Computational models

  • Article
    | Open Access

    Disentangling the impacts of non-pharmaceutical interventions on COVID-19 transmission is challenging as they have been used in different combinations across time and space. This study shows that, early in the epidemic, school/daycare closures and stopping nursing home visits were associated with the biggest reduction in transmission in the United States.

    • Bingyi Yang
    • , Angkana T. Huang
    •  & Derek A. T. Cummings
  • Article
    | Open Access

    Population-based surveys are the gold standard for estimating seroprevalence but are expensive and often only capture a small geographic area or window of time. This study describes a new platform, SCALE-IT, for serosurveillance based on algorithmic sampling of electronic health records, and uses it to estimate the seroprevalence of SARS-CoV-2 in San Francisco.

    • Isobel Routledge
    • , Adrienne Epstein
    •  & Isabel Rodriguez-Barraquer
  • Article
    | Open Access

    Technical advancements have significantly improved early diagnosis of cervical cancer, but accurate diagnosis is still difficult due to various practical factors. Here, the authors develop an artificial intelligence assistive diagnostic solution to improve cervical liquid-based thin-layer cell smear diagnosis according to clinical TBS criteria in a large multicenter study.

    • Xiaohui Zhu
    • , Xiaoming Li
    •  & Yanqing Ding
  • Article
    | Open Access

    Non-coding RNA function is poorly understood, partly due to the challenge of determining RNA secondary (2D) structure. Here, the authors present a framework for the reproducible prediction and visualization of the 2D structure of a wide array of RNAs, which enables linking RNA sequence to function.

    • Blake A. Sweeney
    • , David Hoksza
    •  & Anton I. Petrov
  • Article
    | Open Access

    Many job sectors classified as ‘essential’ have continued operating with limited restrictions during the COVID-19 pandemic, potentially placing workers at higher risk of infection. Here, the authors show that seropositivity rates in workers vary widely across and between job sectors in Geneva, Switzerland.

    • Silvia Stringhini
    • , María-Eugenia Zaballa
    •  & Idris Guessous
  • Article
    | Open Access

    Allele-specific expression in diploid organisms can be quantified by RNA-seq and it is common practice to rely on a single library. Here, the authors show that the standard approach has variable error rate and present Qllelic as a tool to improve reproducibility of allele-specific RNA-seq analysis.

    • Asia Mendelevich
    • , Svetlana Vinogradova
    •  & Alexander A. Gimelbrant
  • Article
    | Open Access

    Single-cell RNA-Seq allows us to observe snapshots of how biological systems change over time at cellular resolution. Here, the authors develop a generative framework that uses time-resolved single-cell data to model how cells change in physical time, including in response to perturbations.

    • Grace Hui Ting Yeo
    • , Sachit D. Saksena
    •  & David K. Gifford
  • Article
    | Open Access

    Multi-layered epigenetic regulation in higher eukaryotes makes it challenging to disentangle the individual effects of modifications on chromatin structure and function. Here, the authors expressed mammalian DNA methyltransferases in yeast, which have no DNA methylation, to show that methylation has intrinsic effects on chromatin structure.

    • Diana Buitrago
    • , Mireia Labrador
    •  & Modesto Orozco
  • Article
    | Open Access

    Association analyses that capture rare and noncoding variants in whole genome sequencing data are limited by factors like statistical power. Here, the authors present KnockoffScreen, a statistical method using the knockoff framework to detect, localise and prioritise rare and common risk variants at genome-wide scale.

    • Zihuai He
    • , Linxi Liu
    •  & Iuliana Ionita-Laza
  • Article
    | Open Access

    Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures, with enormous societal and economic costs. Here, the authors demonstrate the feasibility of a test-trace-quarantine strategy using an agent-based model and detailed data on the Seattle region.

    • Cliff C. Kerr
    • , Dina Mistry
    •  & Daniel J. Klein
  • Article
    | Open Access

    Predicting RNA structure from sequence is challenging due to the relative sparsity of experimentally-determined RNA 3D structures for model training. Here, the authors propose a way to incorporate knowledge on interactions at the atomic and base–base level to refine the prediction of RNA structures.

    • Peng Xiong
    • , Ruibo Wu
    •  & Yaoqi Zhou
  • Article
    | Open Access

    AIM2-ASC inflammasomes are filamentous signalling platforms that play a central role in host innate defence. Here, the authors present the filament cryo-EM structure of the inflammasome receptor AIM2, which is very similar to the adaptor ASC filament structure. By employing Rosetta and Molecular Dynamics simulations the authors provide further insights into the directionality and recognition mechanisms of the individual AIM2 and ASC filaments, which is further validated with biochemical and cellular experiments.

    • Mariusz Matyszewski
    • , Weili Zheng
    •  & Jungsan Sohn
  • Article
    | Open Access

    Several prognostic indices are available to predict the long-term fate of emerging infectious diseases and the effect of their containment measures, including a variety of reproduction numbers. Here, the authors introduce the epidemicity index, a complementary index to evaluate the potential for transient increases of SARS-Cov-2 epidemics.

    • Lorenzo Mari
    • , Renato Casagrandi
    •  & Marino Gatto
  • Article
    | Open Access

    Karyotyping of cancer genomes at the base-level is technically challenging. Here, the authors introduce InfoGenomeR, an algorithm that can infer cancer genome karyotypes from whole-genome sequencing data, and test their model on breast, ovarian and brain cancer samples; and identify private and shared mutations between primary and metastatic cancer samples.

    • Yeonghun Lee
    •  & Hyunju Lee
  • Article
    | Open Access

    The ability to design functional sequences is central to protein engineering and biotherapeutics. Here the authors introduce a deep generative alignment-free model for sequence design applied to highly variable regions and design and test a diverse nanobody library with improved properties for selection experiments.

    • Jung-Eun Shin
    • , Adam J. Riesselman
    •  & Debora S. Marks
  • Article
    | Open Access

    Functional RNA secondary structure is important for the pre-mRNA processing including splicing, cleavage and polyadenylation, and RNA editing. Here the authors present a catalog of conserved long-range RNA structures in the human transcriptome by defining pairs of conserved complementary regions (PCCR) in pre-aligned evolutionarily conserved regions.

    • Svetlana Kalmykova
    • , Marina Kalinina
    •  & Dmitri Pervouchine
  • Article
    | Open Access

    Methods for profiling differences between individual cells are constantly expanding. Here, the authors present a computational framework for the analysis of chromatin accessibility data at the single-cell level that takes into account previous knowledge and data-specific characteristics.

    • Shengquan Chen
    • , Guanao Yan
    •  & Zhixiang Lin
  • Article
    | Open Access

    Likelihood optimization in phylogenetic tree reconstruction is computationally intensive, especially as the number of sequences and taxa included increase. Here, Azouri et al. show how an artificial intelligence approach can reduce computational time without losing accuracy of tree inference.

    • Dana Azouri
    • , Shiran Abadi
    •  & Tal Pupko
  • Article
    | Open Access

    Many countries have closed schools as part of their COVID-19 response. Here, the authors model SARS-CoV-2 transmission on a network of schools and households in England, and find that risk of transmission between schools is lower if primary schools are open than if secondary schools are open.

    • James D. Munday
    • , Katharine Sherratt
    •  & Sebastian Funk
  • Article
    | Open Access

    COVID-19 has caused many healthcare systems to become overwhelmed, potentially impacting patient care. Here, the authors show that COVID-19-related in-hospital mortality rates in Israel increased in periods of moderate or high hospital load, independent of patient characteristics.

    • Hagai Rossman
    • , Tomer Meir
    •  & Malka Gorfine
  • Article
    | Open Access

    Application of the control usually requires complete knowledge of the system, which is rare for biological networks characterized by uncertainty. Klickstein et al. propose an optimal control for uncertain systems represented by network ensembles where only weight distributions for edges are known.

    • Isaac Klickstein
    •  & Francesco Sorrentino
  • Article
    | Open Access

    Single-cell RNA-Seq suffers from heterogeneity in sequencing sparsity and complex differential patterns in gene expression. Here, the authors introduce a graph neural network based on a hypothesis-free deep learning framework as an effective representation of gene expression and cell–cell relationships.

    • Juexin Wang
    • , Anjun Ma
    •  & Dong Xu
  • Article
    | Open Access

    Phylogeographic analyses can provide broad descriptions of the spread of pathogens between populations, but are limited by incomplete sampling. Here, the authors develop an inference framework that reconstructs sequential transmission events and use it to characterise dynamics of dengue in Thailand.

    • Henrik Salje
    • , Amy Wesolowski
    •  & Derek A. T. Cummings
  • Article
    | Open Access

    Transcription factor over-expression-based cellular conversion methods often endure low conversion efficiency. Here the authors show how to increase conversion efficiency by combining a computational method for prioritizing more efficient TF combinations with a transposon-based genomic integration system for delivery.

    • Sascha Jung
    • , Evan Appleton
    •  & Antonio del Sol
  • Article
    | Open Access

    The role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. Here, the authors use an age-structured transmission model fitted to age-specific seroprevalence and hospital admission data to assess the effects of school-based measures during the COVID-19 pandemic in the Netherlands.

    • Ganna Rozhnova
    • , Christiaan H. van Dorp
    •  & Mirjam E. Kretzschmar
  • Article
    | Open Access

    Malaria transmission-blocking vaccines are in development, but roll-out strategies have not been assessed. Here, the authors show that transmission-blocking activity is likely to be higher in the field than in laboratory conditions, and that school-aged children are an important group to target.

    • Joseph D. Challenger
    • , Daniela Olivera Mesa
    •  & Thomas S. Churcher
  • Article
    | Open Access

    Our understanding of the function of many transcripts is still incomplete, limiting the interpretability of transcriptomic data. Here the authors use consensus-independent component analysis, together with a guilt-by-association approach, to improve the prediction of gene function.

    • Carlos G. Urzúa-Traslaviña
    • , Vincent C. Leeuwenburgh
    •  & Rudolf S. N. Fehrmann
  • Article
    | Open Access

    Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. Here, the authors propose an ecology-based computational method to predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome.

    • Akshit Goyal
    • , Tong Wang
    •  & Sergei Maslov
  • Article
    | Open Access

    The selection of a small set of cellular labels to distinguish a subpopulation of cells from a complex mixture is an important task in cell biology. Here the authors propose a method for supervised genetic marker selection using linear programming and provides a Python package scGeneFit that implements this approach.

    • Bianca Dumitrascu
    • , Soledad Villar
    •  & Barbara E. Engelhardt
  • Article
    | Open Access

    Kinases drive fundamental changes in cell state, but predicting kinase activity based on substrate-level changes can be challenging. Here the authors introduce a computational framework that utilizes similarities between substrates to robustly infer kinase activity.

    • Serhan Yılmaz
    • , Marzieh Ayati
    •  & Mehmet Koyutürk
  • Article
    | Open Access

    Social distancing policies aiming to reduce COVID-19 transmission have been reflected in reductions in human mobility. Here, the authors show that reduced mobility is correlated with decreased transmission, but that this relationship weakened over time as social distancing measures were relaxed.

    • Pierre Nouvellet
    • , Sangeeta Bhatia
    •  & Christl A. Donnelly
  • Article
    | Open Access

    The role of children in the spread of COVID-19 is not fully understood, and the circumstances under which schools should be opened are therefore debated. Here, the authors demonstrate protocols by which schools in France can be safely opened without overwhelming the healthcare system.

    • Laura Di Domenico
    • , Giulia Pullano
    •  & Vittoria Colizza
  • Article
    | Open Access

    Metabolites are indicators of health and disease; genetic studies can reveal variants influencing their levels. Here, the authors investigate the contribution of rare, exonic variants on the levels of urine metabolites and generate predictions on metabolic consequences underlying metabolic disease.

    • Yurong Cheng
    • , Pascal Schlosser
    •  & Anna Köttgen
  • Article
    | Open Access

    Human mobility plays a central role in the spread of infectious diseases and can help in forecasting incidence. Here the authors show a comparison of multiple mobility benchmarks in forecasting influenza, and demonstrate the value of a machine-learned mobility map with global coverage at multiple spatial scales.

    • Srinivasan Venkatramanan
    • , Adam Sadilek
    •  & Madhav Marathe
  • Article
    | Open Access

    Spread of SARS-CoV-2 in the early phase of the pandemic has been driven by high population susceptibility, but virus sensitivity to climate may play a role in future outbreaks. Here, the authors simulate SARS-CoV-2 dynamics in winter assuming climate dependence is similar to an endemic coronavirus strain.

    • Rachel E. Baker
    • , Wenchang Yang
    •  & Bryan T. Grenfell
  • Article
    | Open Access

    Genomic prediction of phenotype may be improved by using DNA mutations with functional, evolutionary, and pleiotropic consequences. Here the authors describe a method for genome-wide fine-mapping of QTLs and develop a genotyping array for improved prediction of genetic values for cattle traits.

    • Ruidong Xiang
    • , Iona M. MacLeod
    •  & Michael E. Goddard
  • Article
    | Open Access

    Aberrant splicing is a major contributor to rare disease, but detection accuracy using current methods is limited. Here, the authors develop an algorithm that detects aberrant splicing and intron retention events from RNA-seq data and apply it to diagnosis in mitochondrial disease.

    • Christian Mertes
    • , Ines F. Scheller
    •  & Julien Gagneur