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September 2021, Volume 17, Issue 9
- 1-29 Differential contribution to gene expression prediction of histone modifications at enhancers or promoters
by Mar González-Ramírez & Cecilia Ballaré & Francesca Mugianesi & Malte Beringer & Alexandra Santanach & Enrique Blanco & Luciano Di Croce - 1-29 An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City
by Sheng Zhang & Joan Ponce & Zhen Zhang & Guang Lin & George Karniadakis - 1-32 Envelope reconstruction of speech and music highlights stronger tracking of speech at low frequencies
by Nathaniel J Zuk & Jeremy W Murphy & Richard B Reilly & Edmund C Lalor - 1-35 Inter-trial effects in priming of pop-out: Comparison of computational updating models
by Fredrik Allenmark & Ahu Gokce & Thomas Geyer & Artyom Zinchenko & Hermann J Müller & Zhuanghua Shi - 1-40 On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo
by Charles-Elie Rabier & Vincent Berry & Marnus Stoltz & João D Santos & Wensheng Wang & Jean-Christophe Glaszmann & Fabio Pardi & Celine Scornavacca
August 2021, Volume 17, Issue 8
- 1-9 Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster
by Jamie J Alnasir - 1-10 Ten simple rules for aspiring graduate students
by Andrea I Luppi & Charlotte Coco Newton & Lynde Folsom & Elisa Galliano & Rafael Romero-Garcia - 1-12 Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries
by Benjamin Moore & Patricia Carvajal-López & Paballo Abel Chauke & Marco Cristancho & Victoria Dominguez Del Angel & Selene L Fernandez-Valverde & Amel Ghouila & Piraveen Gopalasingam & Fatma Zahra Guerfali & Alice Matimba & Sarah L Morgan & Guilherme Oliveira & Verena Ras & Alejandro Reyes & Javier De Las Rivas & Nicola Mulder - 1-13 SiGMoiD: A super-statistical generative model for binary data
by Xiaochuan Zhao & Germán Plata & Purushottam D Dixit - 1-13 Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coalescence regime
by Marc Durand - 1-17 An uncertainty-based model of the effects of fixation on choice
by Zhi-Wei Li & Wei Ji Ma - 1-18 Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base
by Tomasz Konopka & Sandra Ng & Damian Smedley - 1-18 Circadian rhythm shows potential for mRNA efficiency and self-organized division of labor in multinucleate cells
by Leif Zinn-Brooks & Marcus L Roper - 1-18 A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers
by Frances L Heredia & Abiel Roche-Lima & Elsie I Parés-Matos - 1-18 PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions
by Seyed Ziaeddin Alborzi & Amina Ahmed Nacer & Hiba Najjar & David W Ritchie & Marie-Dominique Devignes - 1-18 miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
by Ariel A Hippen & Matias M Falco & Lukas M Weber & Erdogan Pekcan Erkan & Kaiyang Zhang & Jennifer Anne Doherty & Anna Vähärautio & Casey S Greene & Stephanie C Hicks - 1-21 A large-scale brain network mechanism for increased seizure propensity in Alzheimer’s disease
by Luke Tait & Marinho A Lopes & George Stothart & John Baker & Nina Kazanina & Jiaxiang Zhang & Marc Goodfellow - 1-22 Unveiling functions of the visual cortex using task-specific deep neural networks
by Kshitij Dwivedi & Michael F Bonner & Radoslaw Martin Cichy & Gemma Roig - 1-22 Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations
by Jenny M Vo-Phamhi & Kevin A Yamauchi & Rafael Gómez-Sjöberg - 1-22 Review of machine learning methods for RNA secondary structure prediction
by Qi Zhao & Zheng Zhao & Xiaoya Fan & Zhengwei Yuan & Qian Mao & Yudong Yao - 1-23 Critical behaviour of the stochastic Wilson-Cowan model
by Antonio de Candia & Alessandro Sarracino & Ilenia Apicella & Lucilla de Arcangelis - 1-24 A multi-objective genetic algorithm to find active modules in multiplex biological networks
by Elva María Novoa-del-Toro & Efrén Mezura-Montes & Matthieu Vignes & Morgane Térézol & Frédérique Magdinier & Laurent Tichit & Anaïs Baudot - 1-24 Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread
by John R Giles & Derek AT Cummings & Bryan T Grenfell & Andrew J Tatem & Elisabeth zu Erbach-Schoenberg & CJE Metcalf & Amy Wesolowski - 1-24 A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes
by Karoline Horgmo Jæger & Andrew G Edwards & Wayne R Giles & Aslak Tveito - 1-25 Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic
by Ritabrata Dutta & Susana N Gomes & Dante Kalise & Lorenzo Pacchiardi - 1-25 The role of memory in non-genetic inheritance and its impact on cancer treatment resistance
by Tyler Cassidy & Daniel Nichol & Mark Robertson-Tessi & Morgan Craig & Alexander R A Anderson - 1-26 Identification of structures for ion channel kinetic models
by Kathryn E Mangold & Wei Wang & Eric K Johnson & Druv Bhagavan & Jonathan D Moreno & Jeanne M Nerbonne & Jonathan R Silva - 1-27 A multi-approach and multi-scale platform to model CD4+ T cells responding to infections
by Kenneth Y Wertheim & Bhanwar Lal Puniy & Alyssa La Fleur & Ab Rauf Shah & Matteo Barberis & Tomáš Helikar - 1-27 Computational identification and experimental characterization of preferred downstream positions in human core promoters
by René Dreos & Anna Sloutskin & Nati Malachi & Diana Ideses & Philipp Bucher & Tamar Juven-Gershon - 1-28 A hidden Markov model reliably characterizes ketamine-induced spectral dynamics in macaque local field potentials and human electroencephalograms
by Indie C Garwood & Sourish Chakravarty & Jacob Donoghue & Meredith Mahnke & Pegah Kahali & Shubham Chamadia & Oluwaseun Akeju & Earl K Miller & Emery N Brown - 1-28 Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence
by Simon M Lichtinger & Adiran Garaizar & Rosana Collepardo-Guevara & Aleks Reinhardt - 1-29 Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters
by Natalie Schaworonkow & Bradley Voytek - 1-30 A probabilistic model for the ultradian timing of REM sleep in mice
by Sung-Ho Park & Justin Baik & Jiso Hong & Hanna Antila & Benjamin Kurland & Shinjae Chung & Franz Weber - 1-30 Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space
by Daisuke Imoto & Nen Saito & Akihiko Nakajima & Gen Honda & Motohiko Ishida & Toyoko Sugita & Sayaka Ishihara & Koko Katagiri & Chika Okimura & Yoshiaki Iwadate & Satoshi Sawai - 1-33 Evaluation and comparison of multi-omics data integration methods for cancer subtyping
by Ran Duan & Lin Gao & Yong Gao & Yuxuan Hu & Han Xu & Mingfeng Huang & Kuo Song & Hongda Wang & Yongqiang Dong & Chaoqun Jiang & Chenxing Zhang & Songwei Jia - 1-33 Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows
by Daniel Schindler & Ted Moldenhawer & Maike Stange & Valentino Lepro & Carsten Beta & Matthias Holschneider & Wilhelm Huisinga - 1-35 Interspike interval correlations in neuron models with adaptation and correlated noise
by Lukas Ramlow & Benjamin Lindner
July 2021, Volume 17, Issue 7
- 1-12 Ten simple rules to improve academic work–life balance
by Michael John Bartlett & Feyza Nur Arslan & Adriana Bankston & Sarvenaz Sarabipour - 1-13 Ten simple rules for attending your first conference
by Elizabeth Leininger & Kelly Shaw & Niema Moshiri & Kelly Neiles & Getiria Onsongo & Anna Ritz - 1-15 POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis
by Pol Castellano-Escuder & Raúl González-Domínguez & Francesc Carmona-Pontaque & Cristina Andrés-Lacueva & Alex Sánchez-Pla - 1-16 Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology
by Adrian J Green & Martin J Mohlenkamp & Jhuma Das & Meenal Chaudhari & Lisa Truong & Robyn L Tanguay & David M Reif - 1-17 Elementary integrate-and-fire process underlies pulse amplitudes in Electrodermal activity
by Sandya Subramanian & Patrick L Purdon & Riccardo Barbieri & Emery N Brown - 1-17 The effect of natural selection on the propagation of protein expression noise to bacterial growth
by Laurens H J Krah & Rutger Hermsen - 1-18 Predicting seasonal influenza using supermarket retail records
by Ioanna Miliou & Xinyue Xiong & Salvatore Rinzivillo & Qian Zhang & Giulio Rossetti & Fosca Giannotti & Dino Pedreschi & Alessandro Vespignani - 1-18 A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network
by Ben G Weinstein & Sarah J Graves & Sergio Marconi & Aditya Singh & Alina Zare & Dylan Stewart & Stephanie A Bohlman & Ethan P White - 1-20 Accurate influenza forecasts using type-specific incidence data for small geographic units
by James Turtle & Pete Riley & Michal Ben-Nun & Steven Riley - 1-20 SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization
by Lei Li & Zhen Gao & Yu-Tian Wang & Ming-Wen Zhang & Jian-Cheng Ni & Chun-Hou Zheng - 1-20 Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors
by Shirit Dvorkin & Reut Levi & Yoram Louzoun - 1-21 Accumulation of continuously time-varying sensory evidence constrains neural and behavioral responses in human collision threat detection
by Gustav Markkula & Zeynep Uludağ & Richard McGilchrist Wilkie & Jac Billington - 1-22 Risk sensitivity and theory of mind in human coordination
by Pedro L Ferreira & Francisco C Santos & Sérgio Pequito - 1-22 Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic
by Tenglong Li & Laura F White - 1-22 ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements
by Xi Chen & Andrew F Neuwald & Leena Hilakivi-Clarke & Robert Clarke & Jianhua Xuan - 1-22 Computational Eurotransplant kidney allocation simulations demonstrate the feasibility and benefit of T-cell epitope matching
by Matthias Niemann & Nils Lachmann & Kirsten Geneugelijk & Eric Spierings - 1-22 Modeling changes in probabilistic reinforcement learning during adolescence
by Liyu Xia & Sarah L Master & Maria K Eckstein & Beth Baribault & Ronald E Dahl & Linda Wilbrecht & Anne Gabrielle Eva Collins - 1-22 Modelling locust foraging: How and why food affects group formation
by Fillipe Georgiou & Jerome Buhl & J E F Green & Bishnu Lamichhane & Ngamta Thamwattana - 1-24 Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes
by Davin Lunz & Gregory Batt & Jakob Ruess & J Frédéric Bonnans - 1-24 Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure
by Toru Niina & Yasuhiro Matsunaga & Shoji Takada - 1-25 A Keller-Segel model for C elegans L1 aggregation
by Leon Avery & Brian Ingalls & Catherine Dumur & Alexander Artyukhin - 1-25 Noise suppression in stochastic genetic circuits using PID controllers
by Saurabh Modi & Supravat Dey & Abhyudai Singh - 1-25 Multitask learning over shared subspaces
by Nicholas Menghi & Kemal Kacar & Will Penny - 1-26 Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans
by Omer Yuval & Yael Iosilevskii & Anna Meledin & Benjamin Podbilewicz & Tom Shemesh - 1-28 Selection of stimulus parameters for enhancing slow wave sleep events with a neural-field theory thalamocortical model
by Felipe A Torres & Patricio Orio & María-José Escobar - 1-30 Adaptive control of movement deceleration during saccades
by Simon P Orozco & Scott T Albert & Reza Shadmehr - 1-31 Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
by Maximilian Hanussek & Felix Bartusch & Jens Krüger - 1-34 On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread
by Meysam Hashemi & Anirudh N Vattikonda & Viktor Sip & Sandra Diaz-Pier & Alexander Peyser & Huifang Wang & Maxime Guye & Fabrice Bartolomei & Marmaduke M Woodman & Viktor K Jirsa - 1-37 Insights into substrate recognition and specificity for IgG by Endoglycosidase S2
by Asaminew H Aytenfisu & Daniel Deredge & Erik H Klontz & Jonathan Du & Eric J Sundberg & Alexander D MacKerell Jr - 1-42 Average beta burst duration profiles provide a signature of dynamical changes between the ON and OFF medication states in Parkinson’s disease
by Benoit Duchet & Filippo Ghezzi & Gihan Weerasinghe & Gerd Tinkhauser & Andrea A Kühn & Peter Brown & Christian Bick & Rafal Bogacz
June 2021, Volume 17, Issue 6
- 1-8 Ten simple rules for doing a postdoc in pharma
by Jitao David Zhang - 1-14 Iliski, a software for robust calculation of transfer functions
by Ali-Kemal Aydin & William D Haselden & Julie Dang & Patrick J Drew & Serge Charpak & Davide Boido - 1-17 Mixture-of-Experts Variational Autoencoder for clustering and generating from similarity-based representations on single cell data
by Andreas Kopf & Vincent Fortuin & Vignesh Ram Somnath & Manfred Claassen - 1-17 A zero inflated log-normal model for inference of sparse microbial association networks
by Vincent Prost & Stéphane Gazut & Thomas Brüls - 1-17 pyTFM: A tool for traction force and monolayer stress microscopy
by Andreas Bauer & Magdalena Prechová & Lena Fischer & Ingo Thievessen & Martin Gregor & Ben Fabry - 1-18 Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER Distance Restraints
by Diego del Alamo & Kevin L Jagessar & Jens Meiler & Hassane S Mchaourab - 1-20 SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data
by Jing Qi & Yang Zhou & Zicen Zhao & Shuilin Jin - 1-21 CytoPy: An autonomous cytometry analysis framework
by Ross J Burton & Raya Ahmed & Simone M Cuff & Sarah Baker & Andreas Artemiou & Matthias Eberl - 1-21 PHENSIM: Phenotype Simulator
by Salvatore Alaimo & Rosaria Valentina Rapicavoli & Gioacchino P Marceca & Alessandro La Ferlita & Oksana B Serebrennikova & Philip N Tsichlis & Bud Mishra & Alfredo Pulvirenti & Alfredo Ferro - 1-22 GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction
by Zhong Li & Kaiyancheng Jiang & Shengwei Qin & Yijun Zhong & Arne Elofsson - 1-22 BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration
by Andreas Deutsch & Josué Manik Nava-Sedeño & Simon Syga & Haralampos Hatzikirou - 1-23 High-affinity P2Y2 and low-affinity P2X7 receptor interaction modulates ATP-mediated calcium signaling in murine osteoblasts
by Nicholas Mikolajewicz & Delaney Smith & Svetlana V Komarova & Anmar Khadra - 1-23 lra: A long read aligner for sequences and contigs
by Jingwen Ren & Mark J P Chaisson - 1-23 Three-dimensional topology optimization model to simulate the external shapes of bone
by Misaki Sakashita & Shintaro Yamasaki & Kentaro Yaji & Atsushi Kawamoto & Shigeru Kondo - 1-24 A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2
by Edward M Hill & Benjamin D Atkins & Matt J Keeling & Louise Dyson & Michael J Tildesley - 1-24 Stochastic optimal feedforward-feedback control determines timing and variability of arm movements with or without vision
by Bastien Berret & Adrien Conessa & Nicolas Schweighofer & Etienne Burdet - 1-24 De novo mutational signature discovery in tumor genomes using SparseSignatures
by Avantika Lal & Keli Liu & Robert Tibshirani & Arend Sidow & Daniele Ramazzotti - 1-28 A549 in-silico 1.0: A first computational model to simulate cell cycle dependent ion current modulation in the human lung adenocarcinoma
by Sonja Langthaler & Theresa Rienmüller & Susanne Scheruebel & Brigitte Pelzmann & Niroj Shrestha & Klaus Zorn-Pauly & Wolfgang Schreibmayer & Andrew Koff & Christian Baumgartner - 1-28 Categorical judgments do not modify sensory representations in working memory
by Long Luu & Alan A Stocker - 1-29 Identifying the combinatorial control of signal-dependent transcription factors
by Ning Wang & Diane Lefaudeux & Anup Mazumder & Jingyi Jessica Li & Alexander Hoffmann - 1-30 Unsupervised logic-based mechanism inference for network-driven biological processes
by Martina Prugger & Lukas Einkemmer & Samantha P Beik & Perry T Wasdin & Leonard A Harris & Carlos F Lopez - 1-31 Learning divisive normalization in primary visual cortex
by Max F Burg & Santiago A Cadena & George H Denfield & Edgar Y Walker & Andreas S Tolias & Matthias Bethge & Alexander S Ecker - 1-32 Novelty is not surprise: Human exploratory and adaptive behavior in sequential decision-making
by He A Xu & Alireza Modirshanechi & Marco P Lehmann & Wulfram Gerstner & Michael H Herzog - 1-35 Behavioral correlates of cortical semantic representations modeled by word vectors
by Satoshi Nishida & Antione Blanc & Naoya Maeda & Masataka Kado & Shinji Nishimoto - 1-51 Embedding optimization reveals long-lasting history dependence in neural spiking activity
by Lucas Rudelt & Daniel González Marx & Michael Wibral & Viola Priesemann
May 2021, Volume 17, Issue 5
- 1-8 Ten steps to investigate a cellular system with mathematical modeling
by Jasia King & Kerbaï Saïd Eroumé & Roman Truckenmüller & Stefan Giselbrecht & Ann E Cowan & Leslie Loew & Aurélie Carlier - 1-13 Ten simple rules for productive lab meetings
by Nigel Golden & Kadambari Devarajan & Cathleen Balantic & Joseph Drake & Michael T Hallworth & Toni Lyn Morelli - 1-14 scHiCTools: A computational toolbox for analyzing single-cell Hi-C data
by Xinjun Li & Fan Feng & Hongxi Pu & Wai Yan Leung & Jie Liu - 1-15 MetaGSCA: A tool for meta-analysis of gene set differential coexpression
by Yan Guo & Hui Yu & Haocan Song & Jiapeng He & Olufunmilola Oyebamiji & Huining Kang & Jie Ping & Scott Ness & Yu Shyr & Fei Ye - 1-17 A deep learning algorithm for 3D cell detection in whole mouse brain image datasets
by Adam L Tyson & Charly V Rousseau & Christian J Niedworok & Sepiedeh Keshavarzi & Chryssanthi Tsitoura & Lee Cossell & Molly Strom & Troy W Margrie - 1-17 Red blood cell phenotyping from 3D confocal images using artificial neural networks
by Greta Simionato & Konrad Hinkelmann & Revaz Chachanidze & Paola Bianchi & Elisa Fermo & Richard van Wijk & Marc Leonetti & Christian Wagner & Lars Kaestner & Stephan Quint - 1-17 On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins
by Edwin Rodriguez Horta & Martin Weigt - 1-18 Effects of incomplete inter-hospital network data on the assessment of transmission dynamics of hospital-acquired infections
by Hanjue Xia & Johannes Horn & Monika J Piotrowska & Konrad Sakowski & André Karch & Hannan Tahir & Mirjam Kretzschmar & Rafael Mikolajczyk - 1-20 What we can and what we cannot see with extracellular multielectrodes
by Chaitanya Chintaluri & Marta Bejtka & Władysław Średniawa & Michał Czerwiński & Jakub M Dzik & Joanna Jędrzejewska-Szmek & Kacper Kondrakiewicz & Ewa Kublik & Daniel K Wójcik - 1-20 Extracting representations of cognition across neuroimaging studies improves brain decoding
by Arthur Mensch & Julien Mairal & Bertrand Thirion & Gaël Varoquaux - 1-20 PRER: A patient representation with pairwise relative expression of proteins on biological networks
by Halil İbrahim Kuru & Mustafa Buyukozkan & Oznur Tastan - 1-21 Hierarchical semantic composition of biosimulation models using bond graphs
by Niloofar Shahidi & Michael Pan & Soroush Safaei & Kenneth Tran & Edmund J Crampin & David P Nickerson - 1-21 Computational phenotyping of brain-behavior dynamics underlying approach-avoidance conflict in major depressive disorder
by Mads L Pedersen & Maria Ironside & Ken-ichi Amemori & Callie L McGrath & Min S Kang & Ann M Graybiel & Diego A Pizzagalli & Michael J Frank - 1-21 CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation
by Christopher J Arthurs & Rostislav Khlebnikov & Alex Melville & Marija Marčan & Alberto Gomez & Desmond Dillon-Murphy & Federica Cuomo & Miguel Silva Vieira & Jonas Schollenberger & Sabrina R Lynch & Christopher Tossas-Betancourt & Kritika Iyer & Sara Hopper & Elizabeth Livingston & Pouya Youssefi & Alia Noorani & Sabrina Ben Ahmed & Foeke J H Nauta & Theodorus M J van Bakel & Yunus Ahmed & Petrus A J van Bakel & Jonathan Mynard & Paolo Di Achille & Hamid Gharahi & Kevin D Lau & Vasilina Filonova & Miquel Aguirre & Nitesh Nama & Nan Xiao & Seungik Baek & Krishna Garikipati & Onkar Sahni & David Nordsletten & C Alberto Figueroa - 1-22 A first-takes-all model of centriole copy number control based on cartwheel elongation
by Marco António Dias Louro & Mónica Bettencourt-Dias & Jorge Carneiro - 1-22 Patterns of selection against centrosome amplification in human cell lines
by Marco António Dias Louro & Mónica Bettencourt-Dias & Claudia Bank - 1-22 Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition
by Christian Schulz & Tjasa Kumelj & Emil Karlsen & Eivind Almaas - 1-23 Model guided trait-specific co-expression network estimation as a new perspective for identifying molecular interactions and pathways
by Juho A J Kontio & Tanja Pyhäjärvi & Mikko J Sillanpää - 1-24 Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10
by Leonard Campanello & Maria K Traver & Hari Shroff & Brian C Schaefer & Wolfgang Losert - 1-24 G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
by Weimiao Wu & Yunqing Liu & Qile Dai & Xiting Yan & Zuoheng Wang - 1-26 Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage
by Jonathan Liu & Donald Hansen & Elizabeth Eck & Yang Joon Kim & Meghan Turner & Simon Alamos & Hernan Garcia - 1-27 A reaction-diffusion network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation in Drosophila
by Claudio D T Barros & Maira A Cardoso & Paulo M Bisch & Helena M Araujo & Francisco J P Lopes - 1-27 Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport
by Daniel Ch Haspinger & Sandra Klinge & Gerhard A Holzapfel - 1-28 Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs
by Antoine Soulé & Vladimir Reinharz & Roman Sarrazin-Gendron & Alain Denise & Jérôme Waldispühl - 1-31 Small subpopulations of β-cells do not drive islet oscillatory [Ca2+] dynamics via gap junction communication
by JaeAnn M Dwulet & Jennifer K Briggs & Richard K P Benninger - 1-33 Evaluation of residue-residue contact prediction methods: From retrospective to prospective
by Huiling Zhang & Zhendong Bei & Wenhui Xi & Min Hao & Zhen Ju & Konda Mani Saravanan & Haiping Zhang & Ning Guo & Yanjie Wei - 1-34 Sequence learning recodes cortical representations instead of strengthening initial ones
by Kristjan Kalm & Dennis Norris
April 2021, Volume 17, Issue 4
- 1-16 MAUI (MBI Analysis User Interface)—An image processing pipeline for Multiplexed Mass Based Imaging
by Alex Baranski & Idan Milo & Shirley Greenbaum & John-Paul Oliveria & Dunja Mrdjen & Michael Angelo & Leeat Keren - 1-16 Mistakes can stabilise the dynamics of rock-paper-scissors games
by Maria Kleshnina & Sabrina S Streipert & Jerzy A Filar & Krishnendu Chatterjee - 1-18 Using Hawkes Processes to model imported and local malaria cases in near-elimination settings
by H Juliette T Unwin & Isobel Routledge & Seth Flaxman & Marian-Andrei Rizoiu & Shengjie Lai & Justin Cohen & Daniel J Weiss & Swapnil Mishra & Samir Bhatt - 1-18 Avoiding the bullies: The resilience of cooperation among unequals
by Michael Foley & Rory Smead & Patrick Forber & Christoph Riedl - 1-20 A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation
by Diego Vidaurre - 1-20 WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans
by Laetitia Hebert & Tosif Ahamed & Antonio C Costa & Liam O’Shaughnessy & Greg J Stephens - 1-20 Temporal dynamics of a CSF1R signaling gene regulatory network involved in epilepsy
by Claude Gérard & Laurane De Mot & Sabine Cordi & Jonathan van Eyll & Frédéric P Lemaigre - 1-21 Behavioral discrimination and time-series phenotyping of birdsong performance
by Avishek Paul & Helen McLendon & Veronica Rally & Jon T Sakata & Sarah C Woolley - 1-21 Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment
by Benjamin Deneu & Maximilien Servajean & Pierre Bonnet & Christophe Botella & François Munoz & Alexis Joly - 1-22 Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions
by Yao Jiang & Hui-Fang Liu & Rong Liu - 1-25 Individual differences in the perception of probability
by Mel W Khaw & Luminita Stevens & Michael Woodford - 1-28 VolPy: Automated and scalable analysis pipelines for voltage imaging datasets
by Changjia Cai & Johannes Friedrich & Amrita Singh & M Hossein Eybposh & Eftychios A Pnevmatikakis & Kaspar Podgorski & Andrea Giovannucci - 1-33 Interactions between all pairs of neighboring trees in 16 forests worldwide reveal details of unique ecological processes in each forest, and provide windows into their evolutionary histories
by Christopher Wills & Bin Wang & Shuai Fang & Yunquan Wang & Yi Jin & James Lutz & Jill Thompson & Kyle E Harms & Sandeep Pulla & Bonifacio Pasion & Sara Germain & Heming Liu & Joseph Smokey & Sheng-Hsin Su & Nathalie Butt & Chengjin Chu & George Chuyong & Chia-Hao Chang-Yang & H S Dattaraja & Stuart Davies & Sisira Ediriweera & Shameema Esufali & Christine Dawn Fletcher & Nimal Gunatilleke & Savi Gunatilleke & Chang-Fu Hsieh & Fangliang He & Stephen Hubbell & Zhanqing Hao & Akira Itoh & David Kenfack & Buhang Li & Xiankun Li & Keping Ma & Michael Morecroft & Xiangcheng Mi & Yadvinder Malhi & Perry Ong & Lillian Jennifer Rodriguez & H S Suresh & I Fang Sun & Raman Sukumar & Sylvester Tan & Duncan Thomas & Maria Uriarte & Xihua Wang & Xugao Wang & T L Yao & Jess Zimmermann - 1-41 Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads
by Rohan N Shah & Alexander J Ruthenburg - 1-45 Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data
by David P Shorten & Richard E Spinney & Joseph T Lizier
March 2021, Volume 17, Issue 3
- 1-9 Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds
by Brian Coventry & David Baker - 1-10 COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data
by Song He & Xinyu Song & Xiaoxi Yang & Jijun Yu & Yuqi Wen & Lianlian Wu & Bowei Yan & Jiannan Feng & Xiaochen Bo - 1-11 PDKit: A data science toolkit for the digital assessment of Parkinson’s Disease
by Cosmin Stamate & Joan Saez Pons & David Weston & George Roussos - 1-15 Ten simple rules for quick and dirty scientific programming
by Gabriel Balaban & Ivar Grytten & Knut Dagestad Rand & Lonneke Scheffer & Geir Kjetil Sandve - 1-16 Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance
by Anton J M Larsson & Christoph Ziegenhain & Michael Hagemann-Jensen & Björn Reinius & Tina Jacob & Tim Dalessandri & Gert-Jan Hendriks & Maria Kasper & Rickard Sandberg - 1-16 JSOM: Jointly-evolving self-organizing maps for alignment of biological datasets and identification of related clusters
by Hong Seo Lim & Peng Qiu - 1-17 Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD
by Yannick Marcon & Tom Bishop & Demetris Avraam & Xavier Escriba-Montagut & Patricia Ryser-Welch & Stuart Wheater & Paul Burton & Juan R González - 1-18 Assessing criticality in pre-seizure single-neuron activity of human epileptic cortex
by Annika Hagemann & Jens Wilting & Bita Samimizad & Florian Mormann & Viola Priesemann - 1-18 Dcmd: Distance-based classification using mixture distributions on microbiome data
by Konstantin Shestopaloff & Mei Dong & Fan Gao & Wei Xu - 1-19 Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks
by Yang Li & Chengxin Zhang & Eric W Bell & Wei Zheng & Xiaogen Zhou & Dong-Jun Yu & Yang Zhang - 1-19 Reconstructing feedback representations in the ventral visual pathway with a generative adversarial autoencoder
by Haider Al-Tahan & Yalda Mohsenzadeh - 1-19 Signal-to-signal neural networks for improved spike estimation from calcium imaging data
by Jilt Sebastian & Mriganka Sur & Hema A Murthy & Mathew Magimai-Doss - 1-20 Predicting microbial growth dynamics in response to nutrient availability
by Olga A Nev & Richard J Lindsay & Alys Jepson & Lisa Butt & Robert E Beardmore & Ivana Gudelj - 1-20 Can subjective pain be inferred from objective physiological data? Evidence from patients with sickle cell disease
by Mark J Panaggio & Daniel M Abrams & Fan Yang & Tanvi Banerjee & Nirmish R Shah - 1-20 Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model
by Gregory L Watson & Di Xiong & Lu Zhang & Joseph A Zoller & John Shamshoian & Phillip Sundin & Teresa Bufford & Anne W Rimoin & Marc A Suchard & Christina M Ramirez - 1-21 Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling
by Yekaterina S Pavlova & David Paez-Espino & Andrew Yu Morozov & Ilya S Belalov - 1-21 Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases
by Janani Durairaj & Elena Melillo & Harro J Bouwmeester & Jules Beekwilder & Dick de Ridder & Aalt D J van Dijk - 1-21 Collective predator evasion: Putting the criticality hypothesis to the test
by Pascal P Klamser & Pawel Romanczuk - 1-22 A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli
by Alexandre Oliveira & Joana Rodrigues & Eugénio Campos Ferreira & Lígia Rodrigues & Oscar Dias - 1-22 Connectivity, reproduction number, and mobility interact to determine communities’ epidemiological superspreader potential in a metapopulation network
by Brandon Lieberthal & Allison M Gardner - 1-23 Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements
by Kseniia Cheloshkina & Maria Poptsova - 1-23 Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models
by Denis A Shah & Erick D De Wolf & Pierce A Paul & Laurence V Madden - 1-23 Health inequities in influenza transmission and surveillance
by Casey M Zipfel & Vittoria Colizza & Shweta Bansal - 1-23 Public Baseline and shared response structures support the theory of antibody repertoire functional commonality
by Matthew I J Raybould & Claire Marks & Aleksandr Kovaltsuk & Alan P Lewis & Jiye Shi & Charlotte M Deane - 1-24 Optimal timing of one-shot interventions for epidemic control
by Francesco Di Lauro & István Z Kiss & Joel C Miller - 1-24 Parameters and determinants of responses to selection in antibody libraries
by Steven Schulz & Sébastien Boyer & Matteo Smerlak & Simona Cocco & Rémi Monasson & Clément Nizak & Olivier Rivoire - 1-25 Modelling the impact of clot fragmentation on the microcirculation after thrombectomy
by Wahbi K El-Bouri & Andrew MacGowan & Tamás I Józsa & Matthew J Gounis & Stephen J Payne - 1-25 Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance
by Vincent Brault & Bastien Mallein & Jean-François Rupprecht - 1-25 Inferring phenomenological models of first passage processes
by Catalina Rivera & David Hofmann & Ilya Nemenman - 1-25 Mechanical coupling in the nitrogenase complex
by Qi Huang & Monika Tokmina-Lukaszewska & Lewis E Johnson & Hayden Kallas & Bojana Ginovska & John W Peters & Lance C Seefeldt & Brian Bothner & Simone Raugei - 1-25 Perturbations both trigger and delay seizures due to generic properties of slow-fast relaxation oscillators
by Alberto Pérez-Cervera & Jaroslav Hlinka - 1-25 Prediction of amphipathic helix—Membrane interactions with Rosetta
by Alican Gulsevin & Jens Meiler - 1-25 Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability
by Javier Rasero & Amy Isabella Sentis & Fang-Cheng Yeh & Timothy Verstynen - 1-25 Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach
by Josh L Espinoza & Chris L Dupont & Aubrie O’Rourke & Sinem Beyhan & Pavel Morales & Amy Spoering & Kirsten J Meyer & Agnes P Chan & Yongwook Choi & William C Nierman & Kim Lewis & Karen E Nelson - 1-26 Principles for data analysis workflows
by Sara Stoudt & Váleri N Vásquez & Ciera C Martinez - 1-27 Linear-nonlinear cascades capture synaptic dynamics
by Julian Rossbroich & Daniel Trotter & John Beninger & Katalin Tóth & Richard Naud - 1-27 Optimal prediction with resource constraints using the information bottleneck
by Vedant Sachdeva & Thierry Mora & Aleksandra M Walczak & Stephanie E Palmer - 1-28 How does Sec63 affect the conformation of Sec61 in yeast?
by Pratiti Bhadra & Lalitha Yadhanapudi & Karin Römisch & Volkhard Helms - 1-29 Fixation patterns in simple choice reflect optimal information sampling
by Frederick Callaway & Antonio Rangel & Thomas L Griffiths - 1-30 Graph of graphs analysis for multiplexed data with application to imaging mass cytometry
by Ya-Wei Eileen Lin & Tal Shnitzer & Ronen Talmon & Franz Villarroel-Espindola & Shruti Desai & Kurt Schalper & Yuval Kluger - 1-30 Neural modelling of the encoding of fast frequency modulation
by Alejandro Tabas & Katharina von Kriegstein
February 2021, Volume 17, Issue 2
- 1-10 Ten simple rules for running and managing virtual internships
by Johannes Werner & Debora Jeske - 1-11 Ten simple rules for engaging with artificial intelligence in biomedicine
by Avni Malik & Paranjay Patel & Lubaina Ehsan & Shan Guleria & Thomas Hartka & Sodiq Adewole & Sana Syed - 1-12 Ten simple rules for starting (and sustaining) an academic data science initiative
by Micaela S Parker & Arlyn E Burgess & Philip E Bourne - 1-12 Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective
by Hwai-Ray Tung & Rick Durrett - 1-13 A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
by Martín Garrido-Rodriguez & Daniel Lopez-Lopez & Francisco M Ortuno & María Peña-Chilet & Eduardo Muñoz & Marco A Calzado & Joaquin Dopazo - 1-15 Freedom to choose between public resources promotes cooperation
by Mohammad Salahshour - 1-15 Evaluating epidemic forecasts in an interval format
by Johannes Bracher & Evan L Ray & Tilmann Gneiting & Nicholas G Reich - 1-15 Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species
by Zutan Li & Hangjin Jiang & Lingpeng Kong & Yuanyuan Chen & Kun Lang & Xiaodan Fan & Liangyun Zhang & Cong Pian - 1-17 Adaptive social contact rates induce complex dynamics during epidemics
by Ronan F Arthur & James H Jones & Matthew H Bonds & Yoav Ram & Marcus W Feldman - 1-18 Deriving fine-scale models of human mobility from aggregated origin-destination flow data
by Constanze Ciavarella & Neil M Ferguson - 1-18 Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
by Florian Huber & Lars Ridder & Stefan Verhoeven & Jurriaan H Spaaks & Faruk Diblen & Simon Rogers & Justin J J van der Hooft - 1-19 Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches
by Judith A Bouman & Julien Riou & Sebastian Bonhoeffer & Roland R Regoes - 1-19 FastTrack: An open-source software for tracking varying numbers of deformable objects
by Benjamin Gallois & Raphaël Candelier - 1-19 A numerical framework for mechano-regulated tendon healing—Simulation of early regeneration of the Achilles tendon
by Thomas Notermans & Petri Tanska & Rami K Korhonen & Hanifeh Khayyeri & Hanna Isaksson - 1-20 Unsupervised manifold learning of collective behavior
by Mathew Titus & George Hagstrom & James R Watson - 1-20 KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions
by Bingjie Xue & Benjamin Jordan & Saqib Rizvi & Kristen M Naegle - 1-20 A mathematical model of the role of aggregation in sonic hedgehog signalling
by Daniel J A Derrick & Kathryn Wolton & Richard A Currie & Marcus John Tindall - 1-20 Evolution of heterogeneous perceptual limits and indifference in competitive foraging
by Richard P Mann - 1-21 When to wake up? The optimal waking-up strategies for starvation-induced persistence
by Yusuke Himeoka & Namiko Mitarai - 1-21 From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach
by Ann-Kristin Becker & Marcus Dörr & Stephan B Felix & Fabian Frost & Hans J Grabe & Markus M Lerch & Matthias Nauck & Uwe Völker & Henry Völzke & Lars Kaderali - 1-21 On the importance of evolving phenotype distributions on evolutionary diversification
by Gil Jorge Barros Henriques & Koichi Ito & Christoph Hauert & Michael Doebeli - 1-22 End-to-end neural system identification with neural information flow
by K Seeliger & L Ambrogioni & Y Güçlütürk & L M van den Bulk & U Güçlü & M A J van Gerven - 1-22 TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations
by Qiao Liu & Lei Xie