Marko Budinich: Biology decoded by computer science

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Marko Budinich is an expert in bioinformatics: he masters biology as well as computing and uses computers’ calculation power to decode the Tara Oceans genetic data. Just after earning his PhD, the Chilean researcher will study for the next 2 years the network of microbes in the Ocean. His mission is to better understand its functioning and the various parameters influencing it. His goal is to develop computer models to provide a broader view of the current and future states of the microbial network.
A few months ago, Marko decided to apply for a position in the “Ocean Plankton, Climate & Development” project, initiated by the Tara Expeditions Foundation and financed by the French Facility for Global Environment (FFEM). This cooperative project is a unique opportunity for him to develop new skills and participate in the new network of researchers set up by the project.

 

His PhD completed, Marko Budinich took a well-deserved break before embarking on the Tara Oceans adventure. “I did a PhD thesis, which takes a lot of energy. That’s why I’m taking a long vacation first,” he says with a smile. Marko will then settle at the marine station* in Roscoff (Brittany) with his wife and 1 year old son. “It’s the first time I’m actually working on the Tara Oceans data, even if I’ve been thinking about it for a long time,” he says. Believing it’s still too early to discuss the future development of his research, Marko prefers to talk about an “idea, an intuition”.

It’s somewhat similar to the algorithms used to analyze communities of individuals or friends on Facebook.

Beyond the dataset

Marko Budinich knows very well why he chose to integrate the Tara Oceans scientific team. First, the Tara Ocean dataset is the most global and exhaustive collected so far. Also, this innovative research is interdisciplinary, bringing together oceanographers, biologists, geneticists, etc. But most importantly, the project is part of an overall goal of understanding how oceans work. “These are fascinating and important matters,” he says enthusiastically. He is prepared to devote his skills to the study of marine plankton. Integrating the moving world of oceanic microorganisms into the standardized universe of computer science is the purpose of bioinformatics. Plankton represent billions of organisms and tens of thousands of species. Given such complexity, the processing power of computers is essential and now available.

To clarify his work, the Chilean researcher uses an analogy that makes sense to most or all of us. “It’s somewhat similar to the algorithms used to analyze communities of individuals or friends on Facebook. These algorithms enable us to understand why communities are organized in a certain way and to identify the factors influencing their development. Computer science plays the same role with regard to planktonic communities. Its goal is to connect all levels of the ecosystem. Biological data give us access to communities. We can then correlate these observations with environmental parameters to identify which ones are the most constraining for the community structure”.

Why this particular interest in a network built by oceanic microbes? Part of the answer lies in this paradox: “We know very little about microbes, yet they govern the Ocean’s biological cycles”.

Modeling is not just about predicting, it’s also about understanding.

Starting from the genome

“We model an organism via all the chemical reactions occurring inside its cells,” he says. Starting from the genome – the complete gene set – we have access to the organism’s proteins, thus allowing a better understanding of metabolism and the chemical reactions involved. By correlating these data with environmental parameters, for instance the amount of nutrients, we can estimate some processes such as the organism’s growth rate.

The bioinformatics tools developed by Marko Budinich have multiple applications. Before starting his PhD, Marko worked for 5 years as an engineer and studied yeast involved in the wine making process and also the metabolism of “extremophiles” bacteria thriving in conditions that are proved to be fatal to most organisms, they are used to extract copper from crude ore, a major economic resource in Chile. For his PhD, his work was to “adapt models developed for a single organism to the whole ecosystem”, therefore to a multitude of living beings.

The Chilean researcher wishes to emphasize the fact that “modeling is not just about predicting, it’s also about understanding. We take all these data and we explore them. They tell us what’s interesting and we have to understand what they suggest.”

 

Marko
Marko Budinich

“Science is a collective effort.”

The bioinformatics tools developed by Marko will not be limited to microbial oceanography. They can be adapted to various environments, like the ones encountered in his country, from arid deserts to Antarctic ecosystems.

Even if Marko hasn’t decided yet exactly what he will study (and potentially discover), he knows how he intends to carry out his research: definitely not alone. “Science is a collective effort. It’s not done by people who work alone in laboratories.” For him, interdisciplinarity allows scientists to approach issues in a different way and understand all the details.

 

*The Roscoff marine station is a research and education center in marine biology and ecology, depending on the French National Center for Scientific Research (CNRS) and Pierre and Marie Curie University (UPMC).

 

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