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August 2019, Volume 15, Issue 8
- 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 - 1-22 Primacy coding facilitates effective odor discrimination when receptor sensitivities are tuned
by David Zwicker - 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 - 1-28 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 - 1-30 DART-ID increases single-cell proteome coverage
by Albert Tian Chen & Alexander Franks & Nikolai Slavov
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 - 1-15 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 - 1-25 Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales
by Joshua M Mueller & Primoz Ravbar & Julie H Simpson & Jean M Carlson - 1-35 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 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 - 1-18 Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features
by David A Knowles & Gina Bouchard & Sylvia Plevritis - 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 - 1-24 Efficient algorithms to discover alterations with complementary functional association in cancer
by Rebecca Sarto Basso & Dorit S Hochbaum & Fabio Vandin - 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 - 1-30 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 - 1-16 The intrinsic dimension of protein sequence evolution
by Elena Facco & Andrea Pagnani & Elena Tea Russo & Alessandro Laio - 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 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 - 1-24 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 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 Contextual influence on confidence judgments in human reinforcement learning
by Maël Lebreton & Karin Bacily & Stefano Palminteri & Jan B Engelmann - 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 - 1-30 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 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 - 1-25 Methods for computing the maximum performance of computational models of fMRI responses
by Agustin Lage-Castellanos & Giancarlo Valente & Elia Formisano & Federico De Martino - 1-27 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 - 1-29 Scalable nonlinear programming framework for parameter estimation in dynamic biological system models
by Sungho Shin & Ophelia S Venturelli & Victor M Zavala - 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
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 - 1-17 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 - 1-19 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 - 1-24 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 - 1-26 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 - 1-19 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 - 1-21 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 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
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 - 1-21 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 - 1-35 Exploring chromatin hierarchical organization via Markov State Modelling
by Zhen Wah Tan & Enrico Guarnera & Igor N Berezovsky
November 2018, Volume 14, Issue 11
- 1-17 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 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 - 1-21 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 - 1-29 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
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 - 1-21 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 - 1-24 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 - 1-30 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 - 1-20 Maintaining maximal metabolic flux by gene expression control
by Robert Planqué & Josephus Hulshof & Bas Teusink & Johannes C Hendriks & Frank J Bruggeman - 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 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 - 1-33 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 - 1-14 Scaling up data curation using deep learning: An application to literature triage in genomic variation resources
by Kyubum Lee & Maria Livia Famiglietti & Aoife McMahon & Chih-Hsuan Wei & Jacqueline Ann Langdon MacArthur & Sylvain Poux & Lionel Breuza & Alan Bridge & Fiona Cunningham & Ioannis Xenarios & Zhiyong Lu - 1-14 SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks
by Rong Zhang & Zhao Ren & Wei Chen - 1-19 Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching
by Martin Raden & Mostafa Mahmoud Mohamed & Syed Mohsin Ali & Rolf Backofen - 1-21 Human Pavlovian fear conditioning conforms to probabilistic learning
by Athina Tzovara & Christoph W Korn & Dominik R Bach - 1-22 A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data
by Tianwei Yu - 1-24 MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction
by Xing Chen & Jun Yin & Jia Qu & Li Huang - 1-25 New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images
by Ilya Patrushev & Christina James-Zorn & Aldo Ciau-Uitz & Roger Patient & Michael J Gilchrist - 1-25 Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings
by Vito Paolo Pastore & Paolo Massobrio & Aleksandar Godjoski & Sergio Martinoia - 1-28 Rare-event sampling of epigenetic landscapes and phenotype transitions
by Margaret J Tse & Brian K Chu & Cameron P Gallivan & Elizabeth L Read - 1-29 Profiling cellular morphodynamics by spatiotemporal spectrum decomposition
by Xiao Ma & Onur Dagliyan & Klaus M Hahn & Gaudenz Danuser - 1-30 Inferring hidden structure in multilayered neural circuits
by Niru Maheswaranathan & David B Kastner & Stephen A Baccus & Surya Ganguli
July 2018, Volume 14, Issue 7
- 1-15 Punishment and inspection for governing the commons in a feedback-evolving game
by Xiaojie Chen & Attila Szolnoki - 1-16 Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning
by Naihui Zhou & Zachary D Siegel & Scott Zarecor & Nigel Lee & Darwin A Campbell & Carson M Andorf & Dan Nettleton & Carolyn J Lawrence-Dill & Baskar Ganapathysubramanian & Jonathan W Kelly & Iddo Friedberg - 1-16 A marginalized two-part Beta regression model for microbiome compositional data
by Haitao Chai & Hongmei Jiang & Lu Lin & Lei Liu - 1-19 Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location?
by Sebastian D Boie & Erin G Connor & Margaret McHugh & Katherine I Nagel & G Bard Ermentrout & John P Crimaldi & Jonathan D Victor - 1-21 PyPhi: A toolbox for integrated information theory
by William G P Mayner & William Marshall & Larissa Albantakis & Graham Findlay & Robert Marchman & Giulio Tononi - 1-23 Gain control with A-type potassium current: IA as a switch between divisive and subtractive inhibition
by Joshua H Goldwyn & Bradley R Slabe & Joseph B Travers & David Terman - 1-34 Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure
by Lukas Grossberger & Francesco P Battaglia & Martin Vinck - 1-38 Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception
by Luigi Acerbi & Kalpana Dokka & Dora E Angelaki & Wei Ji Ma
June 2018, Volume 14, Issue 6
- 1-15 Solving the RNA design problem with reinforcement learning
by Peter Eastman & Jade Shi & Bharath Ramsundar & Vijay S Pande - 1-18 Anticipating epidemic transitions with imperfect data
by Tobias S Brett & Eamon B O’Dea & Éric Marty & Paige B Miller & Andrew W Park & John M Drake & Pejman Rohani - 1-21 Computation predicts rapidly adapting mechanotransduction currents cannot account for tactile encoding in Merkel cell-neurite complexes
by Gregory J Gerling & Lingtian Wan & Benjamin U Hoffman & Yuxiang Wang & Ellen A Lumpkin - 1-22 3D morphology-based clustering and simulation of human pyramidal cell dendritic spines
by Sergio Luengo-Sanchez & Isabel Fernaud-Espinosa & Concha Bielza & Ruth Benavides-Piccione & Pedro Larrañaga & Javier DeFelipe - 1-27 Instance-based generalization for human judgments about uncertainty
by Philipp Schustek & Rubén Moreno-Bote - 1-29 Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions
by Logan C Brooks & David C Farrow & Sangwon Hyun & Ryan J Tibshirani & Roni Rosenfeld - 1-30 The impact of temporal sampling resolution on parameter inference for biological transport models
by Jonathan U Harrison & Ruth E Baker
May 2018, Volume 14, Issue 5
- 1-4 2018 ISCB accomplishments by a senior scientist award
by Christiana N Fogg & Diane E Kovats & Ron Shamir - 1-4 Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago
by Milana Frenkel-Morgenstern & Lonnie Welch & Bruno Gaeta & Diane E Kovats - 1-4 Ten simple rules for writing a cover letter to accompany a job application for an academic position
by Lubomir Tomaska & Jozef Nosek - 1-13 Community-based benchmarking improves spike rate inference from two-photon calcium imaging data
by Philipp Berens & Jeremy Freeman & Thomas Deneux & Nikolay Chenkov & Thomas McColgan & Artur Speiser & Jakob H Macke & Srinivas C Turaga & Patrick Mineault & Peter Rupprecht & Stephan Gerhard & Rainer W Friedrich & Johannes Friedrich & Liam Paninski & Marius Pachitariu & Kenneth D Harris & Ben Bolte & Timothy A Machado & Dario Ringach & Jasmine Stone & Luke E Rogerson & Nicolas J Sofroniew & Jacob Reimer & Emmanouil Froudarakis & Thomas Euler & Miroslav Román Rosón & Lucas Theis & Andreas S Tolias & Matthias Bethge - 1-15 beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types
by Aaron T L Lun & Hervé Pagès & Mike L Smith - 1-21 Bi-stability in cooperative transport by ants in the presence of obstacles
by Jonathan E Ron & Itai Pinkoviezky & Ehud Fonio & Ofer Feinerman & Nir S Gov - 1-23 Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains
by Andreas Petrides & Glenn Vinnicombe - 1-26 Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization
by Marissa Renardy & Tau-Mu Yi & Dongbin Xiu & Ching-Shan Chou - 1-29 A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data
by Aaditya V Rangan & Caroline C McGrouther & John Kelsoe & Nicholas Schork & Eli Stahl & Qian Zhu & Arjun Krishnan & Vicky Yao & Olga Troyanskaya & Seda Bilaloglu & Preeti Raghavan & Sarah Bergen & Anders Jureus & Mikael Landen & Bipolar Disorders Working Group of the Psychiatric Genomics Consortium - 1-34 Optimizing the learning rate for adaptive estimation of neural encoding models
by Han-Lin Hsieh & Maryam M Shanechi
April 2018, Volume 14, Issue 4
- 1-15 RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning
by Ji-Sung Kim & Xin Gao & Andrey Rzhetsky - 1-16 Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer
by Itziar Irurzun-Arana & Alvaro Janda & Sergio Ardanza-Trevijano & Iñaki F Trocóniz - 1-17 Correcting for batch effects in case-control microbiome studies
by Sean M Gibbons & Claire Duvallet & Eric J Alm - 1-23 Using pseudoalignment and base quality to accurately quantify microbial community composition
by Mark Reppell & John Novembre - 1-24 Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape
by David R J Pleydell & Samuel Soubeyrand & Sylvie Dallot & Gérard Labonne & Joël Chadœuf & Emmanuel Jacquot & Gaël Thébaud - 1-25 Compositional clustering in task structure learning
by Nicholas T Franklin & Michael J Frank - 1-26 On the role of extrinsic noise in microRNA-mediated bimodal gene expression
by Marco Del Giudice & Stefano Bo & Silvia Grigolon & Carla Bosia - 1-27 Need for speed: An optimized gridding approach for spatially explicit disease simulations
by Stefan Sellman & Kimberly Tsao & Michael J Tildesley & Peter Brommesson & Colleen T Webb & Uno Wennergren & Matt J Keeling & Tom Lindström - 1-28 Exploiting glycan topography for computational design of Env glycoprotein antigenicity
by Wen-Han Yu & Peng Zhao & Monia Draghi & Claudia Arevalo & Christina B Karsten & Todd J Suscovich & Bronwyn Gunn & Hendrik Streeck & Abraham L Brass & Michael Tiemeyer & Michael Seaman & John R Mascola & Lance Wells & Douglas A Lauffenburger & Galit Alter - 1-31 Computational mechanisms underlying cortical responses to the affordance properties of visual scenes
by Michael F Bonner & Russell A Epstein
March 2018, Volume 14, Issue 3
- 1-14 Across-subjects classification of stimulus modality from human MEG high frequency activity
by Britta U Westner & Sarang S Dalal & Simon Hanslmayr & Tobias Staudigl - 1-18 An evolutionary learning and network approach to identifying key metabolites for osteoarthritis
by Ting Hu & Karoliina Oksanen & Weidong Zhang & Ed Randell & Andrew Furey & Guang Sun & Guangju Zhai - 1-18 From correlation to causation: Estimating effective connectivity from zero-lag covariances of brain signals
by Jonathan Schiefer & Alexander Niederbühl & Volker Pernice & Carolin Lennartz & Jürgen Hennig & Pierre LeVan & Stefan Rotter - 1-18 Activation gating in HCN2 channels
by Sabine Hummert & Susanne Thon & Thomas Eick & Ralf Schmauder & Eckhard Schulz & Klaus Benndorf - 1-19 Bat detective—Deep learning tools for bat acoustic signal detection
by Oisin Mac Aodha & Rory Gibb & Kate E Barlow & Ella Browning & Michael Firman & Robin Freeman & Briana Harder & Libby Kinsey & Gary R Mead & Stuart E Newson & Ivan Pandourski & Stuart Parsons & Jon Russ & Abigel Szodoray-Paradi & Farkas Szodoray-Paradi & Elena Tilova & Mark Girolami & Gabriel Brostow & Kate E Jones - 1-21 Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells
by Yanting Luo & Jianlin He & Xiguang Xu & Ming-an Sun & Xiaowei Wu & Xuemei Lu & Hehuang Xie - 1-24 Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state
by Hao Ge & Pingping Wu & Hong Qian & Xiaoliang Sunney Xie - 1-25 SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data
by Ivan Dotu & Scott I Adamson & Benjamin Coleman & Cyril Fournier & Emma Ricart-Altimiras & Eduardo Eyras & Jeffrey H Chuang - 1-25 speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification
by Charlie Beirnaert & Pieter Meysman & Trung Nghia Vu & Nina Hermans & Sandra Apers & Luc Pieters & Adrian Covaci & Kris Laukens - 1-25 Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders
by Guillaume Viejo & Thomas Cortier & Adrien Peyrache - 1-26 Factors affecting basket catheter detection of real and phantom rotors in the atria: A computational study
by Laura Martinez-Mateu & Lucia Romero & Ana Ferrer-Albero & Rafael Sebastian & José F Rodríguez Matas & José Jalife & Omer Berenfeld & Javier Saiz - 1-26 Dynamic combination of sensory and reward information under time pressure
by Shiva Farashahi & Chih-Chung Ting & Chang-Hao Kao & Shih-Wei Wu & Alireza Soltani - 1-27 Classifying dynamic transitions in high dimensional neural mass models: A random forest approach
by Lauric A Ferrat & Marc Goodfellow & John R Terry
February 2018, Volume 14, Issue 2
- 1-4 Ten simple rules for writing a popular science book
by Adam J Kucharski - 1-13 Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach
by Meenu R Mridula & Ashalatha S Nair & K Satheesh Kumar - 1-16 A maximum-entropy model for predicting chromatin contacts
by Pau Farré & Eldon Emberly - 1-20 A model of risk and mental state shifts during social interaction
by Andreas Hula & Iris Vilares & Terry Lohrenz & Peter Dayan & P Read Montague - 1-21 Control fast or control smart: When should invading pathogens be controlled?
by Robin N Thompson & Christopher A Gilligan & Nik J Cunniffe - 1-23 Prediction of infectious disease epidemics via weighted density ensembles
by Evan L Ray & Nicholas G Reich - 1-26 Interpretation of correlated neural variability from models of feed-forward and recurrent circuits
by Volker Pernice & Rava Azeredo da Silveira - 1-26 Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains
by Sneha Vishwanath & Alexandre G de Brevern & Narayanaswamy Srinivasan