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December 2024, Volume 20, Issue 12
- 1-22 Mapping genes for human face shape: Exploration of univariate phenotyping strategies
by Meng Yuan & Seppe Goovaerts & Michiel Vanneste & Harold Matthews & Hanne Hoskens & Stephen Richmond & Ophir D Klein & Richard A Spritz & Benedikt Hallgrimsson & Susan Walsh & Mark D Shriver & John R Shaffer & Seth M Weinberg & Hilde Peeters & Peter Claes - 1-22 Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform
by Xavier Escriba-Montagut & Yannick Marcon & Augusto Anguita-Ruiz & Demetris Avraam & Jose Urquiza & Andrei S Morgan & Rebecca C Wilson & Paul Burton & Juan R Gonzalez - 1-22 The Burr distribution as a model for the delay between key events in an individual’s infection history
by Nyall Jamieson & Christiana Charalambous & David M Schultz & Ian Hall - 1-22 Estimating the distribution of parameters in differential equations with repeated cross-sectional data
by Hyeontae Jo & Sung Woong Cho & Hyung Ju Hwang - 1-24 A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
by Henri Schmidt & Benjamin J Raphael - 1-24 A multi-scale study of thalamic state-dependent responsiveness
by Jorin Overwiening & Federico Tesler & Domenico Guarino & Alain Destexhe - 1-25 Estimating the time-varying effective reproduction number via Cycle Threshold-based Transformer
by Xin-Yu Zhang & Lan-Lan Yu & Wei-Yi Wang & Gui-Quan Sun & Jian-Cheng Lv & Tao Zhou & Quan-Hui Liu - 1-26 Evolution of cooperation in multichannel games on multiplex networks
by Amit Basak & Supratim Sengupta - 1-27 A framework for modelling desert locust population dynamics and large-scale dispersal
by Renata Retkute & William Thurston & Keith Cressman & Christopher A Gilligan - 1-29 Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling
by Jiyoung Kang & Hae-Jeong Park - 1-31 Marked point process variational autoencoder with applications to unsorted spiking activities
by Ryohei Shibue & Tomoharu Iwata - 1-31 Mathematical basis and toolchain for hierarchical optimization of biochemical networks
by Nisha Ann Viswan & Alexandre Tribut & Manvel Gasparyan & Ovidiu Radulescu & Upinder S Bhalla - 1-32 Neuro-cognitive multilevel causal modeling: A framework that bridges the explanatory gap between neuronal activity and cognition
by Moritz Grosse-Wentrup & Akshey Kumar & Anja Meunier & Manuel Zimmer - 1-37 Parallel development of object recognition in newborn chicks and deep neural networks
by Lalit Pandey & Donsuk Lee & Samantha M W Wood & Justin N Wood - 1-39 Uncovering population contributions to the extracellular potential in the mouse visual system using Laminar Population Analysis
by Atle E Rimehaug & Anders M Dale & Anton Arkhipov & Gaute T Einevoll - 1-43 Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework
by Máté Mohácsi & Márk Patrik Török & Sára Sáray & Luca Tar & Gábor Farkas & Szabolcs Káli - 1-44 Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction
by Akash Bahai & Chee Keong Kwoh & Yuguang Mu & Yinghui Li - 1-46 Extracting interpretable signatures of whole-brain dynamics through systematic comparison
by Annie G Bryant & Kevin Aquino & Linden Parkes & Alex Fornito & Ben D Fulcher
November 2024, Volume 20, Issue 11
- 1-10 Eleven quick tips for properly handling tabular data
by Marla I Hertz & Ashley S McNeill - 1-17 MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm
by Chao Wang & Quan Zou - 1-17 Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function
by Yuanchen Zhao & Otto X Cordero & Mikhail Tikhonov - 1-17 Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models
by Wyatt G Madden & Wei Jin & Benjamin Lopman & Andreas Zufle & Benjamin Dalziel & C Jessica E. Metcalf & Bryan T Grenfell & Max S Y Lau - 1-18 The evolutionary cost of homophily: Social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens
by Shuanger Li & Davorka Gulisija & Oana Carja - 1-19 Socially driven negative feedback regulates activity and energy use in ant colonies
by Maurizio Porfiri & Nicole Abaid & Simon Garnier - 1-21 A new look at TFPI inhibition of factor X activation
by Fabian Santiago & Amandeep Kaur & Shannon Bride & Dougald Monroe & Karin Leiderman & Suzanne Sindi - 1-21 Approximate planning in spatial search
by Marta Kryven & Suhyoun Yu & Max Kleiman-Weiner & Tomer Ullman & Joshua Tenenbaum - 1-21 scGRN-Entropy: Inferring cell differentiation trajectories using single-cell data and gene regulation network-based transfer entropy
by Rui Sun & Wenjie Cao & ShengXuan Li & Jian Jiang & Yazhou Shi & Bengong Zhang - 1-23 A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors
by Alireza Rezvani-Sharif & Hadi Lioe & Steven K Dower & Matthias Pelzing & Con Panousis & Dalton J E Harvie & Ineke L Muir - 1-23 Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
by Robert van Dijk & John Arevalo & Mehrtash Babadi & Anne E Carpenter & Shantanu Singh - 1-23 GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies
by Lin Lin & Rachel L Spreng & Kelly E Seaton & S Moses Dennison & Lindsay C Dahora & Daniel J Schuster & Sheetal Sawant & Peter B Gilbert & Youyi Fong & Neville Kisalu & Andrew J Pollard & Georgia D Tomaras & Jia Li - 1-23 Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing
by Sven B Gould & Jonas Magiera & Carolina García García & Parth K Raval - 1-24 Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics
by Alexandria M Jensen & Peter DeWitt & Brianne M Bettcher & Julia Wrobel & Katerina Kechris & Debashis Ghosh - 1-25 Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion
by Aaron R Allred & Caroline R Austin & Lanna Klausing & Nicholas Boggess & Torin K Clark - 1-25 Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits
by Vitaly V Ganusov & Afsal Kolloli & Selvakumar Subbian - 1-27 Co-contraction embodies uncertainty: An optimal feedforward strategy for robust motor control
by Bastien Berret & Dorian Verdel & Etienne Burdet & Frédéric Jean - 1-30 An inductive bias for slowly changing features in human reinforcement learning
by Noa L Hedrich & Eric Schulz & Sam Hall-McMaster & Nicolas W Schuck - 1-30 A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates
by Baike She & Rebecca Lee Smith & Ian Pytlarz & Shreyas Sundaram & Philip E Paré - 1-32 Teaching deep networks to see shape: Lessons from a simplified visual world
by Christian Jarvers & Heiko Neumann - 1-33 Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations
by Aylin Bircan & Nurdan Kuru & Onur Dereli & Berkay Selçuk & Ogün Adebali
October 2024, Volume 20, Issue 10
- 1-10 Gene signatures for cancer research: A 25-year retrospective and future avenues
by Wei Liu & Huaqin He & Davide Chicco - 1-17 EEG microstate transition cost correlates with task demands
by Giacomo Barzon & Ettore Ambrosini & Antonino Vallesi & Samir Suweis - 1-17 Integrating information from historical data into mechanistic models for influenza forecasting
by Alessio Andronico & Juliette Paireau & Simon Cauchemez - 1-19 Enhancing insights in sexually transmitted infection mapping: Syphilis in Forsyth County, North Carolina, a case study
by Lani Fox & William C Miller & Dionne Gesink & Irene Doherty & Marc Serre - 1-20 IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation
by Haolin Jiang & Yulian Xu & Yunguang Tong & Dong Zhang & Ruhong Zhou - 1-20 Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals
by Michele Gentili & Kimberly Glass & Enrico Maiorino & Brian D Hobbs & Zhonghui Xu & Peter J Castaldi & Michael H Cho & Craig P Hersh & Dandi Qiao & Jarrett D Morrow & Vincent J Carey & John Platig & Edwin K Silverman - 1-21 Best practices for estimating and reporting epidemiological delay distributions of infectious diseases
by Kelly Charniga & Sang Woo Park & Andrei R Akhmetzhanov & Anne Cori & Jonathan Dushoff & Sebastian Funk & Katelyn M Gostic & Natalie M Linton & Adrian Lison & Christopher E Overton & Juliet R C Pulliam & Thomas Ward & Simon Cauchemez & Sam Abbott - 1-21 PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites
by Yun Zuo & Xingze Fang & Jiayong Wan & Wenying He & Xiangrong Liu & Xiangxiang Zeng & Zhaohong Deng - 1-24 Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data
by Safiye Celik & Jan-Christian Hütter & Sandra Melo Carlos & Nathan H Lazar & Rahul Mohan & Conor Tillinghast & Tommaso Biancalani & Marta M Fay & Berton A Earnshaw & Imran S Haque - 1-24 Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer
by Lianghong Chen & Zi Huai Huang & Yan Sun & Mike Domaratzki & Qian Liu & Pingzhao Hu - 1-25 A Computational Framework for Understanding the Impact of Prior Experiences on Pain Perception and Neuropathic Pain
by Malin Ramne & Jon Sensinger - 1-25 Regularizing hyperparameters of interacting neural signals in the mouse cortex reflect states of arousal
by Dmitry R Lyamzin & Andrea Alamia & Mohammad Abdolrahmani & Ryo Aoki & Andrea Benucci - 1-27 Computational joint action: Dynamical models to understand the development of joint coordination
by Cecilia De Vicariis & Vinil T Chackochan & Laura Bandini & Eleonora Ravaschio & Vittorio Sanguineti - 1-27 Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history
by Gabriel A A Silva & Avril M Harder & Kenneth B Kirksey & Samarth Mathur & Janna R Willoughby - 1-28 The optimal spatially-dependent control measures to effectively and economically eliminate emerging infectious diseases
by Fan Xia & Yanni Xiao & Junling Ma - 1-29 Compression-based inference of network motif sets
by Alexis Bénichou & Jean-Baptiste Masson & Christian L Vestergaard - 1-29 Why aphid virus retention needs more attention: Modelling aphid behaviour and virus manipulation in non-persistent plant virus transmission
by Elin K Falla & Nik J Cunniffe - 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