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Content
November 2021, Volume 17, Issue 11
- 1-14 Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data
by Tania Mendonca & Ana A Jones & Jose M Pozo & Sarah Baxendale & Tanya T Whitfield & Alejandro F Frangi - 1-16 Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling
by Danial Pourjafar-Dehkordi & Martin Zacharias - 1-16 The meaning of significant mean group differences for biomarker discovery
by Eva Loth & Jumana Ahmad & Chris Chatham & Beatriz López & Ben Carter & Daisy Crawley & Bethany Oakley & Hannah Hayward & Jennifer Cooke & Antonia San José Cáceres & Danilo Bzdok & Emily Jones & Tony Charman & Christian Beckmann & Thomas Bourgeron & Roberto Toro & Jan Buitelaar & Declan Murphy & Guillaume Dumas - 1-16 The role of competition versus cooperation in microbial community coalescence
by Pablo Lechón-Alonso & Tom Clegg & Jacob Cook & Thomas P Smith & Samraat Pawar - 1-18 Approximate distance correlation for selecting highly interrelated genes across datasets
by Qunlun Shen & Shihua Zhang - 1-19 Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data
by Pavel I Kos & Aleksandra A Galitsyna & Sergey V Ulianov & Mikhail S Gelfand & Sergey V Razin & Alexander V Chertovich - 1-21 Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data
by Torfinn S Madssen & Guro F Giskeødegård & Age K Smilde & Johan A Westerhuis - 1-21 Intriguing effects of selection intensity on the evolution of prosocial behaviors
by Alex McAvoy & Andrew Rao & Christoph Hauert - 1-23 Cluster size distribution of cells disseminating from a primary tumor
by Mrinmoy Mukherjee & Herbert Levine - 1-23 Estimating the dimensionality of the manifold underlying multi-electrode neural recordings
by Ege Altan & Sara A Solla & Lee E Miller & Eric J Perreault - 1-24 Cross-population coupling of neural activity based on Gaussian process current source densities
by Natalie Klein & Joshua H Siegle & Tobias Teichert & Robert E Kass - 1-24 Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones
by Erik B Nordquist & Charles A English & Eugenia M Clerico & Woody Sherman & Lila M Gierasch & Jianhan Chen - 1-25 Comparison of metabolic states using genome-scale metabolic models
by Chaitra Sarathy & Marian Breuer & Martina Kutmon & Michiel E Adriaens & Chris T Evelo & Ilja C W Arts - 1-26 Optimizing network propagation for multi-omics data integration
by Konstantina Charmpi & Manopriya Chokkalingam & Ronja Johnen & Andreas Beyer - 1-26 Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance
by Mathurin Dorel & Bertram Klinger & Tommaso Mari & Joern Toedling & Eric Blanc & Clemens Messerschmidt & Michal Nadler-Holly & Matthias Ziehm & Anja Sieber & Falk Hertwig & Dieter Beule & Angelika Eggert & Johannes H Schulte & Matthias Selbach & Nils Blüthgen - 1-26 A gap-filling algorithm for prediction of metabolic interactions in microbial communities
by Dafni Giannari & Cleo Hanchen Ho & Radhakrishnan Mahadevan - 1-27 Multivariable association discovery in population-scale meta-omics studies
by Himel Mallick & Ali Rahnavard & Lauren J McIver & Siyuan Ma & Yancong Zhang & Long H Nguyen & Timothy L Tickle & George Weingart & Boyu Ren & Emma H Schwager & Suvo Chatterjee & Kelsey N Thompson & Jeremy E Wilkinson & Ayshwarya Subramanian & Yiren Lu & Levi Waldron & Joseph N Paulson & Eric A Franzosa & Hector Corrada Bravo & Curtis Huttenhower - 1-28 Crowd control: Reducing individual estimation bias by sharing biased social information
by Bertrand Jayles & Clément Sire & Ralf H J M Kurvers - 1-34 Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases
by Tunca Doğan & Ece Akhan Güzelcan & Marcus Baumann & Altay Koyas & Heval Atas & Ian R Baxendale & Maria Martin & Rengul Cetin-Atalay - 1-37 Causal inference regulates audiovisual spatial recalibration via its influence on audiovisual perception
by Fangfang Hong & Stephanie Badde & Michael S Landy - 1-38 Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans
by Javier J How & Saket Navlakha & Sreekanth H Chalasani
October 2021, Volume 17, Issue 10
- 1-12 Ten simple rules for training yourself in an emerging field
by Whitney M Woelmer & L M Bradley & Lisa T Haber & David H Klinges & Abigail S L Lewis & Elizabeth J Mohr & Christa L Torrens & Kathryn I Wheeler & Alyssa M Willson - 1-15 A data-driven approach for constructing mutation categories for mutational signature analysis
by Gal Gilad & Mark D M Leiserson & Roded Sharan - 1-16 pyActigraphy: Open-source python package for actigraphy data visualization and analysis
by Grégory Hammad & Mathilde Reyt & Nikita Beliy & Marion Baillet & Michele Deantoni & Alexia Lesoinne & Vincenzo Muto & Christina Schmidt - 1-17 Estimating ectopic beat probability with simplified statistical models that account for experimental uncertainty
by Qingchu Jin & Joseph L Greenstein & Raimond L Winslow - 1-18 A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC
by Jason Bennett & Mikhail Pomaznoy & Akul Singhania & Bjoern Peters - 1-19 RgCop-A regularized copula based method for gene selection in single-cell RNA-seq data
by Snehalika Lall & Sumanta Ray & Sanghamitra Bandyopadhyay - 1-20 Extended graphical lasso for multiple interaction networks for high dimensional omics data
by Yang Xu & Hongmei Jiang & Wenxin Jiang - 1-20 Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample’s infection concentration
by Daniel Cresta & Donald C Warren & Christian Quirouette & Amanda P Smith & Lindey C Lane & Amber M Smith & Catherine A A Beauchemin - 1-21 Steady-state measures of visual suppression
by Daniel H Baker & Greta Vilidaite & Alex R Wade - 1-21 Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities
by Yun Min Song & Hyukpyo Hong & Jae Kyoung Kim - 1-21 Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns
by Maxwell W Libbrecht & Rachel C W Chan & Michael M Hoffman - 1-21 Complexity and diversity in sparse code priors improve receptive field characterization of Macaque V1 neurons
by Ziniu Wu & Harold Rockwell & Yimeng Zhang & Shiming Tang & Tai Sing Lee - 1-22 PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes
by Charlie M Carpenter & Weiming Zhang & Lucas Gillenwater & Cameron Severn & Tusharkanti Ghosh & Russell Bowler & Katerina Kechris & Debashis Ghosh - 1-23 Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention
by Stacy Tessler Lindau & Jennifer A Makelarski & Chaitanya Kaligotla & Emily M Abramsohn & David G Beiser & Chiahung Chou & Nicholson Collier & Elbert S Huang & Charles M Macal & Jonathan Ozik & Elizabeth L Tung - 1-24 Better tired than lost: Turtle ant trail networks favor coherence over short edges
by Arjun Chandrasekhar & James A R Marshall & Cortnea Austin & Saket Navlakha & Deborah M Gordon - 1-25 Tracking calcium dynamics from individual neurons in behaving animals
by Thibault Lagache & Alison Hanson & Jesús E Pérez-Ortega & Adrienne Fairhall & Rafael Yuste - 1-27 How conformity can lead to polarised social behaviour
by Folco Panizza & Alexander Vostroknutov & Giorgio Coricelli - 1-28 Atorvastatin-mediated rescue of cancer-related cognitive changes in combined anticancer therapies
by Junho Lee & Jin Su Kim & Yangjin Kim - 1-28 Visual perception of texture regularity: Conjoint measurements and a wavelet response-distribution model
by Hua-Chun Sun & David St-Amand & Curtis L Baker Jr. & Frederick A A Kingdom - 1-28 Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites
by Bikash K Bhandari & Chun Shen Lim & Daniela M Remus & Augustine Chen & Craig van Dolleweerd & Paul P Gardner - 1-29 Point-estimating observer models for latent cause detection
by Jennifer Laura Lee & Wei Ji Ma - 1-31 Narrative event segmentation in the cortical reservoir
by Peter Ford Dominey - 1-32 Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity
by Daniel E Mattox & Chris Bailey-Kellogg - 1-32 Action planning and control under uncertainty emerge through a desirability-driven competition between parallel encoding motor plans
by Vince Enachescu & Paul Schrater & Stefan Schaal & Vassilios Christopoulos - 1-35 Cortical feedback and gating in odor discrimination and generalization
by Gaia Tavoni & David E Chen Kersen & Vijay Balasubramanian - 1-38 Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans
by Yashika Arora & Pushpinder Walia & Mitsuhiro Hayashibe & Makii Muthalib & Shubhajit Roy Chowdhury & Stephane Perrey & Anirban Dutta
September 2021, Volume 17, Issue 9
- 1-5 Ten simple rules for avoiding predatory publishing scams
by Michelle Leonard & Suzanne Stapleton & Perry Collins & Terry Kit Selfe & Tara Cataldo - 1-6 Ten simple rules for being a faculty advocate of first-year graduate students
by Kevin A Janes - 1-8 Ten simple rules for choosing a PhD supervisor
by Loay Jabre & Catherine Bannon & J Scott P McCain & Yana Eglit - 1-12 Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment
by Sepideh Mazrouee & Susan J Little & Joel O Wertheim - 1-14 Hemodynamics-driven mathematical model of first and second heart sound generation
by Mehrdad Shahmohammadi & Hongxing Luo & Philip Westphal & Richard N Cornelussen & Frits W Prinzen & Tammo Delhaas - 1-16 Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections
by Thomas Beneteau & Christian Selinger & Mircea T Sofonea & Samuel Alizon - 1-16 Ten simple rules for supporting historically underrepresented students in science
by Suchinta Arif & Melanie Duc Bo Massey & Natalie Klinard & Julie Charbonneau & Loay Jabre & Ana Barbosa Martins & Danielle Gaitor & Rhiannon Kirton & Catalina Albury & Karma Nanglu - 1-19 ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves
by Eric D Musselman & Jake E Cariello & Warren M Grill & Nicole A Pelot - 1-20 Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics
by Eric W Bridgeford & Shangsi Wang & Zeyi Wang & Ting Xu & Cameron Craddock & Jayanta Dey & Gregory Kiar & William Gray-Roncal & Carlo Colantuoni & Christopher Douville & Stephanie Noble & Carey E Priebe & Brian Caffo & Michael Milham & Xi-Nian Zuo & Consortium for Reliability and Reproducibility & Joshua T Vogelstein - 1-20 Basis profile curve identification to understand electrical stimulation effects in human brain networks
by Kai J Miller & Klaus-Robert Müller & Dora Hermes - 1-21 Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds
by Alison Pereira Ribeiro & Nádia Felix Felipe da Silva & Fernanda Neiva Mesquita & Priscila de Cássia Souza Araújo & Thierson Couto Rosa & José Neiva Mesquita-Neto - 1-21 Insights into the dynamic trajectories of protein filament division revealed by numerical investigation into the mathematical model of pure fragmentation
by Magali Tournus & Miguel Escobedo & Wei-Feng Xue & Marie Doumic - 1-21 XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers
by Jack B Maguire & Daniele Grattarola & Vikram Khipple Mulligan & Eugene Klyshko & Hans Melo - 1-22 Drug-induced resistance evolution necessitates less aggressive treatment
by Teemu Kuosmanen & Johannes Cairns & Robert Noble & Niko Beerenwinkel & Tommi Mononen & Ville Mustonen - 1-23 Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
by Rui Yin & Johnathan D Guest & Ghazaleh Taherzadeh & Ragul Gowthaman & Ipsa Mittra & Jane Quackenbush & Brian G Pierce - 1-24 Personalized brain stimulation for effective neurointervention across participants
by Nienke E R van Bueren & Thomas L Reed & Vu Nguyen & James G Sheffield & Sanne H G van der Ven & Michael A Osborne & Evelyn H Kroesbergen & Roi Cohen Kadosh - 1-24 Optima TB: A tool to help optimally allocate tuberculosis spending
by Lara Goscé & Gerard J Abou Jaoude & David J Kedziora & Clemens Benedikt & Azfar Hussain & Sarah Jarvis & Alena Skrahina & Dzmitry Klimuk & Henadz Hurevich & Feng Zhao & Nicole Fraser-Hurt & Nejma Cheikh & Marelize Gorgens & David J Wilson & Romesh Abeysuriya & Rowan Martin-Hughes & Sherrie L Kelly & Anna Roberts & Robyn M Stuart & Tom Palmer & Jasmina Panovska-Griffiths & Cliff C Kerr & David P Wilson & Hassan Haghparast-Bidgoli & Jolene Skordis & Ibrahim Abubakar - 1-24 Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model
by Federica Gugole & Luc E Coffeng & Wouter Edeling & Benjamin Sanderse & Sake J de Vlas & Daan Crommelin - 1-25 Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C
by Susana Posada-Céspedes & Gert Van Zyl & Hesam Montazeri & Jack Kuipers & Soo-Yon Rhee & Roger Kouyos & Huldrych F Günthard & Niko Beerenwinkel - 1-25 Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing
by Michael Smith & Rachel Chan & Maaz Khurram & Paul M K Gordon - 1-25 Learning brain dynamics for decoding and predicting individual differences
by Joyneel Misra & Srinivas Govinda Surampudi & Manasij Venkatesh & Chirag Limbachia & Joseph Jaja & Luiz Pessoa - 1-26 Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
by Ilario De Toma & Cesar Sierra & Mara Dierssen - 1-26 Neighbor-enhanced diffusivity in dense, cohesive cell populations
by Hyun Gyu Lee & Kyoung J Lee - 1-28 Latching dynamics as a basis for short-term recall
by Kwang Il Ryom & Vezha Boboeva & Oleksandra Soldatkina & Alessandro Treves - 1-28 Differences in olfactory bulb mitral cell spiking with ortho- and retronasal stimulation revealed by data-driven models
by Michelle F Craft & Andrea K Barreiro & Shree Hari Gautam & Woodrow L Shew & Cheng Ly - 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 - 1-39 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 - 1-17 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 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 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 A T 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 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 - 1-28 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 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
- 1-13 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 - 1-18 Predicting seasonal influenza using supermarket retail records
by Ioanna Miliou & Xinyue Xiong & Salvatore Rinzivillo & Qian Zhang & Giulio Rossetti & Fosca Giannotti & Dino Pedreschi & Alessandro Vespignani - 1-20 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 & Yansen Su - 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 Modelling locust foraging: How and why food affects group formation
by Fillipe Georgiou & Camille 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 - 1-25 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 - 1-34 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 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 - 1-21 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 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 - 1-22 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 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 - 1-31 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 & Antoine 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 - 1-14 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 PRER: A patient representation with pairwise relative expression of proteins on biological networks
by Halil İbrahim Kuru & Mustafa Buyukozkan & Oznur Tastan - 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 G Garcia - 1-26 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 - 1-27 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 - 1-28 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 - 1-20 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 - 1-27 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