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July 2019, Volume 15, Issue 7
- 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 - 1-33 Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks
by Manuel Beiran & Srdjan Ostojic - 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
- 1-13 Social evolution under demographic stochasticity
by David V McLeod & Troy Day - 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 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 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 - 1-21 Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components
by Nicholas Rogers & John Hermiz & Mehran Ganji & Erik Kaestner & Kıvılcım Kılıç & Lorraine Hossain & Martin Thunemann & Daniel R Cleary & Bob S Carter & David Barba & Anna Devor & Eric Halgren & Shadi A Dayeh & Vikash Gilja - 1-21 A local measure of symmetry and orientation for individual spikes of grid cells
by Simon N Weber & Henning Sprekeler - 1-21 A data-driven interactome of synergistic genes improves network-based cancer outcome prediction
by Amin Allahyar & Joske Ubels & Jeroen de Ridder - 1-21 Phylogenies from dynamic networks
by Cornelia Metzig & Oliver Ratmann & Daniela Bezemer & Caroline Colijn - 1-24 Identifying individual risk rare variants using protein structure guided local tests (POINT)
by Rachel Marceau West & Wenbin Lu & Daniel M Rotroff & Melaine A Kuenemann & Sheng-Mao Chang & Michael C Wu & Michael J Wagner & John B Buse & Alison A Motsinger-Reif & Denis Fourches & Jung-Ying Tzeng - 1-25 Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling
by Nitzan Shahar & Tobias U Hauser & Michael Moutoussis & Rani Moran & Mehdi Keramati & NSPN consortium & Raymond J Dolan - 1-25 Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana
by Shayne M Plourde & Prativa Amom & Michelle Tan & Adriana T Dawes & Anna A Dobritsa - 1-25 16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses
by Stephen Woloszynek & Zhengqiao Zhao & Jian Chen & Gail L Rosen - 1-26 Information integration in large brain networks
by Daniel Toker & Friedrich T Sommer - 1-28 Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis
by Hongyu Zhou & Zheng Dong & Gennady Verkhivker & Brian D Zoltowski & Peng Tao - 1-29 Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors
by Lior Tiroshi & Joshua A Goldberg - 1-32 Maps of variability in cell lineage trees
by Damien G Hicks & Terence P Speed & Mohammed Yassin & Sarah M Russell
January 2019, Volume 15, Issue 1
- 1-4 Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
by Arne Elofsson & Berk Hess & Erik Lindahl & Alexey Onufriev & David van der Spoel & Anders Wallqvist - 1-15 Prediction of ultra-high-order antibiotic combinations based on pairwise interactions
by Itay Katzir & Murat Cokol & Bree B Aldridge & Uri Alon - 1-17 Protein—protein binding supersites
by Raji Viswanathan & Eduardo Fajardo & Gabriel Steinberg & Matthew Haller & Andras Fiser - 1-19 Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis
by Xiaohu Hu & Yibo Wang & Amanda Hunkele & Davide Provasi & Gavril W Pasternak & Marta Filizola - 1-20 Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization
by Timothy D Majarian & Robert F Murphy & Seema S Lakdawala - 1-20 A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex
by Margot C Bjoring & C Daniel Meliza - 1-21 Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures
by Jordan J Clark & Mark L Benson & Richard D Smith & Heather A Carlson - 1-23 The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments
by Zachary R Fox & Brian Munsky - 1-23 STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds
by Abdul-Saboor Sheikh & Nicol S Harper & Jakob Drefs & Yosef Singer & Zhenwen Dai & Richard E Turner & Jörg Lücke - 1-23 Deep image reconstruction from human brain activity
by Guohua Shen & Tomoyasu Horikawa & Kei Majima & Yukiyasu Kamitani - 1-24 Sour grapes and sweet victories: How actions shape preferences
by Fabien Vinckier & Lionel Rigoux & Irma T Kurniawan & Chen Hu & Sacha Bourgeois-Gironde & Jean Daunizeau & Mathias Pessiglione - 1-26 PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data
by Yu-Han H Hsu & Claire Churchhouse & Tune H Pers & Josep M Mercader & Andres Metspalu & Krista Fischer & Kristen Fortney & Eric K Morgen & Clicerio Gonzalez & Maria E Gonzalez & Tonu Esko & Joel N Hirschhorn - 1-31 Predicting change: Approximate inference under explicit representation of temporal structure in changing environments
by Dimitrije Marković & Andrea M F Reiter & Stefan J Kiebel
April 2019, Volume 14, Issue 4
- 1-12 CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer
by Thomas D Sherman & Luciane T Kagohara & Raymon Cao & Raymond Cheng & Matthew Satriano & Michael Considine & Gabriel Krigsfeld & Ruchira Ranaweera & Yong Tang & Sandra A Jablonski & Genevieve Stein-O'Brien & Daria A Gaykalova & Louis M Weiner & Christine H Chung & Elana J Fertig
December 2018, Volume 14, Issue 12
- 1-4 One thousand simple rules
by Philip E Bourne & Fran Lewitter & Scott Markel & Jason A Papin - 1-15 Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator
by Daniel Blustein & Ahmed Shehata & Kevin Englehart & Jonathon Sensinger - 1-17 Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
by Danesh Moradigaravand & Martin Palm & Anne Farewell & Ville Mustonen & Jonas Warringer & Leopold Parts - 1-20 On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model
by Brian C Lee & Daniel J Tward & Partha P Mitra & Michael I Miller - 1-21 SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions
by Wen Zhang & Xiang Yue & Guifeng Tang & Wenjian Wu & Feng Huang & Xining Zhang - 1-22 A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins
by Luhao Zhang & Maodong Li & Zhirong Liu - 1-23 Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson’s disease
by Logan L Grado & Matthew D Johnson & Theoden I Netoff - 1-27 Bayesian inference of protein conformational ensembles from limited structural data
by Wojciech Potrzebowski & Jill Trewhella & Ingemar Andre - 1-27 Coherent chaos in a recurrent neural network with structured connectivity
by Itamar Daniel Landau & Haim Sompolinsky - 1-28 A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome
by Jia Lu & Xiaoyi Cao & Sheng Zhong - 1-29 Detection and analysis of spatiotemporal patterns in brain activity
by Rory G Townsend & Pulin Gong - 1-35 Exploring chromatin hierarchical organization via Markov State Modelling
by Zhen Wah Tan & Enrico Guarnera & Igor N Berezovsky
November 2018, Volume 14, Issue 11
- 1-11 Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks
by Ryan R Wick & Louise M Judd & Kathryn E Holt - 1-16 A computational analysis of dynamic, multi-organ inflammatory crosstalk induced by endotoxin in mice
by Ruben Zamora & Sebastian Korff & Qi Mi & Derek Barclay & Lukas Schimunek & Riccardo Zucca & Xerxes D Arsiwalla & Richard L Simmons & Paul Verschure & Timothy R Billiar & Yoram Vodovotz - 1-17 Moth olfactory receptor neurons adjust their encoding efficiency to temporal statistics of pheromone fluctuations
by Marie Levakova & Lubomir Kostal & Christelle Monsempès & Vincent Jacob & Philippe Lucas - 1-18 RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks
by Jun Li & Wei Zhu & Jun Wang & Wenfei Li & Sheng Gong & Jian Zhang & Wei Wang - 1-18 powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire
by Hillary Koch & Dmytro Starenki & Sara J Cooper & Richard M Myers & Qunhua Li - 1-19 Deterministic response strategies in a trial-and-error learning task
by Holger Mohr & Katharina Zwosta & Dimitrije Markovic & Sebastian Bitzer & Uta Wolfensteller & Hannes Ruge - 1-19 Comparative structural dynamic analysis of GTPases
by Hongyang Li & Xin-Qiu Yao & Barry J Grant - 1-21 Prediction and classification in equation-free collective motion dynamics
by Keisuke Fujii & Takeshi Kawasaki & Yuki Inaba & Yoshinobu Kawahara - 1-21 Efficient pedigree recording for fast population genetics simulation
by Jerome Kelleher & Kevin R Thornton & Jaime Ashander & Peter L Ralph - 1-22 A regularity index for dendrites - local statistics of a neuron's input space
by Laura Anton-Sanchez & Felix Effenberger & Concha Bielza & Pedro Larrañaga & Hermann Cuntz - 1-23 Binding of the general anesthetic sevoflurane to ion channels
by Letícia Stock & Juliana Hosoume & Leonardo Cirqueira & Werner Treptow - 1-24 Inferring interaction partners from protein sequences using mutual information
by Anne-Florence Bitbol - 1-25 Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction
by Susann Vorberg & Stefan Seemayer & Johannes Söding - 1-28 Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes
by Weilong Zhao & Xinwei Sher - 1-29 A Bayesian mixture modelling approach for spatial proteomics
by Oliver M Crook & Claire M Mulvey & Paul D W Kirk & Kathryn S Lilley & Laurent Gatto - 1-30 Rosetta FunFolDes – A general framework for the computational design of functional proteins
by Jaume Bonet & Sarah Wehrle & Karen Schriever & Che Yang & Anne Billet & Fabian Sesterhenn & Andreas Scheck & Freyr Sverrisson & Barbora Veselkova & Sabrina Vollers & Roxanne Lourman & Mélanie Villard & Stéphane Rosset & Thomas Krey & Bruno E Correia - 1-33 Modulation of voltage-dependent K+ conductances in photoreceptors trades off investment in contrast gain for bandwidth
by Francisco J H Heras & Mikko Vähäsöyrinki & Jeremy E Niven - 1-34 Comparing Bayesian and non-Bayesian accounts of human confidence reports
by William T Adler & Wei Ji Ma
October 2018, Volume 14, Issue 10
- 1-4 Ten simple rules for developing good reading habits during graduate school and beyond
by Marcos Méndez - 1-4 Ten simple rules when considering retirement
by Philip E Bourne - 1-7 What to know before forecasting the flu
by Prithwish Chakraborty & Bryan Lewis & Stephen Eubank & John S Brownstein & Madhav Marathe & Naren Ramakrishnan - 1-8 Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor
by Richard A Erickson & Michael N Fienen & S Grace McCalla & Emily L Weiser & Melvin L Bower & Jonathan M Knudson & Greg Thain - 1-15 Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function
by Robin Moss & Frank B Sachse & Eloy G Moreno-Galindo & Ricardo A Navarro-Polanco & Martin Tristani-Firouzi & Gunnar Seemann - 1-17 A k -mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria
by Erki Aun & Age Brauer & Veljo Kisand & Tanel Tenson & Maido Remm - 1-19 Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques
by Dominik Wodarz & Pamela J Skinner & David N Levy & Elizabeth Connick - 1-20 meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays
by Sahar Gelfman & Quanli Wang & Yi-Fan Lu & Diana Hall & Christopher D Bostick & Ryan Dhindsa & Matt Halvorsen & K Melodi McSweeney & Ellese Cotterill & Tom Edinburgh & Michael A Beaumont & Wayne N Frankel & Slavé Petrovski & Andrew S Allen & Michael J Boland & David B Goldstein & Stephen J Eglen - 1-21 Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals
by Iksoo Huh & Isabel Mendizabal & Taesung Park & Soojin V Yi - 1-21 Ten quick tips for getting the most scientific value out of numerical data
by Lars Ole Schwen & Sabrina Rueschenbaum - 1-22 Modeling sensory-motor decisions in natural behavior
by Ruohan Zhang & Shun Zhang & Matthew H Tong & Yuchen Cui & Constantin A Rothkopf & Dana H Ballard & Mary M Hayhoe - 1-23 Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data
by Misbah Razzaq & Loïc Paulevé & Anne Siegel & Julio Saez-Rodriguez & Jérémie Bourdon & Carito Guziolowski - 1-24 Predicting B cell receptor substitution profiles using public repertoire data
by Amrit Dhar & Kristian Davidsen & Frederick A Matsen IV & Vladimir N Minin - 1-24 Seizure pathways: A model-based investigation
by Philippa J Karoly & Levin Kuhlmann & Daniel Soudry & David B Grayden & Mark J Cook & Dean R Freestone - 1-28 Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells
by Ernest C Y Ho & Juan Nicolas Malagón & Abha Ahuja & Rama Singh & Ellen Larsen - 1-28 State dependence of stimulus-induced variability tuning in macaque MT
by Joseph A Lombardo & Matthew V Macellaio & Bing Liu & Stephanie E Palmer & Leslie C Osborne - 1-30 A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments
by Katharina Nöh & Sebastian Niedenführ & Martin Beyß & Wolfgang Wiechert
September 2018, Volume 14, Issue 9
- 1-15 Individualised aspiration dynamics: Calculation by proofs
by Bin Wu & Lei Zhou - 1-16 clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
by Davide Risso & Liam Purvis & Russell B Fletcher & Diya Das & John Ngai & Sandrine Dudoit & Elizabeth Purdom - 1-16 Optimal multi-source forecasting of seasonal influenza
by Zeynep Ertem & Dorrie Raymond & Lauren Ancel Meyers - 1-18 Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing
by Hamidreza Jamalabadi & Sarah Alizadeh & Monika Schönauer & Christian Leibold & Steffen Gais - 1-19 Implications of alternative routes to APC/C inhibition by the mitotic checkpoint complex
by Fridolin Gross & Paolo Bonaiuti & Silke Hauf & Andrea Ciliberto - 1-20 Maintaining maximal metabolic flux by gene expression control
by Robert Planqué & Josephus Hulshof & Bas Teusink & Johannes C Hendriks & Frank J Bruggeman - 1-23 Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling
by Tatu Pantsar & Sami Rissanen & Daniel Dauch & Tuomo Laitinen & Ilpo Vattulainen & Antti Poso - 1-24 An information theoretic treatment of sequence-to-expression modeling
by Farzaneh Khajouei & Saurabh Sinha - 1-24 Transition state characteristics during cell differentiation
by Rowan D Brackston & Eszter Lakatos & Michael P H Stumpf - 1-25 Modeling and prediction of clinical symptom trajectories in Alzheimer’s disease using longitudinal data
by Nikhil Bhagwat & Joseph D Viviano & Aristotle N Voineskos & M Mallar Chakravarty & Alzheimer’s Disease Neuroimaging Initiative - 1-25 The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow
by Rosanna Migliore & Carmen A Lupascu & Luca L Bologna & Armando Romani & Jean-Denis Courcol & Stefano Antonel & Werner A H Van Geit & Alex M Thomson & Audrey Mercer & Sigrun Lange & Joanne Falck & Christian A Rössert & Ying Shi & Olivier Hagens & Maurizio Pezzoli & Tamas F Freund & Szabolcs Kali & Eilif B Muller & Felix Schürmann & Henry Markram & Michele Migliore - 1-28 A Markov chain for numerical chromosomal instability in clonally expanding populations
by Sergi Elizalde & Ashley M Laughney & Samuel F Bakhoum - 1-29 Co-evolution networks of HIV/HCV are modular with direct association to structure and function
by Ahmed Abdul Quadeer & David Morales-Jimenez & Matthew R McKay - 1-31 Comparing two classes of biological distribution systems using network analysis
by Lia Papadopoulos & Pablo Blinder & Henrik Ronellenfitsch & Florian Klimm & Eleni Katifori & David Kleinfeld & Danielle S Bassett - 1-33 Informational structures: A dynamical system approach for integrated information
by Francisco J Esteban & Javier A Galadí & José A Langa & José R Portillo & Fernando Soler-Toscano - 1-40 Inferring decoding strategies for multiple correlated neural populations
by Kaushik J Lakshminarasimhan & Alexandre Pouget & Gregory C DeAngelis & Dora E Angelaki & Xaq Pitkow
August 2018, Volume 14, Issue 8
- 1-12 Ten simple rules for measuring the impact of workshops
by Shoaib Sufi & Aleksandra Nenadic & Raniere Silva & Beth Duckles & Iveta Simera & Jennifer A de Beyer & Caroline Struthers & Terhi Nurmikko-Fuller & Louisa Bellis & Wadud Miah & Adriana Wilde & Iain Emsley & Olivier Philippe & Melissa Balzano & Sara Coelho & Heather Ford & Catherine Jones & Vanessa Higgins