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Content
December 2019, Volume 15, Issue 12
- 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 - 1-17 Noise-precision tradeoff in predicting combinations of mutations and drugs
by Avichai Tendler & Anat Zimmer & Avi Mayo & Uri Alon - 1-18 Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features
by David A Knowles & Gina Bouchard & Sylvia Plevritis - 1-18 Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes
by Anupama Sharma & Shakti N Menon & V Sasidevan & Sitabhra Sinha - 1-19 Amplitude cancellation influences the association between frequency components in the neural drive to muscle and the rectified EMG signal
by Jakob Lund Dideriksen & Dario Farina - 1-20 Uncovering functional signature in neural systems via random matrix theory
by Assaf Almog & M Renate Buijink & Ori Roethler & Stephan Michel & Johanna H Meijer & Jos H T Rohling & Diego Garlaschelli - 1-20 DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images
by Victor Kulikov & Syuan-Ming Guo & Matthew Stone & Allen Goodman & Anne Carpenter & Mark Bathe & Victor Lempitsky - 1-20 Forecasting national and regional influenza-like illness for the USA
by Michal Ben-Nun & Pete Riley & James Turtle & David P Bacon & Steven Riley - 1-22 Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG
by Natalie Schaworonkow & Vadim V Nikulin - 1-24 State-aware detection of sensory stimuli in the cortex of the awake mouse
by Audrey J Sederberg & Aurélie Pala & He J V Zheng & Biyu J He & Garrett B Stanley - 1-24 Efficient algorithms to discover alterations with complementary functional association in cancer
by Rebecca Sarto Basso & Dorit S Hochbaum & Fabio Vandin - 1-25 An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis
by Niki Karagianni & Ksanthi Kranidioti & Nikolaos Fikas & Maria Tsochatzidou & Panagiotis Chouvardas & Maria C Denis & George Kollias & Christoforos Nikolaou - 1-27 Parameter estimation and identifiability in a neural population model for electro-cortical activity
by Agus Hartoyo & Peter J Cadusch & David T J Liley & Damien G Hicks - 1-28 Beyond Bouma's window: How to explain global aspects of crowding?
by Adrien Doerig & Alban Bornet & Ruth Rosenholtz & Gregory Francis & Aaron M Clarke & Michael H Herzog - 1-29 Human representation of multimodal distributions as clusters of samples
by Jingwei Sun & Jian Li & Hang Zhang - 1-30 Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias
by Ming Bo Cai & Nicolas W Schuck & Jonathan W Pillow & Yael Niv
April 2019, Volume 15, Issue 4
- 1-7 Ten simple rules for organizing a webinar series
by Faisal M Fadlelmola & Sumir Panji & Azza E Ahmed & Amel Ghouila & Wisdom A Akurugu & Jean-Baka Domelevo Entfellner & Oussema Souiai & Nicola Mulder & H3ABioNet Research working group as members of the H3Africa Consortium - 1-7 Ten simple rules for providing a meaningful research experience to high school students
by Emily A Lescak & Kate M O’Neill & Giovanna M Collu & Subhamoy Das - 1-8 Ten simple rules towards healthier research labs
by Fernando T Maestre - 1-10 Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)
by Hailong Meng & Gur Yaari & Christopher R Bolen & Stefan Avey & Steven H Kleinstein - 1-16 The intrinsic dimension of protein sequence evolution
by Elena Facco & Andrea Pagnani & Elena Tea Russo & Alessandro Laio - 1-16 Revealing evolutionary constraints on proteins through sequence analysis
by Shou-Wen Wang & Anne-Florence Bitbol & Ned S Wingreen - 1-17 Bet-hedging strategies in expanding populations
by Paula Villa Martín & Miguel A Muñoz & Simone Pigolotti - 1-17 Model diagnostics and refinement for phylodynamic models
by Max S Y Lau & Bryan T Grenfell & Colin J Worby & Gavin J Gibson - 1-18 Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs
by Cheng Liang & Shengpeng Yu & Jiawei Luo - 1-19 Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions
by Anne Richelle & Austin W T Chiang & Chih-Chung Kuo & Nathan E Lewis - 1-21 Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length
by Kai Liu & Brian Chu & Jay Newby & Elizabeth L Read & John Lowengrub & Jun Allard - 1-21 Chemical features mining provides new descriptive structure-odor relationships
by Carmen C Licon & Guillaume Bosc & Mohammed Sabri & Marylou Mantel & Arnaud Fournel & Caroline Bushdid & Jerome Golebiowski & Celine Robardet & Marc Plantevit & Mehdi Kaytoue & Moustafa Bensafi - 1-21 Neural crest streaming as an emergent property of tissue interactions during morphogenesis
by András Szabó & Eric Theveneau & Melissa Turan & Roberto Mayor - 1-21 Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms
by Kyriaki Kalimeri & Matteo Delfino & Ciro Cattuto & Daniela Perrotta & Vittoria Colizza & Caroline Guerrisi & Clement Turbelin & Jim Duggan & John Edmunds & Chinelo Obi & Richard Pebody & Ana O Franco & Yamir Moreno & Sandro Meloni & Carl Koppeschaar & Charlotte Kjelsø & Ricardo Mexia & Daniela Paolotti - 1-22 Evolutionary multiplayer games on graphs with edge diversity
by Qi Su & Lei Zhou & Long Wang - 1-23 I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment
by Stelios Pavlidis & Calixte Monast & Matthew J Loza & Patrick Branigan & Kiang F Chung & Ian M Adcock & Yike Guo & Anthony Rowe & Frédéric Baribaud - 1-24 Confidence resets reveal hierarchical adaptive learning in humans
by Micha Heilbron & Florent Meyniel - 1-24 Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size
by Daniel I S Rosenbloom & Peter Bacchetti & Mars Stone & Xutao Deng & Ronald J Bosch & Douglas D Richman & Janet D Siliciano & John W Mellors & Steven G Deeks & Roger G Ptak & Rebecca Hoh & Sheila M Keating & Melanie Dimapasoc & Marta Massanella & Jun Lai & Michele D Sobolewski & Deanna A Kulpa & Michael P Busch & for the Reservoir Assay Validation and Evaluation Network (RAVEN) Study Group - 1-25 A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation
by Marko Järvenpää & Mohamad R Abdul Sater & Georgia K Lagoudas & Paul C Blainey & Loren G Miller & James A McKinnell & Susan S Huang & Yonatan H Grad & Pekka Marttinen - 1-25 Competing evolutionary paths in growing populations with applications to multidrug resistance
by Michael D Nicholson & Tibor Antal - 1-25 Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder
by Abrar E Al-Shaer & George R Flentke & Mark E Berres & Ana Garic & Susan M Smith - 1-25 GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity
by Lex E Flagel & Benjamin K Blackman & Lila Fishman & Patrick J Monnahan & Andrea Sweigart & John K Kelly - 1-27 The relative contribution of color and material in object selection
by Ana Radonjić & Nicolas P Cottaris & David H Brainard - 1-27 Contextual influence on confidence judgments in human reinforcement learning
by Maël Lebreton & Karin Bacily & Stefano Palminteri & Jan B Engelmann - 1-27 Imperfect Bayesian inference in visual perception
by Elina Stengård & Ronald van den Berg - 1-28 TASmania: A bacterial Toxin-Antitoxin Systems database
by Hatice Akarsu & Patricia Bordes & Moise Mansour & Donna-Joe Bigot & Pierre Genevaux & Laurent Falquet - 1-29 A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism
by Oveis Jamialahmadi & Sameereh Hashemi-Najafabadi & Ehsan Motamedian & Stefano Romeo & Fatemeh Bagheri - 1-29 A Bayesian framework for the analysis of systems biology models of the brain
by Joshua Russell-Buckland & Christopher P Barnes & Ilias Tachtsidis - 1-30 SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species
by Đorđe Miladinović & Christine Muheim & Stefan Bauer & Andrea Spinnler & Daniela Noain & Mojtaba Bandarabadi & Benjamin Gallusser & Gabriel Krummenacher & Christian Baumann & Antoine Adamantidis & Steven A Brown & Joachim M Buhmann - 1-34 Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits
by Yifan Gu & Yang Qi & Pulin Gong - 1-35 Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features
by Craig A Magaret & David C Benkeser & Brian D Williamson & Bhavesh R Borate & Lindsay N Carpp & Ivelin S Georgiev & Ian Setliff & Adam S Dingens & Noah Simon & Marco Carone & Christopher Simpkins & David Montefiori & Galit Alter & Wen-Han Yu & Michal Juraska & Paul T Edlefsen & Shelly Karuna & Nyaradzo M Mgodi & Srilatha Edugupanti & Peter B Gilbert - 1-38 Inferring neural circuit structure from datasets of heterogeneous tuning curves
by Takafumi Arakaki & G Barello & Yashar Ahmadian - 1-41 Learning and forgetting using reinforced Bayesian change detection
by Vincent Moens & Alexandre Zénon
March 2019, Volume 15, Issue 3
- 1-16 Spatial clustering and common regulatory elements correlate with coordinated gene expression
by Jingyu Zhang & Hengyu Chen & Ruoyan Li & David A Taft & Guang Yao & Fan Bai & Jianhua Xing - 1-17 Evolutionary model for the unequal segregation of high copy plasmids
by Karin Münch & Richard Münch & Rebekka Biedendieck & Dieter Jahn & Johannes Müller - 1-17 Bacterial surface colonization, preferential attachment and fitness under periodic stress
by Maor Grinberg & Tomer Orevi & Nadav Kashtan - 1-17 Bayes-optimal estimation of overlap between populations of fixed size
by Daniel B Larremore - 1-18 LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities
by Lei Wang & Zhu-Hong You & Xing Chen & Yang-Ming Li & Ya-Nan Dong & Li-Ping Li & Kai Zheng - 1-20 A dynamic power-law sexual network model of gonorrhoea outbreaks
by Lilith K Whittles & Peter J White & Xavier Didelot - 1-20 Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data
by Finlay Campbell & Anne Cori & Neil Ferguson & Thibaut Jombart - 1-21 Latent goal models for dynamic strategic interaction
by Shariq N Iqbal & Lun Yin & Caroline B Drucker & Qian Kuang & Jean-François Gariépy & Michael L Platt & John M Pearson - 1-21 Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence
by Manh Cuong Ngô & Mads Peter Heide-Jørgensen & Susanne Ditlevsen - 1-21 Optimizing the depth and the direction of prospective planning using information values
by Can Eren Sezener & Amir Dezfouli & Mehdi Keramati - 1-21 A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations
by Weiling Li & Lin Lin & Raunaq Malhotra & Lei Yang & Raj Acharya & Mary Poss - 1-24 A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus
by Sifat A Moon & Lee W Cohnstaedt & D Scott McVey & Caterina M Scoglio - 1-24 A spectrum of routing strategies for brain networks
by Andrea Avena-Koenigsberger & Xiaoran Yan & Artemy Kolchinsky & Martijn P van den Heuvel & Patric Hagmann & Olaf Sporns - 1-25 Methods for computing the maximum performance of computational models of fMRI responses
by Agustin Lage-Castellanos & Giancarlo Valente & Elia Formisano & Federico De Martino - 1-25 Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas
by Lawrence W Sheppard & Emma J Defriez & Philip C Reid & Daniel C Reuman - 1-26 Building a mechanistic mathematical model of hepatitis C virus entry
by Mphatso Kalemera & Dilyana Mincheva & Joe Grove & Christopher J R Illingworth - 1-26 A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory
by Rodoniki Athanasiadou & Benjamin Neymotin & Nathan Brandt & Wei Wang & Lionel Christiaen & David Gresham & Daniel Tranchina - 1-27 The gradient of the reinforcement landscape influences sensorimotor learning
by Joshua G A Cashaback & Christopher K Lao & Dimitrios J Palidis & Susan K Coltman & Heather R McGregor & Paul L Gribble - 1-27 Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition
by Marieke Rohde & Kenichi Narioka & Jochen J Steil & Lina K Klein & Marc O Ernst - 1-28 Humans use multi-objective control to regulate lateral foot placement when walking
by Jonathan B Dingwell & Joseph P Cusumano - 1-29 Scalable nonlinear programming framework for parameter estimation in dynamic biological system models
by Sungho Shin & Ophelia S Venturelli & Victor M Zavala - 1-31 Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome
by Bernardo P de Almeida & André F Vieira & Joana Paredes & Mónica Bettencourt-Dias & Nuno L Barbosa-Morais - 1-32 ChIPulate: A comprehensive ChIP-seq simulation pipeline
by Vishaka Datta & Sridhar Hannenhalli & Rahul Siddharthan