Printed from https://ideas.repec.org/s/plo/pcbi008.html
Content
January 2021, Volume 17, Issue 1
- 1-29 Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome
by Marco Aqil & Selen Atasoy & Morten L Kringelbach & Rikkert Hindriks - 1-30 Reconciling kinetic and thermodynamic models of bacterial transcription
by Muir Morrison & Manuel Razo-Mejia & Rob Phillips - 1-32 Online analysis of microendoscopic 1-photon calcium imaging data streams
by Johannes Friedrich & Andrea Giovannucci & Eftychios A Pnevmatikakis - 1-34 Post-lockdown abatement of COVID-19 by fast periodic switching
by Michelangelo Bin & Peter Y K Cheung & Emanuele Crisostomi & Pietro Ferraro & Hugo Lhachemi & Roderick Murray-Smith & Connor Myant & Thomas Parisini & Robert Shorten & Sebastian Stein & Lewi Stone - 1-43 A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans
by Samuel Planton & Timo van Kerkoerle & Leïla Abbih & Maxime Maheu & Florent Meyniel & Mariano Sigman & Liping Wang & Santiago Figueira & Sergio Romano & Stanislas Dehaene
December 2020, Volume 16, Issue 12
- 1-13 CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines
by Dongdong Lin & Hima B Yalamanchili & Xinmin Zhang & Nathan E Lewis & Christina S Alves & Joost Groot & Johnny Arnsdorf & Sara P Bjørn & Tune Wulff & Bjørn G Voldborg & Yizhou Zhou & Baohong Zhang - 1-13 Confidence intervals by constrained optimization—An algorithm and software package for practical identifiability analysis in systems biology
by Ivan Borisov & Evgeny Metelkin - 1-15 Control of filament length by a depolymerizing gradient
by Arnab Datta & David Harbage & Jane Kondev - 1-17 Multiobjective optimization identifies cancer-selective combination therapies
by Otto I Pulkkinen & Prson Gautam & Ville Mustonen & Tero Aittokallio - 1-17 A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease
by Pamela N Luna & Jonathan M Mansbach & Chad A Shaw - 1-18 Optimal adjustment of the human circadian clock in the real world
by Samuel Christensen & Yitong Huang & Olivia J Walch & Daniel B Forger - 1-18 Searching through functional space reveals distributed visual, auditory, and semantic coding in the human brain
by Sreejan Kumar & Cameron T Ellis & Thomas P O’Connell & Marvin M Chun & Nicholas B Turk-Browne - 1-19 FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy
by Daniel F Nino & Daniel Djayakarsana & Joshua N Milstein - 1-21 A mathematical model of local and global attention in natural scene viewing
by Noa Malem-Shinitski & Manfred Opper & Sebastian Reich & Lisa Schwetlick & Stefan A Seelig & Ralf Engbert - 1-21 Drug2ways: Reasoning over causal paths in biological networks for drug discovery
by Daniel Rivas-Barragan & Sarah Mubeen & Francesc Guim Bernat & Martin Hofmann-Apitius & Daniel Domingo-Fernández - 1-21 Practical considerations for measuring the effective reproductive number, Rt
by Katelyn M Gostic & Lauren McGough & Edward B Baskerville & Sam Abbott & Keya Joshi & Christine Tedijanto & Rebecca Kahn & Rene Niehus & James A Hay & Pablo M De Salazar & Joel Hellewell & Sophie Meakin & James D Munday & Nikos I Bosse & Katharine Sherrat & Robin N Thompson & Laura F White & Jana S Huisman & Jérémie Scire & Sebastian Bonhoeffer & Tanja Stadler & Jacco Wallinga & Sebastian Funk & Marc Lipsitch & Sarah Cobey - 1-21 Population variability in the generation and selection of T-cell repertoires
by Zachary Sethna & Giulio Isacchini & Thomas Dupic & Thierry Mora & Aleksandra M Walczak & Yuval Elhanati - 1-22 Quantification of nematic cell polarity in three-dimensional tissues
by André Scholich & Simon Syga & Hernán Morales-Navarrete & Fabián Segovia-Miranda & Hidenori Nonaka & Kirstin Meyer & Walter de Back & Lutz Brusch & Yannis Kalaidzidis & Marino Zerial & Frank Jülicher & Benjamin M Friedrich - 1-22 Reconciling emergences: An information-theoretic approach to identify causal emergence in multivariate data
by Fernando E Rosas & Pedro A M Mediano & Henrik J Jensen & Anil K Seth & Adam B Barrett & Robin L Carhart-Harris & Daniel Bor - 1-23 Modeling habitat connectivity in support of multiobjective species movement: An application to amphibian habitat systems
by Timothy C Matisziw & Ashkan Gholamialam & Kathleen M Trauth - 1-23 A functional theory of bistable perception based on dynamical circular inference
by Pantelis Leptourgos & Vincent Bouttier & Renaud Jardri & Sophie Denève - 1-24 Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging
by Julienne LaChance & Daniel J Cohen - 1-24 Optimal learning with excitatory and inhibitory synapses
by Alessandro Ingrosso - 1-25 The DIOS framework for optimizing infectious disease surveillance: Numerical methods for simulation and multi-objective optimization of surveillance network architectures
by Qu Cheng & Philip A Collender & Alexandra K Heaney & Xintong Li & Rohini Dasan & Charles Li & Joseph A Lewnard & Jonathan L Zelner & Song Liang & Howard H Chang & Lance A Waller & Benjamin A Lopman & Changhong Yang & Justin V Remais - 1-26 Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage
by Samuel P Ingram & Nicholas T Henthorn & John W Warmenhoven & Norman F Kirkby & Ranald I Mackay & Karen J Kirkby & Michael J Merchant - 1-27 Evaluation of CD8 T cell killing models with computer simulations of 2-photon imaging experiments
by Ananya Rastogi & Philippe A Robert & Stephan Halle & Michael Meyer-Hermann - 1-29 Differential effects of propofol and ketamine on critical brain dynamics
by Thomas F Varley & Olaf Sporns & Aina Puce & John Beggs - 1-29 Biologically-informed neural networks guide mechanistic modeling from sparse experimental data
by John H Lagergren & John T Nardini & Ruth E Baker & Matthew J Simpson & Kevin B Flores - 1-30 Accurate prediction of kinase-substrate networks using knowledge graphs
by Vít Nováček & Gavin McGauran & David Matallanas & Adrián Vallejo Blanco & Piero Conca & Emir Muñoz & Luca Costabello & Kamalesh Kanakaraj & Zeeshan Nawaz & Brian Walsh & Sameh K Mohamed & Pierre-Yves Vandenbussche & Colm J Ryan & Walter Kolch & Dirk Fey - 1-32 A generative spiking neural-network model of goal-directed behaviour and one-step planning
by Ruggero Basanisi & Andrea Brovelli & Emilio Cartoni & Gianluca Baldassarre - 1-32 Estimating individuals’ genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data
by Christopher M Pooley & Glenn Marion & Stephen C Bishop & Richard I Bailey & Andrea B Doeschl-Wilson - 1-32 The two kinds of free energy and the Bayesian revolution
by Sebastian Gottwald & Daniel A Braun - 1-32 Unbiased and efficient log-likelihood estimation with inverse binomial sampling
by Bas van Opheusden & Luigi Acerbi & Wei Ji Ma - 1-40 Measuring spectrally-resolved information transfer
by Edoardo Pinzuti & Patricia Wollstadt & Aaron Gutknecht & Oliver Tüscher & Michael Wibral
November 2020, Volume 16, Issue 11
- 1-11 Ten simple rules for starting research in your late teens
by Cameron Mura & Mike Chalupa & Abigail M Newbury & Jack Chalupa & Philip E Bourne - 1-14 Tracking and predicting U.S. influenza activity with a real-time surveillance network
by Sequoia I Leuba & Reza Yaesoubi & Marina Antillon & Ted Cohen & Christoph Zimmer - 1-14 Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy
by Doruk Cakmakci & Emin Onur Karakaslar & Elisa Ruhland & Marie-Pierre Chenard & Francois Proust & Martial Piotto & Izzie Jacques Namer & A Ercument Cicek - 1-15 Quantification of Ebola virus replication kinetics in vitro
by Laura E Liao & Jonathan Carruthers & Sophie J Smither & CL4 Virology Team & Simon A Weller & Diane Williamson & Thomas R Laws & Isabel García-Dorival & Julian Hiscox & Benjamin P Holder & Catherine A A Beauchemin & Alan S Perelson & Martín López-García & Grant Lythe & John N Barr & Carmen Molina-París - 1-15 Testing structural identifiability by a simple scaling method
by Mario Castro & Rob J de Boer - 1-16 EventEpi—A natural language processing framework for event-based surveillance
by Auss Abbood & Alexander Ullrich & Rüdiger Busche & Stéphane Ghozzi - 1-18 The Moran process on 2-chromatic graphs
by Kamran Kaveh & Alex McAvoy & Krishnendu Chatterjee & Martin A Nowak - 1-18 Maximizing the reusability of gene expression data by predicting missing metadata
by Pei-Yau Lung & Dongrui Zhong & Xiaodong Pang & Yan Li & Jinfeng Zhang - 1-18 Inferring a network from dynamical signals at its nodes
by Corey Weistuch & Luca Agozzino & Lilianne R Mujica-Parodi & Ken A Dill - 1-19 Systems biology informed deep learning for inferring parameters and hidden dynamics
by Alireza Yazdani & Lu Lu & Maziar Raissi & George Em Karniadakis - 1-20 Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium
by Román Zapién-Campos & Michael Sieber & Arne Traulsen - 1-20 Biological network growth in complex environments: A computational framework
by Torsten Johann Paul & Philip Kollmannsberger - 1-20 Identifying longevity associated genes by integrating gene expression and curated annotations
by F William Townes & Kareem Carr & Jeffrey W Miller - 1-21 An exact method for quantifying the reliability of end-of-epidemic declarations in real time
by Kris V Parag & Christl A Donnelly & Rahul Jha & Robin N Thompson - 1-21 A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection
by Oliver M Crook & Aikaterini Geladaki & Daniel J H Nightingale & Owen L Vennard & Kathryn S Lilley & Laurent Gatto & Paul D W Kirk - 1-21 Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species
by Yumin Zheng & Haohan Wang & Yang Zhang & Xin Gao & Eric P Xing & Min Xu - 1-22 Modelling pathogen spread in a healthcare network: Indirect patient movements
by Monika J Piotrowska & Konrad Sakowski & André Karch & Hannan Tahir & Johannes Horn & Mirjam E Kretzschmar & Rafael T Mikolajczyk - 1-22 DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
by Maxat Kulmanov & Robert Hoehndorf - 1-25 A dual-feedback loop model of the mammalian circadian clock for multi-input control of circadian phase
by Lindsey S Brown & Francis J Doyle III - 1-26 Dopamine release, diffusion and uptake: A computational model for synaptic and volume transmission
by Kathleen Wiencke & Annette Horstmann & David Mathar & Arno Villringer & Jane Neumann - 1-27 Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells
by Azusa Tanaka & Yasuhiro Ishitsuka & Hiroki Ohta & Akihiro Fujimoto & Jun-ichirou Yasunaga & Masao Matsuoka - 1-30 Interspike intervals within retinal spike bursts combinatorially encode multiple stimulus features
by Toshiyuki Ishii & Toshihiko Hosoya - 1-32 Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins
by Amir Bitran & William M Jacobs & Eugene Shakhnovich - 1-34 Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach
by Howard Bowman & Joseph L Brooks & Omid Hajilou & Alexia Zoumpoulaki & Vladimir Litvak - 1-41 PPM-Decay: A computational model of auditory prediction with memory decay
by Peter M C Harrison & Roberta Bianco & Maria Chait & Marcus T Pearce
October 2020, Volume 16, Issue 10
- 1-8 LocusFocus: Web-based colocalization for the annotation and functional follow-up of GWAS
by Naim Panjwani & Fan Wang & Scott Mastromatteo & Allen Bao & Cheng Wang & Gengming He & Jiafen Gong & Johanna M Rommens & Lei Sun & Lisa J Strug - 1-9 Ten simple rules for building an antiracist lab
by V Bala Chaudhary & Asmeret Asefaw Berhe - 1-9 Ten simple rules for women principal investigators during a pandemic
by Pamela K Kreeger & Amy Brock & Holly C Gibbs & K Jane Grande-Allen & Alice H Huang & Kristyn S Masters & Padmini Rangamani & Michaela R Reagan & Shannon L Servoss - 1-10 Multiscale community detection in Cytoscape
by Akshat Singhal & Song Cao & Christopher Churas & Dexter Pratt & Santo Fortunato & Fan Zheng & Trey Ideker - 1-16 Mathematical model predicts response to chemotherapy in advanced non-resectable non-small cell lung cancer patients treated with platinum-based doublet
by Emilia Kozłowska & Rafał Suwiński & Monika Giglok & Andrzej Świerniak & Marek Kimmel - 1-16 Inferring tumor progression in large datasets
by Mohammadreza Mohaghegh Neyshabouri & Seong-Hwan Jun & Jens Lagergren - 1-18 A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies
by Audrey McCombs & Claus Kadelka - 1-18 Estimation of the force of infection and infectious period of skin sores in remote Australian communities using interval-censored data
by Michael J Lydeamore & Patricia T Campbell & David J Price & Yue Wu & Adrian J Marcato & Will Cuningham & Jonathan R Carapetis & Ross M Andrews & Malcolm I McDonald & Jodie McVernon & Steven Y C Tong & James M McCaw - 1-18 Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals
by Etienne Combrisson & Timothy Nest & Andrea Brovelli & Robin A A Ince & Juan L P Soto & Aymeric Guillot & Karim Jerbi - 1-19 Exploring the sequence fitness landscape of a bridge between protein folds
by Pengfei Tian & Robert B Best - 1-19 Time varying methods to infer extremes in dengue transmission dynamics
by Jue Tao Lim & Yiting Han & Borame Sue Lee Dickens & Lee Ching Ng & Alex R Cook - 1-19 Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness
by Sen Pei & Jeffrey Shaman - 1-20 Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance
by Dharmeshkumar Patel & Jonathan E Barnes & Wayne I L Davies & Deborah L Stenkamp & Jagdish Suresh Patel - 1-20 Genome Complexity Browser: Visualization and quantification of genome variability
by Alexander Manolov & Dmitry Konanov & Dmitry Fedorov & Ivan Osmolovsky & Rinat Vereshchagin & Elena Ilina - 1-21 A mathematical model of flagellar gene regulation and construction in Salmonella enterica
by Kiersten Utsey & James P Keener - 1-21 A genotype imputation method for de-identified haplotype reference information by using recurrent neural network
by Kaname Kojima & Shu Tadaka & Fumiki Katsuoka & Gen Tamiya & Masayuki Yamamoto & Kengo Kinoshita - 1-21 Iterative point set registration for aligning scRNA-seq data
by Amir Alavi & Ziv Bar-Joseph - 1-21 Forecasting influenza in Europe using a metapopulation model incorporating cross-border commuting and air travel
by Sarah C Kramer & Sen Pei & Jeffrey Shaman - 1-21 Paired fruit flies synchronize behavior: Uncovering social interactions in Drosophila melanogaster
by Ugne Klibaite & Joshua W Shaevitz - 1-22 Metabolic pathway inference using multi-label classification with rich pathway features
by Abdur Rahman M. A. Basher & Ryan J McLaughlin & Steven J Hallam - 1-22 A data-driven characterisation of natural facial expressions when giving good and bad news
by David M Watson & Ben B Brown & Alan Johnston - 1-23 Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts
by Andrew F Magee & Sebastian Höhna & Tetyana I Vasylyeva & Adam D Leaché & Vladimir N Minin - 1-23 Reduction in social learning and increased policy uncertainty about harmful intent is associated with pre-existing paranoid beliefs: Evidence from modelling a modified serial dictator game
by Joseph M Barnby & Vaughan Bell & Mitul A Mehta & Michael Moutoussis - 1-24 Learning gene networks underlying clinical phenotypes using SNP perturbation
by Calvin McCarter & Judie Howrylak & Seyoung Kim - 1-24 Likelihood-free nested sampling for parameter inference of biochemical reaction networks
by Jan Mikelson & Mustafa Khammash - 1-25 Significance of trends in gait dynamics
by Klaudia Kozlowska & Miroslaw Latka & Bruce J West - 1-25 Models of SIV rebound after treatment interruption that involve multiple reactivation events
by Christiaan H van Dorp & Jessica M Conway & Dan H Barouch & James B Whitney & Alan S Perelson - 1-26 Intuitive physical reasoning about objects’ masses transfers to a visuomotor decision task consistent with Newtonian physics
by Nils Neupärtl & Fabian Tatai & Constantin A Rothkopf - 1-27 Recurrent neural networks can explain flexible trading of speed and accuracy in biological vision
by Courtney J Spoerer & Tim C Kietzmann & Johannes Mehrer & Ian Charest & Nikolaus Kriegeskorte - 1-27 Reward-predictive representations generalize across tasks in reinforcement learning
by Lucas Lehnert & Michael L Littman & Michael J Frank - 1-27 Penalized regression and model selection methods for polygenic scores on summary statistics
by Jack Pattee & Wei Pan - 1-32 Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis
by Ruijin Wu & Rahul Prabhu & Aysegul Ozkan & Meera Sitharam - 1-32 Optimising age coverage of seasonal influenza vaccination in England: A mathematical and health economic evaluation
by Edward M Hill & Stavros Petrou & Henry Forster & Simon de Lusignan & Ivelina Yonova & Matt J Keeling - 1-38 The covariance perceptron: A new paradigm for classification and processing of time series in recurrent neuronal networks
by Matthieu Gilson & David Dahmen & Rubén Moreno-Bote & Andrea Insabato & Moritz Helias - 1-41 Protein-protein interactions in neurodegenerative diseases: A conspiracy theory
by Travis B Thompson & Pavanjit Chaggar & Ellen Kuhl & Alain Goriely & for the Alzheimer’s Disease Neuroimaging Initiative - 1-42 Biophysically detailed mathematical models of multiscale cardiac active mechanics
by Francesco Regazzoni & Luca Dedè & Alfio Quarteroni - 1-48 Finding, visualizing, and quantifying latent structure across diverse animal vocal repertoires
by Tim Sainburg & Marvin Thielk & Timothy Q Gentner
September 2020, Volume 16, Issue 9
- 1-14 Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule
by Kwang Su Kim & Tatsunari Kondoh & Yusuke Asai & Ayato Takada & Shingo Iwami - 1-16 Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion
by Nikolaus Korfhage & Markus Mühling & Stephan Ringshandl & Anke Becker & Bernd Schmeck & Bernd Freisleben - 1-17 DeepHE: Accurately predicting human essential genes based on deep learning
by Xue Zhang & Wangxin Xiao & Weijia Xiao - 1-18 All-atom simulation of the HET-s prion replication
by Luca Terruzzi & Giovanni Spagnolli & Alberto Boldrini & Jesús R Requena & Emiliano Biasini & Pietro Faccioli - 1-19 Characterizing chromatin folding coordinate and landscape with deep learning
by Wen Jun Xie & Yifeng Qi & Bin Zhang - 1-19 Alcoholic liver disease: A registry view on comorbidities and disease prediction
by Dhouha Grissa & Ditlev Nytoft Rasmussen & Aleksander Krag & Søren Brunak & Lars Juhl Jensen - 1-20 Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
by Ryan E Pavlovicz & Hahnbeom Park & Frank DiMaio - 1-20 NuSeT: A deep learning tool for reliably separating and analyzing crowded cells
by Linfeng Yang & Rajarshi P Ghosh & J Matthew Franklin & Simon Chen & Chenyu You & Raja R Narayan & Marc L Melcher & Jan T Liphardt - 1-20 Minimizing the number of optimizations for efficient community dynamic flux balance analysis
by James D Brunner & Nicholas Chia - 1-21 Increased comparability between RNA-Seq and microarray data by utilization of gene sets
by Frans M van der Kloet & Jeroen Buurmans & Martijs J Jonker & Age K Smilde & Johan A Westerhuis - 1-21 A simple, scalable approach to building a cross-platform transcriptome atlas
by Paul W Angel & Nadia Rajab & Yidi Deng & Chris M Pacheco & Tyrone Chen & Kim-Anh Lê Cao & Jarny Choi & Christine A Wells - 1-22 Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures
by Bo Chen & Wei Xu - 1-22 Prospects for detecting early warning signals in discrete event sequence data: Application to epidemiological incidence data
by Emma Southall & Michael J Tildesley & Louise Dyson - 1-23 Discovering functional sequences with RELICS, an analysis method for CRISPR screens
by Patrick C Fiaux & Hsiuyi V Chen & Poshen B Chen & Aaron R Chen & Graham McVicker - 1-24 Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms
by Rajib Mukherjee & Burcu Beykal & Adam T Szafran & Melis Onel & Fabio Stossi & Maureen G Mancini & Dillon Lloyd & Fred A Wright & Lan Zhou & Michael A Mancini & Efstratios N Pistikopoulos - 1-24 Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data
by Camila P. E. de Souza & Mirela Andronescu & Tehmina Masud & Farhia Kabeer & Justina Biele & Emma Laks & Daniel Lai & Patricia Ye & Jazmine Brimhall & Beixi Wang & Edmund Su & Tony Hui & Qi Cao & Marcus Wong & Michelle Moksa & Richard A Moore & Martin Hirst & Samuel Aparicio & Sohrab P Shah - 1-25 Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images
by William Pilcher & Xingyu Yang & Anastasia Zhurikhina & Olga Chernaya & Yinghan Xu & Peng Qiu & Denis Tsygankov - 1-25 Efficient sensory coding of multidimensional stimuli
by Thomas E Yerxa & Eric Kee & Michael R DeWeese & Emily A Cooper - 1-25 The relative contributions of infectious and mitotic spread to HTLV-1 persistence
by Daniel J Laydon & Vikram Sunkara & Lies Boelen & Charles R M Bangham & Becca Asquith - 1-27 Response nonlinearities in networks of spiking neurons
by Alessandro Sanzeni & Mark H Histed & Nicolas Brunel - 1-27 Inferring a complete genotype-phenotype map from a small number of measured phenotypes
by Zachary R Sailer & Sarah H Shafik & Robert L Summers & Alex Joule & Alice Patterson-Robert & Rowena E Martin & Michael J Harms - 1-27 Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention
by Yunjun Zhang & Thomas Leitner & Jan Albert & Tom Britton - 1-28 Similarities and differences in spatial and non-spatial cognitive maps
by Charley M Wu & Eric Schulz & Mona M Garvert & Björn Meder & Nicolas W Schuck - 1-29 Uncertainty-driven regulation of learning and exploration in adolescents: A computational account
by Marieke Jepma & Jessica V Schaaf & Ingmar Visser & Hilde M Huizenga - 1-39 Fast estimation of time-varying infectious disease transmission rates
by Mikael Jagan & Michelle S deJonge & Olga Krylova & David J D Earn
August 2020, Volume 16, Issue 8
- 1-16 Information transmission from NFkB signaling dynamics to gene expression
by Alok Maity & Roy Wollman - 1-17 Deconvolving the contributions of cell-type heterogeneity on cortical gene expression
by Ellis Patrick & Mariko Taga & Ayla Ergun & Bernard Ng & William Casazza & Maria Cimpean & Christina Yung & Julie A Schneider & David A Bennett & Chris Gaiteri & Philip L De Jager & Elizabeth M Bradshaw & Sara Mostafavi - 1-18 Multiplexing information flow through dynamic signalling systems
by Giorgos Minas & Dan J Woodcock & Louise Ashall & Claire V Harper & Michael R H White & David A Rand - 1-20 Template-based mapping of dynamic motifs in tissue morphogenesis
by Tomer Stern & Stanislav Y Shvartsman & Eric F Wieschaus - 1-20 A novel single-cell based method for breast cancer prognosis
by Xiaomei Li & Lin Liu & Gregory J Goodall & Andreas Schreiber & Taosheng Xu & Jiuyong Li & Thuc D Le - 1-20 Optimising efficacy of antibiotics against systemic infection by varying dosage quantities and times
by Andy Hoyle & David Cairns & Iona Paterson & Stuart McMillan & Gabriela Ochoa & Andrew P Desbois - 1-21 JBrowse Connect: A server API to connect JBrowse instances and users
by Eric Yao & Robert Buels & Lincoln Stein & Taner Z Sen & Ian Holmes - 1-21 Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits
by Craig A Glastonbury & Sara L Pulit & Julius Honecker & Jenny C Censin & Samantha Laber & Hanieh Yaghootkar & Nilufer Rahmioglu & Emilie Pastel & Katerina Kos & Andrew Pitt & Michelle Hudson & Christoffer Nellåker & Nicola L Beer & Hans Hauner & Christian M Becker & Krina T Zondervan & Timothy M Frayling & Melina Claussnitzer & Cecilia M Lindgren - 1-22 Inferring the ancestry of parents and grandparents from genetic data
by Jingwen Pei & Yiming Zhang & Rasmus Nielsen & Yufeng Wu - 1-23 Order matters: How covert value updating during sequential option sampling shapes economic preference
by Chen Hu & Philippe Domenech & Mathias Pessiglione - 1-26 Effect of magnitude and variability of energy of activation in multisite ultrasensitive biochemical processes
by Leonila Lagunes & Lee Bardwell & German A Enciso - 1-27 A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis
by Amrit Dhar & Duncan K Ralph & Vladimir N Minin & Frederick A Matsen IV - 1-27 Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones
by Fabrizio Clarelli & Adam Palmer & Bhupender Singh & Merete Storflor & Silje Lauksund & Ted Cohen & Sören Abel & Pia Abel zur Wiesch - 1-28 Dynamic estimation of auditory temporal response functions via state-space models with Gaussian mixture process noise
by Sina Miran & Alessandro Presacco & Jonathan Z Simon & Michael C Fu & Steven I Marcus & Behtash Babadi - 1-29 Reliable estimation of membrane curvature for cryo-electron tomography
by Maria Salfer & Javier F Collado & Wolfgang Baumeister & Rubén Fernández-Busnadiego & Antonio Martínez-Sánchez - 1-29 Understanding multivariate brain activity: Evaluating the effect of voxelwise noise correlations on population codes in functional magnetic resonance imaging
by Ru-Yuan Zhang & Xue-Xin Wei & Kendrick Kay - 1-29 Modeling time-varying brain networks with a self-tuning optimized Kalman filter
by D Pascucci & M Rubega & G Plomp - 1-34 Buildup and bistability in auditory streaming as an evidence accumulation process with saturation
by Quynh-Anh Nguyen & John Rinzel & Rodica Curtu - 1-39 Task-evoked activity quenches neural correlations and variability across cortical areas
by Takuya Ito & Scott L Brincat & Markus Siegel & Ravi D Mill & Biyu J He & Earl K Miller & Horacio G Rotstein & Michael W Cole
July 2020, Volume 16, Issue 7
- 1-6 Ten simple rules for reading a scientific paper
by Maureen A Carey & Kevin L Steiner & William A Petri Jr - 1-10 Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices
by Joe Hilton & Matt J Keeling - 1-12 A framework to assess the quality and impact of bioinformatics training across ELIXIR
by Kim T Gurwitz & Prakash Singh Gaur & Louisa J Bellis & Lee Larcombe & Eva Alloza & Balint Laszlo Balint & Alexander Botzki & Jure Dimec & Victoria Dominguez del Angel & Pedro L Fernandes & Eija Korpelainen & Roland Krause & Mateusz Kuzak & Loredana Le Pera & Brane Leskošek & Jessica M Lindvall & Diana Marek & Paula A Martinez & Tuur Muyldermans & Ståle Nygård & Patricia M Palagi & Hedi Peterson & Fotis Psomopoulos & Vojtech Spiwok & Celia W G van Gelder & Allegra Via & Marko Vidak & Daniel Wibberg & Sarah L Morgan & Gabriella Rustici - 1-14 Multidimensional phenotyping predicts lifespan and quantifies health in Caenorhabditis elegans
by Céline N Martineau & André E X Brown & Patrick Laurent - 1-19 Socioeconomic bias in influenza surveillance
by Samuel V Scarpino & James G Scott & Rosalind M Eggo & Bruce Clements & Nedialko B Dimitrov & Lauren Ancel Meyers - 1-20 A practical application of generative adversarial networks for RNA-seq analysis to predict the molecular progress of Alzheimer's disease
by Jinhee Park & Hyerin Kim & Jaekwang Kim & Mookyung Cheon - 1-20 iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding
by Huiyuan Chen & Feixiong Cheng & Jing Li - 1-20 Beyond ranking nodes: Predicting epidemic outbreak sizes by network centralities
by Doina Bucur & Petter Holme - 1-20 Using information theory to optimise epidemic models for real-time prediction and estimation
by Kris V Parag & Christl A Donnelly - 1-21 Immunization strategies in networks with missing data
by Samuel F Rosenblatt & Jeffrey A Smith & G Robin Gauthier & Laurent Hébert-Dufresne - 1-21 A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms
by August George & Paola Bisignano & John M Rosenberg & Michael Grabe & Daniel M Zuckerman - 1-22 Estimation of neuron parameters from imperfect observations
by Joseph D Taylor & Samuel Winnall & Alain Nogaret - 1-22 Predicting lymphatic filariasis elimination in data-limited settings: A reconstructive computational framework for combining data generation and model discovery
by Morgan E Smith & Emily Griswold & Brajendra K Singh & Emmanuel Miri & Abel Eigege & Solomon Adelamo & John Umaru & Kenrick Nwodu & Yohanna Sambo & Jonathan Kadimbo & Jacob Danyobi & Frank O Richards & Edwin Michael - 1-23 A novel riboswitch classification based on imbalanced sequences achieved by machine learning
by Solomon Shiferaw Beyene & Tianyi Ling & Blagoj Ristevski & Ming Chen - 1-23 Cortical ignition dynamics is tightly linked to the core organisation of the human connectome
by Samy Castro & Wael El-Deredy & Demian Battaglia & Patricio Orio - 1-24 Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data
by Xian F Mallory & Mohammadamin Edrisi & Nicholas Navin & Luay Nakhleh - 1-24 An in vitro quantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias
by Jennifer L Wilson & Dan Lu & Nick Corr & Aaron Fullerton & James Lu - 1-25 Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data
by Richard J Beck & Dario I Bijker & Joost B Beltman - 1-26 A simple model for learning in volatile environments
by Payam Piray & Nathaniel D Daw - 1-27 Cross-species regulatory sequence activity prediction
by David R Kelley - 1-34 Brain-optimized extraction of complex sound features that drive continuous auditory perception
by Julia Berezutskaya & Zachary V Freudenburg & Umut Güçlü & Marcel A J van Gerven & Nick F Ramsey
June 2020, Volume 16, Issue 6
- 1-13 Measurable health effects associated with the daylight saving time shift
by Hanxin Zhang & Torsten Dahlén & Atif Khan & Gustaf Edgren & Andrey Rzhetsky - 1-15 XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization
by Will Xiao & Gabriel Kreiman - 1-15 Assessing predictors for new post translational modification sites: A case study on hydroxylation
by Damiano Piovesan & Andras Hatos & Giovanni Minervini & Federica Quaglia & Alexander Miguel Monzon & Silvio C E Tosatto - 1-17 Forecasting unprecedented ecological fluctuations
by Samuel R Bray & Bo Wang - 1-17 Sample-based modeling reveals bidirectional interplay between cell cycle progression and extrinsic apoptosis
by Dirke Imig & Nadine Pollak & Frank Allgöwer & Markus Rehm - 1-17 Disease evolution in reaction networks: Implications for a diagnostic problem
by Abolfazl Ramezanpour & Alireza Mashaghi - 1-18 A validation framework for neuroimaging software: The case of population receptive fields
by Garikoitz Lerma-Usabiaga & Noah Benson & Jonathan Winawer & Brian A Wandell - 1-21 Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves
by Federico Sevlever & Juan Pablo Di Bella & Alejandra C Ventura - 1-21 Kilohertz waveforms optimized to produce closed-state Na+ channel inactivation eliminate onset response in nerve conduction block
by Guosheng Yi & Warren M Grill - 1-22 Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data
by Nima Nouri & Steven H Kleinstein - 1-22 Resilience of three-dimensional sinusoidal networks in liver tissue
by Jens Karschau & André Scholich & Jonathan Wise & Hernán Morales-Navarrete & Yannis Kalaidzidis & Marino Zerial & Benjamin M Friedrich - 1-24 Emergence of cooperative bistability and robustness of gene regulatory networks
by Shintaro Nagata & Macoto Kikuchi - 1-25 Combined model-free and model-sensitive reinforcement learning in non-human primates
by Bruno Miranda & W M Nishantha Malalasekera & Timothy E Behrens & Peter Dayan & Steven W Kennerley - 1-25 Realistic modeling of mesoscopic ephaptic coupling in the human brain
by Giulio Ruffini & Ricardo Salvador & Ehsan Tadayon & Roser Sanchez-Todo & Alvaro Pascual-Leone & Emiliano Santarnecchi - 1-26 Natural scene statistics predict how humans pool information across space in surface tilt estimation
by Seha Kim & Johannes Burge - 1-27 Classifying sex and strain from mouse ultrasonic vocalizations using deep learning
by A Ivanenko & P Watkins & M A J van Gerven & K Hammerschmidt & B Englitz - 1-27 A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data
by David Lamparter & Rajat Bhatnagar & Katja Hebestreit & T Grant Belgard & Alice Zhang & Victor Hanson-Smith - 1-27 Brain dynamics for confidence-weighted learning
by Florent Meyniel - 1-27 Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface
by Anna U Lowegard & Marcel S Frenkel & Graham T Holt & Jonathan D Jou & Adegoke A Ojewole & Bruce R Donald - 1-28 Multiscale modeling of human cerebrovasculature: A hybrid approach using image-based geometry and a mathematical algorithm
by Satoshi Ii & Hiroki Kitade & Shunichi Ishida & Yohsuke Imai & Yoshiyuki Watanabe & Shigeo Wada - 1-29 It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology
by Niklas Korsbo & Henrik Jönsson - 1-29 Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites
by Ethan D Evans & Chengzhen Dai & Siavash Isazadeh & Shinkyu Park & Carlo Ratti & Eric J Alm - 1-34 Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model
by Sandra Mayr & Fabian Hauser & Sujitha Puthukodan & Markus Axmann & Janett Göhring & Jaroslaw Jacak
May 2020, Volume 16, Issue 5
- 1-9 Ten Simple Rules for a successful remote postdoc
by Kevin R Burgio & Caitlin McDonough MacKenzie & Stephanie B Borrelle & S K Morgan Ernest & Jacquelyn L Gill & Kurt E Ingeman & Amy Teffer & Ethan P White - 1-9 Ten simple rules for running a successful women-in-STEM organization on an academic campus
by Deborah D Rupert & Alexandra C Nowlan & Oliver H Tam & Molly Gale Hammell - 1-12 Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles
by Alastair M Kilpatrick & Audra Anjum & Lonnie Welch - 1-15 Inference on dengue epidemics with Bayesian regime switching models
by Jue Tao Lim & Borame Sue Dickens & Sun Haoyang & Ng Lee Ching & Alex R Cook - 1-16 Early warning signals in motion inference
by Yuval Hart & Maryam Vaziri-Pashkam & L Mahadevan - 1-17 Calibration of individual-based models to epidemiological data: A systematic review
by C Marijn Hazelbag & Jonathan Dushoff & Emanuel M Dominic & Zinhle E Mthombothi & Wim Delva - 1-17 Microbial communities display alternative stable states in a fluctuating environment
by Clare I Abreu & Vilhelm L Andersen Woltz & Jonathan Friedman & Jeff Gore - 1-18 Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system
by Sinu Paul & Nathan P Croft & Anthony W Purcell & David C Tscharke & Alessandro Sette & Morten Nielsen & Bjoern Peters - 1-18 Ad hoc efforts for advancing data science education
by Orianna DeMasi & Alexandra Paxton & Kevin Koy - 1-19 Towards a data-driven characterization of behavioral changes induced by the seasonal flu
by Nicolò Gozzi & Daniela Perrotta & Daniela Paolotti & Nicola Perra - 1-19 GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm
by Lei Wang & Zhu-Hong You & Yang-Ming Li & Kai Zheng & Yu-An Huang - 1-21 A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type
by Alan Le Goallec & Braden T Tierney & Jacob M Luber & Evan M Cofer & Aleksandar D Kostic & Chirag J Patel - 1-22 Compositional Lotka-Volterra describes microbial dynamics in the simplex
by Tyler A Joseph & Liat Shenhav & Joao B Xavier & Eran Halperin & Itsik Pe’er - 1-22 iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation
by Kai Zheng & Zhu-Hong You & Jian-Qiang Li & Lei Wang & Zhen-Hao Guo & Yu-An Huang