Wageningen, The Netherlands
December 4, 2014
Delft University of Technology (TU Delft) and KeyGene join forces by appointing KeyGene's head of bioinformatics, Roeland van Ham as part-time professor in plant computational biology at TU Delft. With this collaboration TU Delft’s Data Science initiative, that has an excellent reputation in data analytics, and KeyGene aim to change the field in plant genomics research. Since KeyGene is a pioneering company in plant research using ao plant genomics that generates huge amount of complex data, the new position of Roeland van Ham at TU Delft generates great opportunities to turn ‘big data’ into knowledge and knowledge into useful applications for society.
We talked to Roeland about his new and challenging job at Delft University of Technology.
Roeland, this special chair connects biological knowledge with computer models and algorithms. What is the relevance of connecting these research areas?
The relevance is born out of necessity, really. Biology is about variation and variation, unfortunately, makes things very fuzzy. Up to about half a century ago, description and qualitative models helped us to understand the fundamental processes in biology. When challenged, however, to make accurate predictions, such models were insufficient. To deal with fuzziness and complexity when we try to understand biological phenomena, we perform experiments and do measurements on the many different components from which biological systems are built. And we do so on a very large scale, using repetitions under many varying conditions. It is this practice that has turned biology into an information science: we now try to manage massive amounts of data, to connect these and turn them into knowledge and understanding. At many levels, this endeavor has become way too complex to be left to human intuition only. Computational methods, from data management and processing algorithms to statistical and mathematical models, now provide indispensible and novel ways to turn our “Big Data” into knowledge and knowledge into useful applications for society.
What are the main goals of your job?
The overarching theme is predicting a plant’s phenotype from its genotype and to direct biotechnological approaches to steer both in creating better crops.
The primary focus of my research will be on developing and applying new computational approaches. Firstly, to predict the function of genes and other elements in the DNA of plants. And secondly, how these can be altered to give improved performance. Knowing what genes do, how they do it, and how we can improve what they do, helps us enormously creating better agricultural crops.
Two further areas of attention will be on how we can best computationally reconstruct the complex genomes of plants from large amounts of DNA sequencing data, and on how to automate the description of variation in plant traits using digital imaging techniques.
How could your job at Delft University benefit from your work at KeyGene and vice versa?
At KeyGene our primary focus is on turning knowledge into practical applications and innovative products for the seed, agro and food industry. As a high-tech R&D company, we work mostly from the center of that spectrum and we sometimes need to stop when questions get too fundamental. Delft University will provide great opportunities to venture further in that direction and benefit from the environment with ample expertise in technologies. At the same time, in KeyGene we have much plant biology data and knowledge that relate directly to real-life problems in crop improvement. These will provide opportunities for novel research directions in Delft, novel applications for bioinformatics techniques. There will also be excellent training opportunities for students who can take on research questions with direct relevance for industry. Working on bioinformatics in the green domain will also offer inspiration: after all, plants have among the most complex genomes and they provide opportunities for experimentation that are impossible with other types of organisms.
Global challenges such as population growth, climate change and shortages of arable land and water supply are expected to rise. To address these challenges, agriculture has to
produce ‘more with less’. How could this special chair contribute to finding answers?
The challenge is to help shorten the cycle in which new and better performing crop varieties can be developed. Agronomic techniques, and more recently, green biotechnology have been enormously successful in doing so. However, the global developments have also accelerated, so all the challenges remain. The one way forward to create better adapted crops is through understanding of how plants and traits develop and what mechanisms and variation in their genomes underlie traits of agricultural relevance. This is similar to our efforts to really understand the human genome and use this to develop personalized approaches to cure diseases and to help contribute to human health. This too has become an “information” or “Big Data” science in which computational methods to integrate and analyze data are taking us further. It is my ambition, through this chair, to contribute to a similar path in plant biotechnology.
What motivates you?
That’s a package. For one, the fact that I can work and contribute to a most relevant societal challenge, that of global food security, is enormously satisfying. To try and make a real difference is a strong driver to me. To now also being able to do this from both an industrial and academic environment is like having my bread buttered on both sides. And last but not least, to work together with other scientists and young students, from very different backgrounds at the crossroads of scientific disciplines is inspiring, a privilege and outright fun.
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