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September 2022, Volume 18, Issue 9
- 1-27 Towards reliable quantification of cell state velocities
by Valérie Marot-Lassauzaie & Brigitte Joanne Bouman & Fearghal Declan Donaghy & Yasmin Demerdash & Marieke Alida Gertruda Essers & Laleh Haghverdi - 1-27 Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets
by Melissa A Iacovidou & Priscille Barreaux & Simon E F Spencer & Matthew B Thomas & Erin E Gorsich & Kat S Rock - 1-28 A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data
by Ran Su & Haitang Yang & Leyi Wei & Siqi Chen & Quan Zou - 1-28 A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis
by Michela Carlotta Massi & Lorenzo Dominoni & Francesca Ieva & Giovanni Fiorito - 1-28 A hierarchical process model links behavioral aging and lifespan in C. elegans
by Natasha Oswal & Olivier M F Martin & Sofia Stroustrup & Monika Anna Matusiak Bruckner & Nicholas Stroustrup - 1-30 MouseNet: A biologically constrained convolutional neural network model for the mouse visual cortex
by Jianghong Shi & Bryan Tripp & Eric Shea-Brown & Stefan Mihalas & Michael A. Buice - 1-30 Systems-level identification of key transcription factors in immune cell specification
by Cong Liu & Kyla Omilusik & Clara Toma & Nadia S Kurd & John T Chang & Ananda W Goldrath & Wei Wang - 1-31 Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection
by Andrea Di Gioacchino & Jonah Procyk & Marco Molari & John S Schreck & Yu Zhou & Yan Liu & Rémi Monasson & Simona Cocco & Petr Šulc - 1-31 An integrative systems biology approach to overcome venetoclax resistance in acute myeloid leukemia
by Michelle Przedborski & David Sharon & Severine Cathelin & Steven Chan & Mohammad Kohandel - 1-32 Robust inference of population size histories from genomic sequencing data
by Gautam Upadhya & Matthias Steinrücken - 1-32 Investigating differential abundance methods in microbiome data: A benchmark study
by Marco Cappellato & Giacomo Baruzzo & Barbara Di Camillo - 1-32 Utility of constraints reflecting system stability on analyses for biological models
by Yoshiaki Kariya & Masashi Honma & Keita Tokuda & Akihiko Konagaya & Hiroshi Suzuki - 1-35 Interaction between games give rise to the evolution of moral norms of cooperation
by Mohammad Salahshour - 1-36 Ambiguity drives higher-order Pavlovian learning
by Tomislav D Zbozinek & Omar D Perez & Toby Wise & Michael Fanselow & Dean Mobbs
August 2022, Volume 18, Issue 8
- 1-8 Ten simple rules for a successful EU Marie Skłodowska-Curie Actions Postdoctoral (MSCA) fellowship application
by Philipp Baumert & Francesco Cenni & Mikhail L Antonkine - 1-9 Ten simple rules for organizing a special session at a scientific conference
by Davide Chicco & Philip E Bourne - 1-10 Ten simple rules for reporting information on species interactions
by Cristina A Kita & Guillermo Florez-Montero & Sebastián Montoya-Bustamante & Renata L Muylaert & Natalya Zapata-Mesa & Marco A R Mello - 1-11 Understanding the structure of cognitive noise
by Jian-Qiao Zhu & Pablo León-Villagrá & Nick Chater & Adam N Sanborn - 1-14 A simple model of the attentional blink and its modulation by mental training
by Nadav Amir & Naftali Tishby & Israel Nelken - 1-15 VGsim: Scalable viral genealogy simulator for global pandemic
by Vladimir Shchur & Vadim Spirin & Dmitry Sirotkin & Evgeni Burovski & Nicola De Maio & Russell Corbett-Detig - 1-15 Nine quick tips for pathway enrichment analysis
by Davide Chicco & Giuseppe Agapito - 1-16 SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2
by Richard A Stein & Hassane S Mchaourab - 1-17 Ten quick tips for biomarker discovery and validation analyses using machine learning
by Ramon Diaz-Uriarte & Elisa Gómez de Lope & Rosalba Giugno & Holger Fröhlich & Petr V Nazarov & Isabel A Nepomuceno-Chamorro & Armin Rauschenberger & Enrico Glaab - 1-17 iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank
by Wenxiang Zhang & Jialu Hou & Bin Liu - 1-17 Archetypal Analysis for population genetics
by Julia Gimbernat-Mayol & Albert Dominguez Mantes & Carlos D Bustamante & Daniel Mas Montserrat & Alexander G Ioannidis - 1-18 Novel feature selection methods for construction of accurate epigenetic clocks
by Adam Li & Amber Mueller & Brad English & Anthony Arena & Daniel Vera & Alice E Kane & David A Sinclair - 1-19 TreeKnit: Inferring ancestral reassortment graphs of influenza viruses
by Pierre Barrat-Charlaix & Timothy G Vaughan & Richard A Neher - 1-20 Different forms of superspreading lead to different outcomes: Heterogeneity in infectiousness and contact behavior relevant for the case of SARS-CoV-2
by Elise J Kuylen & Andrea Torneri & Lander Willem & Pieter J K Libin & Steven Abrams & Pietro Coletti & Nicolas Franco & Frederik Verelst & Philippe Beutels & Jori Liesenborgs & Niel Hens - 1-21 Cross-fitted instrument: A blueprint for one-sample Mendelian randomization
by William R P Denault & Jon Bohlin & Christian M Page & Stephen Burgess & Astanand Jugessur - 1-21 Avoiding costly mistakes in groups: The evolution of error management in collective decision making
by Alan N Tump & Max Wolf & Pawel Romanczuk & Ralf H J M Kurvers - 1-21 The impact of sparsity in low-rank recurrent neural networks
by Elizabeth Herbert & Srdjan Ostojic - 1-22 Subunit promotion energies for channel opening in heterotetrameric olfactory CNG channels
by Jana Schirmeyer & Thomas Eick & Eckhard Schulz & Sabine Hummert & Christian Sattler & Ralf Schmauder & Klaus Benndorf - 1-24 Spatiotemporal dynamics of human high gamma discriminate naturalistic behavioral states
by Abdulwahab Alasfour & Paolo Gabriel & Xi Jiang & Isaac Shamie & Lucia Melloni & Thomas Thesen & Patricia Dugan & Daniel Friedman & Werner Doyle & Orin Devinsky & David Gonda & Shifteh Sattar & Sonya Wang & Eric Halgren & Vikash Gilja - 1-26 Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics
by Marie Chion & Christine Carapito & Frédéric Bertrand - 1-26 Terminal heterocyst differentiation in the Anabaena patA mutant as a result of post-transcriptional modifications and molecular leakage
by Pau Casanova-Ferrer & Saúl Ares & Javier Muñoz-García - 1-27 Adaptive search space pruning in complex strategic problems
by Ofra Amir & Liron Tyomkin & Yuval Hart - 1-27 How growers make decisions impacts plant disease control
by Rachel E Murray-Watson & Frédéric M Hamelin & Nik J Cunniffe - 1-27 Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm
by Mohammad-Hadi Foroughmand-Araabi & Sama Goliaei & Alice C McHardy - 1-31 A framework for macroscopic phase-resetting curves for generalised spiking neural networks
by Grégory Dumont & Alberto Pérez-Cervera & Boris Gutkin - 1-32 The pursuit of happiness: A reinforcement learning perspective on habituation and comparisons
by Rachit Dubey & Thomas L Griffiths & Peter Dayan - 1-33 Constructive connectomics: How neuronal axons get from here to there using gene-expression maps derived from their family trees
by Stan Kerstjens & Gabriela Michel & Rodney J Douglas
July 2022, Volume 18, Issue 7
- 1-11 Ten simple rules for designing and running a computing minor for bio/chem students
by Rochelle-Jan Reyes & Nina Hosmane & Shasta Ihorn & Milo Johnson & Anagha Kulkarni & Jennifer Nelson & Michael Savvides & Duc Ta & Ilmi Yoon & Pleuni S Pennings - 1-13 Ten simple rules to host an inclusive conference
by Rocío Joo & Andrea Sánchez-Tapia & Sara Mortara & Yanina Bellini Saibene & Heather Turner & Dorothea Hug Peter & Natalia Soledad Morandeira & Matt Bannert & Batool Almazrouq & Elizabeth Hare & Laura Ación & Juan Pablo Narváez-Gómez & Marcela Alfaro Córdoba & Federico Marini & Rita Giordano & Silvia Canelón & Anicet Ebou & Adithi R Upadhya & Joselyn Chávez & Janani Ravi - 1-15 Asymmetric and adaptive reward coding via normalized reinforcement learning
by Kenway Louie - 1-16 Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design
by Jennifer Brennan & Lalit Jain & Sofia Garman & Ann E Donnelly & Erik Scott Wright & Kevin Jamieson - 1-17 Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses
by Wendi Bacon & Alexandra Holinski & Marina Pujol & Meredith Wilmott & Sarah L Morgan & on behalf of the European Molecular Biology Laboratory—European Bioinformatics Institute Training Team - 1-17 Graphia: A platform for the graph-based visualisation and analysis of high dimensional data
by Tom C Freeman & Sebastian Horsewell & Anirudh Patir & Josh Harling-Lee & Tim Regan & Barbara B Shih & James Prendergast & David A Hume & Tim Angus - 1-18 Dimensionality reduction of longitudinal ’omics data using modern tensor factorizations
by Uria Mor & Yotam Cohen & Rafael Valdés-Mas & Denise Kviatcovsky & Eran Elinav & Haim Avron - 1-19 A Bayesian method for identifying associations between response variables and bacterial community composition
by Adrian Verster & Nicholas Petronella & Judy Green & Fernando Matias & Stephen P J Brooks - 1-20 ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients
by Bodhayan Prasad & Cathy McGeough & Amanda Eakin & Tan Ahmed & Dawn Small & Philip Gardiner & Adrian Pendleton & Gary Wright & Anthony J Bjourson & David S Gibson & Priyank Shukla - 1-20 To what extent naringenin binding and membrane depolarization shape mitoBK channel gating—A machine learning approach
by Monika Richter-Laskowska & Paulina Trybek & Piotr Bednarczyk & Agata Wawrzkiewicz-Jałowiecka - 1-20 Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study
by Joseph Chadi Lemaitre & Damiano Pasetto & Mario Zanon & Enrico Bertuzzo & Lorenzo Mari & Stefano Miccoli & Renato Casagrandi & Marino Gatto & Andrea Rinaldo - 1-21 A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission
by Fabian Santiago & Suzanne Sindi - 1-21 AC-PCoA: Adjustment for confounding factors using principal coordinate analysis
by Yu Wang & Fengzhu Sun & Wei Lin & Shuqin Zhang - 1-21 Pooling strategies in V1 can account for the functional and structural diversity across species
by Victor Boutin & Angelo Franciosini & Frédéric Chavane & Laurent U Perrinet - 1-22 nAdder: A scale-space approach for the 3D analysis of neuronal traces
by Minh Son Phan & Katherine Matho & Emmanuel Beaurepaire & Jean Livet & Anatole Chessel - 1-22 Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2
by Jose M Jimenez-Guardeño & Ana Maria Ortega-Prieto & Borja Menendez Moreno & Thomas J A Maguire & Adam Richardson & Juan Ignacio Diaz-Hernandez & Javier Diez Perez & Mark Zuckerman & Albert Mercadal Playa & Carlos Cordero Deline & Michael H Malim & Rocio Teresa Martinez-Nunez - 1-23 Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions
by Saleh Fayaz & Mohammad Amin Fakharian & Ali Ghazizadeh - 1-23 Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data
by Long Liu & Qingyu Meng & Cherry Weng & Qing Lu & Tong Wang & Yalu Wen - 1-25 The accuracy of absolute differential abundance analysis from relative count data
by Kimberly E Roche & Sayan Mukherjee - 1-26 The computational relationship between reinforcement learning, social inference, and paranoia
by Joseph M Barnby & Mitul A Mehta & Michael Moutoussis - 1-27 The spectrum of covariance matrices of randomly connected recurrent neuronal networks with linear dynamics
by Yu Hu & Haim Sompolinsky - 1-28 Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models
by Fabian Fröhlich & Peter K Sorger - 1-28 Physiological characterization of electrodermal activity enables scalable near real-time autonomic nervous system activation inference
by Rafiul Amin & Rose T Faghih - 1-30 Suboptimal human inference can invert the bias-variance trade-off for decisions with asymmetric evidence
by Tahra L Eissa & Joshua I Gold & Krešimir Josić & Zachary P Kilpatrick - 1-31 Suprathreshold perceptual decisions constrain models of confidence
by Shannon M Locke & Michael S Landy & Pascal Mamassian - 1-33 Gaze-dependent evidence accumulation predicts multi-alternative risky choice behaviour
by Felix Molter & Armin W Thomas & Scott A Huettel & Hauke R Heekeren & Peter N C Mohr
June 2022, Volume 18, Issue 6
- 1-12 sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics
by Nadezhda M Belonogova & Gulnara R Svishcheva & Anatoly V Kirichenko & Irina V Zorkoltseva & Yakov A Tsepilov & Tatiana I Axenovich - 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