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June 2024, Volume 20, Issue 6
- 1-28 Synergistic information supports modality integration and flexible learning in neural networks solving multiple tasks
by Alexandra M Proca & Fernando E Rosas & Andrea I Luppi & Daniel Bor & Matthew Crosby & Pedro A M Mediano - 1-28 Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments
by Jeremy VanderDoes & Claire Marceaux & Kenta Yokote & Marie-Liesse Asselin-Labat & Gregory Rice & Jack D Hywood - 1-28 Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection
by Ellie Mainou & Ruy M Ribeiro & Jessica M Conway - 1-33 Beliefs, compulsive behavior and reduced confidence in control
by Lionel Rigoux & Klaas E Stephan & Frederike H Petzschner - 1-40 The stabilized supralinear network accounts for the contrast dependence of visual cortical gamma oscillations
by Caleb J Holt & Kenneth D Miller & Yashar Ahmadian
May 2024, Volume 20, Issue 5
- 1-8 FAIR-USE4OS: Guidelines for creating impactful open-source software
by Raphael Sonabend & Hugo Gruson & Leo Wolansky & Agnes Kiragga & Daniel S Katz - 1-13 PESSA: A web tool for pathway enrichment score-based survival analysis in cancer
by Hong Yang & Ying Shi & Anqi Lin & Chang Qi & Zaoqu Liu & Quan Cheng & Kai Miao & Jian Zhang & Peng Luo - 1-13 MGSurvE: A framework to optimize trap placement for genetic surveillance of mosquito populations
by Héctor M Sánchez C. & David L Smith & John M Marshall - 1-15 The impact of health inequity on spatial variation of COVID-19 transmission in England
by Thomas Rawson & Wes Hinsley & Raphael Sonabend & Elizaveta Semenova & Anne Cori & Neil M Ferguson - 1-19 Clustering and visualization of single-cell RNA-seq data using path metrics
by Andriana Manousidaki & Anna Little & Yuying Xie - 1-20 Inferring fungal growth rates from optical density data
by Tara Hameed & Natasha Motsi & Elaine Bignell & Reiko J Tanaka - 1-20 Machine-learning and mechanistic modeling of metastatic breast cancer after neoadjuvant treatment
by Sebastien Benzekry & Michalis Mastri & Chiara Nicolò & John M L Ebos - 1-21 Leveraging conformal prediction to annotate enzyme function space with limited false positives
by Kerr Ding & Jiaqi Luo & Yunan Luo - 1-22 Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model
by Alexander Massey & Corentin Boennec & Claudia Ximena Restrepo-Ortiz & Christophe Blanchet & Samuel Alizon & Mircea T Sofonea - 1-22 A systematic analysis of regression models for protein engineering
by Richard Michael & Jacob Kæstel-Hansen & Peter Mørch Groth & Simon Bartels & Jesper Salomon & Pengfei Tian & Nikos S Hatzakis & Wouter Boomsma - 1-23 Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration
by James Ryu & Amin Nejatbakhsh & Mahdi Torkashvand & Sahana Gangadharan & Maedeh Seyedolmohadesin & Jinmahn Kim & Liam Paninski & Vivek Venkatachalam - 1-23 A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships
by Alexander Kroll & Sahasra Ranjan & Martin J Lercher - 1-23 Mathematical modeling of the evolution of resistance and aggressiveness of high-grade serous ovarian cancer from patient CA-125 time series
by Kanyarat Jitmana & Jason I Griffiths & Sian Fereday & Anna DeFazio & David Bowtell & for Australian Ovarian Cancer Study & Frederick R Adler - 1-24 Graph topological transformations in space-filling cell aggregates
by Tanmoy Sarkar & Matej Krajnc - 1-24 Astrocytes as a mechanism for contextually-guided network dynamics and function
by Lulu Gong & Fabio Pasqualetti & Thomas Papouin & ShiNung Ching - 1-24 Interpretable online network dictionary learning for inferring long-range chromatin interactions
by Vishal Rana & Jianhao Peng & Chao Pan & Hanbaek Lyu & Albert Cheng & Minji Kim & Olgica Milenkovic - 1-25 Scuphr: A probabilistic framework for cell lineage tree reconstruction
by Hazal Koptagel & Seong-Hwan Jun & Joanna Hård & Jens Lagergren - 1-25 Challenges of COVID-19 Case Forecasting in the US, 2020–2021
by Velma K Lopez & Estee Y Cramer & Robert Pagano & John M Drake & Eamon B O’Dea & Madeline Adee & Turgay Ayer & Jagpreet Chhatwal & Ozden O Dalgic & Mary A Ladd & Benjamin P Linas & Peter P Mueller & Jade Xiao & Johannes Bracher & Alvaro J Castro Rivadeneira & Aaron Gerding & Tilmann Gneiting & Yuxin Huang & Dasuni Jayawardena & Abdul H Kanji & Khoa Le & Anja Mühlemann & Jarad Niemi & Evan L Ray & Ariane Stark & Yijin Wang & Nutcha Wattanachit & Martha W Zorn & Sen Pei & Jeffrey Shaman & Teresa K Yamana & Samuel R Tarasewicz & Daniel J Wilson & Sid Baccam & Heidi Gurung & Steve Stage & Brad Suchoski & Lei Gao & Zhiling Gu & Myungjin Kim & Xinyi Li & Guannan Wang & Lily Wang & Yueying Wang & Shan Yu & Lauren Gardner & Sonia Jindal & Maximilian Marshall & Kristen Nixon & Juan Dent & Alison L Hill & Joshua Kaminsky & Elizabeth C Lee & Joseph C Lemaitre & Justin Lessler & Claire P Smith & Shaun Truelove & Matt Kinsey & Luke C Mullany & Kaitlin Rainwater-Lovett & Lauren Shin & Katharine Tallaksen & Shelby Wilson & Dean Karlen & Lauren Castro & Geoffrey Fairchild & Isaac Michaud & Dave Osthus & Jiang Bian & Wei Cao & Zhifeng Gao & Juan Lavista Ferres & Chaozhuo Li & Tie-Yan Liu & Xing Xie & Shun Zhang & Shun Zheng & Matteo Chinazzi & Jessica T Davis & Kunpeng Mu & Ana Pastore y Piontti & Alessandro Vespignani & Xinyue Xiong & Robert Walraven & Jinghui Chen & Quanquan Gu & Lingxiao Wang & Pan Xu & Weitong Zhang & Difan Zou & Graham Casey Gibson & Daniel Sheldon & Ajitesh Srivastava & Aniruddha Adiga & Benjamin Hurt & Gursharn Kaur & Bryan Lewis & Madhav Marathe & Akhil Sai Peddireddy & Przemyslaw Porebski & Srinivasan Venkatramanan & Lijing Wang & Pragati V Prasad & Jo W Walker & Alexander E Webber & Rachel B Slayton & Matthew Biggerstaff & Nicholas G Reich & Michael A Johansson - 1-26 Marmosets mutually compensate for differences in rhythms when coordinating vigilance
by Nikhil Phaniraj & Rahel K Brügger & Judith M Burkart - 1-27 Data–driven modelling makes quantitative predictions regarding bacteria surface motility
by Daniel L Barton & Yow-Ren Chang & William Ducker & Jure Dobnikar - 1-27 Estimating mutation rates under heterogeneous stress responses
by Lucy Lansch-Justen & Meriem El Karoui & Helen K Alexander - 1-27 Adaptive modeling and inference of higher-order coordination in neuronal assemblies: A dynamic greedy estimation approach
by Shoutik Mukherjee & Behtash Babadi - 1-27 Brain2GAN: Feature-disentangled neural encoding and decoding of visual perception in the primate brain
by Thirza Dado & Paolo Papale & Antonio Lozano & Lynn Le & Feng Wang & Marcel van Gerven & Pieter Roelfsema & Yağmur Güçlütürk & Umut Güçlü - 1-28 Transferable deep generative modeling of intrinsically disordered protein conformations
by Giacomo Janson & Michael Feig - 1-29 Surprise-minimization as a solution to the structural credit assignment problem
by Franz Wurm & Benjamin Ernst & Marco Steinhauser - 1-29 How well do models of visual cortex generalize to out of distribution samples?
by Yifei Ren & Pouya Bashivan - 1-30 Modeling oxygen transport in the brain: An efficient coarse-grid approach to capture perivascular gradients in the parenchyma
by David Pastor-Alonso & Maxime Berg & Franck Boyer & Natalie Fomin-Thunemann & Michel Quintard & Yohan Davit & Sylvie Lorthois - 1-30 Modeling spatial evolution of multi-drug resistance under drug environmental gradients
by Tomas Ferreira Amaro Freire & Zhijian Hu & Kevin B Wood & Erida Gjini - 1-30 Dissecting Bayes: Using influence measures to test normative use of probability density information derived from a sample
by Keiji Ota & Laurence T Maloney - 1-31 Temporal dynamics of short-term neural adaptation across human visual cortex
by Amber Marijn Brands & Sasha Devore & Orrin Devinsky & Werner Doyle & Adeen Flinker & Daniel Friedman & Patricia Dugan & Jonathan Winawer & Iris Isabelle Anna Groen - 1-32 Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization
by Benjamin Antin & Masato Sadahiro & Marta Gajowa & Marcus A Triplett & Hillel Adesnik & Liam Paninski - 1-33 Topological state-space estimation of functional human brain networks
by Moo K Chung & Shih-Gu Huang & Ian C Carroll & Vince D Calhoun & H Hill Goldsmith - 1-33 Artificial neural networks for model identification and parameter estimation in computational cognitive models
by Milena Rmus & Ti-Fen Pan & Liyu Xia & Anne G E Collins - 1-34 The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance
by Charles Mullon & Jorge Peña & Laurent Lehmann - 1-34 Foraging in a non-foraging task: Fitness maximization explains human risk preference dynamics under changing environment
by Yasuhiro Mochizuki & Norihiro Harasawa & Mayank Aggarwal & Chong Chen & Haruaki Fukuda - 1-35 Estimating receptive fields of simple and complex cells in early visual cortex: A convolutional neural network model with parameterized rectification
by Philippe Nguyen & Jinani Sooriyaarachchi & Qianyu Huang & Curtis L Baker Jr. - 1-37 Differential disruptions in population coding along the dorsal-ventral axis of CA1 in the APP/PS1 mouse model of Aβ pathology
by Udaysankar Chockanathan & Krishnan Padmanabhan
April 2024, Volume 20, Issue 4
- 1-8 Ten simple rules for leading a successful undergraduate-intensive research lab
by KJE Hickman & Geoffrey Zahn - 1-14 Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error
by Robert Challen & Anastasia Chatzilena & George Qian & Glenda Oben & Rachel Kwiatkowska & Catherine Hyams & Adam Finn & Krasimira Tsaneva-Atanasova & Leon Danon - 1-16 Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations
by Jong Hyuk Byun & Hye Seon Jeon & Hwi-yeol Yun & Jae Kyoung Kim - 1-19 Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation
by Tianhe Wang & Guy Avraham & Jonathan S Tsay & Sabrina J Abram & Richard B Ivry - 1-19 Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models
by Judith A Bouman & Anthony Hauser & Simon L Grimm & Martin Wohlfender & Samir Bhatt & Elizaveta Semenova & Andrew Gelman & Christian L Althaus & Julien Riou - 1-20 Optimizing strategies for slowing the spread of invasive species
by Adam Lampert - 1-20 Encoding surprise by retinal ganglion cells
by Danica Despotović & Corentin Joffrois & Olivier Marre & Matthew Chalk - 1-21 Non-invasive assessment of stroke volume and cardiovascular parameters based on peripheral pressure waveform
by Kamil Wołos & Leszek Pstras & Malgorzata Debowska & Wojciech Dabrowski & Dorota Siwicka-Gieroba & Jan Poleszczuk - 1-22 DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction
by Hui Liu & Feng Wang & Jian Yu & Yong Pan & Chaoju Gong & Liang Zhang & Lin Zhang - 1-24 HGCLAMIR: Hypergraph contrastive learning with attention mechanism and integrated multi-view representation for predicting miRNA-disease associations
by Dong Ouyang & Yong Liang & Jinfeng Wang & Le Li & Ning Ai & Junning Feng & Shanghui Lu & Shuilin Liao & Xiaoying Liu & Shengli Xie - 1-25 Modeling single cell trajectory using forward-backward stochastic differential equations
by Kevin Zhang & Junhao Zhu & Dehan Kong & Zhaolei Zhang - 1-25 Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains
by Christian Donner & Julian Bartram & Philipp Hornauer & Taehoon Kim & Damian Roqueiro & Andreas Hierlemann & Guillaume Obozinski & Manuel Schröter - 1-25 Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity
by Irena Balzekas & Joshua Trzasko & Grace Yu & Thomas J Richner & Filip Mivalt & Vladimir Sladky & Nicholas M Gregg & Jamie Van Gompel & Kai Miller & Paul E Croarkin & Vaclav Kremen & Gregory A Worrell - 1-26 Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error
by H Robert Frost - 1-26 Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model
by Rui Meng & Kristofer E Bouchard - 1-27 Learning spatio-temporal patterns with Neural Cellular Automata
by Alex D Richardson & Tibor Antal & Richard A Blythe & Linus J Schumacher - 1-27 Dopamine encoding of novelty facilitates efficient uncertainty-driven exploration
by Yuhao Wang & Armin Lak & Sanjay G Manohar & Rafal Bogacz - 1-28 Partial label learning for automated classification of single-cell transcriptomic profiles
by Malek Senoussi & Thierry Artieres & Paul Villoutreix - 1-28 Wagers for work: Decomposing the costs of cognitive effort
by Sarah L Master & Clayton E Curtis & Peter Dayan - 1-29 StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling
by Luca Giudice & Ahmed Mohamed & Tarja Malm - 1-30 MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface
by Adam Husar & Mariam Ordyan & Guadalupe C Garcia & Joel G Yancey & Ali S Saglam & James R Faeder & Thomas M Bartol & Mary B Kennedy & Terrence J Sejnowski - 1-31 Mathematical analysis of left ventricular elastance with respect to afterload change during ejection phase
by Shiro Kato & Yukiko Himeno & Akira Amano - 1-31 Predictive coding networks for temporal prediction
by Beren Millidge & Mufeng Tang & Mahyar Osanlouy & Nicol S Harper & Rafal Bogacz - 1-31 Informing policy via dynamic models: Cholera in Haiti
by Jesse Wheeler & AnnaElaine Rosengart & Zhuoxun Jiang & Kevin Tan & Noah Treutle & Edward L Ionides - 1-32 What does the mean mean? A simple test for neuroscience
by Alejandro Tlaie & Katharine Shapcott & Thijs L van der Plas & James Rowland & Robert Lees & Joshua Keeling & Adam Packer & Paul Tiesinga & Marieke L Schölvinck & Martha N Havenith - 1-32 Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates
by Adrian Lison & Sam Abbott & Jana Huisman & Tanja Stadler - 1-32 Human decision making balances reward maximization and policy compression
by Lucy Lai & Samuel J Gershman
March 2024, Volume 20, Issue 3
- 1-7 Ten simple rules to leverage large language models for getting grants
by Elizabeth Seckel & Brandi Y Stephens & Fatima Rodriguez - 1-10 Raising awareness of uncertain choices in empirical data analysis: A teaching concept toward replicable research practices
by Maximilian M Mandl & Sabine Hoffmann & Sebastian Bieringer & Anna E Jacob & Marie Kraft & Simon Lemster & Anne-Laure Boulesteix - 1-12 Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating
by Jakub Svoboda & Soham Joshi & Josef Tkadlec & Krishnendu Chatterjee - 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