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Content
March 2021, Volume 17, Issue 3
- 1-19 Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks
by Yang Li & Chengxin Zhang & Eric W Bell & Wei Zheng & Xiaogen Zhou & Dong-Jun Yu & Yang Zhang - 1-19 Reconstructing feedback representations in the ventral visual pathway with a generative adversarial autoencoder
by Haider Al-Tahan & Yalda Mohsenzadeh - 1-19 Signal-to-signal neural networks for improved spike estimation from calcium imaging data
by Jilt Sebastian & Mriganka Sur & Hema A Murthy & Mathew Magimai-Doss - 1-20 Predicting microbial growth dynamics in response to nutrient availability
by Olga A Nev & Richard J Lindsay & Alys Jepson & Lisa Butt & Robert E Beardmore & Ivana Gudelj - 1-20 Can subjective pain be inferred from objective physiological data? Evidence from patients with sickle cell disease
by Mark J Panaggio & Daniel M Abrams & Fan Yang & Tanvi Banerjee & Nirmish R Shah - 1-20 Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model
by Gregory L Watson & Di Xiong & Lu Zhang & Joseph A Zoller & John Shamshoian & Phillip Sundin & Teresa Bufford & Anne W Rimoin & Marc A Suchard & Christina M Ramirez - 1-21 Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling
by Yekaterina S Pavlova & David Paez-Espino & Andrew Yu Morozov & Ilya S Belalov - 1-21 Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases
by Janani Durairaj & Elena Melillo & Harro J Bouwmeester & Jules Beekwilder & Dick de Ridder & Aalt D J van Dijk - 1-21 Collective predator evasion: Putting the criticality hypothesis to the test
by Pascal P Klamser & Pawel Romanczuk - 1-22 A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli
by Alexandre Oliveira & Joana Rodrigues & Eugénio Campos Ferreira & Lígia Rodrigues & Oscar Dias - 1-22 Connectivity, reproduction number, and mobility interact to determine communities’ epidemiological superspreader potential in a metapopulation network
by Brandon Lieberthal & Allison M Gardner - 1-23 Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements
by Kseniia Cheloshkina & Maria Poptsova - 1-23 Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models
by Denis A Shah & Erick D De Wolf & Pierce A Paul & Laurence V Madden - 1-23 Health inequities in influenza transmission and surveillance
by Casey M Zipfel & Vittoria Colizza & Shweta Bansal - 1-23 Public Baseline and shared response structures support the theory of antibody repertoire functional commonality
by Matthew I J Raybould & Claire Marks & Aleksandr Kovaltsuk & Alan P Lewis & Jiye Shi & Charlotte M Deane - 1-24 Parameters and determinants of responses to selection in antibody libraries
by Steven Schulz & Sébastien Boyer & Matteo Smerlak & Simona Cocco & Rémi Monasson & Clément Nizak & Olivier Rivoire - 1-25 Modelling the impact of clot fragmentation on the microcirculation after thrombectomy
by Wahbi K El-Bouri & Andrew MacGowan & Tamás I Józsa & Matthew J Gounis & Stephen J Payne - 1-25 Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance
by Vincent Brault & Bastien Mallein & Jean-François Rupprecht - 1-25 Inferring phenomenological models of first passage processes
by Catalina Rivera & David Hofmann & Ilya Nemenman - 1-25 Mechanical coupling in the nitrogenase complex
by Qi Huang & Monika Tokmina-Lukaszewska & Lewis E Johnson & Hayden Kallas & Bojana Ginovska & John W Peters & Lance C Seefeldt & Brian Bothner & Simone Raugei - 1-25 Perturbations both trigger and delay seizures due to generic properties of slow-fast relaxation oscillators
by Alberto Pérez-Cervera & Jaroslav Hlinka - 1-25 Optimal timing of one-shot interventions for epidemic control
by Francesco Di Lauro & István Z Kiss & Joel C Miller - 1-25 Prediction of amphipathic helix—membrane interactions with Rosetta
by Alican Gulsevin & Jens Meiler - 1-25 Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability
by Javier Rasero & Amy Isabella Sentis & Fang-Cheng Yeh & Timothy Verstynen - 1-25 Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach
by Josh L Espinoza & Chris L Dupont & Aubrie O’Rourke & Sinem Beyhan & Pavel Morales & Amy Spoering & Kirsten J Meyer & Agnes P Chan & Yongwook Choi & William C Nierman & Kim Lewis & Karen E Nelson - 1-26 Principles for data analysis workflows
by Sara Stoudt & Váleri N Vásquez & Ciera C Martinez - 1-27 Linear-nonlinear cascades capture synaptic dynamics
by Julian Rossbroich & Daniel Trotter & John Beninger & Katalin Tóth & Richard Naud - 1-27 Optimal prediction with resource constraints using the information bottleneck
by Vedant Sachdeva & Thierry Mora & Aleksandra M Walczak & Stephanie E Palmer - 1-28 How does Sec63 affect the conformation of Sec61 in yeast?
by Pratiti Bhadra & Lalitha Yadhanapudi & Karin Römisch & Volkhard Helms - 1-29 Fixation patterns in simple choice reflect optimal information sampling
by Frederick Callaway & Antonio Rangel & Thomas L Griffiths - 1-30 Graph of graphs analysis for multiplexed data with application to imaging mass cytometry
by Ya-Wei Eileen Lin & Tal Shnitzer & Ronen Talmon & Franz Villarroel-Espindola & Shruti Desai & Kurt Schalper & Yuval Kluger - 1-30 Neural modelling of the encoding of fast frequency modulation
by Alejandro Tabas & Katharina von Kriegstein
February 2021, Volume 17, Issue 2
- 1-10 Ten simple rules for running and managing virtual internships
by Johannes Werner & Debora Jeske - 1-11 Ten simple rules for engaging with artificial intelligence in biomedicine
by Avni Malik & Paranjay Patel & Lubaina Ehsan & Shan Guleria & Thomas Hartka & Sodiq Adewole & Sana Syed - 1-12 Ten simple rules for starting (and sustaining) an academic data science initiative
by Micaela S Parker & Arlyn E Burgess & Philip E Bourne - 1-12 Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective
by Hwai-Ray Tung & Rick Durrett - 1-13 A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
by Martín Garrido-Rodriguez & Daniel Lopez-Lopez & Francisco M Ortuno & María Peña-Chilet & Eduardo Muñoz & Marco A Calzado & Joaquin Dopazo - 1-15 Freedom to choose between public resources promotes cooperation
by Mohammad Salahshour - 1-15 Evaluating epidemic forecasts in an interval format
by Johannes Bracher & Evan L Ray & Tilmann Gneiting & Nicholas G Reich - 1-15 Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species
by Zutan Li & Hangjin Jiang & Lingpeng Kong & Yuanyuan Chen & Kun Lang & Xiaodan Fan & Liangyun Zhang & Cong Pian - 1-17 Adaptive social contact rates induce complex dynamics during epidemics
by Ronan F Arthur & James H Jones & Matthew H Bonds & Yoav Ram & Marcus W Feldman - 1-18 Deriving fine-scale models of human mobility from aggregated origin-destination flow data
by Constanze Ciavarella & Neil M Ferguson - 1-18 Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
by Florian Huber & Lars Ridder & Stefan Verhoeven & Jurriaan H Spaaks & Faruk Diblen & Simon Rogers & Justin J J van der Hooft - 1-19 Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches
by Judith A Bouman & Julien Riou & Sebastian Bonhoeffer & Roland R Regoes - 1-19 FastTrack: An open-source software for tracking varying numbers of deformable objects
by Benjamin Gallois & Raphaël Candelier - 1-19 A numerical framework for mechano-regulated tendon healing—Simulation of early regeneration of the Achilles tendon
by Thomas Notermans & Petri Tanska & Rami K Korhonen & Hanifeh Khayyeri & Hanna Isaksson - 1-20 Unsupervised manifold learning of collective behavior
by Mathew Titus & George Hagstrom & James R Watson - 1-20 KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions
by Bingjie Xue & Benjamin Jordan & Saqib Rizvi & Kristen M Naegle - 1-20 A mathematical model of the role of aggregation in sonic hedgehog signalling
by Daniel J A Derrick & Kathryn Wolton & Richard A Currie & Marcus John Tindall - 1-20 Evolution of heterogeneous perceptual limits and indifference in competitive foraging
by Richard P Mann - 1-21 From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach
by Ann-Kristin Becker & Marcus Dörr & Stephan B Felix & Fabian Frost & Hans J Grabe & Markus M Lerch & Matthias Nauck & Uwe Völker & Henry Völzke & Lars Kaderali - 1-21 On the importance of evolving phenotype distributions on evolutionary diversification
by Gil Jorge Barros Henriques & Koichi Ito & Christoph Hauert & Michael Doebeli - 1-22 End-to-end neural system identification with neural information flow
by K Seeliger & L Ambrogioni & Y Güçlütürk & L M van den Bulk & U Güçlü & M A J van Gerven - 1-22 TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations
by Qiao Liu & Lei Xie - 1-22 When to wake up? The optimal waking-up strategies for starvation-induced persistence
by Yusuke Himeoka & Namiko Mitarai - 1-23 Generating functional protein variants with variational autoencoders
by Alex Hawkins-Hooker & Florence Depardieu & Sebastien Baur & Guillaume Couairon & Arthur Chen & David Bikard - 1-24 A model of developmental canalization, applied to human cranial form
by Philipp Mitteroecker & Ekaterina Stansfield - 1-24 miRNA normalization enables joint analysis of several datasets to increase sensitivity and to reveal novel miRNAs differentially expressed in breast cancer
by Shay Ben-Elazar & Miriam Ragle Aure & Kristin Jonsdottir & Suvi-Katri Leivonen & Vessela N Kristensen & Emiel A M Janssen & Kristine Kleivi Sahlberg & Ole Christian Lingjærde & Zohar Yakhini - 1-24 Dynamics of chromosomal target search by a membrane-integrated one-component receptor
by Linda Martini & Sophie Brameyer & Elisabeth Hoyer & Kirsten Jung & Ulrich Gerland - 1-25 Nonlinear effects of intrinsic dynamics on temporal encoding in a model of avian auditory cortex
by Christof Fehrman & Tyler D Robbins & C Daniel Meliza - 1-25 Evidence for spreading seizure as a cause of theta-alpha activity electrographic pattern in stereo-EEG seizure recordings
by Viktor Sip & Julia Scholly & Maxime Guye & Fabrice Bartolomei & Viktor Jirsa - 1-25 Building clone-consistent ecosystem models
by Gerrit Ansmann & Tobias Bollenbach - 1-25 Impact of between-tissue differences on pan-cancer predictions of drug sensitivity
by John P Lloyd & Matthew B Soellner & Sofia D Merajver & Jun Z Li - 1-25 Functional parcellation of mouse visual cortex using statistical techniques reveals response-dependent clustering of cortical processing areas
by Mari Ganesh Kumar & Ming Hu & Aadhirai Ramanujan & Mriganka Sur & Hema A Murthy - 1-25 Fixation probabilities in graph-structured populations under weak selection
by Benjamin Allen & Christine Sample & Patricia Steinhagen & Julia Shapiro & Matthew King & Timothy Hedspeth & Megan Goncalves - 1-26 Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes
by Johannes Asplund-Samuelsson & Elton P Hudson - 1-26 Dynamics of COVID-19 under social distancing measures are driven by transmission network structure
by Anjalika Nande & Ben Adlam & Justin Sheen & Michael Z Levy & Alison L Hill - 1-26 A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors
by Juan Jiménez-Sánchez & Álvaro Martínez-Rubio & Anton Popov & Julián Pérez-Beteta & Youness Azimzade & David Molina-García & Juan Belmonte-Beitia & Gabriel F Calvo & Víctor M Pérez-García - 1-27 Integrated information structure collapses with anesthetic loss of conscious arousal in Drosophila melanogaster
by Angus Leung & Dror Cohen & Bruno van Swinderen & Naotsugu Tsuchiya - 1-29 Ancestral haplotype reconstruction in endogamous populations using identity-by-descent
by Kelly Finke & Michael Kourakos & Gabriela Brown & Huyen Trang Dang & Shi Jie Samuel Tan & Yuval B Simons & Shweta Ramdas & Alejandro A Schäffer & Rachel L Kember & Maja Bućan & Sara Mathieson - 1-29 Quantitative profiling of protease specificity
by Boris I Ratnikov & Piotr Cieplak & Albert G Remacle & Elise Nguyen & Jeffrey W Smith - 1-29 Role of neutrophil extracellular traps in regulation of lung cancer invasion and metastasis: Structural insights from a computational model
by Junho Lee & Donggu Lee & Sean Lawler & Yangjin Kim - 1-30 Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model
by Jordan Douglas & Rong Zhang & Remco Bouckaert - 1-30 Finding branched pathways in metabolic network via atom group tracking
by Yiran Huang & Yusi Xie & Cheng Zhong & Fengfeng Zhou - 1-31 Data-driven method to infer the seizure propagation patterns in an epileptic brain from intracranial electroencephalography
by Viktor Sip & Meysam Hashemi & Anirudh N Vattikonda & Marmaduke M Woodman & Huifang Wang & Julia Scholly & Samuel Medina Villalon & Maxime Guye & Fabrice Bartolomei & Viktor K Jirsa - 1-31 Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins
by Rahmatullah Roche & Sutanu Bhattacharya & Debswapna Bhattacharya - 1-33 Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning
by Philipp Mergenthaler & Santosh Hariharan & James M Pemberton & Corey Lourenco & Linda Z Penn & David W Andrews - 1-35 Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees
by George G Vega Yon & Duncan C Thomas & John Morrison & Huaiyu Mi & Paul D Thomas & Paul Marjoram - 1-36 Neural surprise in somatosensory Bayesian learning
by Sam Gijsen & Miro Grundei & Robert T Lange & Dirk Ostwald & Felix Blankenburg
January 2021, Volume 17, Issue 1
- 1-10 PEtab—Interoperable specification of parameter estimation problems in systems biology
by Leonard Schmiester & Yannik Schälte & Frank T Bergmann & Tacio Camba & Erika Dudkin & Janine Egert & Fabian Fröhlich & Lara Fuhrmann & Adrian L Hauber & Svenja Kemmer & Polina Lakrisenko & Carolin Loos & Simon Merkt & Wolfgang Müller & Dilan Pathirana & Elba Raimúndez & Lukas Refisch & Marcus Rosenblatt & Paul L Stapor & Philipp Städter & Dantong Wang & Franz-Georg Wieland & Julio R Banga & Jens Timmer & Alejandro F Villaverde & Sven Sahle & Clemens Kreutz & Jan Hasenauer & Daniel Weindl - 1-11 Chemical graph generators
by Mehmet Aziz Yirik & Christoph Steinbeck - 1-12 Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students
by Korryn Bodner & Chris Brimacombe & Emily S Chenery & Ariel Greiner & Anne M McLeod & Stephanie R Penk & Juan S Vargas Soto - 1-16 The risks of using the chi-square periodogram to estimate the period of biological rhythms
by Michael C Tackenberg & Jacob J Hughey - 1-16 Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing
by Bansho Masutani & Shin-ichi Arimura & Shinichi Morishita - 1-17 Friendly-rivalry solution to the iterated n-person public-goods game
by Yohsuke Murase & Seung Ki Baek - 1-18 mbkmeans: Fast clustering for single cell data using mini-batch k-means
by Stephanie C Hicks & Ruoxi Liu & Yuwei Ni & Elizabeth Purdom & Davide Risso - 1-18 The impact of interactions on invasion and colonization resistance in microbial communities
by Helen M Kurkjian & M Javad Akbari & Babak Momeni - 1-18 Real-time resolution of short-read assembly graph using ONT long reads
by Son Hoang Nguyen & Minh Duc Cao & Lachlan J M Coin - 1-18 Estimating the time-varying reproduction number of COVID-19 with a state-space method
by Shinsuke Koyama & Taiki Horie & Shigeru Shinomoto - 1-20 Modeling invasion patterns in the glioblastoma battlefield
by Martina Conte & Sergio Casas-Tintò & Juan Soler - 1-20 Improving probabilistic infectious disease forecasting through coherence
by Graham Casey Gibson & Kelly R Moran & Nicholas G Reich & Dave Osthus - 1-21 Predicting synchronous firing of large neural populations from sequential recordings
by Oleksandr Sorochynskyi & Stéphane Deny & Olivier Marre & Ulisse Ferrari - 1-21 Sensor-based localization of epidemic sources on human mobility networks
by Jun Li & Juliane Manitz & Enrico Bertuzzo & Eric D Kolaczyk - 1-22 Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data
by Andreas Tjärnberg & Omar Mahmood & Christopher A Jackson & Giuseppe-Antonio Saldi & Kyunghyun Cho & Lionel A Christiaen & Richard A Bonneau - 1-22 Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains
by Antonino Casile & Rose T Faghih & Emery N Brown - 1-23 Structured environments foster competitor coexistence by manipulating interspecies interfaces
by Tristan Ursell - 1-24 Active probing to highlight approaching transitions to ictal states in coupled neural mass models
by Vinícius Rezende Carvalho & Márcio Flávio Dutra Moraes & Sydney S Cash & Eduardo Mazoni Andrade Marçal Mendes - 1-24 CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models
by Lillian R Thistlethwaite & Varduhi Petrosyan & Xiqi Li & Marcus J Miller & Sarah H Elsea & Aleksandar Milosavljevic - 1-24 Modeling multi-sensory feedback control of zebrafish in a flow
by Daniel A Burbano-L. & Maurizio Porfiri - 1-25 A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response
by Evanthia Koukouli & Dennis Wang & Frank Dondelinger & Juhyun Park - 1-26 Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference
by Katharine Best & Dan H Barouch & Jeremie Guedj & Ruy M Ribeiro & Alan S Perelson - 1-27 Dissecting the links between reward and loss, decision-making, and self-reported affect using a computational approach
by Vikki Neville & Peter Dayan & Iain D Gilchrist & Elizabeth S Paul & Michael Mendl - 1-27 Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk
by Antanas Kalkauskas & Umberto Perron & Yuxuan Sun & Nick Goldman & Guy Baele & Stephane Guindon & Nicola De Maio - 1-28 Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine
by Linda K Sundermann & Jeff Wintersinger & Gunnar Rätsch & Jens Stoye & Quaid Morris - 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