Genome Informatics in the 21st Century 

Helder Nakaya, Associate Professor at the University of São Paulo, shares his thoughts on the future of informatics, and his experience of meeting a "science hero" for the first time at our 2022 Genome Informatics conference. 

The long-running Genome informatics conference alternates annually between our programme, where is held at the Wellcome Genome Campus, UK and Cold Spring Harbor in the USA. We asked Helder, Associate Professor at the University of São Paulo, and Hospital Israelita Albert Einstein, Brazil about his experience presenting research at this meeting, and his thoughts on informatics in the 21st century.

A Wellcome Connecting Science interview with Helder Nakaya

As co-chair and speaker in the Genome informatics ‘Single cell and spatial omics’ session, tell us about your research in this area?

Our lab is kind of promiscuous with scientific projects. Although our expertise relies on systems immunology and transcriptomics, we like to research other things, such as digital epidemiology, machine learning approaches for image recognition (of parasites), natural language processing, and development of user-friendly computational tools.

In the field of single cell and spatial omics, we are utilising these approaches to investigate the brain tumour microenvironment in mice, but mostly infectious diseases. In the session, I presented results from two unpublished papers: one related to work on the brain (where we borrowed tools from astronomy to analyse spatial single cell data) and one related to a new computational tool for spatial transcriptomics named, ArchipelaGO.

What exciting directions do you see this field moving into in the future?

I already consider spatial transcriptomics the future of molecular biology. But, as people from my group complained the other day “when we master one technique, another bigger and more complex one appears!”. The area of spatial transcriptomics will expand exponentially and will blow up the minds (and maybe the data storage solutions!) of many researchers. I hope the near future brings us a true 3D spatial transcriptomic approach.

How did this conference benefit you and your research?

A lot. Not only did I meet one of the researchers I admire the most (Sarah Teichmann, my session co-chair), I also watched many interesting seminars with unpublished stories, and established new collaborations which I hope will lead to some good research outcomes. And of course, I was able to finally drink a beer at the bar of a friend from Cambridge, Professor Tony Kouzarides!

Helder sharing a stage with Sarah Teichmann


Talking to amazing researchers face-to-face after this pandemic was awesome!

Helder Nakaya, Associate Professor, University of São Paulo

What do you consider to be some of the challenges in the field of genome informatics, particularly for researchers in the Global South?

The biggest challenge for me is how to properly train researchers in genome informatics. There are already plenty of user-friendly computational tools and databases out there. Teaching programming languages to them should not be the focus, but rather using these resources effectively to get the best research answers.

What is your advice to young researchers, especially those from the Global South, wanting to enter the field?

Rather than becoming programming experts, consider focussing on becoming good scientists. After you know what the questions are, you can explore the best ways to answer them. If this requires programming, then you should learn it!

Back to top Back to top