Thanks to some high-profile research projects, basic understanding of the genome — the genetic code that serves as the instruction manual for the growth and development of all living organisms — is relatively widespread. But most people are less familiar with the proteome, which comprises the entire set of proteins expressed by a tissue at any given time. Changes to the proteome over time can give important clues about human health, including stress levels and the presence of certain illnesses.
When he started his PhD in Molecular Biotechnology in 1996, David Tabb became an early entrant into the field of proteomics — the characterization of all proteins in a biological system. By applying his skills as a computer scientist to the analysis of large-scale datasets, David can identify biomarkers for a number of diseases, including cancer and tuberculosis (TB).
When he moved to South Africa at the end of 2015, David’s work changed to fit his new location. Rather than focusing on noncommunicable diseases like cancer, which present some of the greatest health threats in the U.S., he turned his attention to TB, South Africa’s leading cause of death.
With an estimated 360,000 new cases in 2019, South Africa has one of the world’s highest TB burdens. High rates of antibiotic resistance and HIV comorbidities mean that getting TB under control is a top priority for the country, and one potential way to achieve this is with a vaccine. While the existing Bacillus Calmette–Guérin (BCG) vaccine helps protect against certain strains of TB in childhood, many vaccinated patients end up contracting the disease later in life. The ideal situation, David says, would be to develop a vaccine that keeps people TB-free throughout their lives — but there’s still a long way to go before that can be achieved.
“A good TB cure spans six months, and multiple drugs. So even though it’s curable, TB is still awful to get over. And some of the drugs we use to treat it are extremely potent, and have some really nasty side effects. So it would obviously be a whole lot better if nobody ever developed the disease in the first place.”
- David on developing a TB vaccine
During his time at Vanderbilt University, David was part of the Mass Spectrometry Research Center.
[Photo Credit: Vanderbilt University]
David enjoys road-tripping in Ghana with his wife Natasha.
David always found his colleagues at Stellenbosch University had something new to teach him. Kim Stanley (left) was David's first officemate and helped acquaint him with Cape Town. Gerard Tromp (second from left) shared his infectious love for the natural world. Liesel Muller gave David the opportunity to see quality assurance in action, an important aspect of his research at Stellenbosch. Gian van der Spuy (right) was always able to find order in chaos. [Photo Credit: Stellenbosch University]
Working with the Centre for Bioinformatics and Computational Biology at Stellenbosch, David has focused on identifying TB biomarkers in humans and animals. With the importance of biomarkers now increasingly recognized in the field of vaccinology, David’s work in TB proteomics could play a key role in the development of a new vaccine. Unfortunately, though, the COVID-19 pandemic has overshadowed much of South Africa’s progress in fighting TB. With so many financial and human resources now redirected to coronavirus efforts, David’s work in South Africa is on hold for the time being. In January 2021, he relocated to Paris for a one-year placement at the Institut Pasteur, where he continues to work with biomarkers in the Mass Spectrometry for Biology laboratory.Though his work currently focuses on biomarkers for COVID-19 and other infectious diseases, David’s curiosity and drive often lead him into other areas. He has a particular interest in sequencing non-model organisms like hyenas and black soldier flies, which have not historically been selected for extensive study or genetic sequencing. And he’s currently working on a paper that investigates the potential to merge transcriptomics and proteomics for chia seeds — research which could open the door to broader dietary use of this valuable source of polyunsaturated fatty acids.
“I can see that people have downloaded a copy of my article on ResearchGate, and I can see that there's a demand for some paper I've written, and I can make it available and have a conversation about it. I have a feeling of an accomplishment — rather than some nameless person grabbing a PDF file, and my being completely unaware of it, we now have some sort of relationship established.”
- David on making connections through ResearchGate
David is a Missouri native, but spent the better part of 25 years moving around the U.S. for his research. After studying biology and computer science in Arkansas, he began his PhD at the University of Washington in 1996. David’s decision to study molecular biotechnology was one of a few milestones that helped forge his career path: his training under John R. Yates III, a key player in the emerging science of proteomics, solidified David’s interest in the field.
In 1996, tandem mass spectrometers (the instruments that played the same role for proteomics as sequencers did for genomics) began making the shift from the laboratories of instrument specialists to the laboratories of molecular biologists. This meant that huge volumes of mass spectrometry data would soon be available — but how could those data be turned into biological information? David was in the right place at the right time to develop algorithms for handling large-scale proteomics projects.
After spending two years as a postdoctoral researcher at Oak Ridge National Laboratory in Eastern Tennessee, David joined the faculty of Vanderbilt University as an assistant professor in the Department of Biomedical Informatics. During his 10 years in Nashville, David continued to play a key role in helping to develop the proteomics field. In addition to designing the university’s Foundations of Bioinformatics class, David’s lab was a co-creator of the ProteoWizard library — one of the most widely used tools for converting raw data from mass spectrometers. But the most enduring collaboration of his time at Vanderbilt was his involvement in the National Cancer Institute’s Clinical Proteomic Technology Assessment for Cancer (CPTAC) program, where he focused on identifying biomarkers of cancer.
So what brought a tenured professor from a top U.S. university to South Africa? David says some medical issues made him think differently about his work — he wanted a change of pace from the 60-hour weeks and grant writing that dominated his life at Vanderbilt, but also didn’t want to feel he was backing down from career challenges.
“I was left with a conundrum of needing a change,” he says. “But how could I make it a change that feels like an adventure in its own right and not a retreat?”
So when an email from ResearchGate alerted him of a bioinformatics position at Stellenbosch University, just outside of Cape Town, he was intrigued. Moving to South Africa didn’t just mean a new kind of work-life balance; it also presented an opportunity to make a major impact. At the time, the field of bioinformatics in South Africa was rapidly growing, but there weren’t many locals with David’s skillset. When he accepted a teaching position at Stellenbosch in 2015, David was at the forefront of training a whole generation of scientists in proteomics and mass spectrometry. Now, more than five years later, he truly considers South Africa to be home.
