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March 2024, Volume 20, Issue 3
- 1-18 Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation
by Nadin Haase & Wolf Holtkamp & Simon Christ & Dag Heinemann & Marina V Rodnina & Sophia Rudorf - 1-18 Bayesian inference of relative fitness on high-throughput pooled competition assays
by Manuel Razo-Mejia & Madhav Mani & Dmitri Petrov - 1-19 Evolutionary graph theory beyond pairwise interactions: Higher-order network motifs shape times to fixation in structured populations
by Yang Ping Kuo & Oana Carja - 1-20 Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers
by Kosaku Kitagawa & Kwang Su Kim & Masashi Iwamoto & Sanae Hayashi & Hyeongki Park & Takara Nishiyama & Naotoshi Nakamura & Yasuhisa Fujita & Shinji Nakaoka & Kazuyuki Aihara & Alan S Perelson & Lena Allweiss & Maura Dandri & Koichi Watashi & Yasuhito Tanaka & Shingo Iwami - 1-21 Bayesian inference is facilitated by modular neural networks with different time scales
by Kohei Ichikawa & Kunihiko Kaneko - 1-21 A multiscale computational framework for the development of spines in molluscan shells
by Derek E Moulton & Nathanaël Aubert-Kato & Axel A Almet & Atsuko Sato - 1-22 Ten simple rules for pushing boundaries of inclusion at academic events
by Siobhan Mackenzie Hall & Daniel Kochin & Carmel Carne & Patricia Herterich & Kristen Lenay Lewers & Mohamed Abdelhack & Arun Ramasubramanian & Juno Felecia Michael Alphonse & Visotheary Ung & Sara El-Gebali & Christopher Brian Currin & Esther Plomp & Rachel Thompson & Malvika Sharan - 1-23 Enrichment on steps, not genes, improves inference of differentially expressed pathways
by Nicholas Markarian & Kimberly M Van Auken & Dustin Ebert & Paul W Sternberg - 1-23 Learning environment-specific learning rates
by Jonas Simoens & Tom Verguts & Senne Braem - 1-23 kCSD-python, reliable current source density estimation with quality control
by Chaitanya Chintaluri & Marta Bejtka & Władysław Średniawa & Michał Czerwiński & Jakub M Dzik & Joanna Jędrzejewska-Szmek & Daniel K Wójcik - 1-26 Mathematical models of Plasmodium vivax transmission: A scoping review
by Md Nurul Anwar & Lauren Smith & Angela Devine & Somya Mehra & Camelia R Walker & Elizabeth Ivory & Eamon Conway & Ivo Mueller & James M McCaw & Jennifer A Flegg & Roslyn I Hickson - 1-26 Cortical cell assemblies and their underlying connectivity: An in silico study
by András Ecker & Daniela Egas Santander & Sirio Bolaños-Puchet & James B Isbister & Michael W Reimann - 1-27 Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1
by Tyler Cassidy & Kathryn E Stephenson & Dan H Barouch & Alan S Perelson - 1-29 Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data
by Chenyu Wu & Einar Bjarki Gunnarsson & Even Moa Myklebust & Alvaro Köhn-Luque & Dagim Shiferaw Tadele & Jorrit Martijn Enserink & Arnoldo Frigessi & Jasmine Foo & Kevin Leder - 1-31 Bias in the arrival of variation can dominate over natural selection in Richard Dawkins’s biomorphs
by Nora S Martin & Chico Q Camargo & Ard A Louis - 1-33 AI-Aristotle: A physics-informed framework for systems biology gray-box identification
by Nazanin Ahmadi Daryakenari & Mario De Florio & Khemraj Shukla & George Em Karniadakis - 1-33 PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration
by Cecilia Wieder & Juliette Cooke & Clement Frainay & Nathalie Poupin & Russell Bowler & Fabien Jourdan & Katerina J Kechris & Rachel PJ Lai & Timothy Ebbels
February 2024, Volume 20, Issue 2
- 1-11 HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics
by Margaritis Voliotis & Ali Abbara & Julia K Prague & Johannes D Veldhuis & Waljit S Dhillo & Krasimira Tsaneva-Atanasova - 1-13 magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing
by Zhenxing Guo & Daoyu Duan & Wen Tang & Julia Zhu & William S Bush & Liangliang Zhang & Xiaofeng Zhu & Fulai Jin & Hao Feng - 1-18 Connectivity Matrix Seriation via Relaxation
by Alexander Borst - 1-18 A beta-Poisson model for infectious disease transmission
by Joe Hilton & Ian Hall - 1-19 Quantifying the clusterness and trajectoriness of single-cell RNA-seq data
by Hong Seo Lim & Peng Qiu - 1-19 Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology
by Daniele Dall’Olio & Eric Sträng & Amin T Turki & Jesse M Tettero & Martje Barbus & Renate Schulze-Rath & Javier Martinez Elicegui & Tommaso Matteuzzi & Alessandra Merlotti & Luciana Carota & Claudia Sala & Matteo G Della Porta & Enrico Giampieri & Jesús María Hernández-Rivas & Lars Bullinger & Gastone Castellani & with the HARMONY Healthcare Alliance Consortium - 1-20 Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae)
by Sarah Percival & Joyce G Onyenedum & Daniel H Chitwood & Aman Y Husbands - 1-22 A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization
by Lily Monnier & Paul-Henry Cournède - 1-22 Accounting for isoform expression increases power to identify genetic regulation of gene expression
by Nathan LaPierre & Harold Pimentel - 1-22 Robust expansion of phylogeny for fast-growing genome sequence data
by Yongtao Ye & Marcus H Shum & Joseph L Tsui & Guangchuang Yu & David K Smith & Huachen Zhu & Joseph T Wu & Yi Guan & Tommy Tsan-Yuk Lam - 1-22 EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks
by Francesco Pinotti & José Lourenço & Sunetra Gupta & Suman Das Gupta & Joerg Henning & Damer Blake & Fiona Tomley & Tony Barnett & Dirk Pfeiffer & Md Ahasanul Hoque & Guillaume Fournié - 1-23 Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity
by Pan Li & Jae Kyoung Kim - 1-23 Shared input and recurrency in neural networks for metabolically efficient information transmission
by Tomas Barta & Lubomir Kostal - 1-23 Trained recurrent neural networks develop phase-locked limit cycles in a working memory task
by Matthijs Pals & Jakob H Macke & Omri Barak - 1-24 Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians
by Li-Dunn Chen & Michael A Caprio & Devin M Chen & Andrew J Kouba & Carrie K Kouba - 1-24 STGIC: A graph and image convolution-based method for spatial transcriptomic clustering
by Chen Zhang & Junhui Gao & Hong-Yu Chen & Lingxin Kong & Guangshuo Cao & Xiangyu Guo & Wei Liu & Bin Ren & Dong-Qing Wei - 1-24 Sleep deprivation detected by voice analysis
by Etienne Thoret & Thomas Andrillon & Caroline Gauriau & Damien Léger & Daniel Pressnitzer - 1-25 Attractor neural networks with double well synapses
by Yu Feng & Nicolas Brunel - 1-26 Generating synthetic population for simulating the spatiotemporal dynamics of epidemics
by Kemin Zhu & Ling Yin & Kang Liu & Junli Liu & Yepeng Shi & Xuan Li & Hongyang Zou & Huibin Du - 1-27 The geometric evolution of aortic dissections: Predicting surgical success using fluctuations in integrated Gaussian curvature
by Kameel Khabaz & Karen Yuan & Joseph Pugar & David Jiang & Seth Sankary & Sanjeev Dhara & Junsung Kim & Janet Kang & Nhung Nguyen & Kathleen Cao & Newell Washburn & Nicole Bohr & Cheong Jun Lee & Gordon Kindlmann & Ross Milner & Luka Pocivavsek - 1-29 Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference
by Nicholas Tolley & Pedro L C Rodrigues & Alexandre Gramfort & Stephanie R Jones - 1-30 Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex
by Linxing Preston Jiang & Rajesh P N Rao - 1-32 A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites
by Moritz Groden & Hannah M Moessinger & Barbara Schaffran & Javier DeFelipe & Ruth Benavides-Piccione & Hermann Cuntz & Peter Jedlicka - 1-33 The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion
by Martijn A de Jong & Esmée Adegeest & Noémie M L P Bérenger-Currias & Maria Mircea & Roeland M H Merks & Stefan Semrau - 1-41 The successor representation subserves hierarchical abstraction for goal-directed behavior
by Sven Wientjes & Clay B Holroyd
January 2024, Volume 20, Issue 1
- 1-6 Ten simple rules for establishing an experimental lab
by Marcus Kaiser - 1-15 Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand
by Michael J Plank & Leighton Watson & Oliver J Maclaren - 1-15 Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis
by Yong-Jin Huang & Chun-Wei Chang & Chih-hao Hsieh - 1-18 MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks
by Sebastian Himbert & Dorian Gaboo & Emre Brookes & John F Nagle & Maikel C Rheinstädter - 1-19 Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces
by Enrique R Sebastian & Julio Esparza & Liset M. de la Prida - 1-20 Joint representation of molecular networks from multiple species improves gene classification
by Christopher A Mancuso & Kayla A Johnson & Renming Liu & Arjun Krishnan - 1-20 Revealing and reshaping attractor dynamics in large networks of cortical neurons
by Chen Beer & Omri Barak - 1-21 Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex
by Sebastian Idesis & Sebastián Geli & Joshua Faskowitz & Jakub Vohryzek & Yonatan Sanz Perl & Florian Pieper & Edgar Galindo-Leon & Andreas K Engel & Gustavo Deco - 1-22 Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior
by Yoav Ger & Eliya Nachmani & Lior Wolf & Nitzan Shahar - 1-23 Landscape quantifies the intermediate state and transition dynamics in ecological networks
by Jinchao Lv & Jin Wang & Chunhe Li - 1-23 High-performing neural network models of visual cortex benefit from high latent dimensionality
by Eric Elmoznino & Michael F Bonner - 1-24 Transformations of sensory information in the brain suggest changing criteria for optimality
by Tyler S Manning & Emma Alexander & Bruce G Cumming & Gregory C DeAngelis & Xin Huang & Emily A Cooper - 1-24 A neural network model for the evolution of learning in changing environments
by Magdalena Kozielska & Franz J Weissing - 1-24 Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells
by Paul F Lang & David R Penas & Julio R Banga & Daniel Weindl & Bela Novak - 1-24 Explaining the flaws in human random generation as local sampling with momentum
by Lucas Castillo & Pablo León-Villagrá & Nick Chater & Adam Sanborn - 1-25 Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer
by Chin-Hsuan Sophie Lin & Trang Thuy Do & Lee Unsworth & Marta I Garrido - 1-26 Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions
by Paul J N Brodersen & Hannah Alfonsa & Lukas B Krone & Cristina Blanco-Duque & Angus S Fisk & Sarah J Flaherty & Mathilde C C Guillaumin & Yi-Ge Huang & Martin C Kahn & Laura E McKillop & Linus Milinski & Lewis Taylor & Christopher W Thomas & Tomoko Yamagata & Russell G Foster & Vladyslav V Vyazovskiy & Colin J Akerman - 1-26 Inferring country-specific import risk of diseases from the world air transportation network
by Pascal P Klamser & Adrian Zachariae & Benjamin F Maier & Olga Baranov & Clara Jongen & Frank Schlosser & Dirk Brockmann - 1-30 Controlling target brain regions by optimal selection of input nodes
by Karan Kabbur Hanumanthappa Manjunatha & Giorgia Baron & Danilo Benozzo & Erica Silvestri & Maurizio Corbetta & Alessandro Chiuso & Alessandra Bertoldo & Samir Suweis & Michele Allegra - 1-31 PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning
by Anand Ramachandran & Steven S Lumetta & Deming Chen - 1-32 A genome-wide comprehensive analysis of nucleosome positioning in yeast
by Leo Zeitler & Kévin André & Adriana Alberti & Cyril Denby Wilkes & Julie Soutourina & Arach Goldar
December 2023, Volume 19, Issue 12
- 1-6 Ten simple rules for writing a PLOS Computational Biology quick tips article
by Patricia M Palagi & Russell Schwartz & Scott Markel & B F Francis Ouellette - 1-7 Ten simple rules for humane data science
by Hassan Masum & Philip E Bourne - 1-12 resevol: An R package for spatially explicit models of pesticide resistance given evolving pest genomes
by A Bradley Duthie & Rosie Mangan & C Rose McKeon & Matthew C Tinsley & Luc F Bussière - 1-14 Metric information in cognitive maps: Euclidean embedding of non-Euclidean environments
by Tristan Baumann & Hanspeter A Mallot - 1-14 Recurrence risk stratification of hepatocellular carcinomas based on immune gene expression and features extracted from pathological images
by Tao Ding & Xiao Li & Jiu Mo & Gregory Alexander & Jialu Li - 1-15 The influence of saccades on yaw gaze stabilization in fly flight
by Brock A Davis & Jean-Michel Mongeau - 1-15 Using mixture density networks to emulate a stochastic within-host model of Francisella tularensis infection
by Jonathan Carruthers & Thomas Finnie - 1-16 Sparsity in an artificial neural network predicts beauty: Towards a model of processing-based aesthetics
by Nicolas M Dibot & Sonia Tieo & Tamra C Mendelson & William Puech & Julien P Renoult - 1-19 Major depressive disorder and bistability in an HPA-CNS toggle switch
by Ben Ron Mizrachi & Avichai Tendler & Omer Karin & Tomer Milo & Dafna Haran & Avi Mayo & Uri Alon - 1-20 Transcript assembly and annotations: Bias and adjustment
by Qimin Zhang & Mingfu Shao - 1-20 4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction
by Zihao Wang & Songhao Luo & Zhenquan Zhang & Tianshou Zhou & Jiajun Zhang - 1-21 RMDGCN: Prediction of RNA methylation and disease associations based on graph convolutional network with attention mechanism
by Lian Liu & Yumeng Zhou & Xiujuan Lei - 1-24 PyRates—A code-generation tool for modeling dynamical systems in biology and beyond
by Richard Gast & Thomas R Knösche & Ann Kennedy - 1-24 From dawn till dusk: Time-adaptive bayesian optimization for neurostimulation
by John E Fleming & Ines Pont Sanchis & Oscar Lemmens & Angus Denison-Smith & Timothy O West & Timothy Denison & Hayriye Cagnan - 1-25 Learning massive interpretable gene regulatory networks of the human brain by merging Bayesian networks
by Niko Bernaola & Mario Michiels & Pedro Larrañaga & Concha Bielza - 1-27 multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results
by Aastha Khatiwada & Ayse Selen Yilmaz & Bethany J Wolf & Maciej Pietrzak & Dongjun Chung - 1-35 Statistical prediction of microbial metabolic traits from genomes
by Zeqian Li & Ahmed Selim & Seppe Kuehn - 1-38 Estimating neuronal firing density: A quantitative analysis of firing rate map algorithms
by Roddy M Grieves
November 2023, Volume 19, Issue 11
- 1-13 Ten simple rules for students navigating summer research experiences for undergraduates (REU) programs: From application to program completion
by Maria Manzanares & Courtney Peña & Kayla C Kobak & Miranda B Stratton - 1-15 GENERALIST: A latent space based generative model for protein sequence families
by Hoda Akl & Brooke Emison & Xiaochuan Zhao & Arup Mondal & Alberto Perez & Purushottam D Dixit - 1-16 Addressing erroneous scale assumptions in microbe and gene set enrichment analysis
by Kyle C McGovern & Michelle Pistner Nixon & Justin D Silverman - 1-17 A data-driven semi-parametric model of SARS-CoV-2 transmission in the United States
by John M Drake & Andreas Handel & Éric Marty & Eamon B O’Dea & Tierney O’Sullivan & Giovanni Righi & Andrew T Tredennick - 1-18 Assessing the importance of demographic risk factors across two waves of SARS-CoV-2 using fine-scale case data
by Anthony J Wood & Aeron R Sanchez & Paul R Bessell & Rebecca Wightman & Rowland R Kao - 1-19 Attention-based deep clustering method for scRNA-seq cell type identification
by Shenghao Li & Hui Guo & Simai Zhang & Yizhou Li & Menglong Li - 1-20 On convolutional neural networks for selection inference: Revealing the effect of preprocessing on model learning and the capacity to discover novel patterns
by Ryan M Cecil & Lauren A Sugden - 1-21 Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data
by Javier Kipen & Joakim Jaldén - 1-25 Adaptive oscillators support Bayesian prediction in temporal processing
by Keith B Doelling & Luc H Arnal & M Florencia Assaneo - 1-26 BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
by Tyler W H Backman & Christina Schenk & Tijana Radivojevic & David Ando & Jahnavi Singh & Jeffrey J Czajka & Zak Costello & Jay D Keasling & Yinjie Tang & Elena Akhmatskaya & Hector Garcia Martin - 1-26 Interaction between decision-making and motor learning when selecting reach targets in the presence of bias and noise
by Tianyao Zhu & Jason P Gallivan & Daniel M Wolpert & J Randall Flanagan - 1-27 External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration
by Chiara Dazzi & Julia Mehl & Mounir Benamar & Holger Gerhardt & Petra Knaus & Georg N Duda & Sara Checa - 1-27 Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany
by Elisabeth K Brockhaus & Daniel Wolffram & Tanja Stadler & Michael Osthege & Tanmay Mitra & Jonas M Littek & Ekaterina Krymova & Anna J Klesen & Jana S Huisman & Stefan Heyder & Laura M Helleckes & Matthias an der Heiden & Sebastian Funk & Sam Abbott & Johannes Bracher - 1-27 The mechanism of MinD stability modulation by MinE in Min protein dynamics
by William C Carlquist & Eric N Cytrynbaum - 1-27 Tuning social interactions’ strength drives collective response to light intensity in schooling fish
by Tingting Xue & Xu Li & GuoZheng Lin & Ramón Escobedo & Zhangang Han & Xiaosong Chen & Clément Sire & Guy Theraulaz - 1-28 Learning efficient representations of environmental priors in working memory
by Tahra L Eissa & Zachary P Kilpatrick - 1-29 Exploring strategy differences between humans and monkeys with recurrent neural networks
by Ben Tsuda & Barry J Richmond & Terrence J Sejnowski - 1-31 Modeling the diverse effects of divisive normalization on noise correlations
by Oren Weiss & Hayley A Bounds & Hillel Adesnik & Ruben Coen-Cagli - 1-32 Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation
by Sarvesh Nikumbh & Boris Lenhard
October 2023, Volume 19, Issue 10
- 1-16 Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease
by Jaime Cascante-Vega & Marta Galanti & Katharina Schley & Sen Pei & Jeffrey Shaman - 1-16 Establishing brain states in neuroimaging data
by Zalina Dezhina & Jonathan Smallwood & Ting Xu & Federico E Turkheimer & Rosalyn J Moran & Karl J Friston & Robert Leech & Erik D Fagerholm - 1-17 Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization
by Fanni Ojala & Mohamad R Abdul Sater & Loren G Miller & James A McKinnell & Mary K Hayden & Susan S Huang & Yonatan H Grad & Pekka Marttinen - 1-18 Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment
by Aymara Sancho-Araiz & Zinnia P Parra-Guillen & Jean Bragard & Sergio Ardanza & Victor Mangas-Sanjuan & Iñaki F Trocóniz - 1-19 Circadian distribution of epileptiform discharges in epilepsy: Candidate mechanisms of variability
by Isabella Marinelli & Jamie J Walker & Udaya Seneviratne & Wendyl D’Souza & Mark J Cook & Clare Anderson & Andrew P Bagshaw & Stafford L Lightman & Wessel Woldman & John R Terry - 1-19 Lévy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers
by Andrea Falcón-Cortés & Denis Boyer & Maximino Aldana & Gabriel Ramos-Fernández - 1-21 Deep convolutional and conditional neural networks for large-scale genomic data generation
by Burak Yelmen & Aurélien Decelle & Leila Lea Boulos & Antoine Szatkownik & Cyril Furtlehner & Guillaume Charpiat & Flora Jay - 1-21 A 2D model to study how secondary growth affects the self-supporting behaviour of climbing plants
by Giacomo Vecchiato & Tom Hattermann & Michele Palladino & Fabio Tedone & Patrick Heuret & Nick P Rowe & Pierangelo Marcati - 1-22 Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data
by Lorenzo Posani & Francesca Rizzato & Rémi Monasson & Simona Cocco - 1-22 Modeling functional cell types in spike train data
by Daniel N Zdeblick & Eric T Shea-Brown & Daniela M Witten & Michael A Buice - 1-23 Combining the dynamic model and deep neural networks to identify the intensity of interventions during COVID-19 pandemic
by Mengqi He & Sanyi Tang & Yanni Xiao - 1-23 Temperature sensitive contact modes allosterically gate TRPV3
by Daniel Burns & Vincenzo Venditti & Davit A Potoyan - 1-24 Rational social distancing policy during epidemics with limited healthcare capacity
by Simon K Schnyder & John J Molina & Ryoichi Yamamoto & Matthew S Turner - 1-26 Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning
by Philipp D Lösel & Coline Monchanin & Renaud Lebrun & Alejandra Jayme & Jacob J Relle & Jean-Marc Devaud & Vincent Heuveline & Mathieu Lihoreau - 1-26 Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker
by Oliver J Meacock & William M Durham - 1-27 Distilling identifiable and interpretable dynamic models from biological data
by Gemma Massonis & Alejandro F Villaverde & Julio R Banga - 1-29 Recognition and reconstruction of cell differentiation patterns with deep learning
by Robin Dirk & Jonas L Fischer & Simon Schardt & Markus J Ankenbrand & Sabine C Fischer - 1-29 Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis
by Steven A LaBelle & A Marsh Poulson IV & Steve A Maas & Adam Rauff & Gerard A Ateshian & Jeffrey A Weiss - 1-30 Phi fluctuates with surprisal: An empirical pre-study for the synthesis of the free energy principle and integrated information theory
by Christoffer Lundbak Olesen & Peter Thestrup Waade & Larissa Albantakis & Christoph Mathys - 1-32 Rapid runtime learning by curating small datasets of high-quality items obtained from memory
by Joseph Scott German & Guofeng Cui & Chenliang Xu & Robert A Jacobs - 1-35 Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies
by Yilin Gao & Fengzhu Sun - 1-39 Objects guide human gaze behavior in dynamic real-world scenes
by Nicolas Roth & Martin Rolfs & Olaf Hellwich & Klaus Obermayer - 1-45 Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms
by Larissa Albantakis & Leonardo Barbosa & Graham Findlay & Matteo Grasso & Andrew M Haun & William Marshall & William G P Mayner & Alireza Zaeemzadeh & Melanie Boly & Bjørn E Juel & Shuntaro Sasai & Keiko Fujii & Isaac David & Jeremiah Hendren & Jonathan P Lang & Giulio Tononi
September 2023, Volume 19, Issue 9
- 1-13 Ten simple rules for interpreting and evaluating a meta-analysis
by Rebecca B Carlson & Jennifer R Martin & Robert D Beckett - 1-17 An automated interface for sedimentation velocity analysis in SEDFIT
by Peter Schuck & Samuel C To & Huaying Zhao - 1-18 Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics
by Serena Aneli & Piero Fariselli & Elena Chierto & Carla Bini & Carlo Robino & Giovanni Birolo - 1-18 Uncovering specific mechanisms across cell types in dynamical models
by Adrian L Hauber & Marcus Rosenblatt & Jens Timmer - 1-19 Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony
by Seirana Hashemi & Zahra Razaghi-Moghadam & Zoran Nikoloski - 1-20 iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease
by Ziheng Duan & Yi Dai & Ahyeon Hwang & Cheyu Lee & Kaichi Xie & Chutong Xiao & Min Xu & Matthew J Girgenti & Jing Zhang - 1-21 Beyond ℓ1 sparse coding in V1
by Ilias Rentzeperis & Luca Calatroni & Laurent U Perrinet & Dario Prandi - 1-22 Identifying a developmental transition in honey bees using gene expression data
by Bryan C Daniels & Ying Wang & Robert E Page Jr & Gro V Amdam - 1-22 Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England
by James D Munday & Sam Abbott & Sophie Meakin & Sebastian Funk - 1-22 Human-environment feedback and the consistency of proenvironmental behavior
by Claire Ecotière & Sylvain Billiard & Jean-Baptiste André & Pierre Collet & Régis Ferrière & Sylvie Méléard - 1-23 Nowcasting the 2022 mpox outbreak in England
by Christopher E Overton & Sam Abbott & Rachel Christie & Fergus Cumming & Julie Day & Owen Jones & Rob Paton & Charlie Turner & Thomas Ward - 1-24 Measuring uncertainty in human visual segmentation
by Jonathan Vacher & Claire Launay & Pascal Mamassian & Ruben Coen-Cagli - 1-24 Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches
by Zheng Jiang & Yue-Yue Shen & Rong Liu - 1-24 Fixation dynamics on hypergraphs
by Ruodan Liu & Naoki Masuda - 1-26 A role for cortical interneurons as adversarial discriminators
by Ari S Benjamin & Konrad P Kording - 1-26 Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data
by Simon Boutry & Raphaël Helaers & Tom Lenaerts & Miikka Vikkula - 1-27 What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases
by Francis Banville & Dominique Gravel & Timothée Poisot - 1-27 Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding
by Billy Tchounke & Leopoldo Sanchez & Joseph Martin Bell & David Cros - 1-27 Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels
by Erik Nordquist & Guohui Zhang & Shrishti Barethiya & Nathan Ji & Kelli M White & Lu Han & Zhiguang Jia & Jingyi Shi & Jianmin Cui & Jianhan Chen - 1-28 Mixtures of strategies underlie rodent behavior during reversal learning
by Nhat Minh Le & Murat Yildirim & Yizhi Wang & Hiroki Sugihara & Mehrdad Jazayeri & Mriganka Sur - 1-28 Simulation-based inference for efficient identification of generative models in computational connectomics
by Jan Boelts & Philipp Harth & Richard Gao & Daniel Udvary & Felipe Yáñez & Daniel Baum & Hans-Christian Hege & Marcel Oberlaender & Jakob H Macke - 1-29 iCVS—Inferring Cardio-Vascular hidden States from physiological signals available at the bedside
by Neta Ravid Tannenbaum & Omer Gottesman & Azadeh Assadi & Mjaye Mazwi & Uri Shalit & Danny Eytan - 1-31 Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model
by Shuaijie Zhang & Fan Yang & Lijie Wang & Shucheng Si & Jianmei Zhang & Fuzhong Xue - 1-31 Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models
by Matthew J Simpson & Oliver J Maclaren - 1-32 The inhibitory control of traveling waves in cortical networks
by Grishma Palkar & Jian-young Wu & Bard Ermentrout - 1-32 Self-loops in evolutionary graph theory: Friends or foes?
by Nikhil Sharma & Sedigheh Yagoobi & Arne Traulsen - 1-36 Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models
by Christian Tönsing & Bernhard Steiert & Jens Timmer & Clemens Kreutz - 1-45 Error-independent effect of sensory uncertainty on motor learning when both feedforward and feedback control processes are engaged
by Christopher L Hewitson & David M Kaplan & Matthew J Crossley
August 2023, Volume 19, Issue 8
- 1-6 Ten simple rules for writing a technical book
by Jess Haberman & Greg Wilson - 1-12 Ten simple rules for a mom-friendly Academia
by Esther Sebastián-González & Eva Graciá & Alejandra Morán-Ordóñez & Irene Pérez-Ibarra & Ana Sanz-Aguilar & Mar Sobral - 1-14 Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool
by Rebecca K Nash & Samir Bhatt & Anne Cori & Pierre Nouvellet - 1-15 A new method for the analysis of access period experiments, illustrated with whitefly-borne cassava mosaic begomovirus
by Ruairí Donnelly & Christopher A Gilligan - 1-18 Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance
by Johann F Jadebeck & Wolfgang Wiechert & Katharina Nöh - 1-18 Synaptic weights that correlate with presynaptic selectivity increase decoding performance
by Júlia V Gallinaro & Benjamin Scholl & Claudia Clopath - 1-18 Ensemble inference of unobserved infections in networks using partial observations
by Renquan Zhang & Jilei Tai & Sen Pei - 1-19 E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction
by Rahmatullah Roche & Bernard Moussad & Md Hossain Shuvo & Debswapna Bhattacharya - 1-19 Evolutionary dynamics on sequential temporal networks
by Anzhi Sheng & Aming Li & Long Wang - 1-20 Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network
by Wenxing Hu & Lixin Guan & Mengshan Li - 1-20 The specious art of single-cell genomics
by Tara Chari & Lior Pachter - 1-21 Disentangling Abstraction from Statistical Pattern Matching in Human and Machine Learning
by Sreejan Kumar & Ishita Dasgupta & Nathaniel D Daw & Jonathan D Cohen & Thomas L Griffiths - 1-22 iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction
by Lin Yuan & Jiawang Zhao & Zhen Shen & Qinhu Zhang & Yushui Geng & Chun-Hou Zheng & De-Shuang Huang - 1-23 Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model
by Shawn A Means & Mathias W Roesler & Amy S Garrett & Leo Cheng & Alys R Clark - 1-23 In-silico and in-vitro morphometric analysis of intestinal organoids
by Sandra Montes-Olivas & Danny Legge & Abbie Lund & Alexander G Fletcher & Ann C Williams & Lucia Marucci & Martin Homer - 1-23 Scoring epidemiological forecasts on transformed scales
by Nikos I Bosse & Sam Abbott & Anne Cori & Edwin van Leeuwen & Johannes Bracher & Sebastian Funk - 1-23 An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space
by Bastian Volker Helmut Hornung & Nicolas Terrapon - 1-23 Neural network models for influenza forecasting with associated uncertainty using Web search activity trends
by Michael Morris & Peter Hayes & Ingemar J Cox & Vasileios Lampos - 1-24 Curated single cell multimodal landmark datasets for R/Bioconductor
by Kelly B Eckenrode & Dario Righelli & Marcel Ramos & Ricard Argelaguet & Christophe Vanderaa & Ludwig Geistlinger & Aedin C Culhane & Laurent Gatto & Vincent Carey & Martin Morgan & Davide Risso & Levi Waldron - 1-24 STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring
by Azka Javaid & Hildreth Robert Frost - 1-24 Functional and spatial rewiring principles jointly regulate context-sensitive computation
by Jia Li & Ilias Rentzeperis & Cees van Leeuwen - 1-25 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
by Jonathan W Cody & Amy L Ellis-Connell & Shelby L O’Connor & Elsje Pienaar - 1-25 Receptive field sizes and neuronal encoding bandwidth are constrained by axonal conduction delays
by Tim C Hladnik & Jan Grewe - 1-26 From time-series transcriptomics to gene regulatory networks: A review on inference methods
by Malvina Marku & Vera Pancaldi - 1-28 Efficient sampling-based Bayesian Active Learning for synaptic characterization
by Camille Gontier & Simone Carlo Surace & Igor Delvendahl & Martin Müller & Jean-Pascal Pfister - 1-28 Mathematical models of developmental vascular remodelling: A review
by Jessica R Crawshaw & Jennifer A Flegg & Miguel O Bernabeu & James M Osborne - 1-28 VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
by Guillermo Rangel-Pineros & Alexandre Almeida & Martin Beracochea & Ekaterina Sakharova & Manja Marz & Alejandro Reyes Muñoz & Martin Hölzer & Robert D Finn - 1-29 Automatic extraction of actin networks in plants
by Jordan Hembrow & Michael J Deeks & David M Richards - 1-31 Enhancing reinforcement learning models by including direct and indirect pathways improves performance on striatal dependent tasks
by Kim T Blackwell & Kenji Doya - 1-31 Hybrid predictive coding: Inferring, fast and slow
by Alexander Tscshantz & Beren Millidge & Anil K Seth & Christopher L Buckley - 1-31 Redundant representations are required to disambiguate simultaneously presented complex stimuli
by W Jeffrey Johnston & David J Freedman - 1-31 Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
by Ruihao Li & Jordan C Rozum & Morgan M Quail & Mohammad N Qasim & Suzanne S Sindi & Clarissa J Nobile & Réka Albert & Aaron D Hernday - 1-31 Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration
by Caetano Souto-Maior & Yazmin L Serrano Negron & Susan T Harbison - 1-33 Structural identifiability of biomolecular controller motifs with and without flow measurements as model output
by Eivind S Haus & Tormod Drengstig & Kristian Thorsen - 1-34 Geometry of population activity in spiking networks with low-rank structure
by Ljubica Cimeša & Lazar Ciric & Srdjan Ostojic - 1-41 Switching state-space modeling of neural signal dynamics
by Mingjian He & Proloy Das & Gladia Hotan & Patrick L Purdon
July 2023, Volume 19, Issue 7
- 1-16 LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses
by Alexei J Drummond & Kylie Chen & Fábio K Mendes & Dong Xie - 1-17 LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity
by Juan Xie & Hyeongseon Jeon & Gang Xin & Qin Ma & Dongjun Chung - 1-17 Network feature-based phenotyping of leaf venation robustly reconstructs the latent space
by Kohei Iwamasa & Koji Noshita - 1-19 RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure
by Elena Rivas - 1-20 Monte Carlo samplers for efficient network inference
by Zeliha Kilic & Max Schweiger & Camille Moyer & Steve Pressé - 1-20 Continuous action with a neurobiologically inspired computational approach reveals the dynamics of selection history
by Mukesh Makwana & Fan Zhang & Dietmar Heinke & Joo-Hyun Song - 1-21 Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection
by Alain J Mbebi & Zoran Nikoloski - 1-21 The interplay between age structure and cultural transmission
by Anne Kandler & Laurel Fogarty & Folgert Karsdorp - 1-22 Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants
by Ahmed Taha & Mauricio Patón & David R Penas & Julio R Banga & Jorge Rodríguez - 1-22 Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach
by Christian Blau & Linnea Yvonnesdotter & Erik Lindahl - 1-23 Mapping the semi-nested community structure of 3D chromosome contact networks
by Dolores Bernenko & Sang Hoon Lee & Per Stenberg & Ludvig Lizana