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| Open AccessKnowledge graph-based recommendation framework identifies drivers of resistance in EGFR mutant non-small cell lung cancer
Resistance to EGFR inhibitors presents a major obstacle in treating non-small cell lung cancer. Here, the authors develop a recommender system ranking genes based on trade-offs between diverse types of evidence linking them to potential mechanisms of EGFRi resistance.
- Anna Gogleva
- , Dimitris Polychronopoulos
- & Krishna C. Bulusu
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Article
| Open AccessNeural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations
Here, the authors apply a neural relational inference model to infer dynamic networks of interacting residues in protein molecular dynamics simulations. The model can predict allosteric communication pathways and relative free energy changes upon mutations.
- Jingxuan Zhu
- , Juexin Wang
- & Dong Xu
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Article
| Open AccessReconstructing antibody dynamics to estimate the risk of influenza virus infection
Serological classification of influenza infection has classically been based on a four-fold or higher increase in antibody levels, but this approach may not be optimal. Here, the authors develop a Bayesian model to improve identification of infections in serological samples by accounting for individual antibody dynamics.
- Tim K. Tsang
- , Ranawaka A. P. M. Perera
- & Simon Cauchemez
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Article
| Open AccessIdentifying regions for enhanced control of gambiense sleeping sickness in the Democratic Republic of Congo
Gambiense human African trypanosomiasis (sleeping sickness or gHAT) has been targeted for elimination of transmission by 2030. Here, the authors project impacts of gHAT interventions in the Democratic Republic of the Congo and derive a priority list of health zones requiring enhanced control to achieve this target.
- Ching-I Huang
- , Ronald E. Crump
- & Kat S. Rock
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Article
| Open AccessAgent-based modelling of reactive vaccination of workplaces and schools against COVID-19
The authors use an agent-based model to investigate the potential of reactive vaccination strategies for COVID-19 outbreak mitigation. They find that distributing vaccines in schools and workplaces where cases are detected is more impactful than non-reactive strategies in a wide range of epidemic scenarios.
- Benjamin Faucher
- , Rania Assab
- & Chiara Poletto
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| Open AccessA kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity
Cas9 off-target sites can be predicted by many bioinformatics tools. Here the authors present low complexity mechanistic model that characterizes SpCas9 kinetics in free-energy terms, allowing quantitative prediction of off-target activity in bulk-biochemistry, single molecule, and whole-genome profiling experiments.
- Behrouz Eslami-Mossallam
- , Misha Klein
- & Martin Depken
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Article
| Open AccessMQuad enables clonal substructure discovery using single cell mitochondrial variants
Mitochondrial variants are informative endogenous barcodes for clonal substructure. Here, the authors developed a computational method MQuad to effectively detect these clonal informed mtDNA variants from single-cell RNA, DNA or ATAC sequencing data.
- Aaron Wing Cheung Kwok
- , Chen Qiao
- & Yuanhua Huang
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Article
| Open AccessKinetic model of GPCR-G protein interactions reveals allokairic modulation of signaling
Experimentally validated kinetic simulations uncover transient enhancement of GPCR ternary complex formation by allokairic effectors.
- Kelly J. Culhane
- , Tejas M. Gupte
- & Sivaraj Sivaramakrishnan
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Article
| Open AccessPrecision of morphogen gradients in neural tube development
Morphogen gradients encode positional information during development. Here the authors use theory and simulations to suggest a positional accuracy of single gradients that directly explains the observed precision of progenitor domain boundaries.
- Roman Vetter
- & Dagmar Iber
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Article
| Open AccessQuantifying pupil-to-pupil SARS-CoV-2 transmission and the impact of lateral flow testing in English secondary schools
Twice weekly mass testing using lateral flow tests has helped to control pupil-to-pupil transmission in English secondary schools. Here, the authors show that repeat testing of contacts alongside mass testing could greatly reduce absences with only a marginal increase in transmission, compared to isolating contacts.
- Trystan Leng
- , Edward M. Hill
- & Louise Dyson
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Article
| Open AccessSingle-cell gene fusion detection by scFusion
Gene fusions are an important class of mutations in tumor genomes. Here, the authors develop a single-cell gene fusion detection method scFusion and demonstrate its applications in cancer single-cell studies.
- Zijie Jin
- , Wenjian Huang
- & Ruibin Xi
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Article
| Open AccessUncovering interpretable potential confounders in electronic medical records
Randomized clinical trials are often plagued by selection bias, and expert-selected covariates may insufficiently adjust for confounding factors. Here, the authors develop a framework based on natural language processing to uncover interpretable potential confounders from text.
- Jiaming Zeng
- , Michael F. Gensheimer
- & Ross D. Shachter
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Article
| Open AccessFine-scale heterogeneity in population density predicts wave dynamics in dengue epidemics
Population density can influence the dynamics of emerging infections, but the specific effects at a local (within-city) level are not well understood. Here, the authors investigate the influence of population density on dynamics of dengue outbreaks in Rio de Janeiro and propose that this variable holds the key to how space should be aggregated.
- Victoria Romeo-Aznar
- , Laís Picinini Freitas
- & Mercedes Pascual
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Article
| Open AccessVirtual intracranial EEG signals reconstructed from MEG with potential for epilepsy surgery
Dynamic network models offer insight into brain networks affected by epileptic seizures. Here the authors derive ViEEG (virtual intracranial EEG) from non-invasive MEG recordings that show brain areas involved in seizure generation in patients with epilepsy.
- Miao Cao
- , Daniel Galvis
- & Mark J. Cook
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Article
| Open AccessT-cell dysfunction in the glioblastoma microenvironment is mediated by myeloid cells releasing interleukin-10
The tumour microenvironment counteracts immune therapy in Glioblastomas. Authors show here, using spatially resolved and single cell transcriptomics, that dysfunctional T cells are induced by a myeloid cell subset via Interleukin-10 signalling, and inhibition of the downstream JAK/STAT pathway might restore glioblastoma immune therapy responsiveness.
- Vidhya M. Ravi
- , Nicolas Neidert
- & Dieter Henrik Heiland
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Article
| Open AccessUsing language in social media posts to study the network dynamics of depression longitudinally
Depression network connectivity is a risk factor for developing depression. Here the authors show personalised networks of depression-related linguistic features were linked to network connectivity within a self-reported depressive episode.
- Sean W. Kelley
- & Claire M. Gillan
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Article
| Open AccessWhole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies
Metabolically active organelles compete for cytosolic space and resources during metabolism rewiring. Here, the authors develop a computational model of yeast metabolism and resource allocation to predict condition- and compartment-specific proteome constraints that govern metabolic strategies.
- Ibrahim E. Elsemman
- , Angelica Rodriguez Prado
- & Bas Teusink
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Article
| Open AccessA robust method for collider bias correction in conditional genome-wide association studies
Genetic associations can be biased by conditioning on a phenotype. This study presents ‘Slope-Hunter’, a method which uses model-based clustering to correct this bias, even in the presence of genetic correlation, assuming the class of SNPs affecting only the collider explains more variation in the collider than any other class of SNPs.
- Osama Mahmoud
- , Frank Dudbridge
- & Kate Tilling
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| Open AccessSystematic decomposition of sequence determinants governing CRISPR/Cas9 specificity
The sequence determinants governing CRISPR/Cas9 specificity are not fully understood. Here, the authors devise a high-throughput dual-target synthetic system to explore the sequence features associated with CRISPR/Cas9 off-target effect, reveal a set of sequence-dependent rules, and develop an off-target prediction model and a strategy for Cas9-based allele-specific editing.
- Rongjie Fu
- , Wei He
- & Han Xu
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Article
| Open AccessAdvances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data
The deconvolution of cell types is challenging in spatially-resolved transcriptomics. Here, the authors present SpatialDecon, a method for the deconvolution and quantification of cell types in spatial transcriptomics data, and show how it can be used to analyse immune response heterogeneity in cancer.
- Patrick Danaher
- , Youngmi Kim
- & Joseph M. Beechem
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| Open AccessModel-based evaluation of alternative reactive class closure strategies against COVID-19
Reactive school class closures have been widely implemented to mitigate COVID-19 outbreaks. Here, the authors show that, compared to symptom-prompted PCR testing, screening for cases in schools with antigen tests leads to greater reductions in infection rates in both students and the wider community.
- Quan-Hui Liu
- , Juanjuan Zhang
- & Marco Ajelli
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Article
| Open AccessRapid antigen testing as a reactive response to surges in nosocomial SARS-CoV-2 outbreak risk
Healthcare facilities are vulnerable to SARS-CoV-2 introductions and subsequent nosocomial outbreaks. Here, the authors simulate transmission in a long-term care facility with varying containment measures in place and evaluate reactive response with antigen rapid diagnostic testing.
- David R. M. Smith
- , Audrey Duval
- & Laura Temime
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Article
| Open AccessMaximizing response to intratumoral immunotherapy in mice by tuning local retention
Understanding the pharmacokinetics of locally-injected drugs could aid in the design of immunotherapies to maximize their therapeutic effect. Here, by evaluating different IL-2 fusion proteins, the authors show that molecular weight and matrix binding affect anti-tumor immune response and report a pharmacokinetic framework to predict response to intratumoral IL-2 therapy.
- Noor Momin
- , Joseph R. Palmeri
- & K. Dane Wittrup
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Article
| Open AccessFace detection in untrained deep neural networks
Face-selective neurons are observed in the primate visual pathway and are considered as the basis of face detection in the brain. Here, using a hierarchical deep neural network model of the ventral visual stream, the authors suggest that face selectivity arises in the complete absence of training.
- Seungdae Baek
- , Min Song
- & Se-Bum Paik
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Article
| Open AccessSimultaneous estimation of bi-directional causal effects and heritable confounding from GWAS summary statistics
Mendelian Randomization approaches are being increasingly refined, but certain statistical limitations hinder their application to GWAS. Here, the authors propose a new Mendelian Randomization method to estimate bi- directional causal effects and explicitly account for heritable confounding.
- Liza Darrous
- , Ninon Mounier
- & Zoltán Kutalik
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Article
| Open AccessThe effect of COVID-19 vaccination in Italy and perspectives for living with the virus
Vaccination campaigns against COVID-19 are allowing the progressive release of physical distancing restrictions in many countries. Here, the authors assess the impact of the vaccination program in Italy and evaluate possible prospects for reopening the society while at the same time keeping COVID-19 under control.
- Valentina Marziano
- , Giorgio Guzzetta
- & Stefano Merler
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Article
| Open AccessEmulator-based Bayesian optimization for efficient multi-objective calibration of an individual-based model of malaria
Individual-based models have become important tools in the global battle against infectious diseases, yet model complexity can make calibration challenging. Here, the authors propose a Bayesian optimization framework to calibrate a complex malaria transmission simulator.
- Theresa Reiker
- , Monica Golumbeanu
- & Melissa A. Penny
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Article
| Open AccessSARS-CoV-2 transmission across age groups in France and implications for control
In this study, Tran Kiem et al. examine the contribution of different age groups to COVID-19 transmission. Using data from the French epidemic in summer 2020, they report that while individuals aged 80 years and older are more at risk, pandemic control in the absence of vaccines required measures targeted at all age groups.
- Cécile Tran Kiem
- , Paolo Bosetti
- & Simon Cauchemez
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| Open AccessA benchmark study of simulation methods for single-cell RNA sequencing data
Simulation is useful for developing and evaluating computational methods. Here, the authors develop a comprehensive evaluation framework, SimBench, to benchmark Single-cell RNA-seq simulation methods through a diverse collection of experimental datasets.
- Yue Cao
- , Pengyi Yang
- & Jean Yee Hwa Yang
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Article
| Open AccessEcological memory preserves phage resistance mechanisms in bacteria
One might think that complete extinction of a virulent pathogen is the most effective way of saving a population. For a bacteria-phage system, Skanata and Kussell show that sustaining a minimum pathogen level is actually favorable to prevent a complete loss of immunity in the long run.
- Antun Skanata
- & Edo Kussell
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| Open AccessA model of tension-induced fiber growth predicts white matter organization during brain folding
Associations have been established between brain folding and white matter connectivity. Here the authors show that axon elongation, in response to mechanical stresses during cortical expansion and folding, may be sufficient to induce tissue remodeling consistent with white matter organization.
- Kara E. Garcia
- , Xiaojie Wang
- & Christopher D. Kroenke
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Article
| Open AccessMechanical forces drive a reorientation cascade leading to biofilm self-patterning
Bacterial biofilms exhibit complex spatiotemporal pattern formation. Here the authors report a collective cell reorientation cascade in growing Vibrio cholerae biofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure.
- Japinder Nijjer
- , Changhao Li
- & Jing Yan
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Article
| Open AccessTowards inferring nanopore sequencing ionic currents from nucleotide chemical structures
Nanopore sequencing allows users to identify nucleotide sequence from ionic currents. Here, the authors use deep learning to facilitate the de novo identification of modified nucleotides, particularly methylated cytosine and guanine, from the measured ionic currents without the need for controls.
- Hongxu Ding
- , Ioannis Anastopoulos
- & Benedict Paten
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Article
| Open AccessNetwork analysis reveals rare disease signatures across multiple levels of biological organization
Despite the clear causal relationship between genotype and phenotype in rare diseases, identifying the pathobiological mechanisms at various levels of biological organization remains a practical and conceptual challenge. Here, the authors introduce a network approach for evaluating the impact of rare gene defects across biological scales.
- Pisanu Buphamalai
- , Tomislav Kokotovic
- & Jörg Menche
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| Open AccessPotential global impacts of alternative dosing regimen and rollout options for the ChAdOx1 nCoV-19 vaccine
The ChAdOx1 nCoV-19 vaccine requires two doses, but under limited supply single dose regimens have also been considered. Here, the authors show using static transmission modelling that under certain conditions it is optimal to more expediently administer a single dose to a larger proportion of the population.
- Ricardo Aguas
- , Anouska Bharath
- & Rima Shretta
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Article
| Open AccessThe generative capacity of probabilistic protein sequence models
Generative models have become increasingly popular in protein design, yet rigorous metrics that allow the comparison of these models are lacking. Here, the authors propose a set of such metrics and use them to compare three popular models.
- Francisco McGee
- , Sandro Hauri
- & Allan Haldane
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Article
| Open AccessThe impact of the timely birth dose vaccine on the global elimination of hepatitis B
The timely hepatitis B birth dose vaccination is recommended for all new-borns by the WHO, but coverage is inconsistent. Here, the authors model the impact of scaling-up coverage in 110 low and middle income countries and assess how it may be affected by delays for example caused by the COVID-19 pandemic.
- Margaret J. de Villiers
- , Shevanthi Nayagam
- & Timothy B. Hallett
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| Open AccessDesigning the bioproduction of Martian rocket propellant via a biotechnology-enabled in situ resource utilization strategy
Returning from Mars to Earth requires propellant. The authors propose a biotechnology-enabled in situ resource utilization (bioISRU) process to produce a Mars specific rocket propellant, 2,3-butanediol, using cyanobacteria and engineered E. coli, with lower payload mass and energy usage compared to chemical ISRU strategies.
- Nicholas S. Kruyer
- , Matthew J. Realff
- & Pamela Peralta-Yahya
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Article
| Open AccessBayesian log-normal deconvolution for enhanced in silico microdissection of bulk gene expression data
Deconvolution methods reveal individual cell types in complex tissues profiled by bulk methods. Here the authors present a Bayesian deconvolution method that outperforms existing methods when benchmarked on >700 datasets, especially in estimating cell-type-specific gene expression profiles.
- Bárbara Andrade Barbosa
- , Saskia D. van Asten
- & Yongsoo Kim
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Article
| Open AccessGenome-wide detection of cytosine methylations in plant from Nanopore data using deep learning
Existing methods cannot profile genome-wide cytosine DNA methylations (5mCs) in all three contexts with acceptable accuracy. Here, the authors develop a deep learning tool to detect genome-wide 5mCs of all three contexts in plants with high accuracy from Nanopore reads.
- Peng Ni
- , Neng Huang
- & Jianxin Wang
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Article
| Open AccessNationwide rollout reveals efficacy of epidemic control through digital contact tracing
The effectiveness of digital contact tracing for COVID-19 control remains uncertain. Here, the authors use data from the Smittestopp app, used in Norway in spring 2020, and estimate that 80% of nearby devices were detected by the app, and at least 11% of close contacts were not visible to manual contact tracing.
- Ahmed Elmokashfi
- , Joakim Sundnes
- & Olav Lysne
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Article
| Open AccessEfficient and precise single-cell reference atlas mapping with Symphony
The number of single-cell RNA-seq datasets generated is increasing rapidly, making methods that map cell types to well-curated references increasingly important. Here, the authors propose an accurate method for mapping single cells onto a reference atlas in seconds.
- Joyce B. Kang
- , Aparna Nathan
- & Soumya Raychaudhuri
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Article
| Open AccessGeographical drivers and climate-linked dynamics of Lassa fever in Nigeria
Lassa Fever is a rodent-borne viral haemorrhagic fever that is a public health problem in West Africa. Here, the authors develop a spatiotemporal model of the socioecological drivers of disease using surveillance data from Nigeria, and find evidence of climate sensitivity.
- David W. Redding
- , Rory Gibb
- & Chikwe Ihekweazu
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Article
| Open AccessPossible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics
Understanding the potential impacts of new variants of SARS-CoV-2 is important for pandemic planning. Here, the authors develop a model incorporating hypothetical new variants with varying transmissibility and immune evasion properties, and use it to project possible future epidemic waves in the UK.
- Louise Dyson
- , Edward M. Hill
- & Matt J. Keeling
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Article
| Open AccessDynamic memory to alleviate catastrophic forgetting in continual learning with medical imaging
In clinical practice, the continuous progress of image acquisition technology or diagnostic procedures and evolving imaging protocols hamper the utility of machine learning, as prediction accuracy on new data deteriorates. Here, the authors propose a continual learning approach to deal with such domain shifts occurring at unknown time points.
- Matthias Perkonigg
- , Johannes Hofmanninger
- & Georg Langs
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Article
| Open AccessVEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics
Developing interpretable models is a major challenge in single cell deep learning. Here we show that the VEGA variational autoencoder model, whose decoder wiring mirrors gene modules, can provide direct interpretability to the latent space further enabling the inference of biological module activity.
- Lucas Seninge
- , Ioannis Anastopoulos
- & Joshua Stuart
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Article
| Open AccessMapping the glycosyltransferase fold landscape using interpretable deep learning
Glycosyltransferases (GT) are proteins that display extensive sequence and functional variation on a subset of 3D folds. Here, the authors use interpretable deep learning to predict 3D folds from sequence without the need for sequence alignment, which also enables the prediction of GTs with new folds.
- Rahil Taujale
- , Zhongliang Zhou
- & Natarajan Kannan
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Article
| Open AccessModelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape
Rift Valley fever is a zoonotic haemorrhagic fever with complex transmission dynamics influenced by environmental variables and animal movements. Here, the authors develop a metapopulation model incorporating these factors and use it to identify the main drivers of transmission in the Comoros archipelago.
- Warren S. D. Tennant
- , Eric Cardinale
- & Raphaëlle Métras
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Article
| Open AccessGeneralized and scalable trajectory inference in single-cell omics data with VIA
Scalable trajectory inference for multi-omic single cell datasets is challenging in terms of capturing non-tree complex topologies. Here the authors present a method, VIA, that scales to millions of cells across multiple omic modalities using lazy-teleporting random walks.
- Shobana V. Stassen
- , Gwinky G. K. Yip
- & Kevin K. Tsia