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Content
August 2019, Volume 15, Issue 8
- 1-29 Every which way? On predicting tumor evolution using cancer progression models
by Ramon Diaz-Uriarte & Claudia Vasallo - 1-29 Predicting kinase inhibitors using bioactivity matrix derived informer sets
by Huikun Zhang & Spencer S Ericksen & Ching-pei Lee & Gene E Ananiev & Nathan Wlodarchak & Peng Yu & Julie C Mitchell & Anthony Gitter & Stephen J Wright & F Michael Hoffmann & Scott A Wildman & Michael A Newton - 1-29 Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties
by Ljubisa Miskovic & Jonas Béal & Michael Moret & Vassily Hatzimanikatis - 1-30 A mathematical model of calcium dynamics: Obesity and mitochondria-associated ER membranes
by Jung Min Han & Vipul Periwal - 1-33 Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity
by Audrey Denizot & Misa Arizono & U Valentin Nägerl & Hédi Soula & Hugues Berry - 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
- 1-1 Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources
by Yoram Zarai & Tamir Tuller - 1-4 Correction: Temporal Gillespie algorithm: Fast simulation of contagion processes on time-varying networks
by Christian L Vestergaard & Mathieu Génois - 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 - 1-8 Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
by Adam Rule & Amanda Birmingham & Cristal Zuniga & Ilkay Altintas & Shih-Cheng Huang & Rob Knight & Niema Moshiri & Mai H Nguyen & Sara Brin Rosenthal & Fernando Pérez & Peter W Rose - 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 - 1-21 Large vessels as a tree of transmission lines incorporated in the CircAdapt whole-heart model: A computational tool to examine heart-vessel interaction
by Maarten H G Heusinkveld & Wouter Huberts & Joost Lumens & Theo Arts & Tammo Delhaas & Koen D Reesink - 1-21 Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential
by Aleksandra Karolak & Sharan Poonja & Katarzyna A Rejniak - 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 - 1-23 Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks
by Tim Breitenbach & Chunguang Liang & Niklas Beyersdorf & Thomas Dandekar - 1-23 Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: Parameter estimation and epidemiological implications
by Joseph A Lewnard & Benjamin A Lopman & Umesh D Parashar & Aisleen Bennett & Naor Bar-Zeev & Nigel A Cunliffe & Prasanna Samuel & M Lourdes Guerrero & Guillermo Ruiz-Palacios & Gagandeep Kang & Virginia E Pitzer - 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 Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data
by Ketevan Chkhaidze & Timon Heide & Benjamin Werner & Marc J Williams & Weini Huang & Giulio Caravagna & Trevor A Graham & Andrea Sottoriva - 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 - 1-27 Robustness of respiratory rhythm generation across dynamic regimes
by Jonathan E Rubin & Jeffrey C Smith - 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 - 1-29 Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference
by Chunhui Cai & Gregory F Cooper & Kevin N Lu & Xiaojun Ma & Shuping Xu & Zhenlong Zhao & Xueer Chen & Yifan Xue & Adrian V Lee & Nathan Clark & Vicky Chen & Songjian Lu & Lujia Chen & Liyue Yu & Harry S Hochheiser & Xia Jiang & Q Jane Wang & Xinghua Lu - 1-29 Modeling human intuitions about liquid flow with particle-based simulation
by Christopher J Bates & Ilker Yildirim & Joshua B Tenenbaum & Peter Battaglia - 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
- 1-1 Correction: Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria
by The PLOS Computational Biology Staff - 1-1 Correction: From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses
by Sven Zenker & Jonathan Rubin & Gilles Clermont - 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 - 1-15 Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes
by Atsushi Kamimura & Yoshiya J Matsubara & Kunihiko Kaneko & Nobuto Takeuchi - 1-16 Charting pathways to climate change mitigation in a coupled socio-climate model
by Thomas M Bury & Chris T Bauch & Madhur Anand - 1-18 Sequential exploration in the Iowa gambling task: Validation of a new computational model in a large dataset of young and old healthy participants
by Romain Ligneul - 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 Open collaborative writing with Manubot
by Daniel S Himmelstein & Vincent Rubinetti & David R Slochower & Dongbo Hu & Venkat S Malladi & Casey S Greene & Anthony Gitter - 1-21 Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
by Benedict Borer & Meriç Ataman & Vassily Hatzimanikatis & Dani Or - 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 - 1-24 A multi-scale model of gas transport in the lung to study heterogeneous lung ventilation during the multiple-breath washout test
by David Hasler & Pinelopi Anagnostopoulou & Sylvia Nyilas & Philipp Latzin & Johannes Schittny & Dominik Obrist - 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 - 1-26 Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells
by Marzena Mura & Céline Feillet & Roberto Bertolusso & Franck Delaunay & Marek Kimmel - 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 - 1-27 Resurgent Na+ Current Offers Noise Modulation in Bursting Neurons
by Sharmila Venugopal & Soju Seki & David H Terman & Antonios Pantazis & Riccardo Olcese & Martina Wiedau-Pazos & Scott H Chandler - 1-27 Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations
by Hanne Hoitzing & Payam A Gammage & Lindsey Van Haute & Michal Minczuk & Iain G Johnston & Nick S Jones - 1-31 A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model
by Erlend Hodneland & Erik Hanson & Ove Sævareid & Geir Nævdal & Arvid Lundervold & Veronika Šoltészová & Antonella Z Munthe-Kaas & Andreas Deistung & Jürgen R Reichenbach & Jan M Nordbotten - 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 - 1-36 Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model
by Mahua Roy & Stacey D Finley
May 2019, Volume 15, Issue 5
- 1-1 Notice of Republication: Ten simple rules for organizing a webinar series
by The PLOS Computational Biology Staff - 1-2 Wisdom of crowds in computational biology
by Jason A Papin & Feilim Mac Gabhann - 1-2 Correction: How pupil responses track value-based decision-making during and after reinforcement learning
by Joanne C Van Slooten & Sara Jahfari & Tomas Knapen & Jan Theeuwes - 1-7 Ten quick tips for biocuration
by Y Amy Tang & Klemens Pichler & Anja Füllgrabe & Jane Lomax & James Malone & Monica C Munoz-Torres & Drashtti V Vasant & Eleanor Williams & Melissa Haendel - 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 - 1-9 A quick guide for using Microsoft OneNote as an electronic laboratory notebook
by Santiago Guerrero & Andrés López-Cortés & Jennyfer M García-Cárdenas & Pablo Saa & Alberto Indacochea & Isaac Armendáriz-Castillo & Ana Karina Zambrano & Verónica Yumiceba & Andy Pérez-Villa & Patricia Guevara-Ramírez & Oswaldo Moscoso-Zea & Joel Paredes & Paola E Leone & César Paz-y-Miño - 1-11 Ten quick tips for using a Raspberry Pi
by Anthony C Fletcher & Cameron Mura - 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 - 1-16 Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions
by Matti Javanainen & Giray Enkavi & Ramon Guixà-Gonzaléz & Waldemar Kulig & Hector Martinez-Seara & Ilya Levental & Ilpo Vattulainen - 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 - 1-21 Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares
by Yuning Hao & Ming Yan & Blake R Heath & Yu L Lei & Yuying Xie - 1-22 Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG
by Natalie Schaworonkow & Vadim V Nikulin - 1-23 Perturbing low dimensional activity manifolds in spiking neuronal networks
by Emil Wärnberg & Arvind Kumar - 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 - 1-26 Differential sustained and transient temporal processing across visual streams
by Anthony Stigliani & Brianna Jeska & Kalanit Grill-Spector - 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 - 1-30 A neuromechanistic model for rhythmic beat generation
by Amitabha Bose & Áine Byrne & John Rinzel
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 - 1-7 Network motifs and their origins
by Lewi Stone & Daniel Simberloff & Yael Artzy-Randrup - 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 - 1-11 A quick guide for student-driven community genome annotation
by Prashant S Hosmani & Teresa Shippy & Sherry Miller & Joshua B Benoit & Monica Munoz-Torres & Mirella Flores-Gonzalez & Lukas A Mueller & Helen Wiersma-Koch & Tom D’Elia & Susan J Brown & Surya Saha - 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 - 1-20 Physical constraints on accuracy and persistence during breast cancer cell chemotaxis
by Julien Varennes & Hye-ran Moon & Soutick Saha & Andrew Mugler & Bumsoo Han - 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 - 1-21 Approximate Bayesian estimation of coevolutionary arms races
by Scott L Nuismer & Bob Week - 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 Predicting synthetic lethal interactions using conserved patterns in protein interaction networks
by Graeme Benstead-Hume & Xiangrong Chen & Suzanna R Hopkins & Karen A Lane & Jessica A Downs & Frances M G Pearl - 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 A multiscale model of epigenetic heterogeneity-driven cell fate decision-making
by Núria Folguera-Blasco & Rubén Pérez-Carrasco & Elisabet Cuyàs & Javier A Menendez & Tomás Alarcón - 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 BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
by Remco Bouckaert & Timothy G Vaughan & Joëlle Barido-Sottani & Sebastián Duchêne & Mathieu Fourment & Alexandra Gavryushkina & Joseph Heled & Graham Jones & Denise Kühnert & Nicola De Maio & Michael Matschiner & Fábio K Mendes & Nicola F Müller & Huw A Ogilvie & Louis du Plessis & Alex Popinga & Andrew Rambaut & David Rasmussen & Igor Siveroni & Marc A Suchard & Chieh-Hsi Wu & Dong Xie & Chi Zhang & Tanja Stadler & Alexei J Drummond - 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 - 1-31 Isolating and quantifying the role of developmental noise in generating phenotypic variation
by Maria Kiskowski & Tilmann Glimm & Nickolas Moreno & Tony Gamble & Ylenia Chiari - 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
- 1-1 Correction: In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability
by Vasileios Vavourakis & Triantafyllos Stylianopoulos & Peter A Wijeratne - 1-15 Ten principles for machine-actionable data management plans
by Tomasz Miksa & Stephanie Simms & Daniel Mietchen & Sarah Jones - 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 - 1-18 In vitro and in silico multidimensional modeling of oncolytic tumor virotherapy dynamics
by David R Berg & Chetan P Offord & Iris Kemler & Matthew K Ennis & Lawrence Chang & George Paulik & Zeljko Bajzer & Claudia Neuhauser & David Dingli - 1-19 Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations
by Ramu Anandakrishnan & Robin T Varghese & Nicholas A Kinney & Harold R Garner - 1-19 A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows
by Pei-Chi Yang & Shweta Purawat & Pek U Ieong & Mao-Tsuen Jeng & Kevin R DeMarco & Igor Vorobyov & Andrew D McCulloch & Ilkay Altintas & Rommie E Amaro & Colleen E Clancy - 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 - 1-23 Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits
by Florian Eberhardt & Andreas V M Herz & Stefan Häusler - 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 Myopic control of neural dynamics
by David Hocker & Il Memming Park - 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 OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling
by Fangzhou Shen & Renliang Sun & Jie Yao & Jian Li & Qian Liu & Nathan D Price & Chenguang Liu & Zhuo Wang - 1-25 A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell
by Robert John Holash & Brian R MacIntosh - 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 Rapid interpretation of small-angle X-ray scattering data
by Marie Weiel & Ines Reinartz & Alexander Schug - 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 - 1-28 Determination of effective synaptic conductances using somatic voltage clamp
by Songting Li & Nan Liu & Li Yao & Xiaohui Zhang & Douglas Zhou & David Cai - 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 - 1-31 Agent-based modeling of morphogenetic systems: Advantages and challenges
by Chad M Glen & Melissa L Kemp & Eberhard O Voit - 1-32 An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections
by T Alex Perkins & Robert C Reiner Jr. & Guido España & Quirine A ten Bosch & Amit Verma & Kelly A Liebman & Valerie A Paz-Soldan & John P Elder & Amy C Morrison & Steven T Stoddard & Uriel Kitron & Gonzalo M Vazquez-Prokopec & Thomas W Scott & David L Smith - 1-32 ChIPulate: A comprehensive ChIP-seq simulation pipeline
by Vishaka Datta & Sridhar Hannenhalli & Rahul Siddharthan - 1-33 Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks
by Manuel Beiran & Srdjan Ostojic - 1-34 Soma-axon coupling configurations that enhance neuronal coincidence detection
by Joshua H Goldwyn & Michiel W H Remme & John Rinzel - 1-40 Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines
by Paul Van Liedekerke & Johannes Neitsch & Tim Johann & Kevin Alessandri & Pierre Nassoy & Dirk Drasdo - 1-41 Computational geometry for modeling neural populations: From visualization to simulation
by Marc de Kamps & Mikkel Lepperød & Yi Ming Lai
February 2019, Volume 15, Issue 2
- 1-1 Correction: Epistasis in genomic and survival data of cancer patients
by Dariusz Matlak & Ewa Szczurek - 1-13 Social evolution under demographic stochasticity
by David V McLeod & Troy Day - 1-14 Script of Scripts: A pragmatic workflow system for daily computational research
by Gao Wang & Bo Peng - 1-15 Identifying the mechanism for superdiffusivity in mouse fibroblast motility
by Giuseppe Passucci & Megan E Brasch & James H Henderson & Vasily Zaburdaev & M Lisa Manning - 1-15 A numerical approach for a discrete Markov model for progressing drug resistance of cancer
by Masayuki Maeda & Hideaki Yamashita - 1-15 IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis
by Brandon Monier & Adam McDermaid & Cankun Wang & Jing Zhao & Allison Miller & Anne Fennell & Qin Ma - 1-16 Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks
by Ahmed A Metwally & Philip S Yu & Derek Reiman & Yang Dai & Patricia W Finn & David L Perkins - 1-17 Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15
by Sebastian Funk & Anton Camacho & Adam J Kucharski & Rachel Lowe & Rosalind M Eggo & W John Edmunds - 1-17 Structure and variability of delay activity in premotor cortex
by Nir Even-Chen & Blue Sheffer & Saurabh Vyas & Stephen I Ryu & Krishna V Shenoy - 1-17 A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications
by He Peng & Xiangxiang Zeng & Yadi Zhou & Defu Zhang & Ruth Nussinov & Feixiong Cheng - 1-17 How good are pathogenicity predictors in detecting benign variants?
by Abhishek Niroula & Mauno Vihinen - 1-19 Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas
by David G P van IJzendoorn & Karoly Szuhai & Inge H Briaire-de Bruijn & Marie Kostine & Marieke L Kuijjer & Judith V M G Bovée - 1-19 CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis
by Marzieh Ayati & Danica Wiredja & Daniela Schlatzer & Sean Maxwell & Ming Li & Mehmet Koyutürk & Mark R Chance - 1-19 Predictability in process-based ensemble forecast of influenza
by Sen Pei & Mark A Cane & Jeffrey Shaman - 1-19 Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited
by Dave Osthus & Ashlynn R Daughton & Reid Priedhorsky - 1-20 Development and validation of influenza forecasting for 64 temperate and tropical countries
by Sarah C Kramer & Jeffrey Shaman - 1-20 Independent working memory resources for egocentric and allocentric spatial information
by David Aagten-Murphy & Paul M Bays