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Content
April 2022, Volume 18, Issue 4
- 1-7 Ten simple rules for using entrepreneurship skills to improve research careers and culture
by Matt Bawn & David Dent & Philip E Bourne - 1-9 Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit
by Gautam Munglani & Hannes Vogler & Ueli Grossniklaus - 1-10 Ten simple rules for building a successful science start-up
by Tobias Reichmuth & Collin Y Ewald - 1-11 Ten simple rules to ruin a collaborative environment
by Carolyn J Lawrence-Dill & Robyn L Allscheid & Albert Boaitey & Todd Bauman & Edward S Buckler IV & Jennifer L Clarke & Christopher Cullis & Jack Dekkers & Cassandra J Dorius & Shawn F Dorius & David Ertl & Matthew Homann & Guiping Hu & Mary Losch & Eric Lyons & Brenda Murdoch & Zahra-Katy Navabi & Somashekhar Punnuri & Fahad Rafiq & James M Reecy & Patrick S Schnable & Nicole M Scott & Moira Sheehan & Xavier Sirault & Margaret Staton & Christopher K Tuggle & Alison Van Eenennaam & Rachael Voas - 1-17 RNA folding using quantum computers
by Dillion M Fox & Christopher M MacDermaid & Andrea M A Schreij & Magdalena Zwierzyna & Ross C Walker - 1-20 Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention
by Bryan T Mayer & Allan C deCamp & Yunda Huang & Joshua T Schiffer & Raphael Gottardo & Peter B Gilbert & Daniel B Reeves - 1-20 Using topic modeling to detect cellular crosstalk in scRNA-seq
by Alexandrina Pancheva & Helen Wheadon & Simon Rogers & Thomas D Otto - 1-22 Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants
by Nicholas J Ose & Brandon M Butler & Avishek Kumar & I Can Kazan & Maxwell Sanderford & Sudhir Kumar & S Banu Ozkan - 1-22 DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data
by Lijun Cheng & Pratik Karkhanis & Birkan Gokbag & Yueze Liu & Lang Li - 1-27 Microbiome-based disease prediction with multimodal variational information bottlenecks
by Filippo Grazioli & Raman Siarheyeu & Israa Alqassem & Andreas Henschel & Giampaolo Pileggi & Andrea Meiser - 1-27 SUITOR: Selecting the number of mutational signatures through cross-validation
by Donghyuk Lee & Difei Wang & Xiaohong R Yang & Jianxin Shi & Maria Teresa Landi & Bin Zhu - 1-27 Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors
by Nicolas Sundqvist & Nina Grankvist & Jeramie Watrous & Jain Mohit & Roland Nilsson & Gunnar Cedersund - 1-31 Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders
by Yuge Wang & Hongyu Zhao - 1-31 Chaotic and stochastic dynamics of epileptiform-like activities in sclerotic hippocampus resected from patients with pharmacoresistant epilepsy
by Noemi S Araújo & Selvin Z Reyes-Garcia & João A F Brogin & Douglas D Bueno & Esper A Cavalheiro & Carla A Scorza & Jean Faber - 1-33 Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets
by Anuradha Kar & Manuel Petit & Yassin Refahi & Guillaume Cerutti & Christophe Godin & Jan Traas
March 2022, Volume 18, Issue 3
- 1-8 Ten simple rules for principled simulation modelling
by Laurel Fogarty & Madeleine Ammar & Thomas Holding & Adam Powell & Anne Kandler - 1-13 Survival analysis of pathway activity as a prognostic determinant in breast cancer
by Gustavo S Jeuken & Nicholas P Tobin & Lukas Käll - 1-14 Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms
by Noortje G Godijk & Martin C J Bootsma & Henri C van Werkhoven & Valentijn A Schweitzer & Sabine C de Greeff & Annelot F Schoffelen & Marc J M Bonten - 1-14 Constructing benchmark test sets for biological sequence analysis using independent set algorithms
by Samantha Petti & Sean R Eddy - 1-14 Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data
by Pablo M De Salazar & Fred Lu & James A Hay & Diana Gómez-Barroso & Pablo Fernández-Navarro & Elena V Martínez & Jenaro Astray-Mochales & Rocío Amillategui & Ana García-Fulgueiras & Maria D Chirlaque & Alonso Sánchez-Migallón & Amparo Larrauri & María J Sierra & Marc Lipsitch & Fernando Simón & Mauricio Santillana & Miguel A Hernán - 1-15 Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2
by Leonardo Souto Ferreira & Otavio Canton & Rafael Lopes Paixão da Silva & Silas Poloni & Vítor Sudbrack & Marcelo Eduardo Borges & Caroline Franco & Flavia Maria Darcie Marquitti & José Cássio de Moraes & Maria Amélia de Sousa Mascena Veras & Roberto André Kraenkel & Renato Mendes Coutinho - 1-15 Bayesian inference of ancestral recombination graphs
by Ali Mahmoudi & Jere Koskela & Jerome Kelleher & Yao-ban Chan & David Balding - 1-16 A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data
by Snehalika Lall & Sumanta Ray & Sanghamitra Bandyopadhyay - 1-17 Pooled testing of traced contacts under superspreading dynamics
by Stratis Tsirtsis & Abir De & Lars Lorch & Manuel Gomez-Rodriguez - 1-18 SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included
by Jianle Sun & Ruiqi Lyu & Luojia Deng & Qianwen Li & Yang Zhao & Yue Zhang - 1-18 Deep inference of seabird dives from GPS-only records: Performance and generalization properties
by Amédée Roy & Sophie Lanco Bertrand & Ronan Fablet - 1-20 Ten quick tips for deep learning in biology
by Benjamin D Lee & Anthony Gitter & Casey S Greene & Sebastian Raschka & Finlay Maguire & Alexander J Titus & Michael D Kessler & Alexandra J Lee & Marc G Chevrette & Paul Allen Stewart & Thiago Britto-Borges & Evan M Cofer & Kun-Hsing Yu & Juan Jose Carmona & Elana J Fertig & Alexandr A Kalinin & Brandon Signal & Benjamin J Lengerich & Timothy J Triche Jr. & Simina M Boca - 1-20 Transcriptome diversity is a systematic source of variation in RNA-sequencing data
by Pablo E García-Nieto & Ban Wang & Hunter B Fraser - 1-20 Thalamic bursts modulate cortical synchrony locally to switch between states of global functional connectivity in a cognitive task
by Oscar Portoles & Manuel Blesa & Marieke van Vugt & Ming Cao & Jelmer P Borst - 1-21 Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches
by Timos Papadopoulos & Emilia Vynnycky - 1-21 How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments
by Immanuel Meyer & Bnaya Steinmetz & Nadav M Shnerb - 1-22 Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level
by Anđela Davidović & Remy Chait & Gregory Batt & Jakob Ruess - 1-22 Performance of early warning signals for disease re-emergence: A case study on COVID-19 data
by Daniele Proverbio & Françoise Kemp & Stefano Magni & Jorge Gonçalves - 1-22 The role of cell geometry and cell-cell communication in gradient sensing
by Jonathan Fiorentino & Antonio Scialdone - 1-24 Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition
by Shin-ichi Koda & Shinji Saito - 1-26 Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness
by Daniel J Lugar & Ganesh Sriram - 1-26 Automatic wound detection and size estimation using deep learning algorithms
by Héctor Carrión & Mohammad Jafari & Michelle Dawn Bagood & Hsin-ya Yang & Roslyn Rivkah Isseroff & Marcella Gomez - 1-27 Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins
by Lei Wang & Jiangguo Zhang & Dali Wang & Chen Song - 1-29 Encoding time in neural dynamic regimes with distinct computational tradeoffs
by Shanglin Zhou & Sotiris C Masmanidis & Dean V Buonomano - 1-29 Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation
by Yingjing Feng & Caroline H Roney & Jason D Bayer & Steven A Niederer & Mélèze Hocini & Edward J Vigmond - 1-30 Estimating genetic variance contributed by a quantitative trait locus: A random model approach
by Shibo Wang & Fangjie Xie & Shizhong Xu - 1-31 Oscillator decomposition of infant fNIRS data
by Takeru Matsuda & Fumitaka Homae & Hama Watanabe & Gentaro Taga & Fumiyasu Komaki - 1-34 The ability to classify patients based on gene-expression data varies by algorithm and performance metric
by Stephen R Piccolo & Avery Mecham & Nathan P Golightly & Jérémie L Johnson & Dustin B Miller - 1-38 Evolution of innate behavioral strategies through competitive population dynamics
by Tong Liang & Braden A W Brinkman - 1-39 Task-induced neural covariability as a signature of approximate Bayesian learning and inference
by Richard D Lange & Ralf M Haefner - 1-41 Cortical oscillations support sampling-based computations in spiking neural networks
by Agnes Korcsak-Gorzo & Michael G Müller & Andreas Baumbach & Luziwei Leng & Oliver J Breitwieser & Sacha J van Albada & Walter Senn & Karlheinz Meier & Robert Legenstein & Mihai A Petrovici - 1-47 Bayesian calibration, process modeling and uncertainty quantification in biotechnology
by Laura Marie Helleckes & Michael Osthege & Wolfgang Wiechert & Eric von Lieres & Marco Oldiges
February 2022, Volume 18, Issue 2
- 1-7 Ten simple rules for initial data analysis
by Mark Baillie & Saskia le Cessie & Carsten Oliver Schmidt & Lara Lusa & Marianne Huebner & for the Topic Group “Initial Data Analysis” of the STRATOS Initiative - 1-9 Hidden Markov Modeling with HMMTeacher
by Camilo Fuentes-Beals & Alejandro Valdés-Jiménez & Gonzalo Riadi - 1-11 There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk
by Jon Zelner & Nina B Masters & Ramya Naraharisetti & Sanyu A Mojola & Merlin Chowkwanyun & Ryan Malosh - 1-14 Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich
by Liam M Longo & Rachel Kolodny & Shawn E McGlynn - 1-18 Classical mathematical models for prediction of response to chemotherapy and immunotherapy
by Narmin Ghaffari Laleh & Chiara Maria Lavinia Loeffler & Julia Grajek & Kateřina Staňková & Alexander T Pearson & Hannah Sophie Muti & Christian Trautwein & Heiko Enderling & Jan Poleszczuk & Jakob Nikolas Kather - 1-19 Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster
by Katherine E Overman & Daniel M Choi & Kawai Leung & Joshua W Shaevitz & Gordon J Berman - 1-20 Near-term forecasting of companion animal tick paralysis incidence: An iterative ensemble model
by Nicholas J Clark & Tatiana Proboste & Guyan Weerasinghe & Ricardo J Soares Magalhães - 1-20 Inference of trajectory presence by tree dimension and subset specificity by subtree cover
by Lovemore Tenha & Mingzhou Song - 1-21 Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19
by Xian Yang & Shuo Wang & Yuting Xing & Ling Li & Richard Yi Da Xu & Karl J Friston & Yike Guo - 1-21 Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights
by Ramin Khajeh & Francesco Fumarola & LF Abbott - 1-21 Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning
by Indriani P Astono & James S Welsh & Christopher W Rowe & Phillip Jobling - 1-21 Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic
by Yuen Ler Chow & Shantanu Singh & Anne E Carpenter & Gregory P Way - 1-22 A computationally tractable birth-death model that combines phylogenetic and epidemiological data
by Alexander Eugene Zarebski & Louis du Plessis & Kris Varun Parag & Oliver George Pybus - 1-22 High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication
by Nithya Ramakrishnan & Sibi Raj B Pillai & Ranjith Padinhateeri - 1-23 Learning as filtering: Implications for spike-based plasticity
by Jannes Jegminat & Simone Carlo Surace & Jean-Pascal Pfister - 1-24 RNA-Seq is not required to determine stable reference genes for qPCR normalization
by Nirmal Kumar Sampathkumar & Venkat Krishnan Sundaram & Prakroothi S Danthi & Rasha Barakat & Shiden Solomon & Mrityunjoy Mondal & Ivo Carre & Tatiana El Jalkh & Aïda Padilla-Ferrer & Julien Grenier & Charbel Massaad & Jacqueline C Mitchell - 1-25 Evaluating supervised and unsupervised background noise correction in human gut microbiome data
by Leah Briscoe & Brunilda Balliu & Sriram Sankararaman & Eran Halperin & Nandita R Garud - 1-26 Combination and competition between path integration and landmark navigation in the estimation of heading direction
by Sevan K Harootonian & Arne D Ekstrom & Robert C Wilson - 1-26 In silico prediction of HIV-1-host molecular interactions and their directionality
by Haiting Chai & Quan Gu & Joseph Hughes & David L Robertson - 1-27 Meta-control of social learning strategies
by Anil Yaman & Nicolas Bredeche & Onur Çaylak & Joel Z Leibo & Sang Wan Lee - 1-27 Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network
by R Krishnakumaran & Mohammed Raees & Supratim Ray - 1-35 Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts
by Robert C Mines & Tomasz Lipniacki & Xiling Shen - 1-37 Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates
by Alessandra Løchen & James E Truscott & Nicholas J Croucher
January 2022, Volume 18, Issue 1
- 1-16 An initial ‘snapshot’ of sensory information biases the likelihood and speed of subsequent changes of mind
by William Turner & Daniel Feuerriegel & Robert Hester & Stefan Bode - 1-17 CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach
by Mengting Niu & Quan Zou & Chen Lin - 1-18 OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data
by Raga Krishnakumar & Anne M Ruffing - 1-19 Efficient ReML inference in variance component mixed models using a Min-Max algorithm
by Fabien Laporte & Alain Charcosset & Tristan Mary-Huard - 1-19 Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection
by Alasdair D F Clarke & Amelia R Hunt & Anna E Hughes - 1-20 Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution
by Tadamune Kaneko & Macoto Kikuchi - 1-21 Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods
by Richard Jiang & Prashant Singh & Fredrik Wrede & Andreas Hellander & Linda Petzold - 1-22 Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data
by Qi Jiang & Shuo Zhang & Lin Wan - 1-22 Fast and accurate influenza forecasting in the United States with Inferno
by Dave Osthus - 1-22 Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy
by Alexander B Brummer & Xin Yang & Eric Ma & Margarita Gutova & Christine E Brown & Russell C Rockne - 1-23 Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables
by Arno Strouwen & Bart M Nicolaï & Peter Goos - 1-23 Analytical kinetic model of native tandem promoters in E. coli
by Vatsala Chauhan & Mohamed N M Bahrudeen & Cristina S D Palma & Ines S C Baptista & Bilena L B Almeida & Suchintak Dash & Vinodh Kandavalli & Andre S Ribeiro - 1-24 Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach
by Marcell Miski & Bence Márk Keömley-Horváth & Dorina Rákóczi Megyeriné & Attila Csikász-Nagy & Zoltán Gáspári - 1-24 Formation, collective motion, and merging of macroscopic bacterial aggregates
by George Courcoubetis & Manasi S Gangan & Sean Lim & Xiaokan Guo & Stephan Haas & James Q Boedicker - 1-26 The evolutionary maintenance of Lévy flight foraging
by Winston Campeau & Andrew M Simons & Brett Stevens - 1-26 Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach
by Chen Jia & Abhyudai Singh & Ramon Grima - 1-27 Identification of periodic attractors in Boolean networks using a priori information
by Ulrike Münzner & Tomoya Mori & Marcus Krantz & Edda Klipp & Tatsuya Akutsu - 1-28 Discovering adaptation-capable biological network structures using control-theoretic approaches
by Priyan Bhattacharya & Karthik Raman & Arun K Tangirala - 1-29 A lexical approach for identifying behavioural action sequences
by Gautam Reddy & Laura Desban & Hidenori Tanaka & Julian Roussel & Olivier Mirat & Claire Wyart - 1-30 Interpretable machine learning for high-dimensional trajectories of aging health
by Spencer Farrell & Arnold Mitnitski & Kenneth Rockwood & Andrew D Rutenberg - 1-30 Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships
by Nina Kudryashova & Theoklitos Amvrosiadis & Nathalie Dupuy & Nathalie Rochefort & Arno Onken - 1-32 Optimism and pessimism in optimised replay
by Georgy Antonov & Christopher Gagne & Eran Eldar & Peter Dayan
December 2021, Volume 17, Issue 12
- 1-13 Ten simple rules for developing bioinformatics capacity at an academic institution
by Shaun Aron & C Victor Jongeneel & Paballo Abel Chauke & Melek Chaouch & Judit Kumuthini & Lyndon Zass & Fouzia Radouani & Samar Kamal Kassim & Faisal M Fadlelmola & Nicola Mulder - 1-13 Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization
by Fuminari Miura & Ka Yin Leung & Don Klinkenberg & Kylie E C Ainslie & Jacco Wallinga - 1-14 Development of an experiment-split method for benchmarking the generalization of a PTM site predictor: Lysine methylome as an example
by Guoyang Zou & Yang Zou & Chenglong Ma & Jiaojiao Zhao & Lei Li - 1-15 SWIFT: A deep learning approach to prediction of hypoxemic events in critically-Ill patients using SpO2 waveform prediction
by Akshaya V Annapragada & Joseph L Greenstein & Sanjukta N Bose & Bradford D Winters & Sridevi V Sarma & Raimond L Winslow - 1-17 Motif-pattern dependence of biomolecular phase separation driven by specific interactions
by Benjamin G Weiner & Andrew G T Pyo & Yigal Meir & Ned S Wingreen - 1-19 Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016–2018: A hidden Markov modelling study
by Deus Thindwa & Nicole Wolter & Amy Pinsent & Maimuna Carrim & John Ojal & Stefano Tempia & Jocelyn Moyes & Meredith McMorrow & Jackie Kleynhans & Anne von Gottberg & Neil French & PHIRST group & Cheryl Cohen & Stefan Flasche - 1-19 GCAEMDA: Predicting miRNA-disease associations via graph convolutional autoencoder
by Lei Li & Yu-Tian Wang & Cun-Mei Ji & Chun-Hou Zheng & Jian-Cheng Ni & Yan-Sen Su - 1-19 A systems genomics approach uncovers molecular associates of RSV severity
by Matthew N McCall & Chin-Yi Chu & Lu Wang & Lauren Benoodt & Juilee Thakar & Anthony Corbett & Jeanne Holden-Wiltse & Christopher Slaunwhite & Alex Grier & Steven R Gill & Ann R Falsey & David J Topham & Mary T Caserta & Edward E Walsh & Xing Qiu & Thomas J Mariani - 1-19 A spatio-temporal model to reveal oscillator phenotypes in molecular clocks: Parameter estimation elucidates circadian gene transcription dynamics in single-cells
by Måns Unosson & Marco Brancaccio & Michael Hastings & Adam M Johansen & Bärbel Finkenstädt - 1-20 Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble
by Icíar Civantos-Gómez & Javier García-Algarra & David García-Callejas & Javier Galeano & Oscar Godoy & Ignasi Bartomeus - 1-21 Dissociable influences of reward and punishment on adaptive cognitive control
by Xiamin Leng & Debbie Yee & Harrison Ritz & Amitai Shenhav - 1-21 One-carbon metabolism during the menstrual cycle and pregnancy
by Ruby Kim & H Frederik Nijhout & Michael C Reed - 1-22 Combination treatment optimization using a pan-cancer pathway model
by Robin Schmucker & Gabriele Farina & James Faeder & Fabian Fröhlich & Ali Sinan Saglam & Tuomas Sandholm - 1-22 Benchmarking of tools for axon length measurement in individually-labeled projection neurons
by Mario Rubio-Teves & Sergio Díez-Hermano & César Porrero & Abel Sánchez-Jiménez & Lucía Prensa & Francisco Clascá & María García-Amado & José Antonio Villacorta-Atienza - 1-22 Dynamic maximum entropy provides accurate approximation of structured population dynamics
by Katarína Bod’ová & Enikő Szép & Nicholas H Barton - 1-22 Internal state effects on behavioral shifts in freely behaving praying mantises (Tenodera sinensis)
by Shanel C Pickard & David J Bertsch & Zoe Le Garrec & Roy E Ritzmann & Roger D Quinn & Nicholas S Szczecinski - 1-23 DeepCME: A deep learning framework for computing solution statistics of the chemical master equation
by Ankit Gupta & Christoph Schwab & Mustafa Khammash - 1-23 Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?
by Juan Diaz-Colunga & Ramon Diaz-Uriarte - 1-24 Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes
by Lanxin Zhang & Junyu Wang & Max von Kleist - 1-28 Asymmetric and transient properties of reciprocal activity of antagonists during the paw-shake response in the cat
by Jessica R Parker & Alexander N Klishko & Boris I Prilutsky & Gennady S Cymbalyuk - 1-28 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant
by Joseph R Larsen & Margaret R Martin & John D Martin & James B Hicks & Peter Kuhn - 1-30 A data-informed mean-field approach to mapping of cortical parameter landscapes
by Zhuo-Cheng Xiao & Kevin K Lin & Lai-Sang Young - 1-31 Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity
by Elishai Ezra-Tsur & Oren Amsalem & Lea Ankri & Pritish Patil & Idan Segev & Michal Rivlin-Etzion - 1-38 Preparing to move: Setting initial conditions to simplify interactions with complex objects
by Rashida Nayeem & Salah Bazzi & Mohsen Sadeghi & Neville Hogan & Dagmar Sternad - 1-39 Decision prioritization and causal reasoning in decision hierarchies
by Ariel Zylberberg - 1-44 When shared concept cells support associations: Theory of overlapping memory engrams
by Chiara Gastaldi & Tilo Schwalger & Emanuela De Falco & Rodrigo Quian Quiroga & Wulfram Gerstner
November 2021, Volume 17, Issue 11
- 1-12 Identifying prognostic pairwise relationships among bacterial species in microbiome studies
by Sean M Devlin & Axel Martin & Irina Ostrovnaya - 1-14 Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data
by Tania Mendonca & Ana A Jones & Jose M Pozo & Sarah Baxendale & Tanya T Whitfield & Alejandro F Frangi - 1-16 Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling
by Danial Pourjafar-Dehkordi & Martin Zacharias - 1-16 The meaning of significant mean group differences for biomarker discovery
by Eva Loth & Jumana Ahmad & Chris Chatham & Beatriz López & Ben Carter & Daisy Crawley & Bethany Oakley & Hannah Hayward & Jennifer Cooke & Antonia San José Cáceres & Danilo Bzdok & Emily Jones & Tony Charman & Christian Beckmann & Thomas Bourgeron & Roberto Toro & Jan Buitelaar & Declan Murphy & Guillaume Dumas - 1-16 The role of competition versus cooperation in microbial community coalescence
by Pablo Lechón-Alonso & Tom Clegg & Jacob Cook & Thomas P Smith & Samraat Pawar - 1-18 Approximate distance correlation for selecting highly interrelated genes across datasets
by Qunlun Shen & Shihua Zhang - 1-19 Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data
by Pavel I Kos & Aleksandra A Galitsyna & Sergey V Ulianov & Mikhail S Gelfand & Sergey V Razin & Alexander V Chertovich - 1-21 Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data
by Torfinn S Madssen & Guro F Giskeødegård & Age K Smilde & Johan A Westerhuis - 1-21 Intriguing effects of selection intensity on the evolution of prosocial behaviors
by Alex McAvoy & Andrew Rao & Christoph Hauert - 1-23 Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT
by Shahab Sarmashghi & Metin Balaban & Eleonora Rachtman & Behrouz Touri & Siavash Mirarab & Vineet Bafna - 1-23 Cluster size distribution of cells disseminating from a primary tumor
by Mrinmoy Mukherjee & Herbert Levine - 1-23 Estimating the dimensionality of the manifold underlying multi-electrode neural recordings
by Ege Altan & Sara A Solla & Lee E Miller & Eric J Perreault - 1-24 Cross-population coupling of neural activity based on Gaussian process current source densities
by Natalie Klein & Joshua H Siegle & Tobias Teichert & Robert E Kass - 1-24 Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones
by Erik B Nordquist & Charles A English & Eugenia M Clerico & Woody Sherman & Lila M Gierasch & Jianhan Chen - 1-25 Comparison of metabolic states using genome-scale metabolic models
by Chaitra Sarathy & Marian Breuer & Martina Kutmon & Michiel E Adriaens & Chris T Evelo & Ilja C W Arts - 1-26 Optimizing network propagation for multi-omics data integration
by Konstantina Charmpi & Manopriya Chokkalingam & Ronja Johnen & Andreas Beyer - 1-26 Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance
by Mathurin Dorel & Bertram Klinger & Tommaso Mari & Joern Toedling & Eric Blanc & Clemens Messerschmidt & Michal Nadler-Holly & Matthias Ziehm & Anja Sieber & Falk Hertwig & Dieter Beule & Angelika Eggert & Johannes H Schulte & Matthias Selbach & Nils Blüthgen - 1-26 A gap-filling algorithm for prediction of metabolic interactions in microbial communities
by Dafni Giannari & Cleo Hanchen Ho & Radhakrishnan Mahadevan - 1-27 Multivariable association discovery in population-scale meta-omics studies
by Himel Mallick & Ali Rahnavard & Lauren J McIver & Siyuan Ma & Yancong Zhang & Long H Nguyen & Timothy L Tickle & George Weingart & Boyu Ren & Emma H Schwager & Suvo Chatterjee & Kelsey N Thompson & Jeremy E Wilkinson & Ayshwarya Subramanian & Yiren Lu & Levi Waldron & Joseph N Paulson & Eric A Franzosa & Hector Corrada Bravo & Curtis Huttenhower - 1-28 Crowd control: Reducing individual estimation bias by sharing biased social information
by Bertrand Jayles & Clément Sire & Ralf H J M Kurvers - 1-30 A confirmation bias in perceptual decision-making due to hierarchical approximate inference
by Richard D Lange & Ankani Chattoraj & Jeffrey M Beck & Jacob L Yates & Ralf M Haefner - 1-34 Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases
by Tunca Doğan & Ece Akhan Güzelcan & Marcus Baumann & Altay Koyas & Heval Atas & Ian R Baxendale & Maria Martin & Rengul Cetin-Atalay - 1-35 Hybrid dedicated and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals
by Tanner C Dixon & Christina M Merrick & Joni D Wallis & Richard B Ivry & Jose M Carmena - 1-37 Causal inference regulates audiovisual spatial recalibration via its influence on audiovisual perception
by Fangfang Hong & Stephanie Badde & Michael S Landy - 1-38 Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans
by Javier J How & Saket Navlakha & Sreekanth H Chalasani
October 2021, Volume 17, Issue 10
- 1-12 Ten simple rules for training yourself in an emerging field
by Whitney M Woelmer & L M Bradley & Lisa T Haber & David H Klinges & Abigail S L Lewis & Elizabeth J Mohr & Christa L Torrens & Kathryn I Wheeler & Alyssa M Willson - 1-15 A data-driven approach for constructing mutation categories for mutational signature analysis
by Gal Gilad & Mark D M Leiserson & Roded Sharan - 1-16 pyActigraphy: Open-source python package for actigraphy data visualization and analysis
by Grégory Hammad & Mathilde Reyt & Nikita Beliy & Marion Baillet & Michele Deantoni & Alexia Lesoinne & Vincenzo Muto & Christina Schmidt - 1-17 Estimating ectopic beat probability with simplified statistical models that account for experimental uncertainty
by Qingchu Jin & Joseph L Greenstein & Raimond L Winslow - 1-18 A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC
by Jason Bennett & Mikhail Pomaznoy & Akul Singhania & Bjoern Peters - 1-19 Improved prediction of smoking status via isoform-aware RNA-seq deep learning models
by Zifeng Wang & Aria Masoomi & Zhonghui Xu & Adel Boueiz & Sool Lee & Tingting Zhao & Russell Bowler & Michael Cho & Edwin K Silverman & Craig Hersh & Jennifer Dy & Peter J Castaldi - 1-19 RgCop-A regularized copula based method for gene selection in single cell rna-seq data
by Snehalika Lall & Sumanta Ray & Sanghamitra Bandyopadhyay - 1-20 Extended graphical lasso for multiple interaction networks for high dimensional omics data
by Yang Xu & Hongmei Jiang & Wenxin Jiang - 1-20 Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample’s infection concentration
by Daniel Cresta & Donald C Warren & Christian Quirouette & Amanda P Smith & Lindey C Lane & Amber M Smith & Catherine A A Beauchemin - 1-21 Steady-state measures of visual suppression
by Daniel H Baker & Greta Vilidaite & Alex R Wade - 1-21 Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities
by Yun Min Song & Hyukpyo Hong & Jae Kyoung Kim - 1-21 Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns
by Maxwell W Libbrecht & Rachel C W Chan & Michael M Hoffman - 1-21 Complexity and diversity in sparse code priors improve receptive field characterization of Macaque V1 neurons
by Ziniu Wu & Harold Rockwell & Yimeng Zhang & Shiming Tang & Tai Sing Lee - 1-22 PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes
by Charlie M Carpenter & Weiming Zhang & Lucas Gillenwater & Cameron Severn & Tusharkanti Ghosh & Russell Bowler & Katerina Kechris & Debashis Ghosh - 1-23 Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention
by Stacy Tessler Lindau & Jennifer A Makelarski & Chaitanya Kaligotla & Emily M Abramsohn & David G Beiser & Chiahung Chou & Nicholson Collier & Elbert S Huang & Charles M Macal & Jonathan Ozik & Elizabeth L Tung - 1-24 Better tired than lost: Turtle ant trail networks favor coherence over short edges
by Arjun Chandrasekhar & James A R Marshall & Cortnea Austin & Saket Navlakha & Deborah M Gordon - 1-25 Tracking calcium dynamics from individual neurons in behaving animals
by Thibault Lagache & Alison Hanson & Jesús E Pérez-Ortega & Adrienne Fairhall & Rafael Yuste - 1-27 How conformity can lead to polarised social behaviour
by Folco Panizza & Alexander Vostroknutov & Giorgio Coricelli - 1-28 Atorvastatin-mediated rescue of cancer-related cognitive changes in combined anticancer therapies
by Junho Lee & Jin Su Kim & Yangjin Kim - 1-28 Visual perception of texture regularity: Conjoint measurements and a wavelet response-distribution model
by Hua-Chun Sun & David St-Amand & Curtis L Baker Jr. & Frederick A A Kingdom - 1-28 Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites
by Bikash K Bhandari & Chun Shen Lim & Daniela M Remus & Augustine Chen & Craig van Dolleweerd & Paul P Gardner - 1-28 Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts
by Yi Huang & Ishanu Chattopadhyay - 1-29 Point-estimating observer models for latent cause detection
by Jennifer Laura Lee & Wei Ji Ma - 1-31 Narrative event segmentation in the cortical reservoir
by Peter Ford Dominey - 1-32 Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity
by Daniel E Mattox & Chris Bailey-Kellogg - 1-32 Action planning and control under uncertainty emerge through a desirability-driven competition between parallel encoding motor plans
by Vince Enachescu & Paul Schrater & Stefan Schaal & Vassilios Christopoulos - 1-33 Choice history effects in mice and humans improve reward harvesting efficiency
by Samuel López-Yépez Junior & Juliane Martin & Oliver Hulme & Duda Kvitsiani - 1-35 Cortical feedback and gating in odor discrimination and generalization
by Gaia Tavoni & David E Chen Kersen & Vijay Balasubramanian - 1-38 Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans
by Yashika Arora & Pushpinder Walia & Mitsuhiro Hayashibe & Makii Muthalib & Shubhajit Roy Chowdhury & Stephane Perrey & Anirban Dutta
September 2021, Volume 17, Issue 9
- 1-5 Ten simple rules for avoiding predatory publishing scams
by Michelle Leonard & Suzanne Stapleton & Perry Collins & Terry Kit Selfe & Tara Cataldo - 1-6 Ten simple rules for being a faculty advocate of first-year graduate students
by Kevin A Janes - 1-8 Ten simple rules for choosing a PhD supervisor
by Loay Jabre & Catherine Bannon & J Scott P McCain & Yana Eglit - 1-12 Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment
by Sepideh Mazrouee & Susan J Little & Joel O Wertheim - 1-14 Hemodynamics-driven mathematical model of first and second heart sound generation
by Mehrdad Shahmohammadi & Hongxing Luo & Philip Westphal & Richard N Cornelussen & Frits W Prinzen & Tammo Delhaas - 1-16 Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections
by Thomas Beneteau & Christian Selinger & Mircea T Sofonea & Samuel Alizon - 1-16 Ten simple rules for supporting historically underrepresented students in science
by Suchinta Arif & Melanie Duc Bo Massey & Natalie Klinard & Julie Charbonneau & Loay Jabre & Ana Barbosa Martins & Danielle Gaitor & Rhiannon Kirton & Catalina Albury & Karma Nanglu - 1-19 ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves
by Eric D Musselman & Jake E Cariello & Warren M Grill & Nicole A Pelot - 1-20 Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics
by Eric W Bridgeford & Shangsi Wang & Zeyi Wang & Ting Xu & Cameron Craddock & Jayanta Dey & Gregory Kiar & William Gray-Roncal & Carlo Colantuoni & Christopher Douville & Stephanie Noble & Carey E Priebe & Brian Caffo & Michael Milham & Xi-Nian Zuo & Consortium for Reliability and Reproducibility & Joshua T Vogelstein - 1-20 Basis profile curve identification to understand electrical stimulation effects in human brain networks
by Kai J Miller & Klaus-Robert Müller & Dora Hermes - 1-21 Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds
by Alison Pereira Ribeiro & Nádia Felix Felipe da Silva & Fernanda Neiva Mesquita & Priscila de Cássia Souza Araújo & Thierson Couto Rosa & José Neiva Mesquita-Neto - 1-21 Insights into the dynamic trajectories of protein filament division revealed by numerical investigation into the mathematical model of pure fragmentation
by Magali Tournus & Miguel Escobedo & Wei-Feng Xue & Marie Doumic - 1-21 XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers
by Jack B Maguire & Daniele Grattarola & Vikram Khipple Mulligan & Eugene Klyshko & Hans Melo - 1-22 Drug-induced resistance evolution necessitates less aggressive treatment
by Teemu Kuosmanen & Johannes Cairns & Robert Noble & Niko Beerenwinkel & Tommi Mononen & Ville Mustonen - 1-23 Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
by Rui Yin & Johnathan D Guest & Ghazaleh Taherzadeh & Ragul Gowthaman & Ipsa Mittra & Jane Quackenbush & Brian G Pierce - 1-24 Personalized brain stimulation for effective neurointervention across participants
by Nienke E R van Bueren & Thomas L Reed & Vu Nguyen & James G Sheffield & Sanne H G van der Ven & Michael A Osborne & Evelyn H Kroesbergen & Roi Cohen Kadosh - 1-24 Optima TB: A tool to help optimally allocate tuberculosis spending
by Lara Goscé & Gerard J Abou Jaoude & David J Kedziora & Clemens Benedikt & Azfar Hussain & Sarah Jarvis & Alena Skrahina & Dzmitry Klimuk & Henadz Hurevich & Feng Zhao & Nicole Fraser-Hurt & Nejma Cheikh & Marelize Gorgens & David J Wilson & Romesh Abeysuriya & Rowan Martin-Hughes & Sherrie L Kelly & Anna Roberts & Robyn M Stuart & Tom Palmer & Jasmina Panovska-Griffiths & Cliff C Kerr & David P Wilson & Hassan Haghparast-Bidgoli & Jolene Skordis & Ibrahim Abubakar - 1-24 Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model
by Federica Gugole & Luc E Coffeng & Wouter Edeling & Benjamin Sanderse & Sake J de Vlas & Daan Crommelin - 1-25 Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C
by Susana Posada-Céspedes & Gert Van Zyl & Hesam Montazeri & Jack Kuipers & Soo-Yon Rhee & Roger Kouyos & Huldrych F Günthard & Niko Beerenwinkel - 1-25 Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing
by Michael Smith & Rachel Chan & Maaz Khurram & Paul M K Gordon - 1-25 Learning brain dynamics for decoding and predicting individual differences
by Joyneel Misra & Srinivas Govinda Surampudi & Manasij Venkatesh & Chirag Limbachia & Joseph Jaja & Luiz Pessoa - 1-25 Ergodicity-breaking reveals time optimal decision making in humans
by David Meder & Finn Rabe & Tobias Morville & Kristoffer H Madsen & Magnus T Koudahl & Ray J Dolan & Hartwig R Siebner & Oliver J Hulme - 1-26 Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
by Ilario De Toma & Cesar Sierra & Mara Dierssen - 1-26 Neighbor-enhanced diffusivity in dense, cohesive cell populations
by Hyun Gyu Lee & Kyoung J Lee - 1-28 Latching dynamics as a basis for short-term recall
by Kwang Il Ryom & Vezha Boboeva & Oleksandra Soldatkina & Alessandro Treves - 1-28 Differences in olfactory bulb mitral cell spiking with ortho- and retronasal stimulation revealed by data-driven models
by Michelle F Craft & Andrea K Barreiro & Shree Hari Gautam & Woodrow L Shew & Cheng Ly - 1-28 Phenotypic-dependent variability and the emergence of tolerance in bacterial populations
by José Camacho Mateu & Matteo Sireci & Miguel A Muñoz