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June 2022, Volume 18, Issue 6
- 1-14 Ten simple rules for good research practice
by Simon Schwab & Perrine Janiaud & Michael Dayan & Valentin Amrhein & Radoslaw Panczak & Patricia M Palagi & Lars G Hemkens & Meike Ramon & Nicolas Rothen & Stephen Senn & Eva Furrer & Leonhard Held - 1-14 Ten simple rules for succeeding as an underrepresented STEM undergraduate
by Melanie Duc Bo Massey & Suchinta Arif & Shanukie Embuldeniya & Karma Nanglu & Joseph Bielawski - 1-14 Ten simple rules for improving communication among scientists
by Carla Bautista & Narjes Alfuraiji & Anna Drangowska-Way & Karishma Gangwani & Alida de Flamingh & Philip E Bourne - 1-15 Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology
by Laurynas Kalesinskas & Sanjana Gupta & Purvesh Khatri - 1-15 Pulmonary drug delivery and retention: A computational study to identify plausible parameters based on a coupled airway-mucus flow model
by Aranyak Chakravarty & Mahesh V Panchagnula & Alladi Mohan & Neelesh A Patankar - 1-17 Explainable detection of adverse drug reaction with imbalanced data distribution
by Jin Wang & Liang-Chih Yu & Xuejie Zhang - 1-18 SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data
by Christos Maniatis & Catalina A Vallejos & Guido Sanguinetti - 1-18 Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation
by Raphael R Eguchi & Christian A Choe & Po-Ssu Huang - 1-18 Strain design optimization using reinforcement learning
by Maryam Sabzevari & Sandor Szedmak & Merja Penttilä & Paula Jouhten & Juho Rousu - 1-19 HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data
by Qing Xie & Chenggong Han & Victor Jin & Shili Lin - 1-20 Interpretable pairwise distillations for generative protein sequence models
by Christoph Feinauer & Barthelemy Meynard-Piganeau & Carlo Lucibello - 1-21 Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks
by Timon Wittenstein & Nava Leibovich & Andreas Hilfinger - 1-22 A mechanism for punctuating equilibria during mammalian vocal development
by Thiago T Varella & Yisi S Zhang & Daniel Y Takahashi & Asif A Ghazanfar - 1-23 A weighted constraint satisfaction approach to human goal-directed decision making
by Yuxuan Li & James L McClelland - 1-23 Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
by Cosimo Lupo & Natanael Spisak & Aleksandra M Walczak & Thierry Mora - 1-24 Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue
by Sang-Woo Lee & Yoshihiro Morishita - 1-24 Priority-based transformations of stimulus representation in visual working memory
by Quan Wan & Jorge A Menendez & Bradley R Postle - 1-24 A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
by Vítor Vieira & Jorge Ferreira & Miguel Rocha - 1-25 Characterizing collaborative transcription regulation with a graph-based deep learning approach
by Zhenhao Zhang & Fan Feng & Jie Liu - 1-25 Efficient Bayesian inference for mechanistic modelling with high-throughput data
by Simon Martina Perez & Heba Sailem & Ruth E Baker - 1-25 Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data
by Jair Andrade & Jim Duggan - 1-26 Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design
by Jeremy Grignard & Véronique Lamamy & Eva Vermersch & Philippe Delagrange & Jean-Philippe Stephan & Thierry Dorval & François Fages - 1-26 Addressing delayed case reporting in infectious disease forecast modeling
by Lauren J Beesley & Dave Osthus & Sara Y Del Valle - 1-29 Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling
by Niklas Kolbe & Lorenz Hexemer & Lukas-Malte Bammert & Alexander Loewer & Mária Lukáčová-Medvid’ová & Stefan Legewie - 1-29 Direct reciprocity between individuals that use different strategy spaces
by Laura Schmid & Christian Hilbe & Krishnendu Chatterjee & Martin A Nowak - 1-29 Characterizing superspreading potential of infectious disease: Decomposition of individual transmissibility
by Shi Zhao & Marc K C Chong & Sukhyun Ryu & Zihao Guo & Mu He & Boqiang Chen & Salihu S Musa & Jingxuan Wang & Yushan Wu & Daihai He & Maggie H Wang - 1-29 Deciphering clock cell network morphology within the biological master clock, suprachiasmatic nucleus: From the perspective of circadian wave dynamics
by Hyun Kim & Cheolhong Min & Byeongha Jeong & Kyoung J Lee - 1-30 An approximate stochastic optimal control framework to simulate nonlinear neuro-musculoskeletal models in the presence of noise
by Tom Van Wouwe & Lena H Ting & Friedl De Groote - 1-30 Differential methods for assessing sensitivity in biological models
by Rachel Mester & Alfonso Landeros & Chris Rackauckas & Kenneth Lange - 1-31 A method for the inference of cytokine interaction networks
by Joanneke E Jansen & Dominik Aschenbrenner & Holm H Uhlig & Mark C Coles & Eamonn A Gaffney - 1-32 Epidemic management and control through risk-dependent individual contact interventions
by Tapio Schneider & Oliver R A Dunbar & Jinlong Wu & Lucas Böttcher & Dmitry Burov & Alfredo Garbuno-Inigo & Gregory L Wagner & Sen Pei & Chiara Daraio & Raffaele Ferrari & Jeffrey Shaman - 1-33 Towards a more general understanding of the algorithmic utility of recurrent connections
by Brett W Larsen & Shaul Druckmann - 1-33 Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of ‘stripe’ formation in human data
by Pratik Mullick & Sylvain Fontaine & Cécile Appert-Rolland & Anne-Hélène Olivier & William H Warren & Julien Pettré - 1-34 Modeling cortical synaptic effects of anesthesia and their cholinergic reversal
by Bolaji P Eniwaye & Victoria Booth & Anthony G Hudetz & Michal Zochowski - 1-35 Tracking the contribution of inductive bias to individualised internal models
by Balázs Török & David G Nagy & Mariann Kiss & Karolina Janacsek & Dezső Németh & Gergő Orbán - 1-36 Metastable spiking networks in the replica-mean-field limit
by Luyan Yu & Thibaud O Taillefumier
May 2022, Volume 18, Issue 5
- 1-12 Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers
by Luis Fernando Montaño-Gutierrez & Nahuel Manzanaro Moreno & Iseabail L Farquhar & Yu Huo & Lucia Bandiera & Peter S Swain - 1-14 CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
by Maarten J M F Reijnders & Robert M Waterhouse - 1-15 Predicting knee adduction moment response to gait retraining with minimal clinical data
by Nataliya Rokhmanova & Katherine J Kuchenbecker & Peter B Shull & Reed Ferber & Eni Halilaj - 1-15 Enhancing long-term forecasting: Learning from COVID-19 models
by Hazhir Rahmandad & Ran Xu & Navid Ghaffarzadegan - 1-16 Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics
by Christopher I Jarvis & Amy Gimma & Flavio Finger & Tim P Morris & Jennifer A Thompson & Olivier le Polain de Waroux & W John Edmunds & Sebastian Funk & Thibaut Jombart - 1-19 Gene regulation by a protein translation factor at the single-cell level
by Roswitha Dolcemascolo & Lucas Goiriz & Roser Montagud-Martínez & Guillermo Rodrigo - 1-22 Conflict and competition between model-based and model-free control
by Yuqing Lei & Alec Solway - 1-23 Observing others give & take: A computational account of bystanders’ feelings and actions
by Bastien Blain & Joseph Marks & Philipp Czech & Tali Sharot - 1-24 CBEA: Competitive balances for taxonomic enrichment analysis
by Quang P Nguyen & Anne G Hoen & H Robert Frost - 1-24 Uncertainty–guided learning with scaled prediction errors in the basal ganglia
by Moritz Möller & Sanjay Manohar & Rafal Bogacz - 1-24 Linear viscoelastic properties of the vertex model for epithelial tissues
by Sijie Tong & Navreeta K Singh & Rastko Sknepnek & Andrej Košmrlj - 1-26 Analyzing nested experimental designs—A user-friendly resampling method to determine experimental significance
by Rishikesh U Kulkarni & Catherine L Wang & Carolyn R Bertozzi - 1-26 Anomalous diffusion and asymmetric tempering memory in neutrophil chemotaxis
by Peter Dieterich & Otto Lindemann & Mats Leif Moskopp & Sebastien Tauzin & Anna Huttenlocher & Rainer Klages & Aleksei Chechkin & Albrecht Schwab - 1-27 Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences
by Andonis Gerardos & Nicola Dietler & Anne-Florence Bitbol - 1-27 Feature blindness: A challenge for understanding and modelling visual object recognition
by Gaurav Malhotra & Marin Dujmović & Jeffrey S Bowers - 1-29 BOSO: A novel feature selection algorithm for linear regression with high-dimensional data
by Luis V Valcárcel & Edurne San José-Enériz & Xabier Cendoya & Ángel Rubio & Xabier Agirre & Felipe Prósper & Francisco J Planes - 1-30 A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota
by Alice J Sommer & Annette Peters & Martina Rommel & Josef Cyrys & Harald Grallert & Dirk Haller & Christian L Müller & Marie-Abèle C Bind - 1-30 Designing optimal allocations for cancer screening using queuing network models
by Justin Dean & Evan Goldberg & Franziska Michor - 1-32 Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap)
by Reyhaneh Abbasi & Peter Balazs & Maria Adelaide Marconi & Doris Nicolakis & Sarah M Zala & Dustin J Penn - 1-33 Performance-gated deliberation: A context-adapted strategy in which urgency is opportunity cost
by Maximilian Puelma Touzel & Paul Cisek & Guillaume Lajoie - 1-42 A topological data analytic approach for discovering biophysical signatures in protein dynamics
by Wai Shing Tang & Gabriel Monteiro da Silva & Henry Kirveslahti & Erin Skeens & Bibo Feng & Timothy Sudijono & Kevin K Yang & Sayan Mukherjee & Brenda Rubenstein & Lorin Crawford
April 2022, Volume 18, Issue 4
- 1-7 Ten simple rules for using entrepreneurship skills to improve research careers and culture
by Matt Bawn & David Dent & Philip E Bourne - 1-9 Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit
by Gautam Munglani & Hannes Vogler & Ueli Grossniklaus - 1-9 Ten simple rules for getting started with statistics in graduate school
by Rachel A Zitomer & Jessica Karr & Mark Kerstens & Lindsey Perry & Kayla Ruth & Lindsay Adrean & Suzanne Austin & Jamie Cornelius & Jonathan Dachenhaus & Jonathan Dinkins & Alan Harrington & Hankyu Kim & Terrah Owens & Claire Revekant & Vanessa Schroeder & Chelsea Sink & Jonathon J Valente & Ethan Woodis & James W Rivers - 1-10 Ten simple rules for building a successful science start-up
by Tobias Reichmuth & Collin Y Ewald - 1-11 Ten simple rules to ruin a collaborative environment
by Carolyn J Lawrence-Dill & Robyn L Allscheid & Albert Boaitey & Todd Bauman & Edward S Buckler IV & Jennifer L Clarke & Christopher Cullis & Jack Dekkers & Cassandra J Dorius & Shawn F Dorius & David Ertl & Matthew Homann & Guiping Hu & Mary Losch & Eric Lyons & Brenda Murdoch & Zahra-Katy Navabi & Somashekhar Punnuri & Fahad Rafiq & James M Reecy & Patrick S Schnable & Nicole M Scott & Moira Sheehan & Xavier Sirault & Margaret Staton & Christopher K Tuggle & Alison Van Eenennaam & Rachael Voas - 1-17 RNA folding using quantum computers
by Dillion M Fox & Christopher M MacDermaid & Andrea M A Schreij & Magdalena Zwierzyna & Ross C Walker - 1-18 Application of modular response analysis to medium- to large-size biological systems
by Meriem Mekedem & Patrice Ravel & Jacques Colinge - 1-19 Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states
by Amanda L Peiffer & Julie M Garlick & Stephen T Joy & Anna K Mapp & Charles L Brooks III - 1-20 Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention
by Bryan T Mayer & Allan C deCamp & Yunda Huang & Joshua T Schiffer & Raphael Gottardo & Peter B Gilbert & Daniel B Reeves - 1-20 Using topic modeling to detect cellular crosstalk in scRNA-seq
by Alexandrina Pancheva & Helen Wheadon & Simon Rogers & Thomas D Otto - 1-21 Optimizing interneuron circuits for compartment-specific feedback inhibition
by Joram Keijser & Henning Sprekeler - 1-21 Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs
by Vinita Periwal & Stefan Bassler & Sergej Andrejev & Natalia Gabrielli & Kaustubh Raosaheb Patil & Athanasios Typas & Kiran Raosaheb Patil - 1-22 Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa
by Renato Giliberti & Sara Cavaliere & Italia Elisa Mauriello & Danilo Ercolini & Edoardo Pasolli - 1-22 Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants
by Nicholas J Ose & Brandon M Butler & Avishek Kumar & I Can Kazan & Maxwell Sanderford & Sudhir Kumar & S Banu Ozkan - 1-22 DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data
by Lijun Cheng & Pratik Karkhanis & Birkan Gokbag & Yueze Liu & Lang Li - 1-24 Phylogenetic analysis of migration, differentiation, and class switching in B cells
by Kenneth B Hoehn & Oliver G Pybus & Steven H Kleinstein - 1-27 Microbiome-based disease prediction with multimodal variational information bottlenecks
by Filippo Grazioli & Raman Siarheyeu & Israa Alqassem & Andreas Henschel & Giampaolo Pileggi & Andrea Meiser - 1-27 SUITOR: Selecting the number of mutational signatures through cross-validation
by Donghyuk Lee & Difei Wang & Xiaohong R Yang & Jianxin Shi & Maria Teresa Landi & Bin Zhu - 1-27 Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors
by Nicolas Sundqvist & Nina Grankvist & Jeramie Watrous & Jain Mohit & Roland Nilsson & Gunnar Cedersund - 1-29 Cell type-specific mechanisms of information transfer in data-driven biophysical models of hippocampal CA3 principal neurons
by Daniele Linaro & Matthew J Levy & David L Hunt - 1-30 Alpha blocking and 1/fβ spectral scaling in resting EEG can be accounted for by a sum of damped alpha band oscillatory processes
by Rick Evertz & Damien G Hicks & David T J Liley - 1-31 Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders
by Yuge Wang & Hongyu Zhao - 1-31 Chaotic and stochastic dynamics of epileptiform-like activities in sclerotic hippocampus resected from patients with pharmacoresistant epilepsy
by Noemi S Araújo & Selvin Z Reyes-Garcia & João A F Brogin & Douglas D Bueno & Esper A Cavalheiro & Carla A Scorza & Jean Faber - 1-33 Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets
by Anuradha Kar & Manuel Petit & Yassin Refahi & Guillaume Cerutti & Christophe Godin & Jan Traas
March 2022, Volume 18, Issue 3
- 1-8 Ten simple rules for principled simulation modelling
by Laurel Fogarty & Madeleine Ammar & Thomas Holding & Adam Powell & Anne Kandler - 1-13 Survival analysis of pathway activity as a prognostic determinant in breast cancer
by Gustavo S Jeuken & Nicholas P Tobin & Lukas Käll - 1-14 Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms
by Noortje G Godijk & Martin C J Bootsma & Henri C van Werkhoven & Valentijn A Schweitzer & Sabine C de Greeff & Annelot F Schoffelen & Marc J M Bonten - 1-14 Constructing benchmark test sets for biological sequence analysis using independent set algorithms
by Samantha Petti & Sean R Eddy - 1-14 Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data
by Pablo M De Salazar & Fred Lu & James A Hay & Diana Gómez-Barroso & Pablo Fernández-Navarro & Elena V Martínez & Jenaro Astray-Mochales & Rocío Amillategui & Ana García-Fulgueiras & Maria D Chirlaque & Alonso Sánchez-Migallón & Amparo Larrauri & María J Sierra & Marc Lipsitch & Fernando Simón & Mauricio Santillana & Miguel A Hernán - 1-15 Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2
by Leonardo Souto Ferreira & Otavio Canton & Rafael Lopes Paixão da Silva & Silas Poloni & Vítor Sudbrack & Marcelo Eduardo Borges & Caroline Franco & Flavia Maria Darcie Marquitti & José Cássio de Moraes & Maria Amélia de Sousa Mascena Veras & Roberto André Kraenkel & Renato Mendes Coutinho - 1-15 Bayesian inference of ancestral recombination graphs
by Ali Mahmoudi & Jere Koskela & Jerome Kelleher & Yao-ban Chan & David Balding - 1-16 A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data
by Snehalika Lall & Sumanta Ray & Sanghamitra Bandyopadhyay - 1-17 Pooled testing of traced contacts under superspreading dynamics
by Stratis Tsirtsis & Abir De & Lars Lorch & Manuel Gomez-Rodriguez - 1-18 SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included
by Jianle Sun & Ruiqi Lyu & Luojia Deng & Qianwen Li & Yang Zhao & Yue Zhang - 1-18 Deep inference of seabird dives from GPS-only records: Performance and generalization properties
by Amédée Roy & Sophie Lanco Bertrand & Ronan Fablet - 1-20 Ten quick tips for deep learning in biology
by Benjamin D Lee & Anthony Gitter & Casey S Greene & Sebastian Raschka & Finlay Maguire & Alexander J Titus & Michael D Kessler & Alexandra J Lee & Marc G Chevrette & Paul Allen Stewart & Thiago Britto-Borges & Evan M Cofer & Kun-Hsing Yu & Juan Jose Carmona & Elana J Fertig & Alexandr A Kalinin & Brandon Signal & Benjamin J Lengerich & Timothy J Triche Jr. & Simina M Boca - 1-20 Transcriptome diversity is a systematic source of variation in RNA-sequencing data
by Pablo E García-Nieto & Ban Wang & Hunter B Fraser - 1-20 Thalamic bursts modulate cortical synchrony locally to switch between states of global functional connectivity in a cognitive task
by Oscar Portoles & Manuel Blesa & Marieke van Vugt & Ming Cao & Jelmer P Borst - 1-21 Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches
by Timos Papadopoulos & Emilia Vynnycky - 1-21 How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments
by Immanuel Meyer & Bnaya Steinmetz & Nadav M Shnerb - 1-22 Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level
by Anđela Davidović & Remy Chait & Gregory Batt & Jakob Ruess - 1-22 Performance of early warning signals for disease re-emergence: A case study on COVID-19 data
by Daniele Proverbio & Françoise Kemp & Stefano Magni & Jorge Gonçalves - 1-22 The role of cell geometry and cell-cell communication in gradient sensing
by Jonathan Fiorentino & Antonio Scialdone - 1-24 Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition
by Shin-ichi Koda & Shinji Saito - 1-26 Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness
by Daniel J Lugar & Ganesh Sriram - 1-26 Automatic wound detection and size estimation using deep learning algorithms
by Héctor Carrión & Mohammad Jafari & Michelle Dawn Bagood & Hsin-ya Yang & Roslyn Rivkah Isseroff & Marcella Gomez - 1-27 Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins
by Lei Wang & Jiangguo Zhang & Dali Wang & Chen Song - 1-29 Encoding time in neural dynamic regimes with distinct computational tradeoffs
by Shanglin Zhou & Sotiris C Masmanidis & Dean V Buonomano - 1-29 Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation
by Yingjing Feng & Caroline H Roney & Jason D Bayer & Steven A Niederer & Mélèze Hocini & Edward J Vigmond - 1-30 Estimating genetic variance contributed by a quantitative trait locus: A random model approach
by Shibo Wang & Fangjie Xie & Shizhong Xu - 1-31 Oscillator decomposition of infant fNIRS data
by Takeru Matsuda & Fumitaka Homae & Hama Watanabe & Gentaro Taga & Fumiyasu Komaki - 1-34 The ability to classify patients based on gene-expression data varies by algorithm and performance metric
by Stephen R Piccolo & Avery Mecham & Nathan P Golightly & Jérémie L Johnson & Dustin B Miller - 1-38 Evolution of innate behavioral strategies through competitive population dynamics
by Tong Liang & Braden A W Brinkman - 1-39 Task-induced neural covariability as a signature of approximate Bayesian learning and inference
by Richard D Lange & Ralf M Haefner - 1-41 Cortical oscillations support sampling-based computations in spiking neural networks
by Agnes Korcsak-Gorzo & Michael G Müller & Andreas Baumbach & Luziwei Leng & Oliver J Breitwieser & Sacha J van Albada & Walter Senn & Karlheinz Meier & Robert Legenstein & Mihai A Petrovici - 1-46 Bayesian calibration, process modeling and uncertainty quantification in biotechnology
by Laura Marie Helleckes & Michael Osthege & Wolfgang Wiechert & Eric von Lieres & Marco Oldiges
February 2022, Volume 18, Issue 2
- 1-7 Ten simple rules for initial data analysis
by Mark Baillie & Saskia le Cessie & Carsten Oliver Schmidt & Lara Lusa & Marianne Huebner & for the Topic Group “Initial Data Analysis” of the STRATOS Initiative - 1-9 Hidden Markov Modeling with HMMTeacher
by Camilo Fuentes-Beals & Alejandro Valdés-Jiménez & Gonzalo Riadi - 1-11 There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk
by Jon Zelner & Nina B Masters & Ramya Naraharisetti & Sanyu A Mojola & Merlin Chowkwanyun & Ryan Malosh - 1-12 gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support
by M Eric Irrgang & Caroline Davis & Peter M Kasson - 1-18 Classical mathematical models for prediction of response to chemotherapy and immunotherapy
by Narmin Ghaffari Laleh & Chiara Maria Lavinia Loeffler & Julia Grajek & Kateřina Staňková & Alexander T Pearson & Hannah Sophie Muti & Christian Trautwein & Heiko Enderling & Jan Poleszczuk & Jakob Nikolas Kather - 1-19 Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster
by Katherine E Overman & Daniel M Choi & Kawai Leung & Joshua W Shaevitz & Gordon J Berman - 1-20 Near-term forecasting of companion animal tick paralysis incidence: An iterative ensemble model
by Nicholas J Clark & Tatiana Proboste & Guyan Weerasinghe & Ricardo J Soares Magalhães - 1-20 Inference of trajectory presence by tree dimension and subset specificity by subtree cover
by Lovemore Tenha & Mingzhou Song - 1-21 Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19
by Xian Yang & Shuo Wang & Yuting Xing & Ling Li & Richard Yi Da Xu & Karl J Friston & Yike Guo - 1-21 Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights
by Ramin Khajeh & Francesco Fumarola & LF Abbott - 1-21 Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning
by Indriani P Astono & James S Welsh & Christopher W Rowe & Phillip Jobling - 1-21 Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic
by Yuen Ler Chow & Shantanu Singh & Anne E Carpenter & Gregory P Way - 1-22 Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus
by Siyu Wang & Stephanie M Reeve & Graham T Holt & Adegoke A Ojewole & Marcel S Frenkel & Pablo Gainza & Santosh Keshipeddy & Vance G Fowler & Dennis L Wright & Bruce R Donald - 1-22 A computationally tractable birth-death model that combines phylogenetic and epidemiological data
by Alexander Eugene Zarebski & Louis du Plessis & Kris Varun Parag & Oliver George Pybus - 1-22 High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication
by Nithya Ramakrishnan & Sibi Raj B Pillai & Ranjith Padinhateeri - 1-23 Learning as filtering: Implications for spike-based plasticity
by Jannes Jegminat & Simone Carlo Surace & Jean-Pascal Pfister - 1-24 RNA-Seq is not required to determine stable reference genes for qPCR normalization
by Nirmal Kumar Sampathkumar & Venkat Krishnan Sundaram & Prakroothi S Danthi & Rasha Barakat & Shiden Solomon & Mrityunjoy Mondal & Ivo Carre & Tatiana El Jalkh & Aïda Padilla-Ferrer & Julien Grenier & Charbel Massaad & Jacqueline C Mitchell - 1-25 Evaluating supervised and unsupervised background noise correction in human gut microbiome data
by Leah Briscoe & Brunilda Balliu & Sriram Sankararaman & Eran Halperin & Nandita R Garud - 1-26 Combination and competition between path integration and landmark navigation in the estimation of heading direction
by Sevan K Harootonian & Arne D Ekstrom & Robert C Wilson - 1-26 In silico prediction of HIV-1-host molecular interactions and their directionality
by Haiting Chai & Quan Gu & Joseph Hughes & David L Robertson - 1-27 Meta-control of social learning strategies
by Anil Yaman & Nicolas Bredeche & Onur Çaylak & Joel Z Leibo & Sang Wan Lee - 1-27 Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network
by R Krishnakumaran & Mohammed Raees & Supratim Ray - 1-28 Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics
by Leonie van Steijn & Inge M N Wortel & Clément Sire & Loïc Dupré & Guy Theraulaz & Roeland M H Merks - 1-35 Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts
by Robert C Mines & Tomasz Lipniacki & Xiling Shen - 1-38 Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates
by Alessandra Løchen & James E Truscott & Nicholas J Croucher
January 2022, Volume 18, Issue 1
- 1-16 An initial ‘snapshot’ of sensory information biases the likelihood and speed of subsequent changes of mind
by William Turner & Daniel Feuerriegel & Robert Hester & Stefan Bode - 1-17 CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach
by Mengting Niu & Quan Zou & Chen Lin - 1-18 OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data
by Raga Krishnakumar & Anne M Ruffing - 1-19 Efficient ReML inference in variance component mixed models using a Min-Max algorithm
by Fabien Laporte & Alain Charcosset & Tristan Mary-Huard - 1-19 Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection
by Alasdair D F Clarke & Amelia R Hunt & Anna E Hughes - 1-20 Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution
by Tadamune Kaneko & Macoto Kikuchi - 1-21 Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods
by Richard Jiang & Prashant Singh & Fredrik Wrede & Andreas Hellander & Linda Petzold - 1-22 Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data
by Qi Jiang & Shuo Zhang & Lin Wan - 1-22 Fast and accurate influenza forecasting in the United States with Inferno
by Dave Osthus - 1-22 Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy
by Alexander B Brummer & Xin Yang & Eric Ma & Margarita Gutova & Christine E Brown & Russell C Rockne - 1-23 Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables
by Arno Strouwen & Bart M Nicolaï & Peter Goos - 1-23 Analytical kinetic model of native tandem promoters in E. coli
by Vatsala Chauhan & Mohamed N M Bahrudeen & Cristina S D Palma & Ines S C Baptista & Bilena L B Almeida & Suchintak Dash & Vinodh Kandavalli & Andre S Ribeiro - 1-24 Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach
by Marcell Miski & Bence Márk Keömley-Horváth & Dorina Rákóczi Megyeriné & Attila Csikász-Nagy & Zoltán Gáspári - 1-24 Formation, collective motion, and merging of macroscopic bacterial aggregates
by George Courcoubetis & Manasi S Gangan & Sean Lim & Xiaokan Guo & Stephan Haas & James Q Boedicker - 1-26 The evolutionary maintenance of Lévy flight foraging
by Winston Campeau & Andrew M Simons & Brett Stevens - 1-26 Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach
by Chen Jia & Abhyudai Singh & Ramon Grima - 1-27 Identification of periodic attractors in Boolean networks using a priori information
by Ulrike Münzner & Tomoya Mori & Marcus Krantz & Edda Klipp & Tatsuya Akutsu - 1-28 Discovering adaptation-capable biological network structures using control-theoretic approaches
by Priyan Bhattacharya & Karthik Raman & Arun K Tangirala - 1-29 A lexical approach for identifying behavioural action sequences
by Gautam Reddy & Laura Desban & Hidenori Tanaka & Julian Roussel & Olivier Mirat & Claire Wyart - 1-30 Interpretable machine learning for high-dimensional trajectories of aging health
by Spencer Farrell & Arnold Mitnitski & Kenneth Rockwood & Andrew D Rutenberg - 1-30 Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships
by Nina Kudryashova & Theoklitos Amvrosiadis & Nathalie Dupuy & Nathalie Rochefort & Arno Onken - 1-32 Optimism and pessimism in optimised replay
by Georgy Antonov & Christopher Gagne & Eran Eldar & Peter Dayan
December 2021, Volume 17, Issue 12
- 1-13 Ten simple rules for developing bioinformatics capacity at an academic institution
by Shaun Aron & C Victor Jongeneel & Paballo Abel Chauke & Melek Chaouch & Judit Kumuthini & Lyndon Zass & Fouzia Radouani & Samar Kamal Kassim & Faisal M Fadlelmola & Nicola Mulder - 1-13 Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization
by Fuminari Miura & Ka Yin Leung & Don Klinkenberg & Kylie E C Ainslie & Jacco Wallinga - 1-14 Development of an experiment-split method for benchmarking the generalization of a PTM site predictor: Lysine methylome as an example
by Guoyang Zou & Yang Zou & Chenglong Ma & Jiaojiao Zhao & Lei Li - 1-15 SWIFT: A deep learning approach to prediction of hypoxemic events in critically-Ill patients using SpO2 waveform prediction
by Akshaya V Annapragada & Joseph L Greenstein & Sanjukta N Bose & Bradford D Winters & Sridevi V Sarma & Raimond L Winslow - 1-17 Motif-pattern dependence of biomolecular phase separation driven by specific interactions
by Benjamin G Weiner & Andrew G T Pyo & Yigal Meir & Ned S Wingreen - 1-19 Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016–2018: A hidden Markov modelling study
by Deus Thindwa & Nicole Wolter & Amy Pinsent & Maimuna Carrim & John Ojal & Stefano Tempia & Jocelyn Moyes & Meredith McMorrow & Jackie Kleynhans & Anne von Gottberg & Neil French & PHIRST group & Cheryl Cohen & Stefan Flasche - 1-19 GCAEMDA: Predicting miRNA-disease associations via graph convolutional autoencoder
by Lei Li & Yu-Tian Wang & Cun-Mei Ji & Chun-Hou Zheng & Jian-Cheng Ni & Yan-Sen Su - 1-19 A systems genomics approach uncovers molecular associates of RSV severity
by Matthew N McCall & Chin-Yi Chu & Lu Wang & Lauren Benoodt & Juilee Thakar & Anthony Corbett & Jeanne Holden-Wiltse & Christopher Slaunwhite & Alex Grier & Steven R Gill & Ann R Falsey & David J Topham & Mary T Caserta & Edward E Walsh & Xing Qiu & Thomas J Mariani - 1-19 A spatio-temporal model to reveal oscillator phenotypes in molecular clocks: Parameter estimation elucidates circadian gene transcription dynamics in single-cells
by Måns Unosson & Marco Brancaccio & Michael Hastings & Adam M Johansen & Bärbel Finkenstädt - 1-20 Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble
by Icíar Civantos-Gómez & Javier García-Algarra & David García-Callejas & Javier Galeano & Oscar Godoy & Ignasi Bartomeus - 1-21 Dissociable influences of reward and punishment on adaptive cognitive control
by Xiamin Leng & Debbie Yee & Harrison Ritz & Amitai Shenhav - 1-21 One-carbon metabolism during the menstrual cycle and pregnancy
by Ruby Kim & H Frederik Nijhout & Michael C Reed - 1-22 Combination treatment optimization using a pan-cancer pathway model
by Robin Schmucker & Gabriele Farina & James Faeder & Fabian Fröhlich & Ali Sinan Saglam & Tuomas Sandholm - 1-22 Benchmarking of tools for axon length measurement in individually-labeled projection neurons
by Mario Rubio-Teves & Sergio Díez-Hermano & César Porrero & Abel Sánchez-Jiménez & Lucía Prensa & Francisco Clascá & María García-Amado & José Antonio Villacorta-Atienza - 1-22 Dynamic maximum entropy provides accurate approximation of structured population dynamics
by Katarína Bod’ová & Enikő Szép & Nicholas H Barton - 1-22 Internal state effects on behavioral shifts in freely behaving praying mantises (Tenodera sinensis)
by Shanel C Pickard & David J Bertsch & Zoe Le Garrec & Roy E Ritzmann & Roger D Quinn & Nicholas S Szczecinski - 1-23 DeepCME: A deep learning framework for computing solution statistics of the chemical master equation
by Ankit Gupta & Christoph Schwab & Mustafa Khammash - 1-23 Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?
by Juan Diaz-Colunga & Ramon Diaz-Uriarte - 1-24 Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes
by Lanxin Zhang & Junyu Wang & Max von Kleist - 1-28 Asymmetric and transient properties of reciprocal activity of antagonists during the paw-shake response in the cat
by Jessica R Parker & Alexander N Klishko & Boris I Prilutsky & Gennady S Cymbalyuk - 1-28 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant
by Joseph R Larsen & Margaret R Martin & John D Martin & James B Hicks & Peter Kuhn - 1-30 A data-informed mean-field approach to mapping of cortical parameter landscapes
by Zhuo-Cheng Xiao & Kevin K Lin & Lai-Sang Young - 1-31 Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity
by Elishai Ezra-Tsur & Oren Amsalem & Lea Ankri & Pritish Patil & Idan Segev & Michal Rivlin-Etzion - 1-38 Preparing to move: Setting initial conditions to simplify interactions with complex objects
by Rashida Nayeem & Salah Bazzi & Mohsen Sadeghi & Neville Hogan & Dagmar Sternad - 1-39 Decision prioritization and causal reasoning in decision hierarchies
by Ariel Zylberberg - 1-44 When shared concept cells support associations: Theory of overlapping memory engrams
by Chiara Gastaldi & Tilo Schwalger & Emanuela De Falco & Rodrigo Quian Quiroga & Wulfram Gerstner
November 2021, Volume 17, Issue 11
- 1-12 Identifying prognostic pairwise relationships among bacterial species in microbiome studies
by Sean M Devlin & Axel Martin & Irina Ostrovnaya - 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 Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT
by Shahab Sarmashghi & Metin Balaban & Eleonora Rachtman & Behrouz Touri & Siavash Mirarab & Vineet Bafna - 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