Bioanalysis Zone

2012 Young Investigator Award Finalist (Highly Commended): Raphael Bastos Mareschi Aggio


Raphael Aggio


Nominee: Raphael Bastos Mareschi Aggio, University of Auckland, New Zealand

Nominated By: Silas Villas-Bôas, University of Auckland, New Zealand


Supporting Comments: Raphael Aggio is about to complete his PhD studies in the next few months and already has seven published works in the field of metabolomics. Raphael has been my best PhD student so far, he is hard working and dedicated with a very creative mind. Raphael is one of those few hybrid professionals capable of working in two or more fields very comfortably (e.g., biology, chemistry, mathematics and informatics). Owing to his exceptional performance as a young investigator and PhD student, and the success of his brilliantly created, very powerful bioinformatics tools for assisting the analysis and interpretation of metabolomics data – the impact of this in the field of metabolomics evident by the numerous contacts received from different research groups around the world enquiring about the methods – I highly recommend Raphael for the Bioanalysis Young Investigator Award.

Bioanalysis Zone asked Raphael to highlight one of his favorite published articles and explain his reasoning.

Aggio RB, Ruggiero K, Villas-Bôas SG. Pathway activity profiling (PAPi): from the metabolite profile to the metabolic pathway activity. Bioinformatics 26(23), 2969–2976 (2010).

What were the most difficult challenges encountered in this study? And how were they overcome?

Metabolomics data are within the most difficult ‘omics’ data to interpret, largely owing to the convoluted nature of a cell’s metabolism, where a single metabolite may participate in many different metabolic pathways. One of the biggest challenges in the development of PAPi was the de novo translation of metabolite profiles into activities of metabolic pathways. I needed to become a biochemist and a programmer at the same time. For months, I submerged myself into the literature and computational forums, while generating and experimenting with real datasets. After several sleepless nights, I finally developed an algorithm that worked and made biological sense.

Which areas of your research did you find the most interesting/enjoyable and why? By comparison, which were the least agreeable?

The development and validation of the algorithm used by PAPi required me to dive into biochemistry. I spent months trying to understand the cell metabolism, getting fascinated with its complexity and robustness. It is amazing how cell metabolism evolved and became this huge self-regulatory network involving thousands of metabolites, enzymes and cofactors. Although the learning process can be quite cruel, the R-programming part of this study also became very enjoyable after a while. I realized that it is all about practice. The more programming you do, the easier it becomes and the more you enjoy it. On the other hand, preparing the documentation for PAPi was really not fun! Every R-package requires its author to explain in detail how each function works, a process that consumes a huge amount of time and certainly is not that exciting.

Colleague quotes

Here is what some of Raphael ‘s friends and colleagues had to say about him.

Paulina Giraldo, University of Auckland, New Zealand

“Raphael’s key attributes are tenacity and drive, to work through a problem until he solves it; ambition, which drives him to excel and be the best among his peers; and, a sense of humour, which makes working beside him a pleasure! Furthermore, Raphael has not limited his knowledge and activities to his own field of research, which is evidently reflected in the diversity of projects he is involved with. Up-and-coming bioanalysts have a remarkable example of what a young scientist should aim to be – holistic. And, of course, besides science, Raphael is definitely crazy for surfing!”

Augusto Barbosa, University of Auckland, New Zealand

“What struck me about Raphael, at first, was his highly creative mind and his capacity to think outside the box. He is sharp and enjoys coming across problems, as he takes them as opportunities to improve imperfect systems. The differential positive aspects in Raphael, as compared to other Young Investigators, include his charisma, commitment and passion for what he does. These inspire many people and will strengthen his natural talent for leadership in the future of his career. Outside science, Raphael would probably end up building robots to deal with the world’s rubbish, or otherwise a professional surfer.”

Kathy Ruggiero, University of Auckland, New Zealand

“Raphael’s key attributes include curiosity, analytical thinking, determination and teamwork. Other attributes of Raphael include collegiality, patience, generosity and good-hearted. He can definitely capture the audience’s attention and is very reactive in meetings, often proposing straight-to-the-point hypothesis. He enjoys being with people, listening to music, playing guitar and surfing. If he is not in science, he will be engaged in one of these. This is what is behind Raphael’s character, a guy who anyone can count on or have a pleasant chat about any subject – science, politics, religion, music or sports.”

Xavier Duportet
Massachusetts Institute of Technology, USA

“Raphael is definitely a passionate scientist, hard worker, devoted to his research work and with an acute sense of logical thinking. Working with him has been a real pleasure.”


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