska:
  Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease.
• 
  Matthew Macaulay, Aaron E. Darling, Mathieu Fourment:
  Fidelity of hyperbolic space for Bayesian phylogenetic inference.
• 
  Michael W. Irvin, Arvind Ramanathan, Carlos F. Lopez:
  Model certainty in cellular network-driven processes with missing data.
• 
  Deborah A. Powers, Matthew L. Jenior, Glynis L. Kolling, Jason A. Papin:
  Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies.
• 
  Alina Rekena, Marina J. Pinheiro, Nemailla Bonturi, Isma Belouah, Eliise Tammekivi, Koit Herodes, Eduard J. Kerkhoven, Petri-Jaan Lahtvee:
  Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides.
• 
  Krystian Zielinski, Sebastian Pukszta, Malgorzata Mickiewicz, Marta Kotlarz, Piotr Wygocki, Marcin Zielen, Dominika Drzewiecka, Damian Drzyzga, Anna Kloska, Joanna Jakóbkiewicz-Banecka:
  Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data.
• 
  Sean M. Cavany, Guido España, Alun L. Lloyd, Gonzalo M. Vazquez-Prokopec, Helvio Astete, Lance A. Waller, Uriel Kitron, Thomas W. Scott, Amy C. Morrison, Robert C. Reiner Jr., T. Alex Perkins:
  Fusing an agent-based model of mosquito population dynamics with a statistical reconstruction of spatio-temporal abundance patterns.
• 
  Aref Pariz, Daniel Trotter, Axel Hutt, Jérémie Lefebvre:
  Selective control of synaptic plasticity in heterogeneous networks through transcranial alternating current stimulation (tACS).
• 
  Andrea Ortone, Alberto Arturo Vergani, Mahboubeh Ahmadipour, Riccardo Mannella, Alberto Mazzoni:
  Dopamine depletion leads to pathological synchronization of distinct basal ganglia loops in the beta band.
• 
  Chen Zhao, Jialu Zhang, Xiaoyue Hou, Chi Ho Yeung, An Zeng:
  A high-frequency mobility big-data reveals how COVID-19 spread across professions, locations and age groups.
• 
  Stefania Bracci, Jakob Mraz, Astrid Zeman, Gaëlle Leys, Hans P. Op de Beeck:
  The representational hierarchy in human and artificial visual systems in the presence of object-scene regularities.

Corrections

• 
  Nathaniel J. Linden, Boris Kramer, Padmini Rangamani:
  Correction: Bayesian parameter estimation for dynamical models in systems biology.
• 
  PLOS Computational Biology Staff:
  Correction: Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis.
• 
  Paul Manuel Müller, Christian Meisel:
  Correction: Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load.

Volume 19, Number 5, May 2023

Education

• 
  Stefanie Luecke, Allison Schiffman, Apeksha Singh, Helen Huang, Barbara Shannon, Catera L. Wilder:
  Four guiding principles for effective trainee-led STEM community engagement through high school outreach.

Research Articles

• 
  Samuel N. Brudner, John Pearson, Richard Mooney:
  Generative models of birdsong learning link circadian fluctuations in song variability to changes in performance.
• 
  Sydney C. Weiser, Brian R. Mullen, Desiderio Ascencio, James B. Ackman:
  Data-driven segmentation of cortical calcium dynamics.
• 
  Olga Mineeva, Daniel Danciu, Bernhard Schölkopf, Ruth E. Ley, Gunnar Rätsch, Nicholas D. Youngblut:
  ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.
• 
  Deepraj Sarmah, Wesley O. Meredith, Ian K. Weber, Madison R. Price, Marc R. Birtwistle:
  Predicting anti-cancer drug combination responses with a temporal cell state network model.
• 
  Younes Bouhadjar, Dirk J. Wouters, Markus Diesmann, Tom Tetzlaff:
  Coherent noise enables probabilistic sequence replay in spiking neuronal networks.
• 
  Jonathan K. Sakkos, María Santos-Merino, Emmanuel J. Kokarakis, Bowen Li, Miguel Fuentes-Cabrera, Paolo Zuliani, Daniel C. Ducat:
  Predicting partner fitness based on spatial structuring in a light-driven microbial community.
• 
  Yihsuan S. Tsai, Yogitha S. Chareddy, Brandon A. Price, Joel S. Parker, Chad V. Pecot:
  An integrated model for predicting KRAS dependency.
• 
  Tianhe Wang, Yingrui Luo, Richard B. Ivry, Jonathan S. Tsay, Ernst Pöppel, Yan Bao:
  A unitary mechanism underlies adaptation to both local and global environmental statistics in time perception.
• 
  Jacob R. Pennington, Stephen V. David:
  A convolutional neural network provides a generalizable model of natural sound coding by neural populations in auditory cortex.
• 
  Megan M. Sperry, Tomiko Oskotsky, Ivana Maric, Shruti Kaushal, Takako Takeda, Viktor Horvath, Rani K. Powers, Melissa Rodas, Brooke Furlong, Mercy Soong, Pranav Prabhala, Girija Goyal, Kenneth E. Carlson, Ronald J. Wong, Idit Kosti, Brian L. Le, James Logue, Holly Hammond, Matthew Frieman, David K. Stevenson, Donald E. Ingber, Marina Sirota, Richard Novák:
  Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients.
• 
  Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble:
  Matrix prior for data transfer between single cell data types in latent Dirichlet allocation.
• 
  Jennifer L. Rokhsar, Brinkley Raynor, Justin Sheen, Neal D. Goldstein, Michael Z. Levy, Ricardo Castillo-Neyra:
  Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.
• 
  Yi Zheng, Shaoting Tang, Hongwei Zheng, Xin Wang, Longzhao Liu, Yaqian Yang, Yi Zhen, Zhiming Zheng:
  Noise improves the association between effects of local stimulation and structural degree of brain networks.
• 
  Viraaj Jayaram, Aarti Sehdev, Nirag Kadakia, Ethan A. Brown, Thierry Emonet:
  Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments.
• 
  Hengda He, Linbi Hong, Paul Sajda:
  Pupillary response is associated with the reset and switching of functional brain networks during salience processing.
• 
  Eloy Parra-Barrero, Sen Cheng:
  Learning to predict future locations with internally generated theta sequences.
• 
  Sarafa A. Iyaniwura, Notice Ringa, Prince A. Adu, Sunny Mak, Naveed Z. Janjua, Michael A. Irvine, Michael C. Otterstatter:
  Understanding the impact of mobility on COVID-19 spread: A hybrid gravity-metapopulation model of COVID-19.
• 
  Michael F. Hagan, Farzaneh Mohajerani:
  Self-assembly coupled to liquid-liquid phase separation.
• 
  Chao Han, Gwendolyn English, Hannes P. Saal, Giacomo Indiveri, Aditya Gilra, Wolfger von der Behrens, Eleni Vasilaki:
  Modelling novelty detection in the thalamocortical loop.
• 
  Ruolin He, Jinyu Zhang, Yuanzhe Shao, Shaohua Gu, Chen Song, Long Qian, Wen-Bing Yin, Zhiyuan Li:
  Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements.
• 
  Pierre Ekelmans, Nataliya Kraynyukova, Tatjana Tchumatchenko:
  Targeting operational regimes of interest in recurrent neural networks.
• 
  Fariha Akter, Julien Ochala, Arianna Fornili:
  Binding pocket dynamics along the recovery stroke of human β-cardiac myosin.
• 
  Anthony Federico, Joseph Kern, Xaralabos Varelas, Stefano Monti:
  Structure learning for gene regulatory networks.
• 
  Sanmitra Ghosh, Paul J. Birrell, Daniela De Angelis:
  An approximate diffusion process for environmental stochasticity in infectious disease transmission modelling.
• 
  Yvan Rousset, Oliver Ebenhöh, Adélaïde Raguin:
  Stochastic modelling of a three-dimensional glycogen granule synthesis and impact of the branching enzyme.
• 
  Rohith Vedhthaanth Sekar, Patricia J. Oliva, Michael T. Woodside:
  Modelling the structures of frameshift-stimulatory pseudoknots from representative bat coronaviruses.
• 
  Alvaro Fletcher, Zeba Wunderlich, Germán A. Enciso:
  Shadow enhancers mediate trade-offs between transcriptional noise and fidelity.
• 
  Pawel Nalecz-Jawecki, Paolo Armando Gagliardi, Marek Kochanczyk, Coralie Dessauges, Olivier Pertz, Tomasz Lipniacki:
  The MAPK/ERK channel capacity exceeds 6 bit/hour.
• 
  William Sheffler, Erin C. Yang, Quinton Dowling, Yang Hsia, Chelsea N. Fries, Jenna Stanislaw, Mark D. Langowski, Marisa Brandys, Zhe Li, Rebecca Skotheim, Andrew J. Borst, Alena Khmelinskaia, Neil P. King, David Baker:
  Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.
• 
  David Augustin, Ben Lambert, Ken Wang, Antje-Christine Walz, Martin Robinson, David Gavaghan:
  Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data.
• 
  Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin K. Yang:
  Deep self-supervised learning for biosynthetic gene cluster detection and product classification.
• 
  Solène Song, Malek Senoussi, Paul Escande, Paul Villoutreix:
  Random walk informed heterogeneity detection reveals how the lymph node conduit network influences T cells collective exploration behavior.
• 
  Kexin Huang, Yun Zhang, Haoran Gong, Zhengzheng Qiao, Tiangang Wang, Weiling Zhao, Liyu Huang, Xiaobo Zhou:
  Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression.
• 
  Federico Ciotti, Andrea Cimolato, Giacomo Valle, Stanisa Raspopovic:
  Design of an adaptable intrafascicular electrode (AIR) for selective nerve stimulation by model-based optimization.
• 
  Pauline Clin, Frédéric Grognard, Didier Andrivon, Ludovic Mailleret, Frédéric M. Hamelin:
  The proportion of resistant hosts in mixtures should be biased towards the resistance with the lowest breaking cost.
• 
  Kai J. Miller, Klaus-Robert Müller, Gabriela Ojeda Valencia, Harvey Huang, Nicholas M. Gregg, Gregory A. Worrell, Dora Hermes:
  Canonical Response Parameterization: Quantifying the structure of responses to single-pulse intracranial electrical brain stimulation.
• 
  Gaurav Bajpai, Samuel A. Safran:
  Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.
• 
  Michal Michalski, Piotr Setny:
  Two modes of fusogenic action for influenza virus fusion peptide.
• 
  Derek J. Essegian, Valery Chavez, Rabia Khurshid, Jaime R. Merchan, Stephan C. Schürer:
  AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK.
• 
  K. D. Ahlquist, Lauren A. Sugden, Sohini Ramachandran:
  Enabling interpretable machine learning for biological data with reliability scores.
• 
  Sam De Meyer, Daniel Felipe Cruz, Tom De Swaef, Peter Lootens, Jolien De Block, Kevin Bird, Heike Sprenger, Michael Van de Voorde, Stijn Hawinkel, Tom Van Hautegem, Dirk Inzé, Hilde Nelissen, Isabel Roldán-Ruiz, Steven Maere:
  Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression.
• 
  Matthew Beauregard Smith, Zack Booth Simpson, Edward M. Marcotte:
  Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier.
• 
  Marta Sanvicente-García, Albert García-Valiente, Socayna Jouide, Jessica Jaraba-Wallace, Eric Bautista, Marc Escobosa, Avencia Sánchez-Mejías, Marc Güell:
  CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing.
• 
  Junya Sunagawa, Ryo Komorizono, Hyeongki Park, William S. Hart, Robin N. Thompson, Akiko Makino, Keizo Tomonaga, Shingo Iwami, Ryo Yamaguchi:
  Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection.
• 
  Manu Aggarwal, Vipul Periwal:
  Tight basis cycle representatives for persistent homology of large biological data sets.
• 
  Seunghyun Wang, Doheon Lee:
  Identifying prognostic subgroups of luminal-A breast cancer using deep autoencoders and gene expressions.
• 
  Jean-Michel Arbona, Hadi Kabalane, Jeremy Barbier, Arach Goldar, Olivier Hyrien, Benjamin Audit:
  Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.

Correction

• 
  Nikita Sivakumar, Helen V. Warner, Shayn M. Peirce, Matthew Lazzara:
  Correction: A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion.

Volume 19, Number 6, June 2023

Education Articles

• 
  Ilinca I. Ciubotariu, Gundula Bosch:
  Teaching students to R3eason, not merely to solve problem sets: The role of philosophy and visual data communication in accessible data science education.
• 
  Leyla Jael Castro, Patricia M. Palagi, Niall Beard, Teresa K. Attwood, Michelle D. Brazas:
  Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources.
• 
  Leonid Chindelevitch, Maarten van Dongen, Heather Graz, Antonio Pedrotta, Anita Suresh, Swapna Uplekar, Elita Jauneikaite, Nicole E. Wheeler:
  Ten simple rules for the sharing of bacterial genotype - Phenotype data on antimicrobial resistance.

Perspective

• 
  Robin Champieux, Anthony Solomonides, Marisa Conte, Svetlana Rojevsky, Jimmy Phuong, David A. Dorr, Elizabeth Zampino, Adam B. Wilcox, Matthew B. Carson, Kristi L. Holmes:
  Ten simple rules for organizations to support research data sharing.

Research Articles

• 
  Carlos G. Correa, Mark K. Ho, Frederick Callaway, Nathaniel D. Daw, Thomas L. Griffiths:
  Humans decompose tasks by trading off utility and computational cost.
• 
  Spencer J. Fox, Emily Javan, Remy Pasco, Graham Casey Gibson, Briana Betke, José L. Herrera-Diestra, Spencer Woody, Kelly Pierce, Kaitlyn E. Johnson, Maureen Johnson-León, Michael Lachmann, Lauren Ancel Meyers:
  Disproportionate impacts of COVID-19 in a large US city.
• 
  Viet-Anh Nguyen, David W. Bartels, Christopher A. Gilligan:
  Modelling the spread and mitigation of an emerging vector-borne pathogen: Citrus greening in the U.S.
• 
  Maria Kalweit, Andrea M. Burden, Joschka Boedecker, Thomas Hügle, Theresa Burkard:
  Patient groups in Rheumatoid arthritis identified by deep learning respond differently to biologic or targeted synthetic DMARDs.
• 
  Joshua Pickard, Can Chen, Rahmy Salman, Cooper Stansbury, Sion Kim, Amit Surana, Anthony M. Bloch, Indika Rajapakse:
  HAT: Hypergraph analysis toolbox.
• 
  Shozen Dan, Yu Chen, Yining Chen, Mélodie Monod, Veronika K. Jaeger, Samir Bhatt, André Karch, Oliver Ratmann:
  Estimating fine age structure and time trends in human contact patterns from coarse contact data: The Bayesian rate consistency model.
• 
  Itay Kahane, Mark D. M. Leiserson, Roded Sharan:
  A mutation-level covariate model for mutational signatures.
• 
  Hugo Dourado, Wolfram Liebermeister, Oliver Ebenhöh, Martin J. Lercher:
  Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth.
• 
  Casey M. Baker, Yiyang Gong:
  Identifying properties of pattern completion neurons in a computational model of the visual cortex.
• 
  Danelle Marie Larson, Wako Bungula, Casey McKean, Alaina Stockdill, Amber Lee, Frederick Forrest Miller, Killian Davis:
  Quantifying ecosystem states and state transitions of the Upper Mississippi River System using topological data analysis.
• 
  Irán R. Román, Adrian S. Roman, Ji-Chul Kim, Edward W. Large:
  Hebbian learning with elasticity explains how the spontaneous motor tempo affects music performance synchronization.
• 
  Joshua Daniel Rubin, Nicola Alexandra Vogel, Shyam Gopalakrishnan, Peter Wad Sackett, Gabriel Renaud:
  HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph.
• 
  Mohammad Reza Nikmaneshi, Rakesh K. Jain, Lance L. Munn:
  Computational simulations of tumor growth and treatment response: Benefits of high-frequency, low-dose drug regimens and concurrent vascular normalization.
• 
  Julie A. Charlton, Wiktor Mlynarski, Yoon H. Bai, Ann M. Hermundstad, Robbe L. T. Goris:
  Environmental dynamics shape perceptual decision bias.
• 
  Anastasiia Kim, Sanna Sevanto, Eric R. Moore, Nicholas Lubbers:
  Latent Dirichlet Allocation modeling of environmental microbiomes.
• 
  Senbin Zhu, Qian-Hu Jiang, Zhi-Guo Chen, Xiang Zhou, Yan-Ting Jin, Zixin Deng, Feng-Biao Guo:
  Mslar: Microbial synthetic lethal and rescue database.
• 
  Hojeong Kim, Charles J. Heckman:
  A dynamic calcium-force relationship model for sag behavior in fast skeletal muscle.
• 
  Aris Paschalidis, Oliver J. Watson, Ozkan Aydemir, Robert Verity, Jeffrey A. Bailey:
  coiaf: Directly estimating complexity of infection with allele frequencies.
• 
  Lynn K. A. Sörensen, Sander M. Bohté, Dorina De Jong, Heleen A. Slagter, H. Steven Scholte:
  Mechanisms of human dynamic object recognition revealed by sequential deep neural networks.
• 
  Tin Yau Pang, Martin J. Lercher:
  Optimal density of bacterial cells.
• 
  Sean L. Wu, John M. Henry, Daniel T. Citron, Doreen Mbabazi Ssebuliba, Juliet Nakakawa Nsumba, Héctor M. Sánchez C., Oliver J. Brady, Carlos A. Guerra, Guillermo A. García, Austin R. Carter, Heather M. Ferguson, Emmanuel Afolabi Bakare, Simon I. Hay, Robert C. Reiner Jr., Samson S. Kiware, David L. Smith:
  Spatial dynamics of malaria transmission.
• 
  Joy Putney, Tobias Niebur, Leo Wood, Rachel Conn, Simon Sponberg:
  An information theoretic method to resolve millisecond-scale spike timing precision in a comprehensive motor program.
• 
  Ximei Luo, Yansu Wang, Quan Zou, Lei Xu:
  Recall DNA methylation levels at low coverage sites using a CNN model in WGBS.
• 
  Xiru Fan, Cristian Valenzuela, Weijing Zhao, Zi Chen, Dong Wang, Steven J. Mentzer:
  Stochastic simulations of self-organized elastogenesis in the developing lung.
• 
  Jolyon Troscianko, Daniel Osório:
  A model of colour appearance based on efficient coding of natural images.
• 
  Maral Budak, Joseph M. Cicchese, Pauline Maiello, H. Jacob Borish, Alexander G. White, Harris B. Chishti, Jaime Tomko, L. James Frye, Daniel Fillmore, Kara Kracinovsky, Jennifer Sakal, Charles A. Scanga, Philana Ling Lin, Véronique Dartois, Jennifer J. Linderman, JoAnne L. Flynn, Denise E. Kirschner:
  Optimizing tuberculosis treatment efficacy: Comparing the standard regimen with Moxifloxacin-containing regimens.
• 
  Reo Sato, Kanji Shimomura, Kenji Morita:
  Opponent learning with different representations in the cortico-basal ganglia pathways can develop obsession-compulsion cycle.
• 
  Matthys G. Potgieter, Andrew J. M. Nel, Suereta Fortuin, Shaun Garnett, Jerome M. Wendoh, David L. Tabb, Nicola J. Mulder, Jonathan M. Blackburn:
  MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.
• 
  Christopher J. Skalnik, Sean Y. Cheah, Mica Y. Yang, Mattheus B. Wolff, Ryan K. Spangler, Lee Talman, Jerry H. Morrison, Shayn M. Peirce, Eran Agmon, Markus W. Covert:
  Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses.
• 
  Xiaojing Zhu, Heather Shappell, Mark A. Kramer, Catherine Jean Chu, Eric D. Kolaczyk:
  Distinguishing between different percolation regimes in noisy dynamic networks with an application to epileptic seizures.
• 
  Hongliang Li, Bin Liu:
  BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo.
• 
  Robayet Chowdhury, Alexander T. Taguchi, Laimonas Kelbauskas, Phillip Stafford, Chris Diehnelt, Zhan-Gong Zhao, Phillip C. Williamson, Valerie Green, Neal W. Woodbury:
  Modeling the sequence dependence of differential antibody binding in the immune response to infectious disease.
• 
  Jialu Hou, Hang Wei, Bin Liu:
  iPiDA-SWGCN: Identification of piRNA-disease associations based on Supplementarily Weighted Graph Convolutional Network.
• 
  Yohsuke Murase, Seung Ki Baek:
  Grouping promotes both partnership and rivalry with long memory in direct reciprocity.
• 
  Chance M. Nowak, Tyler Quarton, Leonidas Bleris:
  Impact of variability in cell cycle periodicity on cell population dynamics.
• 
  Yang-Han Wu, Yu-An Huang, Jian-Qiang Li, Zhu-Hong You, Peng-Wei Hu, Lun Hu, Victor C. M. Leung, Zhihua Du:
  Knowledge graph embedding for profiling the interaction between transcription factors and their target genes.
• 
  Emiliano Marachlian, Ramón Huerta, Fernando Locatelli:
  Gain modulation and odor concentration invariance in early olfactory networks.
• 
  Jean-David Morel, Jean-Michel Morel, Luis Álvarez:
  Learning from the past: A short term forecast method for the COVID-19 incidence curve.
• 
  Pranav N. Haravu, Miguel Gonzalez, Shelby L. Nathan, Callum F. Ross, Olga Panagiotopoulou, Russell R. Reid:
  The biomechanics of chewing and suckling in the infant: A potential mechanism for physiologic metopic suture closure.
• 
  Celia De Los Angeles Colomina Basanta, Marya Bazzi, Maruan Hijazi, Conrad Bessant, Pedro R. Cutillas:
  Community detection in empirical kinase networks identifies new potential members of signalling pathways.
• 
  Balázs Erdos, Johan A. Westerhuis, Michiel E. Adriaens, Shauna D. O'Donovan, Ren Xie, Cécile M. Singh-Povel, Age K. Smilde, Ilja C. W. Arts:
  Analysis of high-dimensional metabolomics data with complex temporal dynamics using RM-ASCA+.
• 
  Dylan S. Geldenhuys, Shane Josias, Willie Brink, Mulanga Makhubele, Cang Hui, Pietro Landi, Jeremy Bingham, John Hargrove, C. Marijn Hazelbag:
  Deep learning approaches to landmark detection in tsetse wing images.
• 
  Marina Strocchi, Stefano Longobardi, Christoph M. Augustin, Matthias A. F. Gsell, Argyrios Petras, Christopher A. Rinaldi, Edward J. Vigmond, Gernot Plank, Chris J. Oates, Richard D. Wilkinson, Steven A. Niederer:
  Cell to whole organ global sensitivity analysis on a four-chamber heart electromechanics model using Gaussian processes emulators.
• 
  Marissa E. Fassold, Shannon M. Locke, Michael S. Landy:
  Feeling lucky? Prospective and retrospective cues for sensorimotor confidence.
• 
  Lingling Li, Yulu Hu, Yunshan Xu, Sanyi Tang:
  Mathematical modeling the order of driver gene mutations in colorectal cancer.
• 
  Yi-Xuan Xiong, Meng-Guo Wang, Luonan Chen, Xiao-Fei Zhang:
  Cell-type annotation with accurate unseen cell-type identification using multiple references.
• 
  Yishen Jiang, Xin Wang, Longzhao Liu, Ming Wei, Jingwu Zhao, Zhiming Zheng, Shaoting Tang:
  Nonlinear eco-evolutionary games with global environmental fluctuations and local environmental feedbacks.
• 
  Tobias S. Brett, Shweta Bansal, Pejman Rohani:
  Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state.
• 
  Zhenxing Wu, Jianbo Jiang, Fritz W. Lischka, Scott J. McGrane, Yael Porat-Mesenco, Kai Zhao:
  Domestic cat nose functions as a highly efficient coiled parallel gas chromatograph.
• 
  Yimeng Liu, Guy Amit, Xiaolei Zhao, Na Wu, Daqing Li, Amir Bashan:
  Individualized network analysis reveals a link between the gut microbiome, diet intervention and Gestational Diabetes Mellitus.
• 
  Carolina Fernandez Pujol, Elizabeth G. Blundon, Andrew R. Dykstra:
  Laminar specificity of the auditory perceptual awareness negativity: A biophysical modeling study.
• 
  Philip LaPorte, Christian Hilbe, Martin A. Nowak:
  Adaptive dynamics of memory-one strategies in the repeated donation game.
• 
  Nicolas Andres Saffioti, Cora Lilia Alvarez, Zaher Bazzi, María Virginia Gentilini, Gabriel Eduardo Gondolesi, Pablo Julio Schwarzbaum, Julieta Schachter:
  Dynamic recycling of extracellular ATP in human epithelial intestinal cells.
• 
  Shimeng Huang, Elisabeth Ailer, Niki Kilbertus, Niklas Pfister:
  Supervised learning and model analysis with compositional data.

Corrections

• 
  Brian Nils Lundstrom, Thomas J. Richner:
  Correction: Neural adaptation and fractional dynamics as a window to underlying neural excitability.
• 
  Javier Baladron, Julien Vitay, Torsten Fietzek, Fred H. Hamker:
  Correction: The contribution of the basal ganglia and cerebellum to motor learning: A neuro-computational approach.

Volume 19, Number 7, July 2023

Education Articles

• 
  Davide Chicco, Fabio Cumbo, Claudio Angione:
  Ten quick tips for avoiding pitfalls in multi-omics data integration analyses.
• 
  Thomas Shafee, Daniel Mietchen, Tiago Lubiana, Dariusz Jemielniak, Andra Waagmeester:
  Ten quick tips for editing Wikidata.
• 
  Davide Chicco, Umberto Ferraro Petrillo, Giuseppe Cattaneo:
  Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment.

Perspectives

• 
  Brittney G. Borowiec:
  Ten simple rules for scientists engaging in science communication.
• 
  Rachel J. Harding, Patrick Bermudez, Alexander Bernier, Michael J. S. Beauvais, Pierre Bellec, Sean L. Hill, Agah Karakuzu, Bartha M. Knoppers, Paul Pavlidis, Jean-Baptiste Poline, Jane Roskams, Nikola Stikov, Jessica Stone, Stephen C. Strother, CONP Consortium, Alan C. Evans:
  The Canadian Open Neuroscience Platform - An open science framework for the neuroscience community.

Research Articles

• 
  Marius Schneider, Alexander D. Bird, Albert Gidon, Jochen Triesch, Peter Jedlicka, Hermann Cuntz:
  Biological complexity facilitates tuning of the neuronal parameter space.
• 
  Wojciech Pulawski, Andrzej Kolinski, Michal Kolinski:
  Integrative modeling of diverse protein-peptide systems using CABS-dock.
• 
  Leonardo Dalla Porta, Almudena Barbero-Castillo, Jose Manuel Sanchez-Sanchez, Maria V. Sanchez-Vives:
  M-current modulation of cortical slow oscillations: Network dynamics and computational modeling.
• 
  Samantha P. Beik, Leonard A. Harris, Michael A. Kochen, Julien Sage, Vito Quaranta, Carlos F. Lopez:
  Unified tumor growth mechanisms from multimodel inference and dataset integration.
• 
  Cameron Andress, Kalli Kappel, Marcus Elbert Villena, Miroslava Cuperlovic-Culf, Hongbin Yan, Yifeng Li:
  DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design.
• 
  Samuel Campbell, Michelle C. Mendoza, Aravind Rammohan, Matthew E. McKenzie, Tamara Carla Bidone:
  Computational model of integrin adhesion elongation under an actin fiber.
• 
  Shaoke Lou, Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T. Yang, Mark Gerstein:
  Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes.
• 
  Ahmed Taha, Mauricio Patón, David R. Penas, Julio R. Banga, Jorge Rodríguez:
  Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants.
• 
  Adrien Badré, Chongle Pan:
  Explainable multi-task learning improves the parallel estimation of polygenic risk scores for many diseases through shared genetic basis.
• 
  Francisco Páscoa dos Santos, Jakub Vohryzek, Paul F. M. J. Verschure:
  Multiscale effects of excitatory-inhibitory homeostasis in lesioned cortical networks: A computational study.
• 
  Juan Xie, Hyeongseon Jeon, Gang Xin, Qin Ma, Dongjun Chung:
  LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity.
• 
  Brittany Baur, Junha Shin, Jacob Schreiber, Shilu Zhang, Yi Zhang, Mohith Manjunath, Jun S. Song, William Stafford Noble, Sushmita Roy:
  Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation.
• 
  Michael D. Nicholson, David Cheek, Tibor Antal:
  Sequential mutations in exponentially growing populations.
• 
  Yue Hao, Gábor Závodszky, Claudia Tersteeg, Mojtaba Barzegari, Alfons G. Hoekstra:
  Image-based flow simulation of platelet aggregates under different shear rates.
• 
  Dolores Bernenko, Sang Hoon Lee, Per Stenberg, Ludvig Lizana:
  Mapping the semi-nested community structure of 3D chromosome contact networks.
• 
  Sheng Fu, Mark P. Purdue, Han Zhang, Jing Qin, Lei Song, Sonja I. Berndt, Kai Yu:
  Improve the model of disease subtype heterogeneity by leveraging external summary data.
• 
  Tong Liu, Zheng Wang:
  DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.
• 
  Anne Kandler, Laurel Fogarty, Folgert Karsdorp:
  The interplay between age structure and cultural transmission.
• 
  Rebecca K. West, William J. Harrison, Natasha Matthews, Jason B. Mattingley, David K. Sewell:
  Modality independent or modality specific? Common computations underlie confidence judgements in visual and auditory decisions.
• 
  Chiara Venturini, Pablo Sáez:
  A multi-scale clutch model for adhesion complex mechanics.
• 
  Elena Rivas:
  RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure.
• 
  Ying Zhang, Thomas G. Fai:
  Influence of the vessel wall geometry on the wall-induced migration of red blood cells.
• 
  Wan Yang, Jeffrey Shaman:
  Development of Accurate Long-lead COVID-19 Forecast.
• 
  Mukesh Makwana, Fan Zhang, Dietmar Heinke, Joo-Hyun Song:
  Continuous action with a neurobiologically inspired computational approach reveals the dynamics of selection history.
• 
  Zeliha Kilic, Max Schweiger, Camille Moyer, Steve Pressé:
  Monte Carlo samplers for efficient network inference.
• 
  Alexei J. Drummond, Kylie Chen, Fábio K. Mendes, Dong Xie:
  LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses.
• 
  Joseph L. Servadio, Pham Quang Thai, Marc Choisy, Maciej F. Boni:
  Repeatability and timing of tropical influenza epidemics.
• 
  Kohei Iwamasa, Koji Noshita:
  Network feature-based phenotyping of leaf venation robustly reconstructs the latent space.
• 
  Yohsuke Murase, Christian Hilbe:
  Indirect reciprocity with stochastic and dual reputation updates.
• 
  Kris V. Parag, Uri Obolski:
  Risk averse reproduction numbers improve resurgence detection.
• 
  Roger Vargas, Liam Abbott, Daniel Bower, Nicole Frahm, Mike Shaffer, Wen-Han Yu:
  Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.
• 
  Marte J. Sætra, Ada J. Ellingsrud, Marie E. Rognes:
  Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space - A computational study.
• 
  Andrej Vilfan, Andreja Sarlah:
  Theoretical efficiency limits and speed-efficiency trade-off in myosin motors.
• 
  Mizuki Kato, Erik De Schutter:
  Models of Purkinje cell dendritic tree selection during early cerebellar development.
• 
  Zahra Rahaie, Hamid R. Rabiee, Hamid Alinejad-Rokny:
  DeepGenePrior: A deep learning model for prioritizing genes affected by copy number variants.
• 
  Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada:
  Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study.
• 
  Yinmei Ni, Jingwei Sun, Jian Li:
  The shadowing effect of initial expectation on learning asymmetry.
• 
  Philip J. Harrison, Ankit Gupta, Jonne Rietdijk, Håkan Wieslander, Jordi Carreras Puigvert, Polina Georgiev, Carolina Wählby, Ola Spjuth, Ida-Maria Sintorn:
  Evaluating the utility of brightfield image data for mechanism of action prediction.
• 
  Grace Smith-Vidaurre, Valeria Pérez-Marrufo, Elizabeth A. Hobson, Alejandro Salinas-Melgoza, Timothy F. Wright:
  Individual identity information persists in learned calls of introduced parrot populations.
• 
  Giovanni Strona, Corey J. A. Bradshaw, Pedro Cardoso, Nicholas Gotelli, Frédéric Guillaume, Federica Manca, Ville Mustonen, Luis Zaman:
  Time-travelling pathogens and their risk to ecological communities.
• 
  Kwang S. Kim, Jessica L. Gaines, Benjamin Parrell, Vikram Ramanarayanan, Srikantan S. Nagarajan, John F. Houde:
  Mechanisms of sensorimotor adaptation in a hierarchical state feedback control model of speech.
• 
  Xiangrui Ji, Jie Lin:
  Implications of differential size-scaling of cell-cycle regulators on cell size homeostasis.
• 
  Boris Sotomayor-Gómez, Francesco P. Battaglia, Martin A. Vinck:
  SpikeShip: A method for fast, unsupervised discovery of high-dimensional neural spiking patterns.
• 
  Alain J. Mbebi, Zoran Nikoloski:
  Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection.
• 
  Christian Blau, Linnea Yvonnesdotter, Erik Lindahl:
  Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach.

Correction

• 
  PLOS Computational Biology Staff:
  Correction: Opponent learning with different representations in the cortico-basal ganglia pathways can develop obsession-compulsion cycle.

Volume 19, Number 8, August 2023

Editorial

• 
  Feilim Mac Gabhann, Virginia E. Pitzer, Jason A. Papin:
  The blossoming of methods and software in computational biology.

Education Articles

• 
  Jess Haberman, Greg Wilson:
  Ten simple rules for writing a technical book.
• 
  Tiago Lubiana, Rafael Lopes, Pedro Medeiros, Juan Carlo Silva, Andre Nicolau Aquime Goncalves, Vinicius Maracaja-Coutinho, Helder I. Nakaya:
  Ten quick tips for harnessing the power of ChatGPT in computational biology.
• 
  Esther Sebastián-González, Eva Graciá, Alejandra Morán-Ordóñez, Irene Pérez-Ibarra, Ana Sanz-Aguilar, Mar Sobral:
  Ten simple rules for a mom-friendly Academia.

Perspective

• 
  Tara Chari, Lior Pachter:
  The specious art of single-cell genomics.

Reviews

• 
  Jessica R. Crawshaw, Jennifer A. Flegg, Miguel O. Bernabeu, James M. Osborne:
  Mathematical models of developmental vascular remodelling: A review.
• 
  Malvina Marku, Vera Pancaldi:
  From time-series transcriptomics to gene regulatory networks: A review on inference methods.
• 
  Sizhe Qiu, Aidong Yang, Hong Zeng:
  Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.

Research Articles

• 
  Kevin Sawade, Andreas Marx, Christine Peter, Oleksandra Kukharenko:
  Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes.
• 
  Alexander Tscshantz, Beren Millidge, Anil K. Seth, Christopher L. Buckley:
  Hybrid predictive coding: Inferring, fast and slow.
• 
  Atesmachew Hailegiorgis, Yuji Ishida, Nicholson T. Collier, Michio Imamura, Zhenzhen Shi, Vladimir Reinharz, Masataka Tsuge, Danny Barash, Nobuhiko Hiraga, Hiroshi Yokomichi, Chise Tateno, Jonathan Ozik, Susan L. Uprichard, Kazuaki Chayama, Harel Dahari:
  Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics.
• 
  Jesús Cabrera-Álvarez, Nina Doorn, Fernando Maestú, Gianluca Susi:
  Modeling the role of the thalamus in resting-state functional connectivity: Nature or structure.
• 
  Seungdae Baek, Youngjin Park, Se-Bum Paik:
  Species-specific wiring of cortical circuits for small-world networks in the primary visual cortex.
• 
  Jana Masselink, Alexis Cheviet, Caroline Froment-Tilikete, Denis Pélisson, Markus Lappe:
  A triple distinction of cerebellar function for oculomotor learning and fatigue compensation.
• 
  Torkel E. Loman, James C. W. Locke:
  The σB alternative sigma factor circuit modulates noise to generate different types of pulsing dynamics.
• 
  Anzhi Sheng, Aming Li, Long Wang:
  Evolutionary dynamics on sequential temporal networks.
• 
  Joeri van Strien, Felix Evers, Madhurya Lutikurti, Stijn L. Berendsen, Alejandro Garanto, Geert-Jan van Gemert, Alfredo Cabrera-Orefice, Richard J. Rodenburg, Ulrich Brandt, Taco W. A. Kooij, Martijn A. Huynen:
  Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution.
• 
  Hiroshi Koyama, Hisashi Okumura, Atsushi M. Ito, Kazuyuki Nakamura, Tetsuhisa Otani, Kagayaki Kato, Toshihiko Fujimori:
  Effective mechanical potential of cell-cell interaction explains three-dimensional morphologies during early embryogenesis.
• 
  Júlia V. Gallinaro, Benjamin Scholl, Claudia Clopath:
  Synaptic weights that correlate with presynaptic selectivity increase decoding performance.
• 
  Quentin Clairon, Mélanie Prague, Delphine Planas, Timothée Bruel, Laurent Hocqueloux, Thierry Prazuck, Olivier Schwartz, Rodolphe Thiébaut, Jérémie Guedj:
  Modeling the kinetics of the neutralizing antibody response against SARS-CoV-2 variants after several administrations of Bnt162b2.
• 
  Ljubica Cimesa, Lazar Ciric, Srdjan Ostojic:
  Geometry of population activity in spiking networks with low-rank structure.
• 
  Renquan Zhang, Jilei Tai, Sen Pei:
  Ensemble inference of unobserved infections in networks using partial observations.
• 
  Nicholas A. Bianco, Steven H. Collins, C. Karen Liu, Scott L. Delp:
  Simulating the effect of ankle plantarflexion and inversion-eversion exoskeleton torques on center of mass kinematics during walking.
• 
  Michael Mackay, Siyu Huo, Marcus Kaiser:
  Spatial organisation of the mesoscale connectome: A feature influencing synchrony and metastability of network dynamics.
• 
  Gregory Handy, Alla Borisyuk:
  Investigating the ability of astrocytes to drive neural network synchrony.
• 
  Aurélien Marc, Romain Marlin, Flora Donati, Mélanie Prague, Marion Kerioui, Cécile Hérate, Marie Alexandre, Nathalie Dereuddre-Bosquet, Julie Bertrand, Vanessa Contreras, Sylvie Behillil, Pauline Maisonnasse, Sylvie van der Werf, Roger Le Grand, Jérémie Guedj:
  Impact of variants of concern on SARS-CoV-2 viral dynamics in non-human primates.
• 
  Diego Tec-Campos, Camila Posadas, Juan D. Tibocha-Bonilla, Deepan Thiruppathy, Nathan Glonek, Cristal Zuñiga, Alejandro Zepeda, Karsten Zengler:
  The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions.
• 
  W. Jeffrey Johnston, David J. Freedman:
  Redundant representations are required to disambiguate simultaneously presented complex stimuli.
• 
  Hamish Gibbs, Anwar Musah, Omar Seidu, William Ampofo, Franklin Asiedu-Bekoe, Jonathan Gray, Wole Ademola Adewole, James A. Cheshire, Michael Marks, Rosalind M. Eggo:
  Call detail record aggregation methodology impacts infectious disease models informed by human mobility.
• 
  Ruairi Donnelly, Christopher A. Gilligan:
  A new method for the analysis of access period experiments, illustrated with whitefly-borne cassava mosaic begomovirus.
• 
  Caetano Souto-Maior, Yazmin L. Serrano Negron, Susan T. Harbison:
  Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration.
• 
  Yahel Yedidya, Daniel Davis, Yotam Drier:
  SARS-CoV-2 infection perturbs enhancer mediated transcriptional regulation of key pathways.
• 
  Benjamin Raach, Nils Bundgaard, Marika J. Haase, Jörn Starruß, Rocio Sotillo, Megan L. Stanifer, Frederik Graw:
  Influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics within human airway epithelium.
• 
  Ning Wang, Sofia Khan, Laura L. Elo:
  VarSCAT: A computational tool for sequence context annotations of genomic variants.
• 
  Christina Y. Lee, Jenna Diegel, Michael T. France, Jacques Ravel, Kelly B. Arnold:
  Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy.
• 
  Jia Li, Ilias Rentzeperis, Cees van Leeuwen:
  Functional and spatial rewiring principles jointly regulate context-sensitive computation.
• 
  Jérôme Munuera, Marta Ribes Agost, David Bendetowicz, Adrien Kerebel, Valérian Chambon, Brian Lau:
  Intrinsic motivation for choice varies with individual risk attitudes and the controllability of the environment.
• 
  Tim C. Hladnik, Jan Grewe:
  Receptive field sizes and neuronal encoding bandwidth are constrained by axonal conduction delays.
• 
  Johann F. Jadebeck, Wolfgang Wiechert, Katharina Nöh:
  Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance.
• 
  Daniel Wolffram, Sam Abbott, Matthias an der Heiden, Sebastian Funk, Felix Günther, Davide Hailer, Stefan Heyder, Thomas Hotz, Jan van de Kassteele, Helmut Küchenhoff, Sören Müller-Hansen, Diellë Syliqi, Alexander Ullrich, Maximilian Weigert, Melanie Schienle, Johannes Bracher:
  Collaborative nowcasting of COVID-19 hospitalization incidences in Germany.
• 
  Akhilesh Nandan, Aneta Koseska:
  Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals.
• 
  William T. Scott Jr., Sara Benito-Vaquerizo, Johannes Zimmermann, Djordje Bajic, Almut Heinken, María Suárez-Diez, Peter J. Schaap:
  A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia.
• 
  Oualid El Hajouji, Ran Sun, Alban Zammit, Keith Humphreys, Steven M. Asch, Ian Carroll, Catherine M. Curtin, Tina Hernandez-Boussard:
  Prediction of opioid-related outcomes in a medicaid surgical population: Evidence to guide postoperative opiate therapy and monitoring.
• 
  Sandra Montes-Olivas, Danny Legge, Abbie Lund, Alexander G. Fletcher, Ann C. Williams, Lucia Marucci, Martin E. Homer:
  In-silico and in-vitro morphometric analysis of intestinal organoids.
• 
  Salvador Chulián, Bernadette J. Stolz, Álvaro Martínez-Rubio, Cristina Blázquez Goñi, Juan F. Rodríguez Gutiérrez, Teresa Caballero Velázquez, Águeda Molinos Quintana, Manuel Ramirez-Orellana, Ana Castillo Robleda, José Luis Fuster Soler, Alfredo Minguela Puras, María V. Martínez Sánchez, María Rosa, Víctor M. Pérez-García, Helen M. Byrne:
  The shape of cancer relapse: Topological data analysis predicts recurrence in paediatric acute lymphoblastic leukaemia.
• 
  Oscar D. Murillo, Varduhi Petrosyan, Emily L. LaPlante, Lacey E. Dobrolecki, Michael T. Lewis, Aleksandar Milosavljevic:
  Deconvolution of cancer cell states by the XDec-SM method.
• 
  Peter Czuppon, Troy Day, Florence Débarre, François Blanquart:
  A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance.
• 
  Kun Mi, Lei Sun, Yixuan Hou, Xin Cai, Kaixiang Zhou, Wenjin Ma, Xiangyue Xu, Yuanhu Pan, Zhenli Liu, Lingli Huang:
  A physiologically based pharmacokinetic model to optimize the dosage regimen and withdrawal time of cefquinome in pigs.
• 
  Bastian Volker Helmut Hornung, Nicolas Terrapon:
  An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space.
• 
  Li Xie, Lei Xie:
  Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning.
• 
  Kim T. Blackwell, Kenji Doya:
  Enhancing reinforcement learning models by including direct and indirect pathways improves performance on striatal dependent tasks.
• 
  Camille Gontier, Simone Carlo Surace, Igor Delvendahl, Martin Müller, Jean-Pascal Pfister:
  Efficient sampling-based Bayesian Active Learning for synaptic characterization.
• 
  Isaline Guex, Christian Mazza, Manupriyam Dubey, Maxime Batsch, Renyi Li, Jan Roelof van der Meer:
  Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding.
• 
  Connor J. Moore, Christopher P. Holstege, Jason A. Papin:
  Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses.
• 
  Xuan Liu, Wen Zhang:
  A subcomponent-guided deep learning method for interpretable cancer drug response prediction.
• 
  Ariel Nikas, Hasan Ahmed, Mia Moore, Veronika Zarnitsyna, Rustom Antia:
  When does humoral memory enhance infection?
• 
  Azka Javaid, Hildreth Robert Frost:
  STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring.
• 
  Ruihao Li, Jordan C. Rozum, Morgan M. Quail, Mohammad N. Qasim, Suzanne S. Sindi, Clarissa J. Nobile, Réka Albert, Aaron D. Hernday:
  Inferring gene regulatory networks using transcriptional profiles as dynamical attractors.
• 
  Jonathan W. Cody, Amy L. Ellis-Connell, Shelby L. O'Connor, Elsje Pienaar:
  Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load.
• 
  Kelly B. Eckenrode, Dario Righelli, Marcel Ramos, Ricard Argelaguet, Christophe Vanderaa, Ludwig Geistlinger, Aedín C. Culhane, Laurent Gatto, Vincent J. Carey, Martin Morgan, Davide Risso, Levi Waldron:
  Curated single cell multimodal landmark datasets for R/Bioconductor.
• 
  Pan Ye Li, Alex Roxin:
  Rapid memory encoding in a recurrent network model with behavioral time scale synaptic plasticity.
• 
  Sreejan Kumar, Ishita Dasgupta, Nathaniel D. Daw, Jonathan D. Cohen, Thomas L. Griffiths:
  Disentangling Abstraction from Statistical Pattern Matching in Human and Machine Learning.
• 
  Atara Neugroschl, Irina E. Catrina:
  TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary structure(s) of RNA targets.
• 
  Wenxing Hu, Lixin Guan, Mengshan Li:
  Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network.
• 
  Zhenyu Zhang, Akihiko Nishimura, Nídia S. Trovão, Joshua L. Cherry, Andrew J. Holbrook, Xiang Ji, Philippe Lemey, Marc A. Suchard:
  Accelerating Bayesian inference of dependency between mixed-type biological traits.
• 
  Mingjian He, Proloy Das, Gladia Hotan, Patrick L. Purdon:
  Switching state-space modeling of neural signal dynamics.
• 
  Michael Morris, Peter Hayes, Ingemar J. Cox, Vasileios Lampos:
  Neural network models for influenza forecasting with associated uncertainty using Web search activity trends.
• 
  Eivind S. Haus, Tormod Drengstig, Kristian Thorsen:
  Structural identifiability of biomolecular controller motifs with and without flow measurements as model output.
• 
  Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina A. Sakharova, Manja Marz, Alejandro Reyes, Martin Hölzer, Robert D. Finn:
  VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.
• 
  Rebecca K. Nash, Samir Bhatt, Anne Cori, Pierre Nouvellet:
  Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool.
• 
  Nikos I. Bosse, Sam Abbott, Anne Cori, Edwin van Leeuwen, Johannes Bracher, Sebastian Funk:
  Scoring epidemiological forecasts on transformed scales.
• 
  Shawn Means, Mathias W. Roesler, Amy S. Garrett, Leo K. Cheng, Alys R. Clark:
  Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model.
• 
  Jonathan Morgan, Alan E. Lindsay:
  Modulation of antigen discrimination by duration of immune contacts in a kinetic proofreading model of T cell activation with extreme statistics.
• 
  Jordan Hembrow, Michael J. Deeks, David M. Richards:
  Automatic extraction of actin networks in plants.
• 
  Lin Yuan, Jiawang Zhao, Zhen Shen, Qinhu Zhang, Yushui Geng, Chun-Hou Zheng, De-Shuang Huang:
  iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction.
• 
  Olivier Dennler, François Coste, Samuel Blanquart, Catherine Belleannée, Nathalie Théret:
  Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family.
• 
  Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, Debswapna Bhattacharya:
  E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction.

Methods

• 
  Arthur Menezes, Saki Takahashi, Isobel Routledge, C. Jessica E. Metcalf, Andrea L. Graham, James A. Hay:
  serosim: An R package for simulating serological data arising from vaccination, epidemiological and antibody kinetics processes.

Software

• 
  Agnete T. Lundgaard, Frédéric Burdet, Troels Siggaard, David Westergaard, Danai Vagiaki, Lisa Cantwell, Timo Röder, Dorte Vistisen, Thomas Sparsø, Giuseppe N. Giordano, Mark Ibberson, Karina Banasik, Søren Brunak:
  BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus.

Volume 19, Number 9, September 2023

Education Articles

• 
  Joshua Atienza, Anjalee Benedict, Lincoln D. Stein, Kashif Pirzada, Cheryl White, Shraddha Pai:
  Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy.
• 
  Rebecca B. Carlson, Jennifer R. Martin, Robert D. Beckett:
  Ten simple rules for interpreting and evaluating a meta-analysis.
• 
  Casper de Visser, Lennart F. Johansson, Purva Kulkarni, Hailiang Mei, Pieter B. T. Neerincx, K. Joeri van der Velde, Peter Horvatovich, Alain J. van Gool, Morris A. Swertz, Peter A. C. 't Hoen, Anna Niehues:
  Ten quick tips for building FAIR workflows.

Research Articles

• 
  Hola Adrakey, Gavin J. Gibson, Sandrine Eveillard, Sylvie Malembic-Maher, Frédéric Fabre:
  Bayesian inference for spatio-temporal stochastic transmission of plant disease in the presence of roguing: A case study to characterise the dispersal of Flavescence dorée.
• 
  Zhengqing Zhou, Dianjie Li, Ziheng Zhao, Shuyu Shi, Jianghua Wu, Jianwei Li, Jingpeng Zhang, Ke Gui, Yu Zhang, Qi Ouyang, Heng Mei, Yu Hu, Fangting Li:
  Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients.
• 
  Kun Zhang, Zhichu Xia, Shudong Huang, Gui-Quan Sun, Jiancheng Lv, Marco Ajelli, Keisuke Ejima, Quan-Hui Liu:
  Evaluating the impact of test-trace-isolate for COVID-19 management and alternative strategies.
• 
  Nikhil Sharma, Sedigheh Yagoobi, Arne Traulsen:
  Self-loops in evolutionary graph theory: Friends or foes?
• 
  Roberta Maria Lorenzi, Alice Geminiani, Yann Zerlaut, Marialaura De Grazia, Alain Destexhe, Claudia A. M. Gandini Wheeler-Kingshott, Fulvia Palesi, Claudia Casellato, Egidio D'Angelo:
  A multi-layer mean-field model of the cerebellum embedding microstructure and population-specific dynamics.
• 
  Bo Yuan, Shulei Wang:
  RSim: A reference-based normalization method via rank similarity.
• 
  Ronan F. Arthur, May Levin, Alexandre Labrogere, Marcus W. Feldman:
  Age-differentiated incentives for adaptive behavior during epidemics produce oscillatory and chaotic dynamics.
• 
  Grishma Palkar, Jian-young Wu, Bard Ermentrout:
  The inhibitory control of traveling waves in cortical networks.
• 
  Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J. P. de Esch, Bart A. Westerman:
  Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks.
• 
  Neta Ravid Tannenbaum, Omer Gottesman, Azadeh Assadi, Mjaye Mazwi, Uri Shalit, Danny Eytan:
  iCVS - Inferring Cardio-Vascular hidden States from physiological signals available at the bedside.
• 
  Francis Banville, Dominique Gravel, Timothée Poisot:
  What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases.
• 
  Peter Schuck, Samuel C. To, Huaying Zhao:
  An automated interface for sedimentation velocity analysis in SEDFIT.
• 
  Leijun Ye, Jianfeng Feng, Chunhe Li:
  Controlling brain dynamics: Landscape and transition path for working memory.
• 
  Zheng Jiang, Yue-Yue Shen, Rong Liu:
  Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches.
• 
  Lucía Graña-Miraglia, Nadia Morales-Lizcano, Pauline W. Wang, David M. Hwang, Yvonne C. W. Yau, Valerie J. Waters, David S. Guttman:
  Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis.
• 
  Joanna N. de Klerk, Erin E. Gorsich, John D. Grewar, Benjamin D. Atkins, Warren S. D. Tennant, Karien Labuschagne, Michael J. Tildesley:
  Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach.
• 
  Charlie M. Sexton, Anthony N. Burkitt, Hinze Hogendoorn:
  Spike-timing dependent plasticity partially compensates for neural delays in a multi-layered network of motion-sensitive neurons.
• 
  Tomohiro Otani, Nozomi Nishimura, Hiroshi Yamashita, Satoshi Ii, Shigeki Yamada, Yoshiyuki Watanabe, Marie Oshima, Shigeo Wada:
  Computational modeling of multiscale collateral blood supply in a whole-brain-scale arterial network.
• 
  Jelmer P. Borst, Sean Aubin, Terrence C. Stewart:
  A whole-task brain model of associative recognition that accounts for human behavior and neuroimaging data.
• 
  Christopher L. Hewitson, David M. Kaplan, Matthew J. Crossley:
  Error-independent effect of sensory uncertainty on motor learning when both feedforward and feedback control processes are engaged.
• 
  Jay A. Hennig, Sandra A. Romero Pinto, Takahiro Yamaguchi, Scott W. Linderman, Naoshige Uchida, Samuel J. Gershman:
  Emergence of belief-like representations through reinforcement learning.
• 
  Ziheng Duan, Yi Dai, Ahyeon Hwang, Cheyu Lee, Kaichi Xie, Chutong Xiao, Min Xu, Matthew J. Girgenti, Jing Zhang:
  iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease.
• 
  Billy Tchounke, Leopoldo Sanchez, Joseph Martin Bell, David Cros:
  Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding.
• 
  Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao, Guijun Zhang:
  Pathfinder: Protein folding pathway prediction based on conformational sampling.
• 
  Shuming Liu, Cong Wang, Andrew P. Latham, Xinqiang Ding, Bin Zhang:
  OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates.
• 
  Tom Arthur, Samuel J. Vine, Gavin Buckingham, Mark J. Brosnan, Mark R. Wilson, David John Harris:
  Testing predictive coding theories of autism spectrum disorder using models of active inference.
• 
  Luca Mantovanelli, Dmitrii S. Linnik, Michiel Punter, Hildeberto Jardón-Kojakhmetov, Wojciech M. Smigiel, Bert Poolman:
  Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli.
• 
  Yves Carpentier Solorio, Florent Lemaître, Bassam Jabbour, Olivier Tastet, Nathalie Arbour, Elie Bou Assi:
  Classification of T lymphocyte motility behaviors using a machine learning approach.
• 
  James D. Munday, Sam Abbott, Sophie Meakin, Sebastian Funk:
  Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England.
• 
  Ilias Rentzeperis, Luca Calatroni, Laurent U. Perrinet, Dario Prandi:
  Beyond ℓ1 sparse coding in V1.
• 
  Adrian L. Hauber, Marcus Rosenblatt, Jens Timmer:
  Uncovering specific mechanisms across cell types in dynamical models.
• 
  Nhat Minh Le, Murat Yildirim, Yizhi Wang, Hiroki Sugihara, Mehrdad Jazayeri, Mriganka Sur:
  Mixtures of strategies underlie rodent behavior during reversal learning.
• 
  Simon Boutry, Raphaël Helaers, Tom Lenaerts, Miikka Vikkula:
  Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data.
• 
  Erik B. Nordquist, Guohui Zhang, Shrishti Barethiya, Nathan Ji, Kelli M. White, Lu Han, Zhiguang Jia, Jingyi Shi, Jianmin Cui, Jianhan Chen:
  Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels.
• 
  Elias Vera-Siguenza, Cristina Escribano-Gonzalez, Irene Serrano-Gonzalo, Kattri-Liis Eskla, Fabian Spill, Daniel Tennant:
  Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model.
• 
  Claire Ecotière, Sylvain Billiard, Jean-Baptiste André, Pierre Collet, Régis Ferrière, Sylvie Méléard:
  Human-environment feedback and the consistency of proenvironmental behavior.
• 
  Serena Aneli, Piero Fariselli, Elena Chierto, Carla Bini, Carlo Robino, Giovanni Birolo:
  Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics.
• 
  Zengmiao Wang, Peiyi Wu, Lin Wang, Bingying Li, Yonghong Liu, Yuxi Ge, Ruixue Wang, Ligui Wang, Hua Tan, Chieh-Hsi Wu, Marko Laine, Henrik Salje, Hongbin Song:
  Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study.
• 
  Christopher E. Overton, Sam Abbott, Rachel Christie, Fergus Cumming, Julie Day, Owen Jones, Rob Paton, Charlie Turner, Thomas Ward:
  Nowcasting the 2022 mpox outbreak in England.
• 
  Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski:
  Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony.
• 
  Bayarbaatar Amgalan, Chi-Ping Day, Teresa M. Przytycka:
  Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression.
• 
  Emanuel Cunha, Miguel Silva, Inês Chaves, Hüseyin Demirci, Davide Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Dias:
  The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.
• 
  Sofia Farina, Valérie Voorsluijs, Sonja Fixemer, David S. Bouvier, Susanne Claus, Mark H. Ellisman, Stéphane P. A. Bordas, Alexander Skupin:
  Mechanistic multiscale modelling of energy metabolism in human astrocytes reveals the impact of morphology changes in Alzheimer's Disease.
• 
  Bryan C. Daniels, Ying Wang, Robert E. Page Jr., Gro V. Amdam:
  Identifying a developmental transition in honey bees using gene expression data.
• 
  Mansooreh Ahmadian, Christian Rickert, Angela Minic, Julia Wrobel, Benjamin G. Bitler, Fuyong Xing, Michael Angelo, Elena W. Y. Hsieh, Debashis Ghosh, Kimberly R. Jordan:
  A platform-independent framework for phenotyping of multiplex tissue imaging data.
• 
  Shuaijie Zhang, Fan Yang, Lijie Wang, Shucheng Si, Jianmei Zhang, Fuzhong Xue:
  Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model.
• 
  Christian Tönsing, Bernhard Steiert, Jens Timmer, Clemens Kreutz:
  Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models.
• 
  Xu Pan, Annie DeForge, Odelia Schwartz:
  Generalizing biological surround suppression based on center surround similarity via deep neural network models.
• 
  Jan Boelts, Philipp Harth, Richard Gao, Daniel Udvary, Felipe Yáñez, Daniel Baum, Hans-Christian Hege, Marcel Oberländer, Jakob H. Macke:
  Simulation-based inference for efficient identification of generative models in computational connectomics.
• 
  Jonathan Vacher, Claire Launay, Pascal Mamassian, Ruben Coen Cagli:
  Measuring uncertainty in human visual segmentation.
• 
  Ruodan Liu, Naoki Masuda:
  Fixation dynamics on hypergraphs.
• 
  Antoine De Comite, Philippe Lefèvre, Frédéric Crevecoeur:
  Continuous evaluation of cost-to-go for flexible reaching control and online decisions.
• 
  Thao Vu, Souvik Seal, Tusharkanti Ghosh, Mansooreh Ahmadian, Julia Wrobel, Debashis Ghosh:
  FunSpace: A functional and spatial analytic approach to cell imaging data using entropy measures.
• 
  Ari S. Benjamin, Konrad P. Kording:
  A role for cortical interneurons as adversarial discriminators.
• 
  Stephen R. Piccolo, Paul Denny, Andrew Luxton-Reilly, Samuel H. Payne, Perry G. Ridge:
  Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course.
• 
  Yolanda Larriba, Ivy C. Mason, Richa Saxena, Frank A. J. L. Scheer, Cristina Rueda:
  CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans.
• 
  Jaron C. Thompson, Victor M. Zavala, Ophelia S. Venturelli:
  Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions.
• 
  Jasper Landman, Sjoerd M. Verduyn Lunel, Willem K. Kegel:
  Transcription factor competition facilitates self-sustained oscillations in single gene genetic circuits.
• 
  Matthew J. Simpson, Oliver J. Maclaren:
  Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models.

Software

• 
  Yiming Zhang, Ran Zhou, Lunxu Liu, Lu Chen, Yuan Wang:
  Trackplot: A flexible toolkit for combinatorial analysis of genomic data.

Volume 19, Number 10, October 2023

Research Articles

• 
  Aran Nayebi, Nathan C. L. Kong, Chengxu Zhuang, Justin L. Gardner, Anthony M. Norcia, Daniel L. K. Yamins:
  Mouse visual cortex as a limited resource system that self-learns an ecologically-general representation.
• 
  Qing Li, Yang Yu, Pathum Kossinna, Theodore Lun, Wenyuan Liao, Qingrun Zhang:
  XA4C: eXplainable representation learning via Autoencoders revealing Critical genes.
• 
  Rolf J. Lorentzen, Geir Nævdal, Ove Sævareid, Erlend Hodneland, Erik Andreas Hanson, Antonella Munthe-Kaas:
  Perfusion estimation using synthetic MRI-based measurements and a porous media flow model.
• 
  Qiantong Liang, Johnny Yang, Wai-Tong Louis Fan, Wing-Cheong Lo:
  Patch formation driven by stochastic effects of interaction between viruses and defective interfering particles.
• 
  Cong Liu, Zengmiao Wang, Jun Wang, Chengyu Liu, Mengchi Wang, Vu Ngo, Wei Wang:
  Predicting regional somatic mutation rates using DNA motifs.
• 
  Kaiyun Guan, Erin R. Curtis, Daniel J. Lew, Timothy C. Elston:
  Particle-based simulations reveal two positive feedback loops allow relocation and stabilization of the polarity site during yeast mating.
• 
  Philipp D. Lösel, Coline Monchanin, Renaud Lebrun, Alejandra Jayme, Jacob J. Relle, Jean-Marc Devaud, Vincent Heuveline, Mathieu Lihoreau:
  Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning.
• 
  Aymara Sancho-Araiz, Zinnia P. Parra-Guillen, Jean Bragard, Sergio Ardanza-Trevijano, Victor Mangas-Sanjuan, Iñaki F. Trocóniz:
  Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment.
• 
  Marius Faiß, Dan Stowell:
  Adaptive representations of sound for automatic insect recognition.
• 
  Simone Pompei, Edoardo Bella, Joshua S. Weitz, Jacopo Grilli, Marco Cosentino Lagomarsino:
  Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer.
• 
  Joseph German, Guofeng Cui, Chenliang Xu, Robert A. Jacobs:
  Rapid runtime learning by curating small datasets of high-quality items obtained from memory.
• 
  Isabella Marinelli, Jamie J. Walker, Udaya Seneviratne, Wendyl D'Souza, Mark J. Cook, Clare Anderson, Andrew P. Bagshaw, Stafford Lightman, Wessel Woldman, John R. Terry:
  Circadian distribution of epileptiform discharges in epilepsy: Candidate mechanisms of variability.
• 
  Kailas Shankar Honasoge, Zeynep Karagöz, Benjamin T. Goult, Haguy Wolfenson, Vanessa L. S. LaPointe, Aurélie Carlier:
  Force-dependent focal adhesion assembly and disassembly: A computational study.
• 
  Oliver J. Meacock, William M. Durham:
  Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker.
• 
  Junpeng Zhang, Lin Liu, Xuemei Wei, Chunwen Zhao, Sijing Li, Jiuyong Li, Thuc Duy Le:
  Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers.
• 
  Jennifer S. Lord, Michael B. Bonsall:
  Mechanistic modelling of within-mosquito viral dynamics: Insights into infection and dissemination patterns.
• 
  Leah L. Weber, Chuanyi Zhang, Idoia Ochoa, Mohammed El-Kebir:
  Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.
• 
  Daniel N. Zdeblick, Eric Shea-Brown, Daniela M. Witten, Michael A. Buice:
  Modeling functional cell types in spike train data.
• 
  Joseph D. Valencia, David A. Hendrix:
  Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task.
• 
  Evan Cudone, Amelia M. Lower, Robert A. McDougal:
  Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories.
• 
  Rituparna Khan, Xian F. Mallory:
  Assessing the performance of methods for cell clustering from single-cell DNA sequencing data.
• 
  Felix Benjamin Kern, Zenas C. Chao:
  Short-term neuronal and synaptic plasticity act in synergy for deviance detection in spiking networks.
• 
  Daniel Burns, Vincenzo Venditti, Davit A. Potoyan:
  Temperature sensitive contact modes allosterically gate TRPV3.
• 
  Maximiliano S. Beckel, Bruno Kaufman, Marcelo Yanovsky, Ariel Chernomoretz:
  Conserved and divergent signals in 5' splice site sequences across fungi, metazoa and plants.
• 
  Andrea Falcón-Cortés, Denis Boyer, Maximino Aldana, Gabriel Ramos-Fernandez:
  Lévy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers.
• 
  Simon K. Schnyder, John J. Molina, Ryoichi Yamamoto, Matthew S. Turner:
  Rational social distancing policy during epidemics with limited healthcare capacity.
• 
  Yilin Gao, Fengzhu Sun:
  Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies.
• 
  Catherine G. Triandafillou, Rosalind Wenshan Pan, Aaron R. Dinner, D. Allan Drummond:
  Pervasive, conserved secondary structure in highly charged protein regions.
• 
  Zalina Dezhina, Jonathan Smallwood, Ting Xu, Federico E. Turkheimer, Rosalyn J. Moran, Karl J. Friston, Robert Leech, Erik D. Fagerholm:
  Establishing brain states in neuroimaging data.
• 
  Giacomo Vecchiato, Tom Hattermann, Michele Palladino, Fabio Tedone, Patrick Heuret, Nick P. Rowe, Pierangelo Marcati:
  A 2D model to study how secondary growth affects the self-supporting behaviour of climbing plants.
• 
  Larissa Albantakis, Leonardo S. Barbosa, Graham Findlay, Matteo Grasso, Andrew M. Haun, William Marshall, William G. P. Mayner, Alireza Zaeemzadeh, Mélanie Boly, Bjørn Erik Juel, Shuntaro Sasai, Keiko Fujii, Isaac David, Jeremiah Hendren, Jonathan P. Lang, Giulio Tononi:
  Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms.
• 
  Kevin Lloyd, Peter Dayan:
  Reframing dopamine: A controlled controller at the limbic-motor interface.
• 
  Mengqi He, Sanyi Tang, Yanni Xiao:
  Combining the dynamic model and deep neural networks to identify the intensity of interventions during COVID-19 pandemic.
• 
  Torkel E. Loman, Yingbo Ma, Vasily Ilin, Shashi Gowda, Niklas Korsbo, Nikhil Yewale, Chris Rackauckas, Samuel A. Isaacson:
  Catalyst: Fast and flexible modeling of reaction networks.
• 
  Hadi Zolfaghari, Mervyn Andiapen, Andreas Baumbach, Anthony Mathur, Rich R. Kerswell:
  Wall shear stress and pressure patterns in aortic stenosis patients with and without aortic dilation captured by high-performance image-based computational fluid dynamics.
• 
  Emilia P. Piwek, Mark G. Stokes, Christopher Summerfield:
  A recurrent neural network model of prefrontal brain activity during a working memory task.
• 
  Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga:
  Distilling identifiable and interpretable dynamic models from biological data.
• 
  Scott D. Uhlrich, Antoine Falisse, Lukasz Kidzinski, Julie Muccini, Michael Ko, Akshay S. Chaudhari, Jennifer L. Hicks, Scott L. Delp:
  OpenCap: Human movement dynamics from smartphone videos.
• 
  Mauricio Alexander de Moura Ferreira, Wendel Batista da Silveira, Zoran Nikoloski:
  PARROT: Prediction of enzyme abundances using protein-constrained metabolic models.
• 
  Carole Chevalier, Jérôme Dorignac, Yahaya Ibrahim, Armelle Choquet, Alexandre David, Julie Ripoll, Eric Rivals, Frédéric Geniet, Nils-Ole Walliser, John Palmeri, Andrea Parmeggiani, Jean-Charles Walter:
  Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.
• 
  Daniel Williamson, William Tasker-Brown, James A. H. Murray, Angharad R. Jones, Leah R. Band:
  Modelling how plant cell-cycle progression leads to cell size regulation.
• 
  Vivian Hecht, Kevin Dong, Sreshtaa Rajesh, Polina Shpilker, Siddarth Wekhande, Noam Shoresh:
  Analyzing histone ChIP-seq data with a bin-based probability of being signal.
• 
  Christoffer Lundbak Olesen, Peter Thestrup Waade, Larissa Albantakis, Christoph Mathys:
  Phi fluctuates with surprisal: An empirical pre-study for the synthesis of the free energy principle and integrated information theory.
• 
  Christopher T. Boughter, Martin Meier-Schellersheim:
  An integrated approach to the characterization of immune repertoires using AIMS: An Automated Immune Molecule Separator.
• 
  T. J. Sego, James P. Sluka, Herbert M. Sauro, James A. Glazier:
  Tissue Forge: Interactive biological and biophysics simulation environment.
• 
  Robert Epp, Chaim Glück, Nadine Felizitas Binder, Mohamad El Amki, Bruno Weber, Susanne Wegener, Patrick Jenny, Franca Schmid:
  The role of leptomeningeal collaterals in redistributing blood flow during stroke.
• 
  Thomas B. K. Watkins, Emma C. Colliver, Matthew R. Huska, Tom L. Kaufmann, Emilia L. Lim, Cody B. Duncan, Kerstin Haase, Peter Van Loo, Charles Swanton, Nicholas McGranahan, Roland F. Schwarz:
  Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
• 
  Steven A. LaBelle, A. Marsh Poulson IV, Steve A. Maas, Adam Rauff, Gerard A. Ateshian, Jeffrey A. Weiss:
  Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis.
• 
  Loveday E. Lewin, Kate G. Daniels, Laurence D. Hurst:
  Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation.
• 
  Nicolas Roth, Martin Rolfs, Olaf Hellwich, Klaus Obermayer:
  Objects guide human gaze behavior in dynamic real-world scenes.
• 
  Fanni Ojala, Mohamad R. Abdul Sater, Loren G. Miller, James A. McKinnell, Mary K. Hayden, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen:
  Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization.
• 
  Amoldeep S. Kainth, Gabriela A. Haddad, Johnathon M. Hall, Alexander J. Ruthenburg:
  Merging short and stranded long reads improves transcript assembly.
• 
  Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco:
  Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data.
• 
  Ghazaleh Soleimani, Rayus Kupliki, Martin P. Paulus, Hamed Ekhtiari:
  Dose-response in modulating brain function with transcranial direct current stimulation: From local to network levels.
• 
  Taniel S. Winner, Michael C. Rosenberg, Kanishk Jain, Trisha M. Kesar, Lena H. Ting, Gordon J. Berman:
  Discovering individual-specific gait signatures from data-driven models of neuromechanical dynamics.
• 
  Manuel Guerrero-Hurtado, Manuel García-Villalba, Alejandro Gonzalo, Pablo Martínez-Legazpi, Andrew M. Kahn, Elliot R. McVeigh, Javier Bermejo, Juan C. del Álamo, Oscar Flores:
  Efficient multi-fidelity computation of blood coagulation under flow.
• 
  Jaime Cascante-Vega, Marta Galanti, Katharina Schley, Sen Pei, Jeffrey Shaman:
  Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease.
• 
  Robin Dirk, Jonas L. Fischer, Simon Schardt, Markus J. Ankenbrand, Sabine C. Fischer:
  Recognition and reconstruction of cell differentiation patterns with deep learning.
• 
  Burak Yelmen, Aurélien Decelle, Leila Lea Boulos, Antoine Szatkownik, Cyril Furtlehner, Guillaume Charpiat, Flora Jay:
  Deep convolutional and conditional neural networks for large-scale genomic data generation.
• 
  Maxwell Neal, Deepan Thiruppathy, Karsten Zengler:
  Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R.

Corrections

• 
  Fateme Pourhasanzade, Swami Iyer, Jesslyn Tjendra, Lotta Landor, Selina Våge:
  Correction: Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence.
• 
  Jérôme Munuera, Marta Ribes Agost, David Bendetowicz, Adrien Kerebel, Valérian Chambon, Brian Lau:
  Correction: Intrinsic motivation for choice varies with individual risk attitudes and the controllability of the environment.
• 
  PLOS Computational Biology Staff:
  Correction: Hybrid predictive coding: Inferring, fast and slow.
• 
  PLOS Computational Biology Staff:
  Correction: A quantitative modelling approach for DNA repair on a population scale.
• 
  Xiyun Zhang, Gabriela Lobinska, Michal Feldman, Eddie Dekel, Martin A. Nowak, Yitzhak Pilpel, Yonatan Pauzner, Baruch Barzel, Ady Pauzner:
  Correction: A spatial vaccination strategy to reduce the risk of vaccine-resistant variants.

Methods

• 
  Aniket Ravan, Ruopei Feng, Martin Gruebele, Yann R. Chemla:
  Rapid automated 3-D pose estimation of larval zebrafish using a physical model-trained neural network.

Software

• 
  Jan Kosinski, Marek Zywicki:
  AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals.

Volume 19, Number 11, November 2023

Education

• 
  Maria Manzanares, Courtney Peña, Kayla C. Kobak, Miranda B. Stratton:
  Ten simple rules for students navigating summer research experiences for undergraduates (REU) programs: From application to program completion.

Research Articles

• 
  Tianyao Zhu, Jason P. Gallivan, Daniel M. Wolpert, J. Randall Flanagan:
  Interaction between decision-making and motor learning when selecting reach targets in the presence of bias and noise.
• 
  Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto d'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna:
  A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing.
• 
  Javier Kipen, Joakim Jaldén:
  Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data.
• 
  Sevada Hovsepyan, Itsaso Olasagasti, Anne-Lise Giraud:
  Rhythmic modulation of prediction errors: A top-down gating role for the beta-range in speech processing.
• 
  Remziye E. Wessel, Sepideh Dolatshahi:
  Quantitative mechanistic model reveals key determinants of placental IgG transfer and informs prenatal immunization strategies.
• 
  Mikkel Elle Lepperød, Tristan M. Stöber, Torkel Hafting, Marianne Fyhn, Konrad Paul Körding:
  Inferring causal connectivity from pairwise recordings and optogenetics.
•