Making sense of genomic data: COVID-19 web-based bioinformatics

Duration: 3 weeks, 5 hrs per week

Start date: 25 July 2022. The course will run ‘live’ for 3 weeks from the start date. Once this period is over, you will be able to join and complete the course, but there will be no live monitoring of the forums. Update: Educators will be available to learners taking this course between 21 Nov – 2 Dec 2022.

Free to join, and a free certificate of achievement will be provided on satisfactory completion.

Why join this course?
Over the past decade, sequencing technologies have become more accessible and sequencing data has increased exponentially. However, bioinformatics capacity is still limited. On this three-week course, you will learn the basics of bioinformatics concepts and explore the web-based tools used for viral data and sequencing analyses. The course was developed in collaboration with members of the COG-UK consortium and international experts from around the world.

Who is this course for?

This course is designed for diagnostic and healthcare professionals, researchers, and anyone involved in the testing and analysis of disease samples. It will also be useful to researchers specialising in web-based bioinformatics, diagnostics, diseases or pandemics.

Lead Educators

Carolina Castañeda Garcia
PhD candidate at the International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Mexico.

I am passionate about education and I have prior experience in teaching, biochemical engineering and cancer research. Currently, I am a PhD candidate in biomedical sciences at the National Autonomous University of Mexico (UNAM). My research focuses on the detection of genetic variations, both common and rare, that increase a person’s risk of developing cancer, specifically melanoma. I am interested in evaluating cancer risk by environmental or intrinsic factors. I use sequencing data analysis to identify mutations, guarantee the quality of the data, and analyse how the genomic variations segregate in the general population, as well as, how it affects biological pathways in order to evaluate the effect that any mutation has on the likelihood of developing cancer.

Claudine Nkera-Gutabara
PhD candidate in Human Genetics at the Sydney Brenner Institute for Molecular Bioscience, Division of Human Genetics from the University of Witwatersrand, South Africa.

My PhD is a joint collaborative project with the CSIR Bioengineering and Integrated Genomics Research Group. I have a background in Biological Sciences and Human Genetics and have published a review on my latest research focus – microbiomics. My current research involves the development of a bioinformatics pipeline for the characterization of the South African gut microbiome to reveal associations to different diets, lifestyles and socioeconomic statuses. The sequencing platforms being used to generate this novel data are 16S PacBio long-read and Illumina shotgun metagenomics sequencing, and I have expertise in the analysis of this data.

Dr Tanya Golubchik
Senior lecturer in computational microbiology at the Sydney Institute for Infectious Diseases, University of Sydney Australia.

I am a computational biologist whose research focuses on the genomics of microbial pathogens of public health concern, particularly pathogen evolution during infection. My work with the Big Data Institute at the University of Oxford and with Sydney Institute for Infectious Diseases at the University of Sydney uses deep-sequencing data to analyse the diversity and population dynamics of bacterial and viral pathogens at scale, including most recently, in SARS-CoV-2. I have a particular interest in using novel targeted metagenomics methods to sequence pathogen genomes directly from clinical samples, to gain insights into underlying genetic diversity: for example, learning how SARS-CoV-2 variants arise and are transmitted.

Tracey Calvert-Joshua
Bioinformatician at the South African National Bioinformatics Institute, South Africa.

I am a bioinformatician and PhD student at the South African National Bioinformatics Institute (SANBI) in Cape Town, South Africa. When I say I love data, I mean everything from blockchain technology, metaphysics, social science and biology to random trivia. I’ve also published a book called “The Yummy JellyBeans of Relationships” – which is based on Bertie Botts jellybeans in Harry Potter….and I never even liked Harry Potter when I wrote it. More recently I’ve also dabbled in E-commerce where I sell inspirational clothing. My mom probably thinks I’m confused. But I’m just curious. Curiosity did NOT kill the cat. Ok, maybe Schrodinger’s?

Varun Shamanna
Senior bioinformatician at the Central Research Laboratory, Kempegowda Institute of Medical Sciences, India.

I am a senior bioinformatician at the Central research laboratory, KIMS, India. Also, I am pursuing my PhD in Microbial genomics with a specific focus on Klebsiella pneumoniae. I am involved in the sequencing and analysis of WHO ESKAPE pathogens as a part of the Global Health Research Unit (GHRU) project funded by the National Institute for Health Research (NIHR). As a part of the Indian SARS-CoV-2 Genomics Consortium (INSACOG), we are also sequencing SARS-CoV-2 genomes and analysing them as a part of the national surveillance program. Some of my key interests are building pipelines using Nextflow, pathogen genomics and SARS-CoV-2.

Course Developer

Dr Liã Bárbara Arruda
Wellcome Connecting Science, UK

Contributors
The course also features contributions from the following distinguished scientists, including:

Dr Ana Beatriz Villaseñor – Brigham and Women’s Hospital, Harvard Medical School, USA
Brian Kariithi – University of the Witwatersrand, South Africa
David Twesigomwe – Sydney Brenner Institute for Molecular Bioscience, South Africa
Eunice Niyobuntu – University of the Witwatersrand, South Africa
Dr Rebecca Rockett – University of Sydney, Australia
Muthumeenakshi Bhaskaran – Central Research Laboratory, KIMS
Nischita Subramanya – Central Research Laboratory, KIMS, India
Shreedhanya Marathe – Central Research Laboratory, KIMS, India
Merlin Abraham-Davies – University of Exeter, UK