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February 2021, Volume 17, Issue 2
- 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 Aggregative cycles evolve as a solution to conflicts in social investment
by Leonardo Miele & Silvia De Monte - 1-16 Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing
by Bansho Masutani & Shin-ichi Arimura & Shinichi Morishita - 1-16 Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers
by Sara Ibrahim Omar & Meng Zhao & Rohith Vedhthaanth Sekar & Sahar Arbabi Moghadam & Jack A Tuszynski & Michael T Woodside - 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 - 1-19 Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology
by Hamed Khakzad & Lotta Happonen & Yasaman Karami & Sounak Chowdhury & Gizem Ertürk Bergdahl & Michael Nilges & Guy Tran Van Nhieu & Johan Malmström & Lars Malmström - 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 - 1-25 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 - 1-25 Modeling multi-sensory feedback control of zebrafish in a flow
by Daniel A Burbano-L. & Maurizio Porfiri - 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 - 1-28 Model based planners reflect on their model-free propensities
by Rani Moran & Mehdi Keramati & Raymond J Dolan - 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 Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission
by David William Eyre & Mirjam Laager & A Sarah Walker & Ben S Cooper & Daniel J Wilson & on behalf of the CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare) - 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
- 1-9 IOCBIO Kinetics: An open-source software solution for analysis of data traces
by Marko Vendelin & Martin Laasmaa & Mari Kalda & Jelena Branovets & Niina Karro & Karina Barsunova & Rikke Birkedal - 1-10 Ten quick tips for making things findable
by Sarah Lin & Ibraheem Ali & Greg Wilson - 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 Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing
by Sean C Anderson & Andrew M Edwards & Madi Yerlanov & Nicola Mulberry & Jessica E Stockdale & Sarafa A Iyaniwura & Rebeca C Falcao & Michael C Otterstatter & Michael A Irvine & Naveed Z Janjua & Daniel Coombs & Caroline Colijn - 1-15 Proteostasis is adaptive: Balancing chaperone holdases against foldases
by Adam MR de Graff & David E Mosedale & Tilly Sharp & Ken A Dill & David J Grainger - 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 Neural diffusivity and pre-emptive epileptic seizure intervention
by Erik D Fagerholm & Chayanin Tangwiriyasakul & Karl J Friston & Inês R Violante & Steven Williams & David W Carmichael & Suejen Perani & Federico E Turkheimer & Rosalyn J Moran & Robert Leech & Mark P Richardson - 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 Simple models including energy and spike constraints reproduce complex activity patterns and metabolic disruptions
by Tanguy Fardet & Anna Levina - 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 - 1-29 Bursting in cerebellar stellate cells induced by pharmacological agents: Non-sequential spike adding
by Saeed Farjami & Ryan P D Alexander & Derek Bowie & Anmar Khadra - 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 - 1-31 Value-complexity tradeoff explains mouse navigational learning
by Nadav Amir & Reut Suliman & Maayan Tal & Sagiv Shifman & Naftali Tishby & Israel Nelken - 1-31 Development of a hybrid model for a partially known intracellular signaling pathway through correction term estimation and neural network modeling
by Dongheon Lee & Arul Jayaraman & Joseph S Kwon - 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
- 1-8 Ten simple rules for writing a paper about scientific software
by Joseph D Romano & Jason H Moore - 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 - 1-23 Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
by Kael Dai & Sergey L Gratiy & Yazan N Billeh & Richard Xu & Binghuang Cai & Nicholas Cain & Atle E Rimehaug & Alexander J Stasik & Gaute T Einevoll & Stefan Mihalas & Christof Koch & Anton Arkhipov - 1-24 Ten simple rules for writing Dockerfiles for reproducible data science
by Daniel Nüst & Vanessa Sochat & Ben Marwick & Stephen J Eglen & Tim Head & Tony Hirst & Benjamin D Evans - 1-24 Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein
by Dylan Girodat & Avik K Pati & Daniel S Terry & Scott C Blanchard & Karissa Y Sanbonmatsu - 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 - 1-27 Poisson balanced spiking networks
by Camille E Rullán Buxó & Jonathan W Pillow - 1-30 Interspike intervals within retinal spike bursts combinatorially encode multiple stimulus features
by Toshiyuki Ishii & Toshihiko Hosoya - 1-30 Precise determination of input-output mapping for multimodal gene circuits using data from transient transfection
by Christoph Stelzer & Yaakov Benenson - 1-31 Neural mass modeling of slow-fast dynamics of seizure initiation and abortion
by Elif Köksal Ersöz & Julien Modolo & Fabrice Bartolomei & Fabrice Wendling - 1-31 Spatial considerations in the resolution of inflammation: Elucidating leukocyte interactions via an experimentally-calibrated agent-based model
by Anahita Bayani & Joanne L Dunster & Jonathan J Crofts & Martin R Nelson - 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
- 1-7 Ten simple rules for organizing a data science workshop
by Alise Ponsero & Ryan Bartelme & Gustavo de Oliveira Almeida & Alex Bigelow & Reetu Tuteja & Holly Ellingson & Tyson Swetnam & Nirav Merchant & Maliaca Oxnam & Eric Lyons - 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 - 1-14 Dynamical persistence in high-diversity resource-consumer communities
by Itay Dalmedigos & Guy Bunin - 1-15 Membrane thinning and lateral gating are consistent features of BamA across multiple species
by Jinchan Liu & James C Gumbart - 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 A Bayesian non-parametric mixed-effects model of microbial growth curves
by Peter D Tonner & Cynthia L Darnell & Francesca M L Bushell & Peter A Lund & Amy K Schmid & Scott C Schmidler - 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 Estimating effective population size changes from preferentially sampled genetic sequences
by Michael D Karcher & Luiz Max Carvalho & Marc A Suchard & Gytis Dudas & Vladimir N Minin - 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 - 1-23 Delayed global feedback in the genesis and stability of spatiotemporal excitation patterns in paced biological excitable media
by Zhen Song & Zhilin Qu - 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 - 1-33 Timescales of motor memory formation in dual-adaptation
by Marion Forano & David W Franklin - 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 Refractory density model of cortical direction selectivity: Lagged-nonlagged, transient-sustained, and On-Off thalamic neuron-based mechanisms and intracortical amplification
by Anton Chizhov & Natalia Merkulyeva - 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
- 1-4 Ten simple rules for writing scientific op-ed articles
by Hoe-Han Goh & Philip Bourne - 1-7 Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates
by Pleuni Pennings & Mayra M Banuelos & Francisca L Catalan & Victoria R Caudill & Bozhidar Chakalov & Selena Hernandez & Jeanice Jones & Chinomnso Okorie & Sepideh Modrek & Rori Rohlfs & Nicole Adelstein - 1-10 Ten simple rules on how to write a standard operating procedure
by Susanne Hollmann & Marcus Frohme & Christoph Endrullat & Andreas Kremer & Domenica D’Elia & Babette Regierer & Alina Nechyporenko & on behalf of Cost Action CA15110 - 1-11 Ten simple rules to make your research more sustainable
by Anne-Laure Ligozat & Aurélie Névéol & Bénédicte Daly & Emmanuelle Frenoux - 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 - 1-18 Ten simple rules for open human health research
by Aïda Bafeta & Jason Bobe & Jon Clucas & Pattie Pramila Gonsalves & Célya Gruson-Daniel & Kathy L Hudson & Arno Klein & Anirudh Krishnakumar & Anna McCollister-Slipp & Ariel B Lindner & Dusan Misevic & John A Naslund & Camille Nebeker & Aki Nikolaidis & Irene Pasquetto & Gabriela Sanchez & Matthieu Schapira & Tohar Scheininger & Félix Schoeller & Anibal Sólon Heinsfeld & François Taddei - 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 - 1-21 Microtubule instability driven by longitudinal and lateral strain propagation
by Maxim Igaev & Helmut Grubmüller - 1-22 Aberrant computational mechanisms of social learning and decision-making in schizophrenia and borderline personality disorder
by Lara Henco & Andreea O Diaconescu & Juha M Lahnakoski & Marie-Luise Brandi & Sophia Hörmann & Johannes Hennings & Alkomiet Hasan & Irina Papazova & Wolfgang Strube & Dimitris Bolis & Leonhard Schilbach & Christoph Mathys - 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