Swapnil Mishra
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View article: Differential gut transmission of IncP plasmid clades involving hypervirulent Klebsiella pneumoniae reveals plasmid-specific ecological adaptation
Differential gut transmission of IncP plasmid clades involving hypervirulent Klebsiella pneumoniae reveals plasmid-specific ecological adaptation Open
Conjugative plasmids can drive the global spread of antimicrobial resistance (AMR) in Enterobacterales. Hypervirulent Klebsiella pneumoniae (hvKp) increasingly acquire AMR plasmids, raising concern about convergent hypervirulent drug-resis…
View article: Incorporating human mobility to enhance epidemic response and estimate real-time reproduction numbers
Incorporating human mobility to enhance epidemic response and estimate real-time reproduction numbers Open
Human mobility plays a critical role in the transmission dynamics of infectious diseases, influencing both their spread and the effectiveness of control measures. In the process of quantifying the real-time situation of an epidemic, the in…
View article: The Role of Climate Change in the Expansion of Dengue
The Role of Climate Change in the Expansion of Dengue Open
Climate change-related weather and extreme events are increasing in intensity and frequency, affecting infectious disease transmission globally. Dengue, a climate-sensitive vector-borne disease, to which over half the world’s population is…
View article: Host-pathogen network and eco-evolutionary drivers of avian influenza transmission in wild birds
Host-pathogen network and eco-evolutionary drivers of avian influenza transmission in wild birds Open
View article: Dengue transmission heterogeneity across Indonesia’s archipelago: climate-driven spatiotemporal patterns and policy implications
Dengue transmission heterogeneity across Indonesia’s archipelago: climate-driven spatiotemporal patterns and policy implications Open
Indonesia is the country with the highest dengue burden in Southeast Asia, with 488 of 514 districts reporting dengue cases annually across its 17,000-island archipelago. Despite the substantial dengue burden, spatiotemporal transmission p…
View article: Robert Verity, Anne Cori, Swapnil Mishra, Seth Flaxman and Samir Bhatt's contribution to the Discussion of “Some statistical aspects of the Covid-19 response” by Wood <i>et al</i>
Robert Verity, Anne Cori, Swapnil Mishra, Seth Flaxman and Samir Bhatt's contribution to the Discussion of “Some statistical aspects of the Covid-19 response” by Wood <i>et al</i> Open
View article: Evaluating Age-Dependent Transmission and Vaccination Policy in Singapore’s SARS-CoV-2 Epidemic: A Computational Modelling Approach
Evaluating Age-Dependent Transmission and Vaccination Policy in Singapore’s SARS-CoV-2 Epidemic: A Computational Modelling Approach Open
The SARS-CoV-2 pandemic in Singapore revealed pronounced age-specific differences in disease transmission and severity. To investigate these dynamics, we developed a semi-mechanistic Bayesian hierarchical model that jointly estimated SARS-…
View article: Sub-consensus haploid variant calling in Long-read sequencing technology
Sub-consensus haploid variant calling in Long-read sequencing technology Open
Background Next-generation sequencing (NGS) has become crucial in epidemiology, particularly for tracking viral evolution during outbreaks. While Oxford Nanopore Technologies (ONT) sequencing has gained popularity due to its long-read capa…
View article: Addressing survey fatigue bias in longitudinal social contact studies to improve pandemic preparedness
Addressing survey fatigue bias in longitudinal social contact studies to improve pandemic preparedness Open
Social contact surveys are an important tool to assess infection risks within populations, and the effect of non-pharmaceutical interventions on social behaviour during disease outbreaks, epidemics, and pandemics. Numerous longitudinal soc…
View article: Estimating dengue force of infection from age-stratified surveillance data in Java, Indonesia
Estimating dengue force of infection from age-stratified surveillance data in Java, Indonesia Open
Targeted dengue interventions require reliable estimates of transmission intensity and population immunity at the local level. The force of infection (FOI) provides an objective measure of transmission intensity, but its estimation traditi…
View article: Estimating the worst-case scenario for malaria parasite rate in sub-Saharan Africa
Estimating the worst-case scenario for malaria parasite rate in sub-Saharan Africa Open
Malaria remains a leading cause of morbidity and mortality worldwide, with sub-Saharan Africa bearing the highest burden. Stalled progress under an inadequate budget and the expectation that funding would be further constrained [1, 2] call…
View article: Incorporating human mobility to enhance epidemic response and estimate real-time reproduction numbers
Incorporating human mobility to enhance epidemic response and estimate real-time reproduction numbers Open
Human mobility plays a critical role in the transmission dynamics of infectious diseases, influencing both their spread and the effectiveness of control measures. In the process of quantifying the real-time situation of an epidemic, the in…
View article: Exploring the potential and limitations of deep learning and explainable AI for longitudinal life course analysis
Exploring the potential and limitations of deep learning and explainable AI for longitudinal life course analysis Open
Background Understanding the complex interplay between life course exposures, such as adverse childhood experiences and environmental factors, and disease risk is essential for developing effective public health interventions. Traditional …
View article: Exploring the Potential and Limitations of Deep Learning and Explainable AI for Longitudinal Life Course Analysis
Exploring the Potential and Limitations of Deep Learning and Explainable AI for Longitudinal Life Course Analysis Open
Background: Understanding the complex interplay between life course exposures, such as adverse childhood experiences and environmental factors, and disease risk is essential for developing effective public health interventions. Traditional…
View article: Evidential time-to-event prediction with calibrated uncertainty quantification
Evidential time-to-event prediction with calibrated uncertainty quantification Open
View article: National investment case development for pathogen genomics
National investment case development for pathogen genomics Open
View article: Genetic diversity of Indian Bacillus thuringiensis isolates through a comparative study of ARDRA and 16S rRNA sequencing methods
Genetic diversity of Indian Bacillus thuringiensis isolates through a comparative study of ARDRA and 16S rRNA sequencing methods Open
View article: Ethnicity and anthropometric deficits in children: A cross-sectional analysis of national survey data from 18 countries in sub-Saharan Africa
Ethnicity and anthropometric deficits in children: A cross-sectional analysis of national survey data from 18 countries in sub-Saharan Africa Open
Child anthropometric deficits remain a major public health problem in Sub-Saharan Africa (SSA) and are a key target of the UN Sustainable Development Goals (SDGs). The SDGs recommend disaggregation of health indicators by ethnic group. How…
View article: Towards pandemic preparedness: ability to estimate high-resolution social contact patterns from longitudinal surveys
Towards pandemic preparedness: ability to estimate high-resolution social contact patterns from longitudinal surveys Open
Social contact surveys are an important tool to assess infection risks within populations, and the effect of non-pharmaceutical interventions on social behaviour during disease outbreaks, epidemics, and pandemics. Numerous longitudinal soc…
View article: Uncertainty-Aware Regression for Socio-Economic Estimation via Multi-View Remote Sensing
Uncertainty-Aware Regression for Socio-Economic Estimation via Multi-View Remote Sensing Open
Remote sensing imagery offers rich spectral data across extensive areas for Earth observation. Many attempts have been made to leverage these data with transfer learning to develop scalable alternatives for estimating socio-economic condit…
View article: Evidential time-to-event prediction model with well-calibrated uncertainty estimation
Evidential time-to-event prediction model with well-calibrated uncertainty estimation Open
Time-to-event analysis, or Survival analysis, provides valuable insights into clinical prognosis and treatment recommendations. However, this task is typically more challenging than other regression tasks due to the censored observations. …
View article: Towards pandemic preparedness: ability to estimate high-resolution social contact patterns from longitudinal surveys
Towards pandemic preparedness: ability to estimate high-resolution social contact patterns from longitudinal surveys Open
Social contact surveys are an important tool to assess infection risks within populations, and the effect of non-pharmaceutical interventions on social behaviour during disease outbreaks, epidemics, and pandemics. Numerous longitudinal soc…
View article: KidSat: satellite imagery to map childhood poverty dataset and benchmark
KidSat: satellite imagery to map childhood poverty dataset and benchmark Open
Satellite imagery has emerged as an important tool to analyse demographic, health, and development indicators. While various deep learning models have been built for these tasks, each is specific to a particular problem, with few standard …
View article: The interaction of disease transmission, mortality, and economic output over the first 2 years of the COVID-19 pandemic
The interaction of disease transmission, mortality, and economic output over the first 2 years of the COVID-19 pandemic Open
Background The COVID-19 pandemic has caused over 7.02 million deaths as of January 2024 and profoundly affected most countries’ Gross Domestic Product (GDP). Here, we study the interaction of SARS-CoV-2 transmission, mortality, and economi…
View article: Differential responses of SARS-CoV-2 variants to environmental drivers during their selective sweeps
Differential responses of SARS-CoV-2 variants to environmental drivers during their selective sweeps Open
Previous work has shown that environmental variables affect SARS-CoV-2 transmission, but it is unclear whether different strains show similar environmental responses. Here we leverage genetic data on the transmission of three (Alpha, Delta…
View article: Comparative impact assessment of COVID-19 policy interventions in five South Asian countries using reported and estimated unreported death counts during 2020-2021
Comparative impact assessment of COVID-19 policy interventions in five South Asian countries using reported and estimated unreported death counts during 2020-2021 Open
There has been raging discussion and debate around the quality of COVID death data in South Asia. According to WHO, of the 5.5 million reported COVID-19 deaths from 2020-2021, 0.57 million (10%) were contributed by five low and middle inco…
View article: Life course analysis using deep learning approaches: a simulation study
Life course analysis using deep learning approaches: a simulation study Open
Life course theory seeks to explain the cause of negative health outcomes in an individual’s life through intricate interactions between different exposure events. The methodology used in life course theory requires longitudinal cohort dat…
View article: Cumulative sleep restriction and subsequent recovery sleep: Effects on subjective sleepiness, vigilance, and executive functions
Cumulative sleep restriction and subsequent recovery sleep: Effects on subjective sleepiness, vigilance, and executive functions Open
Objective: Cumulative partial sleep loss is more often practical eventually among aircrew. The sleep loss encountered on the weekdays is generally compensated by taking restorative sleep on the weekends. This study aimed to examine the sub…
View article: Ethnicity and anthropometric deficits in children: a cross-sectional analysis of national survey data from 18 countries in sub-Saharan Africa
Ethnicity and anthropometric deficits in children: a cross-sectional analysis of national survey data from 18 countries in sub-Saharan Africa Open
Background Anthropometric deficits persist in sub-Saharan Africa (SSA) despite sustained improvements in nutrition, disease burden and living conditions. The UN Sustainable Development Goals advocate for disaggregation of health indicators…
View article: Application of referenced thermodynamic integration to Bayesian model selection
Application of referenced thermodynamic integration to Bayesian model selection Open
Evaluating normalising constants is important across a range of topics in statistical learning, notably Bayesian model selection. However, in many realistic problems this involves the integration of analytically intractable, high-dimension…