COVID-19

Scientists and engineers worldwide continue to fight the COVID-19 pandemic. Here are some examples of their work in epidemiology, diagnostics, and public health.

COVID-19 Research and Development with MATLAB and Simulink

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Early Th2 inflammation in the upper respiratory mucosa as a predictor of severe COVID-19 and modulation by early treatment with inhaled corticosteroids: a mechanistic analysis

Jonathan R. Baker et al, Respiratory Medicine, April 7 2022
paper

SARS-CoV-2 infection results in immune responses in the respiratory tract and peripheral blood that suggest mechanisms of disease severity

Wuji Zhang et al, Nature Communications, May 19 2022
paper

Sex differences in global metabolomic profiles of COVID-19 patients

Rocio Diaz Escarcega et al, Cell Death & Disease, May 14 2022
paper

Multivariate profile and acute-phase correlates of cognitive deficits in a COVID-19 hospitalised cohort

Adam Hampshire et al, eClinical Medicine, April 28 2020
paper

Maternal psychological distress during the COVID-19 pandemic and structural changes of the human fetal brain

Yan-Chiao Lu et al, Nature: Communications Medicine, May 26 2022
paper, MATLAB code

An efficient nonstandard computer method to solve a compartmental epidemiological model for COVID-19 with vaccination and population migration

Jorge E. Herrera-Serrano et al, Computer Methods and Programs in Biomedicine, June 2022
paper, MATLAB code (Appendix A)

Remotely Monitoring COVID-19 Patient Health Condition Using Metaheuristics Convolute Networks from IoT-Based Wearable Device Health Data

Mustafa Musa Jaber et al, Sensors, February 5 2022
paper

Systematic evaluating and modeling of SARS-CoV-2 UVC disinfection

Sebastian Freeman et al, Nature: Scientific Reports, April 7 2022
paper

Systemic inflammatory syndrome in COVID-19–SISCoV study: systematic review and meta-analysis

Debjyoti Dhar et al, Pediatric Research, May 18 2021
paper

Functional and microstructural brain abnormalities, fatigue, and cognitive dysfunction after mild COVID-19

Lucas Scardua Silva et al, medRxiv, December 6 2021
preprint and SPM software

SARS-CoV-2 virus transfers to skin through contact with contaminated solids

Saeed Behzadinasab et al, Nature: Scientific Reports, November 24 2021
paper

Mathematical modeling of COVID-19 transmission dynamics between healthcare workers and community

Lemjini Masandawa et al, Results in Physics, September 6 2021
paper

Characterization of the Second Wave of COVID-19 in India

Rajesh Ranjan et al, medRxiv, May 2 2021
paper preprint

Smartphone science: apps test and track infectious diseases

Sandeep Ravindran, Nature, May 10 2021
paper

COVID-19 pathophysiology may be driven by an imbalance in the renin-angiotensin-aldosterone system

Susanne Rysz et al, Nature Communications, April 23 2021
paper

Modelling personal cautiousness during the COVID-19 pandemic: a case study for Turkey and Italy

Hatice Bulut et al, Nonlinear Dyn, February 20 2021
paper

A novel methodology for epidemic risk assessment of COVID-19 outbreak

A. Pluchino et al, Nature: Scientific Reports, March 5 2021
paper

Toolbox to simulate and mitigate COVID-19 propagation

Zahrate El Oula Frihi et al, SoftwareX, June 2021
paper and GitHub MATLAB code repo

Mathematical model of COVID-19 intervention scenarios for São Paulo—Brazil

Osmar Pinto Neto et al, Nature Communications, January 18 2021
paper and Zenodo code

An extended Weight Kernel Density Estimation model forecasts COVID-19 onset risk and identifies spatiotemporal variations of lockdown effects in China

Wenzhong Shi et al, Communications Biology, 2021
paper and Zenodo code

MSC-NTF (NurOwn^®) exosomes: a novel therapeutic modality in the mouse LPS-induced ARDS model

Haggai Kaspi et al, Stem Cell Research & Therapy, January 19 2021
paper

Forecasting of medical equipment demand and outbreak spreading based on deep long short‑term memory network: the COVID‑19 pandemic in Turkey

Erdinç Koç and Muammer Türkoğlu, Signal, Image and Video Processing, September 8 2020
paper

Retinal findings in patients with COVID-19: Results from the SERPICO-19 study

Alessandro Invernizzi et al, The Lancet, September 20 2020
paper with ARIA - retinal vessel analysis MATLAB code

Modeling Social Distancing Strategies to Prevent SARS-CoV-2 Spread in Israel: A Cost-Effectiveness Analysis

Amir Shlomai et al, Value in Health, December 9 2020
paper

Fast detection of SARS-CoV-2 RNA via the integration of plasmonic thermocycling and fluorescence detection in a portable device

Jiyong Cheong et al, Nature Biomedical Engineering, December 3 2020
paper

In-host Mathematical Modelling of COVID-19 in Humans

Esteban A. Hernandez-Vargas and Jorge X. Velasco-Hernandez, Annual Reviews in Control, September 30 2020
paper

Immune responses to SARS-CoV-2 in three children of parents with symptomatic COVID-19

Shidan Tosif et al, Nature Communications, November 11 2020
paper

Testing sewage to home in on Covid-19

Scott Murray, Institute for Data, Systems, and Society, October 28, 2020
article, paper with MATLAB code

The geography of COVID-19 spread in Italy and implications for the relaxation of confinement measures

Enrico Bertuzzo et al, Nature, August 26 2020
paper

Second Version of a COVID-19 Simulator

Cleve Moler, Cleve's Corner, March 29, 2020
blog post and MATLAB code and app

Evidence for content-dependent timing of real-life events during COVID-19 crisis

Keren Taub et al, Scientific Reports, June 2 2022
paper

Application of genetic algorithm combined with improved SEIR model in predicting the epidemic trend of COVID-19, China

Zhenzhen Qiu et al, Scientific Reports, May 26 2022
paper

HIV and COVID-19 co-infection: A mathematical model and optimal control

N. Ringa et al, Informatics in Medicine Unlocked, 2022
paper

COVID-DeepPredictor: Recurrent Neural Network to Predict SARS-CoV-2 and Other Pathogenic Viruses

Indrajit Saha et al, Frontiers in Genetics, February 11 2021
paper and MATLAB code

Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function

Sk. Sarif Hassan et al, International Journal of Biological Macromolecules, January 1 2022
paper and related article

Cognitive deficits in people who have recovered from COVID-19

Adam Hampshire et al, EClinical Medicine, July 22 2021
paper

Modeling serological testing to inform relaxation of social distancing for COVID-19 control

Alicia N. M. Kraay et al, Nature Communications, December 3 2021
paper and MATLAB code

Transmission of SARS-CoV-2 during air travel: a descriptive and modelling study

Jinjun Zhang et al, Infectious Diseases, August 31 2021
paper

ANFIS-Net for automatic detection of COVID-19

Afnan Al-ali et al, Nature: Scientific Reports, August 27 2021
paper

Temporal Dynamics of COVID-19 Outbreak and Future Projections: A Data-Driven Approach

Rajesh Ranjan, Transactions of the Indian National Academy of Engineering, June 6 2020
paper

Face masks effectively limit the probability of SARS-CoV-2 transmission

Yafang Cheng et al, Science, May 20 2021
paper, MATLAB code and data

Modeling vaccination rollouts, SARS-CoV-2 variants and the requirement for non-pharmaceutical interventions in Italy

Giulia Giordano et al, Nature Medicine, April 16 2021
paper

Cognitive impairment and altered cerebral glucose metabolism in the subacute stage of COVID-19

Jonas A Hosp et al, BRAIN: A Journal of Neurology, April 3 2021
paper

Real-time tracking and prediction of COVID-19 infection using digital proxies of population mobility and mixing

Kathy Leung et al, Nature Communications, March 8 2021
paper

Modelling uncertainty in the relative risk of exposure to the SARS-CoV-2 virus by airborne aerosol transmission in well mixed indoor air

Benjamin Jones et al, Building and Environment, March 15 2021
paper

COVID-19 intervention models: An initial aggressive treatment strategy for controlling the infection

Bismark Oduro and Vusi Mpendulo Magagula, Infect Dis Model, January 23 2021
paper

Controlling COVID-19 Outbreaks with Financial Incentives

Chaeyoung Lee et al, International Journal of Environmental Research and Public Health, January 15 2021
paper

The optimal lockdown intensity for COVID-19

Jonathan P. Caulkins et al, Journal of Mathematical Economics, February 3 2021
paper

Electricity demand during pandemic times: The case of the COVID-19 in Spain

I. Santiago et al, Energy Policy, January 2021
paper

Optimal COVID-19 quarantine and testing strategies

Chad R. Wells et al, Nature Communications, 2021
paper

Management strategies in a SEIR-type model of COVID 19 community spread

Anca Rǎdulescu et al, Nature: Scientific Reports, December 4 2020
paper

Variation of quantified infection rates of mixed samples to enhance rapid testing during an epidemic

Usama Kadri, Health Systems, September 13 2020
paper

Development of the Intelligent Pneumatic Sewing Platform for Mask Production

Hao-Ting Lin, IEEExplore, July 28 2020
paper

Avoiding COVID-19: Aerosol Guidelines

Matthew Evans, medRxiv, June 5 2020
paper preprint

Multiscale 3-dimensional pathology findings of COVID-19 diseased lung using high-resolution cleared tissue microscopy

Guang Li et al, bioRxiv, April 20, 2020
paper preprint

COVID-19 SimBiology SEIR Model Examples

Fulden Buyukozturk, MATLAB File Exchange, May 29 2020

COVID-19 Spread Predictor

Ahmed Abel-Gawad, MATLAB File Exchange, July 18th
MATLAB code

Cerebral Micro-Structural Changes in COVID-19 Patients – An MRI-based 3-month Follow-up Study

Yiping Lu et al, The Lancet, August 3 2020
paper

A new estimation method for COVID-19 time-varying reproduction number using active cases

Agus Hasan et al, Scientific Reports, April 23 2022
paper, MATLAB code and datasets

The role of kidney dysfunction in COVID-19 and the influence of age

Edoardo La Porta et al, Scientific Reports, May 23 2022
paper

Optimal control problem arising from COVID-19 transmission model with rapid-test

Dipo Aldila et al, Results in Physics, June 2022
paper

SARS-CoV-2 spike protein induces cognitive deficit and anxiety-like behavior in mouse via non-cell autonomous hippocampal neuronal death

Junyoung Oh et al, Nature: Scientific Reports, March 31 2022
paper

Decision-Making Behaviour Evolution Among Pork Supply and Demand Subjects Under Normalisation of COVID-19 Prevention and Control: A Case Study in China

Li Ma et al, Frontiers in Public Health, March 17 2022
paper

Long-term forecasting of the COVID-19 epidemic

University College London, January 15 2022
forecast

Automated COVID-19 and Heart Failure Detection Using DNA Pattern Technique with Cough Sounds

Mehmet Ali Kobat et al, Diagnostics, October 22 2021
paper

Machine learning detects SARS-CoV-2 and variants rapidly on DNA aptamer metasurfaces

Hulya Torun et al, medRxiv, August 8 2021
paper preprint

Characterizing long COVID in an international cohort: 7 months of symptoms and their impact

Hannah E. Davis et al, EClinical Medicine, July 15 2021
paper

Data-driven estimation of COVID-19 community prevalence through wastewater-based epidemiology

Xuan Li et al, Science of the Total Environment, October 2021
paper

Compartmental Model Suggests Importance of Innate Immune Response to COVID‑19 Infection in Rhesus Macaques

Ericka Mochan et al, Bulletin of Mathematical Biology, May 26 2021
paper

Modeling the cardiac response to hemodynamic changes associated with COVID-19: a computational study

Luca Dede et al, Mathematical Biosciences and Engineering,
April 15 2021
paper

A single dose of recombinant VSV-ΔG-spike vaccine provides protection against SARS-CoV-2 challenge

Yfat Yahalom-Ronen et al, Nature Communications,
December 16 2020
paper

Seismic evidence of the COVID-19 lockdown measures: a case study from eastern Sicily (Italy)

Andrea Cannata et al, EGU: Solid Earth, February 2 2021
paper

Principal Component Analysis Applications in COVID-19 Genome Sequence Studies

Bo Wang and Lin Jiang, Cognitive Computation, January 13 2021
paper

Comparative cost-effectiveness of SARS-CoV-2 testing strategies in the USA: a modelling study

Zhanwei Du et al, The Lancet: Public Health, February 4 2021
paper

Rapid SARS-CoV-2 Detection and Classification Using Phase Imaging with Computational Specificity

Neha Goswami et al, bioRxiv, December 12 2020
paper preprint

The effect of weather data on the spread of COVID-19 in Jordan

Eman Abdelhafez et al, Environmental Science and Pollution Research, January 9 2021
paper

Design of 3D-printable nasopharyngeal swabs in MATLAB for COVID-19 testing

Yilun Sun et al, Transactions on Additive Manufacturing Meets Medicine, September 9 2020
paper

Automated subject-specific mask design and tissue loading evaluation framework using GIBBON

Kevin Moerman, Twitter, April 2020
post and MATLAB code

Classification of Covid-19 Coronavirus, Pneumonia and Healthy Lungs in CT Scans Using Q-Deformed Entropy and Deep Learning Features

Ali Hasan et al, Entropy, April 2020
paper

A quantitative and qualitative analysis of the COVID-19 pandemic model

Sarbaz Khoshnaw et al, Chaos, Solitons & Fractals, September 2020
paper

First-wave COVID-19 transmissability and severity in China outside Hubei after control measures, and second-wave scenario planning: a modelling impact assessment

Kathy Leung et al, The Lancet, April 8, 2020
paper

A COVID-19 Epidemiological Model for Community and Policy Maker Use

Alex De Visscher, Concordia University, arXiv, March 19, 2020
paper preprint with model code

The math behind epidemics

Alison Hill, Physics Today, November 1 2020
paper, MATLAB code

Influence of wind and relative humidity on the social distancing effectiveness to prevent COVID-19 airborne transmission: A numerical study

Yu Feng et al, Journal of Aerosol Science, September 2020
paper

How to determine when COVID-19 pool testing will be most effective

Behind the Headlines, mathworks.com, August 6 2020
blog post

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Ventilator Research and Development Resources

Most of these MATLAB and Simulink examples and research papers were used to help with the ventilator shortage in early 2020. Others are foundational references.