- Oxford University Press, Bioinformatics 
- Journal of Translational Medicine
- Frontiers in Immunology

Bioinformatics for COVID-19 References by Journal

Machine Learning models can be used to better understand the proteins and complexes that are incvolved with the novel Coronavirus. This includes producing predictions of pandemic regarding hospitalizations, patient outcomes, and simulations.

Machine Learning Analysis 

Understanding of COVID-19 target-ligand interactions represents a key challenge, particularly in observing the interactions in vitro. To combat this, the 
COVID-19 Docking Server was developed. It is a web server that predicts binding modes between COVID-19 targets and ligands (small molecules, peptides, antibodies, etc). 

In a very short time, many proteins essential to SARS-CoV-2 have been discovered by researchers in China, including the main protease and spike protein in binding with angiotensin-converting enzyme 2 (ACE2) (this is the primary mode of entry that SARS-CoV-2 uses when initiating cell entry).

As of May 2020, 181 structures were released in the Protein Data Bank, which were  related to 11 different kinds of SARS-CoV-2 proteins.

Structures of the other proteins remain unknown, so the modeled structures of SARS-CoV-2 in the dock server are based on the homologous structures of SARS-CoV, due to high amino acid identity between the two coronaviruses (77.2%). 


INTRODUCTION: COVID-19 Docking Server 

- AI-based programs are trained with large amounts of existing data for their individual purposes. The two types used in this study are:
- (1) Fluency, the AI-based binding affinity prediction platform, which was used on existing FDA approved drugs to test their binding to ACE2 or TMPRSS2 which are 2 proteins used by the virus to enter cells. 
- (2) The Disease Cancelling Technology platform, which was used to assess different drugs' ability to induce gene expression signals that counteract disease-associated signals (identified by examining existing data on gene expression in mouse models). 

Methods of Using Bioinformatics to Identify Potential Therapeutics for COVID-19

- The main benefits of using these unbiased AI programs are (1) speed and (2) widespread availability. 
- Because time is of an essence  in a pandemic, these programs can aid in identifying existing drugs for repurposing and select candidates for clinical trials. 

Benefits of Using Bioinformatics 

Virus-CKB or the viral-associated disease-specific chemogenomics knowledgebase is a platform created to quickly predict existing FDA-approved drugs which can be repurposed and progress to clinical trials to be used to treat COVID-19. New and effective anti-COVID-19 drugs are in urgent need, but discovering new drugs can take up to 8 years, can cost up to $2 billion and have low approval ratings, hence why re-purposing drugs could be useful. Essentially, the database was created to make viral infection research easier.


The Virus-CKB Platform

Computational vaccinology involves using tools that facilitate in silico prediction of immune responses to pathogens by:
- Epitope (art of an antigen molecule to which an antibody attaches itself) mapping
- Antigen selection
- Immunogen design

Use of Bioinformatics in Vaccine Development for COVID-19

Combines computational and statistical techniques, mathematics, and engineering to analyze and interpret biological data of patients affected by COVID-19

Smith College

- Bioinformatics

- Biomaterials

- Biosensors

- Biomechanical Engineering

- Biomedical Optics

- Clinical Engineering

- Genetic Engineering

- Neural Engineering

- Tissue Engineering

- Medical Devices

- Pharmaceutical Engineering

- Rehabilitation Engineering

- Diagnostics and Testing

- Prevention

- Treatment and Cure


Focuses of Biomedical engineering for COVID-19 

Wikipedia

Medical devices encompass essentially all health care products that do not mainly use chemical (pharmaceutical) or biological (vaccines) approaches to diagnose, monitor, and treat patients with COVID-19. Examples include medical imaging, implants, bionics/artificial organs, and biomedical sensors.

- Medical Ventilators for COVID-19

- Medical Ventilator Alternatives for COVID-19

- Biosenors for COVID-19

- Personal Protective Equipment (PPE) for COVID-19

- CT imaging for COVID-19

- Prophylactic Dressings for COVID-19

- Continuous Positive Airway Pressure (CPAP) Devices for COVID-19

Medical Devices for COVID-19

Bioinformatics for COVID-19

Manipulates genomes of organisms, such as animal models, and the virus to develop and/or test therapeutics for COVID-19 

Genetic Engineering for COVID-19

Utilizes light to trigger biochemical reactions in order to detect and treat patients affected by COVID-19

- Photodynamic Therapy (PDT)-based Virotherapy for COVID-19

- Plasmonic Photothermal (PTT)-based Diagnosis for COVID-19

- Plasmonic Photothermal (PTT)-based Treatment for COVID-19

- Photocatalytic Process-based Treatment for COVID-19

Biomedical Optics for COVID-19

Tissue engineering aims to restore damaged tissues or organs by applying engineering and materials principles at the cellular level. It is used interchangeably with "regenerative medicine," which also focuses on providing cures, rather than treatments, for chronic damages to the body due to COVID-19

Tissue Engineering for COVID-19

Applies mechanical engineering principles to biological systems of COVID-19 patients to advance their health

Biomechanical Engineering for COVID-19

Engineers are currently synthesizing new medications to treat patients with COVID-19.

Pharmaceutical Engineering for COVID-19

Deals with the actual implementation of medical devices and reports issues, typically associated with the design of the devices, to improve their implementation

Clinical Engineering for COVID-19

Engineered materials, such as polymers and ceramics, that interact with biological systems of affected patients for medical purposes

- Nanomaterials for COVID-19

Biomaterials for COVID-19

Applies engineering techniques to repair and/or enhance neural systems damaged by COVID-19

Neural Engineering for COVID-19

Focuses on providing technical solutions to affected individuals with disabilities 

Rehabilitation Engineering for COVID-19

Biomedical engineers have put in extensive time and research in testing methods and diagnostics regarding the novel coronavirus. The test results of the population have provided mathematical models to visualize the pandemic, alternatively the private sector has produced a high-volume of nasopharyngeal, throat, and nasal test kits by bioengineering front-runners including: Abbot, Xpert, Lightmix, and Genmark.

Diagnostics and Testing with Biomedical Engineering

Biomedical Engineering involves designing equipment to aid in the treatment of medical conditions.

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