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October 2024, Volume 20, Issue 10
- 1-32 Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson’s disease
by Adam M Roth & John H Buggeln & Joanna E Hoh & Jonathan M Wood & Seth R Sullivan & Truc T Ngo & Jan A Calalo & Rakshith Lokesh & Susanne M Morton & Stephen Grill & John J Jeka & Michael J Carter & Joshua G A Cashaback - 1-34 Learning probability distributions of sensory inputs with Monte Carlo predictive coding
by Gaspard Oliviers & Rafal Bogacz & Alexander Meulemans - 1-38 Bayesian polynomial neural networks and polynomial neural ordinary differential equations
by Colby Fronk & Jaewoong Yun & Prashant Singh & Linda Petzold - 1-39 Mcadet: A feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection
by Saishi Cui & Sina Nassiri & Issa Zakeri - 1-45 A flexible generative algorithm for growing in silico placentas
by Diana C de Oliveira & Hani Cheikh Sleiman & Kelly Payette & Jana Hutter & Lisa Story & Joseph V Hajnal & Daniel C Alexander & Rebecca J Shipley & Paddy J Slator
September 2024, Volume 20, Issue 9
- 1-9 Ten simple rules for successfully carrying out funded research projects
by Diego A Forero & Walter H Curioso & Wei Wang - 1-11 Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting
by Anis Ur Rahman & Gleb Tikhonov & Jari Oksanen & Tuomas Rossi & Otso Ovaskainen - 1-12 Ten quick tips for ensuring machine learning model validity
by Wilson Wen Bin Goh & Mohammad Neamul Kabir & Sehwan Yoo & Limsoon Wong - 1-17 Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies
by Adrian J Green & Lisa Truong & Preethi Thunga & Connor Leong & Melody Hancock & Robyn L Tanguay & David M Reif - 1-17 Bayesian clustering with uncertain data
by Kath Nicholls & Paul D W Kirk & Chris Wallace - 1-18 Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases
by Joseph Shingleton & David Mustard & Steven Dyke & Hannah Williams & Emma Bennett & Thomas Finnie - 1-19 Calibrating dimension reduction hyperparameters in the presence of noise
by Justin Lin & Julia Fukuyama - 1-20 Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency
by Eslam Abousamra & Marlin Figgins & Trevor Bedford - 1-20 Construct prognostic models of multiple myeloma with pathway information incorporated
by Shuo Wang & ShanJin Wang & Wei Pan & YuYang Yi & Junyan Lu - 1-21 A hierarchy of metabolite exchanges in metabolic models of microbial species and communities
by Ylva Katarina Wedmark & Jon Olav Vik & Ove Øyås - 1-22 HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures
by Olav N L Aga & Morten Brun & Kazeem A Dauda & Ramon Diaz-Uriarte & Konstantinos Giannakis & Iain G Johnston - 1-23 Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter
by Jolanda Malamud & Sinan Guloksuz & Ruud van Winkel & Philippe Delespaul & Marc A F De Hert & Catherine Derom & Evert Thiery & Nele Jacobs & Bart P F Rutten & Quentin J M Huys - 1-23 Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data
by Michiel Stock & Wim Van Criekinge & Dimitri Boeckaerts & Steff Taelman & Maxime Van Haeverbeke & Pieter Dewulf & Bernard De Baets - 1-23 HELP: A computational framework for labelling and predicting human common and context-specific essential genes
by Ilaria Granata & Lucia Maddalena & Mario Manzo & Mario Rosario Guarracino & Maurizio Giordano - 1-23 The primacy model and the structure of olfactory space
by Hamza Giaffar & Sergey Shuvaev & Dmitry Rinberg & Alexei A Koulakov - 1-24 Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model
by Yanpeng Yang & Yanyi Zheng & Quan Zou & Jian Li & Hailin Feng - 1-24 SEMbap: Bow-free covariance search and data de-correlation
by Mario Grassi & Barbara Tarantino - 1-24 Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments
by Janice Yang & Neil J Daily & Taylor K Pullinger & Tetsuro Wakatsuki & Eric A Sobie - 1-25 Impact of phylogeny on the inference of functional sectors from protein sequence data
by Nicola Dietler & Alia Abbara & Subham Choudhury & Anne-Florence Bitbol - 1-25 Learning to integrate parts for whole through correlated neural variability
by Zhichao Zhu & Yang Qi & Wenlian Lu & Jianfeng Feng - 1-28 GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments
by Cecile Le Sueur & Magnus Rattray & Mikhail Savitski - 1-29 A Physics-Informed Neural Network approach for compartmental epidemiological models
by Caterina Millevoi & Damiano Pasetto & Massimiliano Ferronato - 1-31 Finding the rhythm: Humans exploit nonlinear intrinsic dynamics of compliant systems in periodic interaction tasks
by Annika Schmidt & Marion Forano & Arne Sachtler & Davide Calzolari & Bernhard M Weber & David W Franklin & Alin Albu-Schäffer - 1-31 Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing
by Breanne Sparta & Timothy Hamilton & Gunalan Natesan & Samuel D Aragones & Eric J Deeds - 1-32 Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803
by Tobias Pfennig & Elena Kullmann & Tomáš Zavřel & Andreas Nakielski & Oliver Ebenhöh & Jan Červený & Gábor Bernát & Anna Barbara Matuszyńska - 1-43 The role of training variability for model-based and model-free learning of an arbitrary visuomotor mapping
by Carlos A Velázquez-Vargas & Nathaniel D Daw & Jordan A Taylor
August 2024, Volume 20, Issue 8
- 1-11 Ten simple rules for successfully managing EU research grants
by David G Pina - 1-16 Rhythmidia: A modern tool for circadian period analysis of filamentous fungi
by Alex T Keeley & Jeffrey M Lotthammer & Jacqueline F Pelham - 1-21 Bird song comparison using deep learning trained from avian perceptual judgments
by Lies Zandberg & Veronica Morfi & Julia M George & David F Clayton & Dan Stowell & Robert F Lachlan - 1-21 Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands
by Catherine M Byrne & Ana Citlali Márquez & Bing Cai & Daniel Coombs & Soren Gantt - 1-21 Upper bounds for integrated information
by Alireza Zaeemzadeh & Giulio Tononi - 1-22 Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention
by Keyvan Mahjoory & Andreas Bahmer & Molly J Henry - 1-22 Diffusion model predicts the geometry of actin cytoskeleton from cell morphology
by Honghan Li & Shiyou Liu & Shinji Deguchi & Daiki Matsunaga - 1-22 The rules of multiplayer cooperation in networks of communities
by Diogo L Pires & Mark Broom - 1-22 scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization
by Yuqing Qian & Quan Zou & Mengyuan Zhao & Yi Liu & Fei Guo & Yijie Ding - 1-23 iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites
by Lin Yuan & Ling Zhao & Jinling Lai & Yufeng Jiang & Qinhu Zhang & Zhen Shen & Chun-Hou Zheng & De-Shuang Huang - 1-23 Attentional selection and communication through coherence: Scope and limitations
by Priscilla E Greenwood & Lawrence M Ward - 1-23 COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms
by Teemu J Rintala & Vittorio Fortino - 1-25 Influence of surprise on reinforcement learning in younger and older adults
by Christoph Koch & Ondrej Zika & Rasmus Bruckner & Nicolas W Schuck - 1-25 Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions
by Efrat Cohen-Davidi & Isana Veksler-Lublinsky - 1-25 Reliable estimation of tree branch lengths using deep neural networks
by Anton Suvorov & Daniel R Schrider - 1-26 Understanding patient-derived tumor organoid growth through an integrated imaging and mathematical modeling framework
by Einar Bjarki Gunnarsson & Seungil Kim & Brandon Choi & J Karl Schmid & Karn Kaura & Heinz-Josef Lenz & Shannon M Mumenthaler & Jasmine Foo - 1-28 scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data
by Fengdi Zhao & Xin Ma & Bing Yao & Qing Lu & Li Chen - 1-31 Signatures of hierarchical temporal processing in the mouse visual system
by Lucas Rudelt & Daniel González Marx & F Paul Spitzner & Benjamin Cramer & Johannes Zierenberg & Viola Priesemann - 1-32 A general model unifying the adaptive, transient and sustained properties of ON and OFF auditory neural responses
by Ulysse Rançon & Timothée Masquelier & Benoit R Cottereau - 1-32 Interacting particle models on the impact of spatially heterogeneous human behavioral factors on dynamics of infectious diseases
by Yunfeng Xiong & Chuntian Wang & Yuan Zhang
July 2024, Volume 20, Issue 7
- 1-12 BCI Toolbox: An open-source python package for the Bayesian causal inference model
by Haocheng Zhu & Ulrik Beierholm & Ladan Shams - 1-12 Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
by Patrick Bryant & Frank Noé - 1-14 Nine quick tips for open meta-analyses
by David Moreau & Kristina Wiebels - 1-15 Fixation times on directed graphs
by David A Brewster & Martin A Nowak & Josef Tkadlec - 1-17 Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong
by Yiu-Chung Lau & Songwei Shan & Dong Wang & Dongxuan Chen & Zhanwei Du & Eric H Y Lau & Daihai He & Linwei Tian & Peng Wu & Benjamin J Cowling & Sheikh Taslim Ali - 1-17 Detection of disease-specific signatures in B cell repertoires of lymphomas using machine learning
by Paul Schmidt-Barbo & Gabriel Kalweit & Mehdi Naouar & Lisa Paschold & Edith Willscher & Christoph Schultheiß & Bruno Märkl & Stefan Dirnhofer & Alexandar Tzankov & Mascha Binder & Maria Kalweit - 1-17 Competitive advantages of T-even phage lysis inhibition in response to secondary infection
by Ulrik Hvid & Namiko Mitarai - 1-19 When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty
by Nathan J Doyle & Fergus Cumming & Robin N Thompson & Michael J Tildesley - 1-20 Nonlinear fusion is optimal for a wide class of multisensory tasks
by Marcus Ghosh & Gabriel Béna & Volker Bormuth & Dan F M Goodman - 1-21 Identifying cell states in single-cell RNA-seq data at statistically maximal resolution
by Pascal Grobecker & Thomas Sakoparnig & Erik van Nimwegen - 1-21 Probabilistic neural transfer function estimation with Bayesian system identification
by Nan Wu & Isabel Valera & Fabian Sinz & Alexander Ecker & Thomas Euler & Yongrong Qiu - 1-22 Generating information-dense promoter sequences with optimal string packing
by Virgile Andreani & Eric J South & Mary J Dunlop - 1-23 Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations
by Yingjun Ma & Yuanyuan Ma - 1-23 Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers
by David R Penas & Meysam Hashemi & Viktor K Jirsa & Julio R Banga - 1-23 Identifying topologically associating domains using differential kernels
by Luka Maisuradze & Megan C King & Ivan V Surovtsev & Simon G J Mochrie & Mark D Shattuck & Corey S O’Hern - 1-23 Quantifying massively parallel microbial growth with spatially mediated interactions
by Florian Borse & Dovydas Kičiatovas & Teemu Kuosmanen & Mabel Vidal & Guillermo Cabrera-Vives & Johannes Cairns & Jonas Warringer & Ville Mustonen - 1-24 Estimating error rates for single molecule protein sequencing experiments
by Matthew Beauregard Smith & Kent VanderVelden & Thomas Blom & Heather D Stout & James H Mapes & Tucker M Folsom & Christopher Martin & Angela M Bardo & Edward M Marcotte - 1-24 Detecting and quantifying heterogeneity in susceptibility using contact tracing data
by Beth M Tuschhoff & David A Kennedy - 1-25 scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics
by Gustavo Magaña-López & Laurence Calzone & Andrei Zinovyev & Loïc Paulevé - 1-26 Modeling soybean growth: A mixed model approach
by Maud Delattre & Yusuke Toda & Jessica Tressou & Hiroyoshi Iwata - 1-27 A low-dimensional approximation of optimal confidence
by Pierre Le Denmat & Tom Verguts & Kobe Desender - 1-27 Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission
by Elias Rosenblatt & Jonathan D Cook & Graziella V DiRenzo & Evan H Campbell Grant & Fernando Arce & Kim M Pepin & F Javiera Rudolph & Michael C Runge & Susan Shriner & Daniel P Walsh & Brittany A Mosher - 1-28 FedGMMAT: Federated generalized linear mixed model association tests
by Wentao Li & Han Chen & Xiaoqian Jiang & Arif Harmanci - 1-32 Jointly efficient encoding and decoding in neural populations
by Simone Blanco Malerba & Aurora Micheli & Michael Woodford & Rava Azeredo da Silveira - 1-36 NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies
by Thomas Couppey & Louis Regnacq & Roland Giraud & Olivier Romain & Yannick Bornat & Florian Kolbl - 1-37 An integrative approach to protein sequence design through multiobjective optimization
by Lu Hong & Tanja Kortemme - 1-37 Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis
by Harry Saxton & Xu Xu & Torsten Schenkel & Richard H Clayton & Ian Halliday
June 2024, Volume 20, Issue 6
- 1-9 Ten simple rules for implementing electronic lab notebooks (ELNs)
by Justine Vandendorpe & Beatrix Adam & Jeanne Wilbrandt & Birte Lindstädt & Konrad U Förstner - 1-9 Ten simple rules for computational biologists collaborating with wet lab researchers
by Mark D Robinson & Peiying Cai & Martin Emons & Reto Gerber & Pierre-Luc Germain & Samuel Gunz & Siyuan Luo & Giulia Moro & Emanuel Sonder & Anthony Sonrel & Jiayi Wang & David Wissel & Izaskun Mallona - 1-10 Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club
by Roberto Efraín Díaz & Stephanie A Wankowicz - 1-16 Knotted artifacts in predicted 3D RNA structures
by Bartosz A Gren & Maciej Antczak & Tomasz Zok & Joanna I Sulkowska & Marta Szachniuk - 1-16 ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning
by Youcheng Li & Leann Lac & Qian Liu & Pingzhao Hu - 1-16 Older adults select different but not simpler strategies than younger adults in risky choice
by Florian Bolenz & Thorsten Pachur - 1-17 Missing data in amortized simulation-based neural posterior estimation
by Zijian Wang & Jan Hasenauer & Yannik Schälte - 1-19 mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics
by Kris Sankaran & Pratheepa Jeganathan - 1-20 Infection patterns in simple and complex contagion processes on networks
by Diego Andrés Contreras & Giulia Cencetti & Alain Barrat - 1-20 Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways
by Leopold Zehetner & Diana Széliová & Barbara Kraus & Juan A Hernandez Bort & Jürgen Zanghellini - 1-21 Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data
by Tina Yao & Endrit Pajaziti & Michael Quail & Silvia Schievano & Jennifer Steeden & Vivek Muthurangu - 1-21 GEM-based computational modeling for exploring metabolic interactions in a microbial community
by Soraya Mirzaei & Mojtaba Tefagh - 1-22 Beyond homogeneity: Assessing the validity of the Michaelis–Menten rate law in spatially heterogeneous environments
by Seolah Shin & Seok Joo Chae & Seunggyu Lee & Jae Kyoung Kim - 1-22 Zero-shot denoising of microscopy images recorded at high-resolution limits
by Sebastian Salwig & Jakob Drefs & Jörg Lücke - 1-23 An algorithm to build synthetic temporal contact networks based on close-proximity interactions data
by Audrey Duval & Quentin J Leclerc & Didier Guillemot & Laura Temime & Lulla Opatowski - 1-23 Machine learning prediction of malaria vaccine efficacy based on antibody profiles
by Jacqueline Wistuba-Hamprecht & Bernhard Reuter & Rolf Fendel & Stephen L Hoffman & Joseph J Campo & Philip L Felgner & Peter G Kremsner & Benjamin Mordmüller & Nico Pfeifer - 1-24 Strong association between genomic 3D structure and CRISPR cleavage efficiency
by Shaked Bergman & Tamir Tuller - 1-26 Threshold-awareness in adaptive cancer therapy
by MingYi Wang & Jacob G Scott & Alexander Vladimirsky - 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