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Content
April 2020, Volume 16, Issue 4
- 1-22 Comparison of methods for rhythm analysis of complex animals’ acoustic signals
by Lara S Burchardt & Mirjam Knörnschild - 1-22 LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer
by Junpeng Zhang & Taosheng Xu & Lin Liu & Wu Zhang & Chunwen Zhao & Sijing Li & Jiuyong Li & Nini Rao & Thuc Duy Le - 1-23 Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
by Lisa-Katrin Schätzle & Ali Hadizadeh Esfahani & Andreas Schuppert - 1-24 Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis
by Yuanchao Zhang & Man S Kim & Erin R Reichenberger & Ben Stear & Deanne M Taylor - 1-25 DOT: Gene-set analysis by combining decorrelated association statistics
by Olga A Vsevolozhskaya & Min Shi & Fengjiao Hu & Dmitri V Zaykin - 1-25 The drift diffusion model as the choice rule in inter-temporal and risky choice: A case study in medial orbitofrontal cortex lesion patients and controls
by Jan Peters & Mark D’Esposito - 1-26 Multiview learning for understanding functional multiomics
by Nam D Nguyen & Daifeng Wang - 1-28 Multiple-target tracking in human and machine vision
by Shiva Kamkar & Fatemeh Ghezloo & Hamid Abrishami Moghaddam & Ali Borji & Reza Lashgari - 1-30 Learning action-oriented models through active inference
by Alexander Tschantz & Anil K Seth & Christopher L Buckley - 1-32 Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology
by Sean L Wu & Héctor M Sánchez C. & John M Henry & Daniel T Citron & Qian Zhang & Kelly Compton & Biyonka Liang & Amit Verma & Derek A T Cummings & Arnaud Le Menach & Thomas W Scott & Anne L Wilson & Steven W Lindsay & Catherine L Moyes & Penny A Hancock & Tanya L Russell & Thomas R Burkot & John M Marshall & Samson Kiware & Robert C Reiner Jr & David L Smith - 1-33 Generalizing to generalize: Humans flexibly switch between compositional and conjunctive structures during reinforcement learning
by Nicholas T Franklin & Michael J Frank - 1-34 eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
by Augusto Anguita-Ruiz & Alberto Segura-Delgado & Rafael Alcalá & Concepción M Aguilera & Jesús Alcalá-Fdez - 1-35 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
by Christopher T Lee & Justin G Laughlin & Nils Angliviel de La Beaumelle & Rommie E Amaro & J Andrew McCammon & Ravi Ramamoorthi & Michael Holst & Padmini Rangamani - 1-42 Discovery of hierarchical representations for efficient planning
by Momchil S Tomov & Samyukta Yagati & Agni Kumar & Wanqian Yang & Samuel J Gershman - 1-44 Striatal network modeling in Huntington’s Disease
by Adam Ponzi & Scott J Barton & Kendra D Bunner & Claudia Rangel-Barajas & Emily S Zhang & Benjamin R Miller & George V Rebec & James Kozloski
March 2020, Volume 16, Issue 3
- 1-12 ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data
by Lisa M Bramer & Amanda M White & Kelly G Stratton & Allison M Thompson & Daniel Claborne & Kirsten Hofmockel & Lee Ann McCue - 1-14 Quantifying the roles of vomiting, diarrhea, and residents vs. staff in norovirus transmission in U.S. nursing home outbreaks
by Carly Adams & David Young & Paul A Gastañaduy & Prabasaj Paul & Zach Marsh & Aron J Hall & Benjamin A Lopman - 1-14 A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015
by Ellen Brooks-Pollock & Leon Danon & Hester Korthals Altes & Jennifer A Davidson & Andrew M T Pollock & Dick van Soolingen & Colin Campbell & Maeve K Lalor - 1-16 The use of mixture density networks in the emulation of complex epidemiological individual-based models
by Christopher N Davis & T Deirdre Hollingsworth & Quentin Caudron & Michael A Irvine - 1-17 Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex
by Dmitrii S Shcherbinin & Vlad A Belousov & Mikhail Shugay - 1-19 Detecting critical slowing down in high-dimensional epidemiological systems
by Tobias Brett & Marco Ajelli & Quan-Hui Liu & Mary G Krauland & John J Grefenstette & Willem G van Panhuis & Alessandro Vespignani & John M Drake & Pejman Rohani - 1-20 CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data
by Thilde Terkelsen & Anders Krogh & Elena Papaleo - 1-21 Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines
by Elba Raimúndez & Simone Keller & Gwen Zwingenberger & Karolin Ebert & Sabine Hug & Fabian J Theis & Dieter Maier & Birgit Luber & Jan Hasenauer - 1-21 The spread of a wild plant pathogen is driven by the road network
by Elina Numminen & Anna-Liisa Laine - 1-22 Parallel Tempering with Lasso for model reduction in systems biology
by Sanjana Gupta & Robin E C Lee & James R Faeder - 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 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 - 1-34 A simplified modelling framework facilitates more complex representations of plant circadian clocks
by Mathias Foo & Declan G Bates & Ozgur E Akman
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 - 1-13 Ten Simple Rules to becoming a principal investigator
by John S Tregoning & Jason E McDermott - 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 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 - 1-23 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 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 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
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 - 1-16 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 - 1-18 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 - 1-14 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 - 1-21 Overlap matrix completion for predicting drug-associated indications
by Mengyun Yang & Huimin Luo & Yaohang Li & Fang-Xiang Wu & Jianxin Wang - 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 - 1-24 Regulatory context drives conservation of glycine riboswitch aptamers
by Matt Crum & Nikhil Ram-Mohan & Michelle M Meyer - 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 - 1-29 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
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 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 Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences
by Ilya Plyusnin & Liisa Holm & Petri Törönen - 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
- 1-5 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 - 1-15 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 - 1-18 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 Categorical encoding of decision variables in orbitofrontal cortex
by Arno Onken & Jue Xie & Stefano Panzeri & Camillo Padoa-Schioppa - 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 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 - 1-30 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 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 - 1-17 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 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 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 - 1-28 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 - 1-23 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 - 1-26 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 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 - 1-29 Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties
by Ljubisa Miskovic & Jonas Béal & Michael Moret & Vassily Hatzimanikatis - 1-34 Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation
by Michael A Colman - 1-35 Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions
by Joel A Paulson & Marc Martin-Casas & Ali Mesbah - 1-35 A generative learning model for saccade adaptation
by Carlos R Cassanello & Florian Ostendorf & Martin Rolfs - 1-35 Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI
by Georgia Koppe & Hazem Toutounji & Peter Kirsch & Stefanie Lis & Daniel Durstewitz
July 2019, Volume 15, Issue 7
- 1-5 Think: Theory for Africa
by Christopher B Currin & Phumlani N Khoza & Alexander D Antrobus & Peter E Latham & Tim P Vogels & Joseph V Raimondo - 1-8 Ten simple rules for giving an effective academic job talk
by Shayna A Sura & Lauren L Smith & Monique R Ambrose & C Eduardo Guerra Amorim & Annabel C Beichman & Ana C R Gomez & Mark Juhn & Gaurav S Kandlikar & Julie S Miller & Jazlyn Mooney & Riley O Mummah & Kirk E Lohmueller & James O Lloyd-Smith - 1-14 Disease gene prediction for molecularly uncharacterized diseases
by Juan J Cáceres & Alberto Paccanaro - 1-17 Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas
by Víctor M Pérez-García & Luis E Ayala-Hernández & Juan Belmonte-Beitia & Philippe Schucht & Michael Murek & Andreas Raabe & Juan Sepúlveda - 1-22 With an eye on uncertainty: Modelling pupillary responses to environmental volatility
by Peter Vincent & Thomas Parr & David Benrimoh & Karl J Friston - 1-22 Depressive symptoms are associated with blunted reward learning in social contexts
by Lou Safra & Coralie Chevallier & Stefano Palminteri - 1-22 Primacy coding facilitates effective odor discrimination when receptor sensitivities are tuned
by David Zwicker - 1-23 Information-theoretic analysis of multivariate single-cell signaling responses
by Tomasz Jetka & Karol Nienałtowski & Tomasz Winarski & Sławomir Błoński & Michał Komorowski - 1-24 Machine and deep learning meet genome-scale metabolic modeling
by Guido Zampieri & Supreeta Vijayakumar & Elisabeth Yaneske & Claudio Angione - 1-25 Foraging as an evidence accumulation process
by Jacob D Davidson & Ahmed El Hady - 1-26 Human online adaptation to changes in prior probability
by Elyse H Norton & Luigi Acerbi & Wei Ji Ma & Michael S Landy - 1-26 Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers
by Jessica M Conway & Alan S Perelson & Jonathan Z Li - 1-26 Identifying determinants of persistent MRSA bacteremia using mathematical modeling
by Tsuyoshi Mikkaichi & Michael R Yeaman & Alexander Hoffmann & MRSA Systems Immunobiology Group - 1-28 A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth
by Shiva Rudraraju & Derek E Moulton & Régis Chirat & Alain Goriely & Krishna Garikipati - 1-29 Dimensionality in recurrent spiking networks: Global trends in activity and local origins in connectivity
by Stefano Recanatesi & Gabriel Koch Ocker & Michael A Buice & Eric Shea-Brown - 1-30 DART-ID increases single-cell proteome coverage
by Albert Tian Chen & Alexander Franks & Nikolai Slavov - 1-32 Reservoir computing model of prefrontal cortex creates novel combinations of previous navigation sequences from hippocampal place-cell replay with spatial reward propagation
by Nicolas Cazin & Martin Llofriu Alonso & Pablo Scleidorovich Chiodi & Tatiana Pelc & Bruce Harland & Alfredo Weitzenfeld & Jean-Marc Fellous & Peter Ford Dominey
June 2019, Volume 15, Issue 6
- 1-4 Ten simple rules for successfully hosting an intern at a scientific software company
by Kristine Briedis & Yi-Shiou Chen & Scott Markel - 1-12 From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training
by Annette McGrath & Katherine Champ & Catherine A Shang & Ellen van Dam & Cath Brooksbank & Sarah L Morgan - 1-13 Telling ecological networks apart by their structure: A computational challenge
by Matthew J Michalska-Smith & Stefano Allesina - 1-15 Evolution of interface binding strengths in simplified model of protein quaternary structure
by Alexander S Leonard & Sebastian E Ahnert - 1-15 Evidence accumulation is biased by motivation: A computational account
by Filip Gesiarz & Donal Cahill & Tali Sharot - 1-19 Ten quick tips for effective dimensionality reduction
by Lan Huong Nguyen & Susan Holmes - 1-20 Learning to use past evidence in a sophisticated world model
by Sanjeevan Ahilan & Rebecca B Solomon & Yannick-André Breton & Kent Conover & Ritwik K Niyogi & Peter Shizgal & Peter Dayan - 1-21 DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences
by Ingoo Lee & Jongsoo Keum & Hojung Nam - 1-21 Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome
by Kymberleigh A Pagel & Danny Antaki & AoJie Lian & Matthew Mort & David N Cooper & Jonathan Sebat & Lilia M Iakoucheva & Sean D Mooney & Predrag Radivojac - 1-21 Modeling the temporal dynamics of the gut microbial community in adults and infants
by Liat Shenhav & Ori Furman & Leah Briscoe & Mike Thompson & Justin D Silverman & Itzhak Mizrahi & Eran Halperin - 1-22 EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame
by Rohan V Koodli & Benjamin Keep & Katherine R Coppess & Fernando Portela & Eterna participants & Rhiju Das - 1-25 Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales
by Joshua M Mueller & Primoz Ravbar & Julie H Simpson & Jean M Carlson - 1-27 Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis
by Takaaki Yonekura & Akitoshi Iwamoto & Hironori Fujita & Munetaka Sugiyama - 1-33 Models that learn how humans learn: The case of decision-making and its disorders
by Amir Dezfouli & Kristi Griffiths & Fabio Ramos & Peter Dayan & Bernard W Balleine - 1-34 Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies
by Payam Piray & Amir Dezfouli & Tom Heskes & Michael J Frank & Nathaniel D Daw - 1-35 How single neuron properties shape chaotic dynamics and signal transmission in random neural networks
by Samuel P Muscinelli & Wulfram Gerstner & Tilo Schwalger
May 2019, Volume 15, Issue 5
- 1-7 Ten simple rules for carrying out and writing meta-analyses
by Diego A Forero & Sandra Lopez-Leon & Yeimy González-Giraldo & Pantelis G Bagos - 1-12 Comprehensively benchmarking applications for detecting copy number variation
by Le Zhang & Wanyu Bai & Na Yuan & Zhenglin Du - 1-12 Modeling enamel matrix secretion in mammalian teeth
by Teemu J Häkkinen & S Susanna Sova & Ian J Corfe & Leo Tjäderhane & Antti Hannukainen & Jukka Jernvall - 1-14 The statistics of epidemic transitions
by John M Drake & Tobias S Brett & Shiyang Chen & Bogdan I Epureanu & Matthew J Ferrari & Éric Marty & Paige B Miller & Eamon B O’Dea & Suzanne M O’Regan & Andrew W Park & Pejman Rohani - 1-16 Identification of avian flapping motion from non-volant winged dinosaurs based on modal effective mass analysis
by Yaser Saffar Talori & Jing-Shan Zhao & Yun-Fei Liu & Wen-Xiu Lu & Zhi-Heng Li & Jingmai Kathleen O'Connor - 1-16 Interacting cells driving the evolution of multicellular life cycles
by Yuanxiao Gao & Arne Traulsen & Yuriy Pichugin