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Content
April 2023, Volume 19, Issue 4
- 1-16 Bridging the gap between mechanistic biological models and machine learning surrogates
by Ioana M Gherman & Zahraa S Abdallah & Wei Pang & Thomas E Gorochowski & Claire S Grierson & Lucia Marucci - 1-18 Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
by Krystian Zieliński & Sebastian Pukszta & Małgorzata Mickiewicz & Marta Kotlarz & Piotr Wygocki & Marcin Zieleń & Dominika Drzewiecka & Damian Drzyzga & Anna Kloska & Joanna Jakóbkiewicz-Banecka - 1-20 Fidelity of hyperbolic space for Bayesian phylogenetic inference
by Matthew Macaulay & Aaron Darling & Mathieu Fourment - 1-20 Shape-driven deep neural networks for fast acquisition of aortic 3D pressure and velocity flow fields
by Endrit Pajaziti & Javier Montalt-Tordera & Claudio Capelli & Raphaël Sivera & Emilie Sauvage & Michael Quail & Silvia Schievano & Vivek Muthurangu - 1-20 Gate-based quantum computing for protein design
by Mohammad Hassan Khatami & Udson C Mendes & Nathan Wiebe & Philip M Kim - 1-21 Fusing an agent-based model of mosquito population dynamics with a statistical reconstruction of spatio-temporal abundance patterns
by Sean M Cavany & Guido España & Alun L Lloyd & Gonzalo M Vazquez-Prokopec & Helvio Astete & Lance A Waller & Uriel Kitron & Thomas W Scott & Amy C Morrison & Robert C Reiner Jr & T Alex Perkins - 1-21 Multi-view clustering by CPS-merge analysis with application to multimodal single-cell data
by Lixiang Zhang & Lin Lin & Jia Li - 1-23 High rifampicin peak plasma concentrations accelerate the slow phase of bacterial decline in tuberculosis patients: Evidence for heteroresistance
by Antal Martinecz & Martin J Boeree & Andreas H Diacon & Rodney Dawson & Colin Hemez & Rob E Aarnoutse & Pia Abel zur Wiesch - 1-24 Minor variations in multicellular life cycles have major effects on adaptation
by Hanna Isaksson & Åke Brännström & Eric Libby - 1-27 Recurrent predictive coding models for associative memory employing covariance learning
by Mufeng Tang & Tommaso Salvatori & Beren Millidge & Yuhang Song & Thomas Lukasiewicz & Rafal Bogacz - 1-28 Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference
by Aidan B Estelle & August George & Elisar J Barbar & Daniel M Zuckerman - 1-29 Efficient coding of natural scenes improves neural system identification
by Yongrong Qiu & David A Klindt & Klaudia P Szatko & Dominic Gonschorek & Larissa Hoefling & Timm Schubert & Laura Busse & Matthias Bethge & Thomas Euler - 1-31 Model certainty in cellular network-driven processes with missing data
by Michael W Irvin & Arvind Ramanathan & Carlos F Lopez
March 2023, Volume 19, Issue 3
- 1-7 Ten simple rules for serving as an editor
by Cameron Mura & Philip E Bourne - 1-10 Ten (not so) simple rules for clinical trial data-sharing
by Claude Pellen & Anne Le Louarn & Gilliosa Spurrier-Bernard & Evelyne Decullier & Jean-Marie Chrétien & Eric Rosenthal & Gérard Le Goff & David Moher & John P A Ioannidis & Florian Naudet - 1-12 The effect of non-linear signal in classification problems using gene expression
by Benjamin J Heil & Jake Crawford & Casey S Greene - 1-13 A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya
by Ruth Nanjala & Festus Nyasimi & Daniel Masiga & Caleb Kipkurui Kibet - 1-15 Robust deep learning object recognition models rely on low frequency information in natural images
by Zhe Li & Josue Ortega Caro & Evgenia Rusak & Wieland Brendel & Matthias Bethge & Fabio Anselmi & Ankit B Patel & Andreas S Tolias & Xaq Pitkow - 1-16 Predicting functional effects of ion channel variants using new phenotypic machine learning methods
by Christian Malte Boßelmann & Ulrike B S Hedrich & Holger Lerche & Nico Pfeifer - 1-17 Ten simple rules for socially responsible science
by Alon Zivony & Rasha Kardosh & Liadh Timmins & Niv Reggev - 1-18 Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load
by Paul Manuel Müller & Christian Meisel - 1-18 Hindcasts and forecasts of suicide mortality in US: A modeling study
by Sasikiran Kandula & Mark Olfson & Madelyn S Gould & Katherine M Keyes & Jeffrey Shaman - 1-19 Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates
by Christoffer Norn & Ingemar André - 1-19 Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins
by Carlos A Gandarilla-Pérez & Sergio Pinilla & Anne-Florence Bitbol & Martin Weigt - 1-19 CustOmics: A versatile deep-learning based strategy for multi-omics integration
by Hakim Benkirane & Yoann Pradat & Stefan Michiels & Paul-Henry Cournède - 1-19 MGAE-DC: Predicting the synergistic effects of drug combinations through multi-channel graph autoencoders
by Peng Zhang & Shikui Tu - 1-21 Inferring protein fitness landscapes from laboratory evolution experiments
by Sameer D’Costa & Emily C Hinds & Chase R Freschlin & Hyebin Song & Philip A Romero - 1-21 Macroscopic resting state model predicts theta burst stimulation response: A randomized trial
by Neda Kaboodvand & Behzad Iravani & Martijn P van den Heuvel & Jonas Persson & Robert Boden - 1-22 Inferring feature importance with uncertainties with application to large genotype data
by Pål Vegard Johnsen & Inga Strümke & Mette Langaas & Andrew Thomas DeWan & Signe Riemer-Sørensen - 1-22 Modelling daily weight variation in honey bee hives
by Karina Arias-Calluari & Theotime Colin & Tanya Latty & Mary Myerscough & Eduardo G Altmann - 1-24 Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression
by Christophe Le Priol & Chloé-Agathe Azencott & Xavier Gidrol - 1-24 Validation framework for epidemiological models with application to COVID-19 models
by Kimberly A Dautel & Ephraim Agyingi & Pras Pathmanathan - 1-25 A new method for the joint estimation of instantaneous reproductive number and serial interval during epidemics
by Chenxi Dai & Dongsheng Zhou & Bo Gao & Kaifa Wang - 1-26 A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer
by Delora Baptista & Pedro G Ferreira & Miguel Rocha - 1-27 Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning
by Bercem Dutagaci & Bingbing Duan & Chenxi Qiu & Craig D Kaplan & Michael Feig - 1-28 One model fits all: Combining inference and simulation of gene regulatory networks
by Elias Ventre & Ulysse Herbach & Thibault Espinasse & Gérard Benoit & Olivier Gandrillon - 1-28 BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach
by Mahmood Kalemati & Mojtaba Zamani Emani & Somayyeh Koohi - 1-28 Global nonlinear approach for mapping parameters of neural mass models
by Dominic M Dunstan & Mark P Richardson & Eugenio Abela & Ozgur E Akman & Marc Goodfellow - 1-29 Coding of object location by heterogeneous neural populations with spatially dependent correlations in weakly electric fish
by Myriah Haggard & Maurice J Chacron - 1-31 OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer
by Anni S Halkola & Kaisa Joki & Tuomas Mirtti & Marko M Mäkelä & Tero Aittokallio & Teemu D Laajala - 1-38 Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity
by Máté László Telek & Elisenda Feliu
February 2023, Volume 19, Issue 2
- 1-13 A linear discriminant analysis model of imbalanced associative learning in the mushroom body compartment
by David Lipshutz & Aneesh Kashalikar & Shiva Farashahi & Dmitri B Chklovskii - 1-14 Forecasting upper respiratory tract infection burden using high-dimensional time series data and forecast combinations
by Jue Tao Lim & Kelvin Bryan Tan & John Abisheganaden & Borame L Dickens - 1-17 Neural adaptation and fractional dynamics as a window to underlying neural excitability
by Brian Nils Lundstrom & Thomas J Richner - 1-20 Interpreting T-cell search “strategies” in the light of evolution under constraints
by Inge M N Wortel & Johannes Textor - 1-20 iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures
by Joris J R Louwen & Satria A Kautsar & Sven van der Burg & Marnix H Medema & Justin J J van der Hooft - 1-23 Evolutionary dynamics of hyperbolic language
by Madison S Krieger - 1-23 Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs
by Rion Brattig Correia & Alain Barrat & Luis M Rocha - 1-24 Functional duality in group criticality via ambiguous interactions
by Takayuki Niizato & Hisashi Murakami & Takuya Musha - 1-24 Simulation-based inference for non-parametric statistical comparison of biomolecule dynamics
by Hippolyte Verdier & François Laurent & Alhassan Cassé & Christian L Vestergaard & Christian G Specht & Jean-Baptiste Masson - 1-24 AI reveals insights into link between CD33 and cognitive impairment in Alzheimer’s Disease
by Tamara Raschka & Meemansa Sood & Bruce Schultz & Aybuge Altay & Christian Ebeling & Holger Fröhlich - 1-28 Temporal progression along discrete coding states during decision-making in the mouse gustatory cortex
by Liam Lang & Giancarlo La Camera & Alfredo Fontanini - 1-29 LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics
by Giulio Ruffini & Giada Damiani & Diego Lozano-Soldevilla & Nikolas Deco & Fernando E Rosas & Narsis A Kiani & Adrián Ponce-Alvarez & Morten L Kringelbach & Robin Carhart-Harris & Gustavo Deco - 1-31 Non-destructive classification of unlabeled cells: Combining an automated benchtop magnetic resonance scanner and artificial intelligence
by Philipp Fey & Daniel Ludwig Weber & Jannik Stebani & Philipp Mörchel & Peter Jakob & Jan Hansmann & Karl-Heinz Hiller & Daniel Haddad - 1-31 Unsupervised learning reveals interpretable latent representations for translucency perception
by Chenxi Liao & Masataka Sawayama & Bei Xiao - 1-41 Criticality in probabilistic models of spreading dynamics in brain networks: Epileptic seizures
by S Amin Moosavi & Wilson Truccolo
January 2023, Volume 19, Issue 1
- 1-4 Ten simple rules for defining a computational biology project
by William Stafford Noble - 1-11 Ten simple rules for implementing open and reproducible research practices after attending a training course
by Verena Heise & Constance Holman & Hung Lo & Ekaterini Maria Lyras & Mark Christopher Adkins & Maria Raisa Jessica Aquino & Konstantinos I Bougioukas & Katherine O Bray & Martyna Gajos & Xuanzong Guo & Corinna Hartling & Rodrigo Huerta-Gutierrez & Miroslava Jindrová & Joanne P M Kenney & Adrianna P Kępińska & Laura Kneller & Elena Lopez-Rodriguez & Felix Mühlensiepen & Angela Richards & Gareth Richards & Maximilian Siebert & James A Smith & Natalie Smith & Nicolai Stransky & Sirpa Tarvainen & Daniela Sofia Valdes & Kayleigh L Warrington & Nina-Maria Wilpert & Disa Witkowska & Mirela Zaneva & Jeanette Zanker & Tracey L Weissgerber - 1-19 Surround suppression in mouse auditory cortex underlies auditory edge detection
by Omri David Gilday & Benedikt Praegel & Ido Maor & Tav Cohen & Israel Nelken & Adi Mizrahi - 1-19 Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks
by Polina Lakrisenko & Paul Stapor & Stephan Grein & Łukasz Paszkowski & Dilan Pathirana & Fabian Fröhlich & Glenn Terje Lines & Daniel Weindl & Jan Hasenauer - 1-20 A dual graph neural network for drug–drug interactions prediction based on molecular structure and interactions
by Mei Ma & Xiujuan Lei - 1-20 Interspecific comparison of gene expression profiles using machine learning
by Artem S Kasianov & Anna V Klepikova & Alexey V Mayorov & Gleb S Buzanov & Maria D Logacheva & Aleksey A Penin - 1-23 Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit
by Yibo Zhao & Nikoleta Vavouraki & Ruth C Lovering & Valentina Escott-Price & Kirsten Harvey & Patrick A Lewis & Claudia Manzoni - 1-26 RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks
by Souvik Seal & Qunhua Li & Elle Butler Basner & Laura M Saba & Katerina Kechris - 1-26 Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons
by Yann Roussel & Csaba Verasztó & Dimitri Rodarie & Tanguy Damart & Michael Reimann & Srikanth Ramaswamy & Henry Markram & Daniel Keller - 1-26 Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering
by Theresa Ullmann & Stefanie Peschel & Philipp Finger & Christian L Müller & Anne-Laure Boulesteix - 1-27 Bayesian reconstruction of memories stored in neural networks from their connectivity
by Sebastian Goldt & Florent Krzakala & Lenka Zdeborová & Nicolas Brunel - 1-27 One dimensional approximations of neuronal dynamics reveal computational strategy
by Connor Brennan & Adeeti Aggarwal & Rui Pei & David Sussillo & Alex Proekt - 1-28 Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis
by Caleb M Phillips & Ernesto A B F Lima & Manasa Gadde & Angela M Jarrett & Marissa Nichole Rylander & Thomas E Yankeelov - 1-28 Skilled motor control of an inverted pendulum implies low entropy of states but high entropy of actions
by Nicola Catenacci Volpi & Martin Greaves & Dari Trendafilov & Christoph Salge & Giovanni Pezzulo & Daniel Polani - 1-29 Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates
by Alexander P Browning & Matthew J Simpson - 1-29 Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability
by Ryan J Murphy & Gency Gunasingh & Nikolas K Haass & Matthew J Simpson - 1-30 Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics
by Oshane O Thomas & Hongyu Shen & Ryan L Raaum & William E H Harcourt-Smith & John D Polk & Mark Hasegawa-Johnson - 1-31 Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia
by Edoardo Pinzuti & Patricia Wollstadt & Oliver Tüscher & Michael Wibral - 1-33 Ecological landscapes guide the assembly of optimal microbial communities
by Ashish B George & Kirill S Korolev - 1-34 Environmental uncertainty and the advantage of impulsive choice strategies
by Diana C Burk & Bruno B Averbeck - 1-44 Improving the validity of neuroimaging decoding tests of invariant and configural neural representation
by Fabian A Soto & Sanjay Narasiwodeyar - 1-46 Relating local connectivity and global dynamics in recurrent excitatory-inhibitory networks
by Yuxiu Shao & Srdjan Ostojic
December 2022, Volume 18, Issue 12
- 1-6 Ten simple rules for launching an academic research career
by Jason A Papin & Jessica Keim-Malpass & Sana Syed - 1-10 Ten simple rules for failing successfully in academia
by Stefan Gaillard & Tara van Viegen & Michele Veldsman & Melanie I Stefan & Veronika Cheplygina - 1-10 Ten simple rules for creating a sense of belonging in your research group
by Nidia Ruedas-Gracia & Crystal M Botham & Amber R Moore & Courtney Peña - 1-12 tension: A Python package for FORCE learning
by Lu Bin Liu & Attila Losonczy & Zhenrui Liao - 1-15 Ten quick tips for sequence-based prediction of protein properties using machine learning
by Qingzhen Hou & Katharina Waury & Dea Gogishvili & K Anton Feenstra - 1-15 Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments
by Yulia Fridman & Zihan Wang & Sergei Maslov & Akshit Goyal - 1-16 Recalibrating probabilistic forecasts of epidemics
by Aaron Rumack & Ryan J Tibshirani & Roni Rosenfeld - 1-17 Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden
by Fanny Bergström & Felix Günther & Michael Höhle & Tom Britton - 1-18 Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods
by Marion F S Fischer & James E Crowe & Jens Meiler - 1-18 scDSSC: Deep Sparse Subspace Clustering for scRNA-seq Data
by HaiYun Wang & JianPing Zhao & ChunHou Zheng & YanSen Su - 1-19 Ten simple rules for empowering women in STEM
by Patricia Guevara-Ramírez & Viviana A Ruiz-Pozo & Santiago Cadena-Ullauri & Gabriela Salazar-Navas & Ana Acosta Bedón & J Faustino V-Vázquez & Ana Karina Zambrano - 1-19 Improved visualization of high-dimensional data using the distance-of-distance transformation
by Jinke Liu & Martin Vinck - 1-20 Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data
by Nana Wei & Yating Nie & Lin Liu & Xiaoqi Zheng & Hua-Jun Wu - 1-21 Allosteric regulation in STAT3 interdomains is mediated by a rigid core: SH2 domain regulation by CCD in D170A variant
by Tingting Zhao & Nischal Karki & Brian D Zoltowski & Devin A Matthews - 1-21 Eleven quick tips for data cleaning and feature engineering
by Davide Chicco & Luca Oneto & Erica Tavazzi - 1-22 ToMExO: A probabilistic tree-structured model for cancer progression
by Mohammadreza Mohaghegh Neyshabouri & Jens Lagergren - 1-23 Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images
by Tomonori Ogane & Daisuke Noshiro & Toshio Ando & Atsuko Yamashita & Yuji Sugita & Yasuhiro Matsunaga - 1-23 Model-based prioritization for acquiring protection
by Sarah M Tashjian & Toby Wise & Dean Mobbs - 1-23 Input correlations impede suppression of chaos and learning in balanced firing-rate networks
by Rainer Engelken & Alessandro Ingrosso & Ramin Khajeh & Sven Goedeke & L F Abbott - 1-23 A fast lasso-based method for inferring higher-order interactions
by Kieran Elmes & Astra Heywood & Zhiyi Huang & Alex Gavryushkin - 1-24 Monitoring real-time transmission heterogeneity from incidence data
by Yunjun Zhang & Tom Britton & Xiaohua Zhou - 1-25 Interacting active surfaces: A model for three-dimensional cell aggregates
by Alejandro Torres-Sánchez & Max Kerr Winter & Guillaume Salbreux - 1-26 Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction
by Yi-Heng Zhu & Chengxin Zhang & Dong-Jun Yu & Yang Zhang - 1-28 Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation
by Olivier Mailhot & Vincent Frappier & François Major & Rafael J Najmanovich - 1-28 Comparing T cell receptor repertoires using optimal transport
by Branden J Olson & Stefan A Schattgen & Paul G Thomas & Philip Bradley & Frederick A Matsen IV - 1-31 A phylogenetic approach to inferring the order in which mutations arise during cancer progression
by Yuan Gao & Jeff Gaither & Julia Chifman & Laura Kubatko - 1-33 Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework
by Yansong Wang & Zilong Hou & Yuning Yang & Ka-chun Wong & Xiangtao Li - 1-34 Bayesian inference of multi-point macromolecular architecture mixtures at nanometre resolution
by Peter A Embacher & Tsvetelina E Germanova & Emanuele Roscioli & Andrew D McAinsh & Nigel J Burroughs - 1-36 Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
by Jakub W Wojciechowski & Emirhan Tekoglu & Marlena Gąsior-Głogowska & Virginie Coustou & Natalia Szulc & Monika Szefczyk & Marta Kopaczyńska & Sven J Saupe & Witold Dyrka - 1-37 The effects of base rate neglect on sequential belief updating and real-world beliefs
by Brandon K Ashinoff & Justin Buck & Michael Woodford & Guillermo Horga - 1-39 A method to estimate the cellular composition of the mouse brain from heterogeneous datasets
by Dimitri Rodarie & Csaba Verasztó & Yann Roussel & Michael Reimann & Daniel Keller & Srikanth Ramaswamy & Henry Markram & Marc-Oliver Gewaltig
November 2022, Volume 18, Issue 11
- 1-10 Ten simple rules for running a summer research program
by Joseph C Ayoob & Juan S Ramírez-Lugo - 1-12 Ten simple rules to cultivate belonging in collaborative data science research teams
by Kaitlyn M Gaynor & Therese Azevedo & Clarissa Boyajian & Julien Brun & Amber E Budden & Allie Cole & Samantha Csik & Joe DeCesaro & Halina Do-Linh & Joan Dudney & Carmen Galaz García & Scout Leonard & Nicholas J Lyon & Althea Marks & Julia Parish & Alexandra A Phillips & Courtney Scarborough & Joshua Smith & Marcus Thompson & Camila Vargas Poulsen & Caitlin R Fong - 1-12 SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more
by Hasan Balci & Ugur Dogrusoz & Yusuf Ziya Ozgul & Perman Atayev - 1-12 Ten simple rules for funding scientific open source software
by Carly Strasser & Kate Hertweck & Josh Greenberg & Dario Taraborelli & Elizabeth Vu - 1-17 Effective resistance against pandemics: Mobility network sparsification for high-fidelity epidemic simulations
by Alexander Mercier & Samuel Scarpino & Cristopher Moore - 1-21 Sampling effects and measurement overlap can bias the inference of neuronal avalanches
by Joao Pinheiro Neto & F Paul Spitzner & Viola Priesemann - 1-24 Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease
by Massimo Cavallaro & Juliana Coelho & Derren Ready & Valerie Decraene & Theresa Lamagni & Noel D McCarthy & Dan Todkill & Matt J Keeling - 1-24 Deep reinforcement learning for optimal experimental design in biology
by Neythen J Treloar & Nathan Braniff & Brian Ingalls & Chris P Barnes - 1-24 Optimized phylogenetic clustering of HIV-1 sequence data for public health applications
by Connor Chato & Yi Feng & Yuhua Ruan & Hui Xing & Joshua Herbeck & Marcia Kalish & Art F Y Poon - 1-26 Efficient inference and identifiability analysis for differential equation models with random parameters
by Alexander P Browning & Christopher Drovandi & Ian W Turner & Adrianne L Jenner & Matthew J Simpson - 1-27 Statistical perspective on functional and causal neural connectomics: The Time-Aware PC algorithm
by Rahul Biswas & Eli Shlizerman - 1-27 Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners
by Himangi Srivastava & Michael J Lippincott & Jordan Currie & Robert Canfield & Maggie P Y Lam & Edward Lau - 1-28 Inferring a spatial code of cell-cell interactions across a whole animal body
by Erick Armingol & Abbas Ghaddar & Chintan J Joshi & Hratch Baghdassarian & Isaac Shamie & Jason Chan & Hsuan-Lin Her & Samuel Berhanu & Anushka Dar & Fabiola Rodriguez-Armstrong & Olivia Yang & Eyleen J O’Rourke & Nathan E Lewis - 1-28 Tracking human skill learning with a hierarchical Bayesian sequence model
by Noémi Éltető & Dezső Nemeth & Karolina Janacsek & Peter Dayan - 1-28 Brain-wide connectome inferences using functional connectivity MultiVariate Pattern Analyses (fc-MVPA)
by Alfonso Nieto-Castanon - 1-29 A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion
by Nikita Sivakumar & Helen V Warner & Shayn M Peirce & Matthew J Lazzara - 1-29 Social dilemmas of sociality due to beneficial and costly contagion
by Daniel B Cooney & Dylan H Morris & Simon A Levin & Daniel I Rubenstein & Pawel Romanczuk - 1-32 Inferring parameters of cancer evolution in chronic lymphocytic leukemia
by Nathan D Lee & Ivana Bozic - 1-33 Inference of B cell clonal families using heavy/light chain pairing information
by Duncan K Ralph & Frederick A Matsen IV - 1-35 Computationally efficient mechanism discovery for cell invasion with uncertainty quantification
by Daniel J VandenHeuvel & Christopher Drovandi & Matthew J Simpson - 1-38 Look twice: A generalist computational model predicts return fixations across tasks and species
by Mengmi Zhang & Marcelo Armendariz & Will Xiao & Olivia Rose & Katarina Bendtz & Margaret Livingstone & Carlos Ponce & Gabriel Kreiman - 1-40 Probabilistic program inference in network-based epidemiological simulations
by Niklas Smedemark-Margulies & Robin Walters & Heiko Zimmermann & Lucas Laird & Christian van der Loo & Neela Kaushik & Rajmonda Caceres & Jan-Willem van de Meent - 1-41 The geometry of representational drift in natural and artificial neural networks
by Kyle Aitken & Marina Garrett & Shawn Olsen & Stefan Mihalas
October 2022, Volume 18, Issue 10
- 1-8 Ten simple rules for successfully supporting first-generation/low-income (FLI) students in STEM
by Courtney Peña & Nidia Ruedas-Gracia & Jennifer R Cohen & Ngoc Tran & Miranda B Stratton - 1-11 Ten simple rules for creating and sustaining antiracist graduate programs
by Edgar Perez-Lopez & Larisa Gavrilova & Janice Disla & Melissa Goodlad & Dalena Ngo & Arabi Seshappan & Farhana Sharmin & Jesus Cisneros & Christopher T Kello & Asmeret Asefaw Berhe - 1-14 Deep mendelian randomization: Investigating the causal knowledge of genomic deep learning models
by Stephen Malina & Daniel Cizin & David A Knowles - 1-15 Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men
by Sara Andresen & Suraj Balakrishna & Catrina Mugglin & Axel J Schmidt & Dominique L Braun & Alex Marzel & Thanh Doco Lecompte & Katharine EA Darling & Jan A Roth & Patrick Schmid & Enos Bernasconi & Huldrych F Günthard & Andri Rauch & Roger D Kouyos & Luisa Salazar-Vizcaya & the Swiss HIV Cohort Study - 1-16 Random-effects meta-analysis of effect sizes as a unified framework for gene set analysis
by Mohammad A Makrooni & Dónal O’Shea & Paul Geeleher & Cathal Seoighe - 1-17 Magnitude-sensitive reaction times reveal non-linear time costs in multi-alternative decision-making
by James A R Marshall & Andreagiovanni Reina & Célia Hay & Audrey Dussutour & Angelo Pirrone - 1-17 Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains
by Sabrin Hilau & Sophia Katz & Tanya Wasserman & Ruth Hershberg & Yonatan Savir - 1-17 Altered expression response upon repeated gene repression in single yeast cells
by Lea Schuh & Igor Kukhtevich & Poonam Bheda & Melanie Schulz & Maria Bordukova & Robert Schneider & Carsten Marr - 1-18 HAL-X: Scalable hierarchical clustering for rapid and tunable single-cell analysis
by James Anibal & Alexandre G Day & Erol Bahadiroglu & Liam O’Neil & Long Phan & Alec Peltekian & Amir Erez & Mariana Kaplan & Grégoire Altan-Bonnet & Pankaj Mehta - 1-18 Fast and interpretable consensus clustering via minipatch learning
by Luqin Gan & Genevera I Allen - 1-19 Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin
by Annie M Westerlund & Akshay Sridhar & Leo Dahl & Alma Andersson & Anna-Yaroslava Bodnar & Lucie Delemotte - 1-19 Parameterized syncmer schemes improve long-read mapping
by Abhinav Dutta & David Pellow & Ron Shamir - 1-20 MetaLP: An integrative linear programming method for protein inference in metaproteomics
by Shichao Feng & Hong-Long Ji & Huan Wang & Bailu Zhang & Ryan Sterzenbach & Chongle Pan & Xuan Guo - 1-20 Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond
by Kody A Waldstein & Jirong Yi & Myung Cho & Raghu Mudumbai & Xiaodong Wu & Steven M Varga & Weiyu Xu - 1-20 An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA
by Gerardo Chowell & Sushma Dahal & Amna Tariq & Kimberlyn Roosa & James M Hyman & Ruiyan Luo - 1-20 A deep learning approach to real-time HIV outbreak detection using genetic data
by Michael D Kupperman & Thomas Leitner & Ruian Ke - 1-22 Disentangling choice value and choice conflict in sequential decisions under risk
by Laura Fontanesi & Amitai Shenhav & Sebastian Gluth - 1-22 Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins
by Javier A Romero & Paulina Putko & Mateusz Urbańczyk & Krzysztof Kazimierczuk & Anna Zawadzka-Kazimierczuk - 1-24 Chaos in synthetic microbial communities
by Behzad D Karkaria & Angelika Manhart & Alex J H Fedorec & Chris P Barnes - 1-24 Stochastic dynamics of Type-I interferon responses
by Benjamin D Maier & Luis U Aguilera & Sven Sahle & Pascal Mutz & Priyata Kalra & Christopher Dächert & Ralf Bartenschlager & Marco Binder & Ursula Kummer - 1-25 The value of confidence: Confidence prediction errors drive value-based learning in the absence of external feedback
by Lena Esther Ptasczynski & Isa Steinecker & Philipp Sterzer & Matthias Guggenmos - 1-27 EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number
by Oswaldo Gressani & Jacco Wallinga & Christian L Althaus & Niel Hens & Christel Faes - 1-27 Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans
by Yuxiang Wu & Shang Wu & Xin Wang & Chengtian Lang & Quanshi Zhang & Quan Wen & Tianqi Xu - 1-28 Efficient Bayesian inference for stochastic agent-based models
by Andreas Christ Sølvsten Jørgensen & Atiyo Ghosh & Marc Sturrock & Vahid Shahrezaei - 1-28 Emergent multilevel selection in a simple spatial model of the evolution of altruism
by Rutger Hermsen - 1-28 Structured random receptive fields enable informative sensory encodings
by Biraj Pandey & Marius Pachitariu & Bingni W Brunton & Kameron Decker Harris - 1-30 Hippocampal and medial prefrontal cortices encode structural task representations following progressive and interleaved training schedules
by Sam C Berens & Chris M Bird - 1-34 Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis
by Chen Jia & Abhyudai Singh & Ramon Grima - 1-38 Multiple bumps can enhance robustness to noise in continuous attractor networks
by Raymond Wang & Louis Kang - 1-39 Reaction-diffusion models in weighted and directed connectomes
by Oliver Schmitt & Christian Nitzsche & Peter Eipert & Vishnu Prathapan & Marc-Thorsten Hütt & Claus C Hilgetag - 1-48 Bayesian parameter estimation for dynamical models in systems biology
by Nathaniel J Linden & Boris Kramer & Padmini Rangamani
September 2022, Volume 18, Issue 9
- 1-13 Graph-based algorithms for Laplace transformed coalescence time distributions
by Gertjan Bisschop - 1-14 Comparing and linking machine learning and semi-mechanistic models for the predictability of endemic measles dynamics
by Max S Y Lau & Alex Becker & Wyatt Madden & Lance A Waller & C Jessica E Metcalf & Bryan T Grenfell - 1-16 PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization
by Wenhui Yan & Wending Tang & Lihua Wang & Yannan Bin & Junfeng Xia - 1-16 Generalism drives abundance: A computational causal discovery approach
by Chuliang Song & Benno I Simmons & Marie-Josée Fortin & Andrew Gonzalez - 1-16 Strange attractor of a narwhal (Monodon monoceros)
by Evgeny A Podolskiy & Mads Peter Heide-Jørgensen - 1-16 Bayesian estimation of community size and overlap from random subsamples
by Erik K Johnson & Daniel B Larremore - 1-17 Testing microbiome associations with survival times at both the community and individual taxon levels
by Yingtian Hu & Yunxiao Li & Glen A Satten & Yi-Juan Hu - 1-19 Optimal anti-amyloid-beta therapy for Alzheimer’s disease via a personalized mathematical model
by Wenrui Hao & Suzanne Lenhart & Jeffrey R Petrella - 1-19 An expert judgment model to predict early stages of the COVID-19 pandemic in the United States
by Thomas McAndrew & Nicholas G Reich - 1-19 Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays
by Luke Ternes & Jia-Ren Lin & Yu-An Chen & Joe W Gray & Young Hwan Chang - 1-20 MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes
by Lin Zhang & Likai Chen & Xiaoqian (Annie) Yu & Claire Duvallet & Siavash Isazadeh & Chengzhen Dai & Shinkyu Park & Katya Frois-Moniz & Fabio Duarte & Carlo Ratti & Eric J Alm & Fangqiong Ling - 1-20 EpiBeds: Data informed modelling of the COVID-19 hospital burden in England
by Christopher E Overton & Lorenzo Pellis & Helena B Stage & Francesca Scarabel & Joshua Burton & Christophe Fraser & Ian Hall & Thomas A House & Chris Jewell & Anel Nurtay & Filippo Pagani & Katrina A Lythgoe - 1-20 Extracting individual characteristics from population data reveals a negative social effect during honeybee defence
by Tatjana Petrov & Matej Hajnal & Julia Klein & David Šafránek & Morgane Nouvian - 1-20 What lies underneath: Precise classification of brain states using time-dependent topological structure of dynamics
by Fernando Soler-Toscano & Javier A Galadí & Anira Escrichs & Yonatan Sanz Perl & Ane López-González & Jacobo D Sitt & Jitka Annen & Olivia Gosseries & Aurore Thibaut & Rajanikant Panda & Francisco J Esteban & Steven Laureys & Morten L Kringelbach & José A Langa & Gustavo Deco - 1-21 A quantitative modelling approach for DNA repair on a population scale
by Leo Zeitler & Cyril Denby Wilkes & Arach Goldar & Julie Soutourina - 1-22 ceRNAR: An R package for identification and analysis of ceRNA-miRNA triplets
by Yi-Wen Hsiao & Lin Wang & Tzu-Pin Lu - 1-22 Fast and accurate Ab Initio Protein structure prediction using deep learning potentials
by Robin Pearce & Yang Li & Gilbert S Omenn & Yang Zhang - 1-23 A normative model of peripersonal space encoding as performing impact prediction
by Zdenek Straka & Jean-Paul Noel & Matej Hoffmann - 1-23 Optimizing laboratory-based surveillance networks for monitoring multi-genotype or multi-serotype infections
by Qu Cheng & Philip A Collender & Alexandra K Heaney & Aidan McLoughlin & Yang Yang & Yuzi Zhang & Jennifer R Head & Rohini Dasan & Song Liang & Qiang Lv & Yaqiong Liu & Changhong Yang & Howard H Chang & Lance A Waller & Jon Zelner & Joseph A Lewnard & Justin V Remais - 1-24 Using Fluorescence Recovery After Photobleaching data to uncover filament dynamics
by J C Dallon & Cécile Leduc & Christopher P Grant & Emily J Evans & Sandrine Etienne-Manneville & Stéphanie Portet - 1-24 Comparing human and model-based forecasts of COVID-19 in Germany and Poland
by Nikos I Bosse & Sam Abbott & Johannes Bracher & Habakuk Hain & Billy J Quilty & Mark Jit & Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group & Edwin van Leeuwen & Anne Cori & Sebastian Funk - 1-24 Optimal control methods for nonlinear parameter estimation in biophysical neuron models
by Nirag Kadakia - 1-26 Patterns of asymmetry and energy cost generated from predictive simulations of hemiparetic gait
by Russell T Johnson & Nicholas A Bianco & James M Finley - 1-27 Towards reliable quantification of cell state velocities
by Valérie Marot-Lassauzaie & Brigitte Joanne Bouman & Fearghal Declan Donaghy & Yasmin Demerdash & Marieke Alida Gertruda Essers & Laleh Haghverdi - 1-27 Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets
by Melissa A Iacovidou & Priscille Barreaux & Simon E F Spencer & Matthew B Thomas & Erin E Gorsich & Kat S Rock - 1-28 A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data
by Ran Su & Haitang Yang & Leyi Wei & Siqi Chen & Quan Zou - 1-28 A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis
by Michela Carlotta Massi & Lorenzo Dominoni & Francesca Ieva & Giovanni Fiorito - 1-28 A hierarchical process model links behavioral aging and lifespan in C. elegans
by Natasha Oswal & Olivier M F Martin & Sofia Stroustrup & Monika Anna Matusiak Bruckner & Nicholas Stroustrup - 1-30 MouseNet: A biologically constrained convolutional neural network model for the mouse visual cortex
by Jianghong Shi & Bryan Tripp & Eric Shea-Brown & Stefan Mihalas & Michael A. Buice - 1-30 Systems-level identification of key transcription factors in immune cell specification
by Cong Liu & Kyla Omilusik & Clara Toma & Nadia S Kurd & John T Chang & Ananda W Goldrath & Wei Wang - 1-31 Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection
by Andrea Di Gioacchino & Jonah Procyk & Marco Molari & John S Schreck & Yu Zhou & Yan Liu & Rémi Monasson & Simona Cocco & Petr Šulc - 1-31 An integrative systems biology approach to overcome venetoclax resistance in acute myeloid leukemia
by Michelle Przedborski & David Sharon & Severine Cathelin & Steven Chan & Mohammad Kohandel - 1-32 Robust inference of population size histories from genomic sequencing data
by Gautam Upadhya & Matthias Steinrücken - 1-32 Investigating differential abundance methods in microbiome data: A benchmark study
by Marco Cappellato & Giacomo Baruzzo & Barbara Di Camillo - 1-32 Utility of constraints reflecting system stability on analyses for biological models
by Yoshiaki Kariya & Masashi Honma & Keita Tokuda & Akihiko Konagaya & Hiroshi Suzuki