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Content
March 2020, Volume 16, Issue 3
- 1-22 Parallel Tempering with Lasso for model reduction in systems biology
by Sanjana Gupta & Robin E C Lee & James R Faeder - 1-22 A plausible accelerating function of intermediate states in cancer metastasis
by Hanah Goetz & Juan R Melendez-Alvarez & Luonan Chen & Xiao-Jun Tian - 1-23 SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures
by Kunal Kathuria & Aakrosh Ratan - 1-24 Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating
by Keri A McKiernan & Anna K Koster & Merritt Maduke & Vijay S Pande - 1-25 Modeling binary and graded cone cell fate patterning in the mouse retina
by Kiara C Eldred & Cameron Avelis & Robert J Johnston Jr & Elijah Roberts - 1-25 Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity
by Mariama Jaiteh & Ismael Rodríguez-Espigares & Jana Selent & Jens Carlsson - 1-25 Deconvolution of calcium imaging data using marked point processes
by Ryohei Shibue & Fumiyasu Komaki - 1-26 Mechanisms underlying attraction to odors in walking Drosophila
by Liangyu Tao & Siddhi Ozarkar & Vikas Bhandawat - 1-27 PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
by Guillaume Gautreau & Adelme Bazin & Mathieu Gachet & Rémi Planel & Laura Burlot & Mathieu Dubois & Amandine Perrin & Claudine Médigue & Alexandra Calteau & Stéphane Cruveiller & Catherine Matias & Christophe Ambroise & Eduardo P C Rocha & David Vallenet - 1-28 Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization
by Rafael R Bravo & Etienne Baratchart & Jeffrey West & Ryan O Schenck & Anna K Miller & Jill Gallaher & Chandler D Gatenbee & David Basanta & Mark Robertson-Tessi & Alexander R A Anderson - 1-30 Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments
by Hanna Märkle & Aurélien Tellier - 1-34 A simplified modelling framework facilitates more complex representations of plant circadian clocks
by Mathias Foo & Declan G Bates & Ozgur E Akman - 1-45 Computational and robotic modeling reveal parsimonious combinations of interactions between individuals in schooling fish
by Liu Lei & Ramón Escobedo & Clément Sire & Guy Theraulaz
February 2020, Volume 16, Issue 2
- 1-9 Ten simple rules for getting started on Twitter as a scientist
by Veronika Cheplygina & Felienne Hermans & Casper Albers & Natalia Bielczyk & Ionica Smeets - 1-12 SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases
by Paul Hager & Hans-Werner Mewes & Meino Rohlfs & Christoph Klein & Tim Jeske - 1-13 Ten Simple Rules to becoming a principal investigator
by John S Tregoning & Jason E McDermott - 1-16 Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic
by Susanne Reimering & Sebastian Muñoz & Alice C McHardy - 1-17 RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
by Kosuke Hamazaki & Hiroyoshi Iwata - 1-18 Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells
by Toshinori Namba & Shuji Ishihara - 1-18 Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies
by Shuang Song & Wei Jiang & Lin Hou & Hongyu Zhao - 1-19 Orbit Image Analysis: An open-source whole slide image analysis tool
by Manuel Stritt & Anna K Stalder & Enrico Vezzali - 1-19 Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network
by Andrei Zinovyev & Urszula Czerwinska & Laura Cantini & Emmanuel Barillot & Klaus M Frahm & Dima L Shepelyansky - 1-19 Non-ohmic tissue conduction in cardiac electrophysiology: Upscaling the non-linear voltage-dependent conductance of gap junctions
by Daniel E Hurtado & Javiera Jilberto & Grigory Panasenko - 1-19 Inferring TF activation order in time series scRNA-Seq studies
by Chieh Lin & Jun Ding & Ziv Bar-Joseph - 1-20 Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
by Aleksandr Kovaltsuk & Matthew I J Raybould & Wing Ki Wong & Claire Marks & Sebastian Kelm & James Snowden & Johannes Trück & Charlotte M Deane - 1-20 Navigable maps of structural brain networks across species
by Antoine Allard & M Ángeles Serrano - 1-21 Surprise response as a probe for compressed memory states
by Hadar Levi-Aharoni & Oren Shriki & Naftali Tishby - 1-21 Bayesian inference and comparison of stochastic transcription elongation models
by Jordan Douglas & Richard Kingston & Alexei J Drummond - 1-21 Changes-of-mind in the absence of new post-decision evidence
by Nadim A A Atiya & Arkady Zgonnikov & Denis O’Hora & Martin Schoemann & Stefan Scherbaum & KongFatt Wong-Lin - 1-23 Early prediction of antigenic transitions for influenza A/H3N2
by Lauren A Castro & Trevor Bedford & Lauren Ancel Meyers - 1-23 A generative growth model for thalamocortical axonal branching in primary visual cortex
by Pegah Kassraian-Fard & Michael Pfeiffer & Roman Bauer - 1-23 Predicting colorectal cancer risk from adenoma detection via a two-type branching process model
by Brian M Lang & Jack Kuipers & Benjamin Misselwitz & Niko Beerenwinkel - 1-24 The SONATA data format for efficient description of large-scale network models
by Kael Dai & Juan Hernando & Yazan N Billeh & Sergey L Gratiy & Judit Planas & Andrew P Davison & Salvador Dura-Bernal & Padraig Gleeson & Adrien Devresse & Benjamin K Dichter & Michael Gevaert & James G King & Werner A H Van Geit & Arseny V Povolotsky & Eilif Muller & Jean-Denis Courcol & Anton Arkhipov - 1-24 Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein
by Joël R Pradines & Victor Farutin & Nicholas A Cilfone & Abouzar Ghavami & Elma Kurtagic & Jamey Guess & Anthony M Manning & Ishan Capila - 1-24 Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors
by Cristina Vaghi & Anne Rodallec & Raphaëlle Fanciullino & Joseph Ciccolini & Jonathan P Mochel & Michalis Mastri & Clair Poignard & John M L Ebos & Sébastien Benzekry - 1-24 The relation between crosstalk and gene regulation form revisited
by Rok Grah & Tamar Friedlander - 1-26 Doubting what you already know: Uncertainty regarding state transitions is associated with obsessive compulsive symptoms
by Isaac Fradkin & Casimir Ludwig & Eran Eldar & Jonathan D Huppert - 1-27 Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials
by Daniel B Reeves & Yunda Huang & Elizabeth R Duke & Bryan T Mayer & E Fabian Cardozo-Ojeda & Florencia A Boshier & David A Swan & Morgane Rolland & Merlin L Robb & John R Mascola & Myron S Cohen & Lawrence Corey & Peter B Gilbert & Joshua T Schiffer - 1-27 From cells to tissue: How cell scale heterogeneity impacts glioblastoma growth and treatment response
by Jill A Gallaher & Susan C Massey & Andrea Hawkins-Daarud & Sonal S Noticewala & Russell C Rockne & Sandra K Johnston & Luis Gonzalez-Cuyar & Joseph Juliano & Orlando Gil & Kristin R Swanson & Peter Canoll & Alexander R A Anderson - 1-27 Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit
by Florian Ott & Dimitrije Marković & Alexander Strobel & Stefan J Kiebel - 1-28 Stochastic optimal open-loop control as a theory of force and impedance planning via muscle co-contraction
by Bastien Berret & Frédéric Jean - 1-29 Multi-state design of flexible proteins predicts sequences optimal for conformational change
by Marion F Sauer & Alexander M Sevy & James E Crowe Jr. & Jens Meiler - 1-29 Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein
by Lenka Stejskal & William D Lees & David S Moss & Machaela Palor & Richard J Bingham & Adrian J Shepherd & Joe Grove
January 2020, Volume 16, Issue 1
- 1-11 Collaboration leads to cooperation on sparse networks
by Simon D Angus & Jonathan Newton - 1-12 BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis
by Manoj Kumar & Cameron T Ellis & Qihong Lu & Hejia Zhang & Mihai Capotă & Theodore L Willke & Peter J Ramadge & Nicholas B Turk-Browne & Kenneth A Norman - 1-13 Limits on amplifiers of natural selection under death-Birth updating
by Josef Tkadlec & Andreas Pavlogiannis & Krishnendu Chatterjee & Martin A Nowak - 1-14 Increasing growth rate slows adaptation when genotypes compete for diffusing resources
by Jeremy M Chacón & Allison K Shaw & William R Harcombe - 1-16 The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations
by Christie A Bahlai & Elise F Zipkin - 1-17 Interpreting neural decoding models using grouped model reliance
by Simon Valentin & Maximilian Harkotte & Tzvetan Popov - 1-17 Learning from animals: How to Navigate Complex Terrains
by Henghui Zhu & Hao Liu & Armin Ataei & Yonatan Munk & Thomas Daniel & Ioannis Ch Paschalidis - 1-17 VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning
by Jiwoong Kim & David E Greenberg & Reed Pifer & Shuang Jiang & Guanghua Xiao & Samuel A Shelburne & Andrew Koh & Yang Xie & Xiaowei Zhan - 1-17 Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism
by Melanie Gerken & Sergej Kakorin & Kamel Chibani & Karl-Josef Dietz - 1-18 A single reaction-diffusion equation for the multifarious eruptions of urticaria
by Sungrim Seirin-Lee & Yuhki Yanase & Shunsuke Takahagi & Michihiro Hide - 1-19 Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power
by Vaitea Opuu & Giuliano Nigro & Thomas Gaillard & Emmanuelle Schmitt & Yves Mechulam & Thomas Simonson - 1-20 Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs
by Benjamin Allen & Christine Sample & Robert Jencks & James Withers & Patricia Steinhagen & Lori Brizuela & Joshua Kolodny & Darren Parke & Gabor Lippner & Yulia A Dementieva - 1-21 Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming
by Jake P Taylor-King & Asbjørn N Riseth & Will Macnair & Manfred Claassen - 1-22 Tissue-guided LASSO for prediction of clinical drug response using preclinical samples
by Edward W Huang & Ameya Bhope & Jing Lim & Saurabh Sinha & Amin Emad - 1-23 Computational optimization of associative learning experiments
by Filip Melinscak & Dominik R Bach - 1-24 A new method for inferring timetrees from temporally sampled molecular sequences
by Sayaka Miura & Koichiro Tamura & Qiqing Tao & Louise A Huuki & Sergei L Kosakovsky Pond & Jessica Priest & Jiamin Deng & Sudhir Kumar - 1-24 A system for tracking whisker kinematics and whisker shape in three dimensions
by Rasmus S Petersen & Andrea Colins Rodriguez & Mathew H Evans & Dario Campagner & Michaela S E Loft - 1-25 Emergence of social inequality in the spatial harvesting of renewable public goods
by Jaideep Joshi & Åke Brännström & Ulf Dieckmann - 1-31 Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model
by Rocío Vega & Manuel Carretero & Rui D M Travasso & Luis L Bonilla - 1-32 Emergence and suppression of cooperation by action visibility in transparent games
by Anton M Unakafov & Thomas Schultze & Alexander Gail & Sebastian Moeller & Igor Kagan & Stephan Eule & Fred Wolf
December 2019, Volume 15, Issue 12
- 1-10 Nine quick tips for analyzing network data
by Vincent Miele & Catherine Matias & Stéphane Robin & Stéphane Dray - 1-12 Molecular sampling at logarithmic rates for next-generation sequencing
by Caroline Horn & Julia Salzman - 1-14 Benchmarking network algorithms for contextualizing genes of interest
by Abby Hill & Scott Gleim & Florian Kiefer & Frederic Sigoillot & Joseph Loureiro & Jeremy Jenkins & Melody K Morris - 1-16 Motion prediction enables simulated MR-imaging of freely moving model organisms
by Markus Reischl & Mazin Jouda & Neil MacKinnon & Erwin Fuhrer & Natalia Bakhtina & Andreas Bartschat & Ralf Mikut & Jan G Korvink - 1-16 Statistical inference in ensemble modeling of cellular metabolism
by Tuure Hameri & Marc-Olivier Boldi & Vassily Hatzimanikatis - 1-17 Representation learning of genomic sequence motifs with convolutional neural networks
by Peter K Koo & Sean R Eddy - 1-18 Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15
by Akira Endo & Mitsuo Uchida & Adam J Kucharski & Sebastian Funk - 1-18 CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data
by Kai Kang & Qian Meng & Igor Shats & David M Umbach & Melissa Li & Yuanyuan Li & Xiaoling Li & Leping Li - 1-19 Statistics of correlated percolation in a bacterial community
by Xiaoling Zhai & Joseph W Larkin & Kaito Kikuchi & Samuel E Redford & Ushasi Roy & Gürol M Süel & Andrew Mugler - 1-19 Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication
by Razie Yousefi & Maga Rowicka - 1-20 Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters
by Christine Jandrasits & Stefan Kröger & Walter Haas & Bernhard Y Renard - 1-20 Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs
by Yongcui Wang & Shilong Chen & Luonan Chen & Yong Wang - 1-21 Overlap matrix completion for predicting drug-associated indications
by Mengyun Yang & Huimin Luo & Yaohang Li & Fang-Xiang Wu & Jianxin Wang - 1-21 Protons in small spaces: Discrete simulations of vesicle acidification
by Apeksha Singh & Frank V Marcoline & Salome Veshaguri & Aimee W Kao & Marcel Bruchez & Joseph A Mindell & Dimitrios Stamou & Michael Grabe - 1-21 The effect of inhibition on rate code efficiency indicators
by Tomas Barta & Lubomir Kostal - 1-21 Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models
by Colette Mair & Sema Nickbakhsh & Richard Reeve & Jim McMenamin & Arlene Reynolds & Rory N Gunson & Pablo R Murcia & Louise Matthews - 1-23 Incomplete information about the partner affects the development of collaborative strategies in joint action
by Vinil T Chackochan & Vittorio Sanguineti - 1-23 From energy to cellular forces in the Cellular Potts Model: An algorithmic approach
by Elisabeth G Rens & Leah Edelstein-Keshet - 1-23 Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
by Giacomo Janson & Alessandro Grottesi & Marco Pietrosanto & Gabriele Ausiello & Giulia Guarguaglini & Alessandro Paiardini - 1-23 Probing neural networks for dynamic switches of communication pathways
by Holger Finger & Richard Gast & Christian Gerloff & Andreas K Engel & Peter König - 1-23 NUFEB: A massively parallel simulator for individual-based modelling of microbial communities
by Bowen Li & Denis Taniguchi & Jayathilake Pahala Gedara & Valentina Gogulancea & Rebeca Gonzalez-Cabaleiro & Jinju Chen & Andrew Stephen McGough & Irina Dana Ofiteru & Thomas P Curtis & Paolo Zuliani - 1-24 Regulatory context drives conservation of glycine riboswitch aptamers
by Matt Crum & Nikhil Ram-Mohan & Michelle M Meyer - 1-24 Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation
by Marina A Ferreira & Evangeline Despin-Guitard & Fernando Duarte & Pierre Degond & Eric Theveneau - 1-25 Inferring reaction network structure from single-cell, multiplex data, using toric systems theory
by Shu Wang & Jia-Ren Lin & Eduardo D Sontag & Peter K Sorger - 1-25 Stability of spontaneous, correlated activity in mouse auditory cortex
by Richard F Betzel & Katherine C Wood & Christopher Angeloni & Maria Neimark Geffen & Danielle S Bassett - 1-25 The dynamics of motor learning through the formation of internal models
by Camilla Pierella & Maura Casadio & Ferdinando A Mussa-Ivaldi & Sara A Solla - 1-26 Chemotaxis in external fields: Simulations for active magnetic biological matter
by Agnese Codutti & Klaas Bente & Damien Faivre & Stefan Klumpp - 1-26 A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation
by Matthew C Pharris & Neal M Patel & Tyler G VanDyk & Thomas M Bartol & Terrence J Sejnowski & Mary B Kennedy & Melanie I Stefan & Tamara L Kinzer-Ursem - 1-28 Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model
by John E Mittler & James T Murphy & Sarah E Stansfield & Kathryn Peebles & Geoffrey S Gottlieb & Neil F Abernethy & Molly C Reid & Steven M Goodreau & Joshua T Herbeck - 1-29 Autistic traits influence the strategic diversity of information sampling: Insights from two-stage decision models
by Haoyang Lu & Li Yi & Hang Zhang - 1-30 ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest
by Jiajin Li & Brandon Jew & Lingyu Zhan & Sungoo Hwang & Giovanni Coppola & Nelson B Freimer & Jae Hoon Sul - 1-38 Neuronal population model of globular bushy cells covering unit-to-unit variability
by Go Ashida & Helen T Heinermann & Jutta Kretzberg
November 2019, Volume 15, Issue 11
- 1-17 Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process
by Jifan Shi & Tiejun Li & Luonan Chen & Kazuyuki Aihara - 1-19 Uncovering the subtype-specific temporal order of cancer pathway dysregulation
by Sahand Khakabimamaghani & Dujian Ding & Oliver Snow & Martin Ester - 1-19 Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S
by Nicholas G Reich & Craig J McGowan & Teresa K Yamana & Abhinav Tushar & Evan L Ray & Dave Osthus & Sasikiran Kandula & Logan C Brooks & Willow Crawford-Crudell & Graham Casey Gibson & Evan Moore & Rebecca Silva & Matthew Biggerstaff & Michael A Johansson & Roni Rosenfeld & Jeffrey Shaman - 1-19 Feasibility of functional magnetic resonance imaging of ocular dominance and orientation preference in primary visual cortex
by Marilia Menezes de Oliveira & James C Pang & Peter A Robinson & Xiaochen Liu & Mark M Schira - 1-23 No substantial change in the balance between model-free and model-based control via training on the two-step task
by Elmar D Grosskurth & Dominik R Bach & Marcos Economides & Quentin J M Huys & Lisa Holper - 1-23 Neural field models for latent state inference: Application to large-scale neuronal recordings
by Michael E Rule & David Schnoerr & Matthias H Hennig & Guido Sanguinetti - 1-24 Forecasting dengue and influenza incidences using a sparse representation of Google trends, electronic health records, and time series data
by Prashant Rangarajan & Sandeep K Mody & Madhav Marathe - 1-27 Predicting neuronal dynamics with a delayed gain control model
by Jingyang Zhou & Noah C Benson & Kendrick Kay & Jonathan Winawer - 1-27 Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences
by Ilya Plyusnin & Liisa Holm & Petri Törönen - 1-27 A novel network control model for identifying personalized driver genes in cancer
by Wei-Feng Guo & Shao-Wu Zhang & Tao Zeng & Yan Li & Jianxi Gao & Luonan Chen - 1-27 Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer
by Miranda D Stobbe & Gian A Thun & Andrea Diéguez-Docampo & Meritxell Oliva & Justin P Whalley & Emanuele Raineri & Ivo G Gut - 1-28 Anticipatory coadaptation of ankle stiffness and sensorimotor gain for standing balance
by Charlotte Le Mouel & Romain Brette - 1-28 A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology
by Chen Zhao & Adam C Mirando & Richard J Sové & Thalyta X Medeiros & Brian H Annex & Aleksander S Popel - 1-29 A model of how depth facilitates scene-relative object motion perception
by Oliver W Layton & D C Niehorster - 1-29 Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets
by M S Vijayabaskar & Debbie K Goode & Nadine Obier & Monika Lichtinger & Amber M L Emmett & Fatin N Zainul Abidin & Nisar Shar & Rebecca Hannah & Salam A Assi & Michael Lie-A-Ling & Berthold Gottgens & Georges Lacaud & Valerie Kouskoff & Constanze Bonifer & David R Westhead - 1-32 Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps
by Yichen Zheng & Thomas Wiehe - 1-34 Large-scale cortical travelling waves predict localized future cortical signals
by David M Alexander & Tonio Ball & Andreas Schulze-Bonhage & Cees van Leeuwen - 1-35 Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture
by Jilin W J L Wang & Fabrizio Lombardi & Xiyun Zhang & Christelle Anaclet & Plamen Ch Ivanov - 1-37 Tonic exploration governs both flexibility and lapses
by R Becket Ebitz & Brianna J Sleezer & Hank P Jedema & Charles W Bradberry & Benjamin Y Hayden
October 2019, Volume 15, Issue 10
- 1-1 Correction: Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism
by The PLOS Computational Biology Staff - 1-1 Correction: Bayesian hypothesis testing and experimental design for two-photon imaging data
by Luke E Rogerson & Zhijian Zhao & Katrin Franke & Thomas Euler & Philipp Berens - 1-1 Correction: Generation of Binary Tree-Child phylogenetic networks
by Gabriel Cardona & Joan Carles Pons & Celine Scornavacca - 1-1 Correction: Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer
by Shyam Kumar Sudhakar & Sungho Hong & Ivan Raikov & Rodrigo Publio & Claus Lang & Thomas Close & Daqing Guo & Mario Negrello & Erik de Schutter - 1-1 Correction: Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer
by Margaret P Chapman & Tyler Risom & Anil J Aswani & Ellen M Langer & Rosalie C Sears & Claire J Tomlin - 1-5 Ten simple rules to aid in achieving a vision
by Philip E Bourne - 1-9 Ten simple rules for providing optimal administrative support to research teams
by Romina Garrido & Casandra A Trowbridge & Nana Tamura - 1-9 TAPES: A tool for assessment and prioritisation in exome studies
by Alexandre Xavier & Rodney J Scott & Bente A Talseth-Palmer - 1-15 Color improves edge classification in human vision
by Camille Breuil & Ben J Jennings & Simon Barthelmé & Nathalie Guyader & Frederick A A Kingdom - 1-16 Uncovering and characterizing splice variants associated with survival in lung cancer patients
by Sean West & Sushil Kumar & Surinder K Batra & Hesham Ali & Dario Ghersi - 1-16 A simulation of the random and directed motion of dendritic cells in chemokine fields
by Avery Parr & Nicholas R Anderson & Daniel A Hammer - 1-17 A Kuramoto model of self-other integration across interpersonal synchronization strategies
by Ole Adrian Heggli & Joana Cabral & Ivana Konvalinka & Peter Vuust & Morten L Kringelbach - 1-18 The folded X-pattern is not necessarily a statistical signature of decision confidence
by Manuel Rausch & Michael Zehetleitner - 1-18 Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort
by Gabriel Balaban & Brian P Halliday & Wenjia Bai & Bradley Porter & Carlotta Malvuccio & Pablo Lamata & Christopher A Rinaldi & Gernot Plank & Daniel Rueckert & Sanjay K Prasad & Martin J Bishop - 1-20 Fungal feature tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi
by Guillermo Vidal-Diez de Ulzurrun & Tsung-Yu Huang & Ching-Wen Chang & Hung-Che Lin & Yen-Ping Hsueh - 1-21 A computational account of threat-related attentional bias
by Toby Wise & Jochen Michely & Peter Dayan & Raymond J Dolan - 1-22 Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature
by Qiao Liu & Di He & Lei Xie - 1-23 Estimating influenza incidence using search query deceptiveness and generalized ridge regression
by Reid Priedhorsky & Ashlynn R Daughton & Martha Barnard & Fiona O’Connell & Dave Osthus - 1-24 Phylogenetic correlations can suffice to infer protein partners from sequences
by Guillaume Marmier & Martin Weigt & Anne-Florence Bitbol - 1-26 Hypergraph-based connectivity measures for signaling pathway topologies
by Nicholas Franzese & Adam Groce & T M Murali & Anna Ritz - 1-27 Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity
by Siva Venkadesh & Alexander O Komendantov & Diek W Wheeler & David J Hamilton & Giorgio A Ascoli - 1-27 Categorical encoding of decision variables in orbitofrontal cortex
by Arno Onken & Jue Xie & Stefano Panzeri & Camillo Padoa-Schioppa - 1-27 Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations
by Carmichael F Ong & Thomas Geijtenbeek & Jennifer L Hicks & Scott L Delp - 1-27 Surfactant delivery in rat lungs: Comparing 3D geometrical simulation model with experimental instillation
by Alireza Kazemi & Bruno Louis & Daniel Isabey & Gary F Nieman & Louis A Gatto & Joshua Satalin & Sarah Baker & James B Grotberg & Marcel Filoche - 1-28 Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling
by Parul Maheshwari & Hao Du & Jen Sheen & Sarah M Assmann & Reka Albert - 1-28 SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways
by Elisa Salviato & Vera Djordjilović & Monica Chiogna & Chiara Romualdi - 1-29 Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers
by David J Wooten & Sarah M Groves & Darren R Tyson & Qi Liu & Jing S Lim & Réka Albert & Carlos F Lopez & Julien Sage & Vito Quaranta - 1-29 Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein
by Ruchi Lohia & Reza Salari & Grace Brannigan - 1-29 Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations
by Bogdan Barz & Jennifer Loschwitz & Birgit Strodel - 1-30 Evaluation of linear and non-linear activation dynamics models for insect muscle
by Nalin Harischandra & Anthony J Clare & Jure Zakotnik & Laura M L Blackburn & Tom Matheson & Volker Dürr - 1-31 Bayesian inference of neuronal assemblies
by Giovanni Diana & Thomas T J Sainsbury & Martin P Meyer - 1-31 Combinations of low-level and high-level neural processes account for distinct patterns of context-dependent choice
by Mehran Spitmaan & Oihane Horno & Emily Chu & Alireza Soltani - 1-32 Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals
by Neil J Bruce & Daniele Narzi & Daniel Trpevski & Siri C van Keulen & Anu G Nair & Ursula Röthlisberger & Rebecca C Wade & Paolo Carloni & Jeanette Hellgren Kotaleski - 1-32 Delayed feedback embedded in perception-action coordination cycles results in anticipation behavior during synchronized rhythmic action: A dynamical systems approach
by Iran R Roman & Auriel Washburn & Edward W Large & Chris Chafe & Takako Fujioka
September 2019, Volume 15, Issue 9
- 1-10 Ten simple rules for helping newcomers become contributors to open projects
by Dan Sholler & Igor Steinmacher & Denae Ford & Mara Averick & Mike Hoye & Greg Wilson - 1-13 EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology
by Sébastien Picault & Yu-Lin Huang & Vianney Sicard & Sandie Arnoux & Gaël Beaunée & Pauline Ezanno - 1-14 Perspective: Dimensions of the scientific method
by Eberhard O Voit - 1-14 Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination
by Alexander D Becker & Amy Wesolowski & Ottar N Bjørnstad & Bryan T Grenfell - 1-15 On measuring selection in cancer from subclonal mutation frequencies
by Ivana Bozic & Chay Paterson & Bartlomiej Waclaw - 1-17 Designing combination therapies with modeling chaperoned machine learning
by Yin Zhang & Julie M Huynh & Guan-Sheng Liu & Richard Ballweg & Kayenat S Aryeh & Andrew L Paek & Tongli Zhang - 1-17 Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints
by Srinivasan Venkatramanan & Jiangzhuo Chen & Arindam Fadikar & Sandeep Gupta & Dave Higdon & Bryan Lewis & Madhav Marathe & Henning Mortveit & Anil Vullikanti - 1-17 MHC binding affects the dynamics of different T-cell receptors in different ways
by Bernhard Knapp & P Anton van der Merwe & Omer Dushek & Charlotte M Deane - 1-18 Quantifying model evidence for yellow fever transmission routes in Africa
by Katy A M Gaythorpe & Kévin Jean & Laurence Cibrelus & Tini Garske - 1-18 Deconvolving multiplexed protease signatures with substrate reduction and activity clustering
by Qinwei Zhuang & Brandon Alexander Holt & Gabriel A Kwong & Peng Qiu - 1-19 Network trade-offs and homeostasis in Arabidopsis shoot architectures
by Adam Conn & Arjun Chandrasekhar & Martin van Rongen & Ottoline Leyser & Joanne Chory & Saket Navlakha - 1-20 Close spatial arrangement of mutants favors and disfavors fixation
by Yunming Xiao & Bin Wu - 1-21 Executable pathway analysis using ensemble discrete-state modeling for large-scale data
by Rohith Palli & Mukta G Palshikar & Juilee Thakar - 1-21 Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data
by Allison L Hicks & Nicole Wheeler & Leonor Sánchez-Busó & Jennifer L Rakeman & Simon R Harris & Yonatan H Grad - 1-22 Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform
by Anna Matveeva & Michael Fichtner & Katherine McAllister & Christopher McCann & Marc Sturrock & Daniel B Longley & Jochen H M Prehn - 1-22 Fast and near-optimal monitoring for healthcare acquired infection outbreaks
by Bijaya Adhikari & Bryan Lewis & Anil Vullikanti & José Mauricio Jiménez & B Aditya Prakash - 1-22 Time scales and wave formation in non-linear spatial public goods games
by Gregory J Kimmel & Philip Gerlee & Philipp M Altrock - 1-22 Multi-cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space
by Michaëlle N Mayalu & Min-Cheol Kim & H Harry Asada - 1-22 Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making
by Amir Dezfouli & Bernard W Balleine - 1-24 Loop analysis of blood pressure/volume homeostasis
by Bruno Burlando & Franco Blanchini & Giulia Giordano - 1-24 Benchmarking network propagation methods for disease gene identification
by Sergio Picart-Armada & Steven J Barrett & David R Willé & Alexandre Perera-Lluna & Alex Gutteridge & Benoit H Dessailly - 1-26 The FACTS model of speech motor control: Fusing state estimation and task-based control
by Benjamin Parrell & Vikram Ramanarayanan & Srikantan Nagarajan & John Houde - 1-27 LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes
by Olivier Collier & Véronique Stoven & Jean-Philippe Vert - 1-28 Cost-benefit trade-offs in decision-making and learning
by Nura Sidarus & Stefano Palminteri & Valérian Chambon - 1-29 Generation of Binary Tree-Child phylogenetic networks
by Gabriel Cardona & Joan Carles Pons & Celine Scornavacca - 1-31 A flexible and generalizable model of online latent-state learning
by Amy L Cochran & Josh M Cisler - 1-33 Estimating information in time-varying signals
by Sarah Anhala Cepeda-Humerez & Jakob Ruess & Gašper Tkačik - 1-34 Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons
by Timothy Rumbell & James Kozloski - 1-38 Characterizing and dissociating multiple time-varying modulatory computations influencing neuronal activity
by Kaiser Niknam & Amir Akbarian & Kelsey Clark & Yasin Zamani & Behrad Noudoost & Neda Nategh - 1-42 Prepaid parameter estimation without likelihoods
by Merijn Mestdagh & Stijn Verdonck & Kristof Meers & Tim Loossens & Francis Tuerlinckx - 1-43 Invariant neural responses for sensory categories revealed by the time-varying information for communication calls
by Julie E Elie & Frédéric E Theunissen
August 2019, Volume 15, Issue 8
- 1-8 Twelve quick tips for designing sound dynamical models for bioprocesses
by Francis Mairet & Olivier Bernard - 1-14 Directed migration shapes cooperation in spatial ecological public goods games
by Felix Funk & Christoph Hauert - 1-16 Reappraising the utility of Google Flu Trends
by Sasikiran Kandula & Jeffrey Shaman - 1-17 PanoView: An iterative clustering method for single-cell RNA sequencing data
by Ming-Wen Hu & Dong Won Kim & Sheng Liu & Donald J Zack & Seth Blackshaw & Jiang Qian - 1-17 Network analyses to quantify effects of host movement in multilevel disease transmission models using foot and mouth disease in Cameroon as a case study
by Laura W Pomeroy & Hyeyoung Kim & Ningchuan Xiao & Mark Moritz & Rebecca Garabed - 1-19 Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer
by Morgan Craig & Kamran Kaveh & Alec Woosley & Andrew S Brown & David Goldman & Elliot Eton & Ravindra M Mehta & Andrew Dhawan & Kazuya Arai & M Mamunur Rahman & Sidi Chen & Martin A Nowak & Aaron Goldman - 1-22 On the optimal design of metabolic RNA labeling experiments
by Alexey Uvarovskii & Isabel S Naarmann-de Vries & Christoph Dieterich - 1-23 Variation in plastic responses to light results from selection in different competitive environments—A game theoretical approach using virtual plants
by Franca J Bongers & Jacob C Douma & Yoh Iwasa & Ronald Pierik & Jochem B Evers & Niels P R Anten - 1-23 FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics
by Michael Gabel & Tobias Hohl & Andrea Imle & Oliver T Fackler & Frederik Graw - 1-25 The formation of preference in risky choice
by Moshe Glickman & Orian Sharoni & Dino J Levy & Ernst Niebur & Veit Stuphorn & Marius Usher - 1-25 Machine learning-based microarray analyses indicate low-expression genes might collectively influence PAH disease
by Song Cui & Qiang Wu & James West & Jiangping Bai - 1-25 Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability
by Vladimir A Fedorov & Philipp S Orekhov & Ekaterina G Kholina & Artem A Zhmurov & Fazoil I Ataullakhanov & Ilya B Kovalenko & Nikita B Gudimchuk - 1-25 Learning to synchronize: How biological agents can couple neural task modules for dealing with the stability-plasticity dilemma
by Pieter Verbeke & Tom Verguts - 1-26 Tracking Pseudomonas aeruginosa transmissions due to environmental contamination after discharge in ICUs using mathematical models
by Thi Mui Pham & Mirjam Kretzschmar & Xavier Bertrand & Martin Bootsma & on behalf of COMBACTE-MAGNET Consortium - 1-27 Bayesian hypothesis testing and experimental design for two-photon imaging data
by Luke E Rogerson & Zhijian Zhao & Katrin Franke & Thomas Euler & Philipp Berens - 1-28 A computational model for gonadotropin releasing cells in the teleost fish medaka
by Geir Halnes & Simen Tennøe & Trude M Haug & Gaute T Einevoll & Finn-Arne Weltzien & Kjetil Hodne - 1-28 Transient crosslinking kinetics optimize gene cluster interactions
by Benjamin Walker & Dane Taylor & Josh Lawrimore & Caitlin Hult & David Adalsteinsson & Kerry Bloom & M Gregory Forest - 1-28 Predicting the effects of deep brain stimulation using a reduced coupled oscillator model
by Gihan Weerasinghe & Benoit Duchet & Hayriye Cagnan & Peter Brown & Christian Bick & Rafal Bogacz