Quick Q&A with the Bioinformatics in Medical Genetics Group

In our series of Quick Q&As with scientists who work in the NLM’s National Center for Biotechnology Information (NCBI), we’re pleased to introduce the three members of the Bioinformatics in Medical Genetics Group.

The leader of the group, Alejandro Schäffer, shares a memorable lesson. Mike Gertz tells how his family influenced his career. And Eric Nawrocki reveals how an article in US News and World Report shaped his future.

Read more Quick Q&As with NCBI scientists.

As always, please feel free to share, like, and comment.

Quick Q&A with Schäffer, Gertz, and Nawrocki
Question Alejandro Schäffer, PhD E. Michael Gertz, PhD Eric Nawrocki, PhD
casual headshot of Alejandro Schäffer casual headshot of Michael Gertz headshot of Eric Nawrocki
In lay terms, what is the focus of your NLM research? I work in three areas: 1) biological sequence analysis, 2) medical genetics, especially immunogenetics, and 3) cancer genomics. I’ve been studying the evolution of cancer within human tumors. Cells within tumors continue to evolve even after the tumor has become cancerous. The diversity and ongoing evolution of cancer may be what enables some tumors to continue to evade the immune system and medical treatment, and to develop resistance. I work on biological sequence analysis projects. Several of them focus on a certain type of biological sequences called functional RNA gene sequences. These sequences are somewhat rare in genomes, where most gene sequences encode proteins. Functional RNAs do not code for proteins, but function directly as RNAs. Because they do not encode proteins, functional RNAs are more difficult to find in the millions of DNA sequence letters or nucleotides present in organisms’ genomes.

I develop a software program called Infernal that attempts to identify RNA genes. It takes advantage of the fact that many RNAs form specific shapes or structures by looking for sequences that can fold into those specific shapes.

Why is it significant, in your opinion? Sequence analysis is central to understanding almost any topic in molecular biology. Medical genetics and cancer genomics are significant because the problems and data are always about health and disease. Evolution occurs by chance, but there are rules to the game of chance. The hope is always that the more we learn these rules, the better we will be able to determine which tumors are truly dangerous, and the better we will be able to target and kill these cancers. Many functional RNAs are not well understood, partly because they are difficult to identify in genomes and study by comparative sequence analysis, but they are just as biologically important as easier to find protein-coding genes. Infernal offers a powerful way to find them that can lead to biological insights.
What or who inspired you to pursue your career? My father, Juan Jorge Schäffer (1930-2017), was a mathematician and engineer and Renaissance person. He had a difficult first half of his life, being forced to emigrate in 1938-39 from Austria to Uruguay, and again in 1968 from Uruguay to the United States. Nevertheless, his perpetual quest for knowledge and mathematical talent enabled him to have a long career as a university professor.

My undergraduate mentor, Jon Louis Bentley, instilled in me a passion for algorithms.

My first programming teacher, Paul Hilfinger, made computer programming fun. I still remember Hilfinger’s first lesson: “No matter what happens, resist the temptation to punch the computer screen.”

My father was a doctor and my mother a nurse, so there was always an interest in biology and medicine in my family. My talents were more in mathematics, but I follow somewhat in their footsteps, lending my knowledge to interdisciplinary work. I wanted to work in research as long as I can remember. My father was a high school science teacher, which probably nudged me towards science, and I’ve been fascinated with biology, the amazing complexity of living things, and the power of evolution ever since I took my first biology class.
How did you get started in your career? I studied math and computer science as an undergraduate and got my doctorate in theoretical computer science. I got my start in computational biology in 1992 by applying the algorithmic techniques that Prof. Bentley taught me to speed up a widely used piece of software in medical genetics. I got a degree in mathematics, specifically computational mathematics, which opened many doors. I remember reading a US News and World Report article when I was in college about “Careers of the Future” that stated that a lot of jobs would be available in coming years to people with backgrounds in both computer science and biology. I was currently trying to decide between those two majors, and that article led me to major in both. When I graduated, I was fortunate enough to be accepted and enter into a graduate program in computational biology, where I became immersed in the world of academic research.
What really gets you jazzed about science and research? I enjoy collaborating with smart people who can teach me new things. I like to choose who I work with first and what I work on second. I love the possibility, directly or indirectly, of helping people. Plus, it has been fascinating.  There are endless surprises in biology. The idea that you can discover something that’s been true for millions or billions of years, but that no one has ever known about.
If you weren’t doing this work, what other profession might you have pursued? Accounting. My interest in algorithms got started because analyzing the performance of an existing algorithm requires a combination of math, computer science, and accounting. Our most interesting neighbor when I was growing up was Yuji Ijiri (1935-2017), an accounting professor who invented triple-entry bookkeeping. I would likely have been in a different area of mathematics or computer science. I really do have a love for it. If I wasn’t doing scientific research, I think I would have tried to be a doctor or work in health care because that is something that always interested me as well.
Tell us something surprising about yourself. I was born in the southern hemisphere—in Montevideo, Uruguay. When life in the United States does not make sense, I say, “I see everything upside down because I was born in the southern hemisphere.” I surfed my way through graduate school. I’ve always really loved watching movies, but I refuse to watch movie previews because I think that they ruin a movie by showing you way too much about what’s going to happen.

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