Alexander V. Alekseyenko, PhD
Associate Professor of Biomedical Informatics in the Department of Public Health Sciences and Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina; Graduate Director of Joint Clemson-MUSC PhD program in Biomedical Data Science and Informatics; Founding Director Program for Human Microbiome Research
- BSc, Computer Science, Case Western Reserve University, Cleveland
- MSc, Biomathematics, University of California, Los Angeles
- PhD, Biomathematics, University of California, Los Angeles
- Postdoctoral Fellow in Bioinformatics, European Bioinformatics Institute, UK
- Postdoctoral Scholar in Statistics, Stanford University
How I describe my work to those outside the field
I say that I’m a data scientist working on improving human health by understanding the function of the microbiome: the microbes that live in and on us. I develop algorithm and statistical methods to learn from host-microbiome data and how to leverage it for health outcome prediction. I lead a team of biologists, programmers, and statisticians to interpret the interactions of the microbiota with their humans. This helps us understand what causes diseases and how to predict the disease course. When asked what I teach, I say that I lead the biomedical data science and informatics PhD training program at MUSC.
Years of experience
I started when I was a research assistant back doing bioinformatics in structural genetics lab when I was an undergrad in 2001. So, since 2001.
Applying computers to solve problems in biology interested me when I was an undergraduate. This was in 2001, when the dot com thing was happening. I wanted to do something different; and the most different in our Computer Science department was Cenk Sahinalp, who was doing bioinformatics. I started working with him. Later, I’ve always complained that the computer science curriculum is not very thorough on math. And so, for my graduate degree, I wanted to do more math. I found this small bioinformatics program at UCLA and it was just what I wanted. UCLA was also developing bioinformatics training so it was a good fit for me, and I decided to become a biomathematician with an interest in bioinformatics. Informatics does not restrict me and actually allows me to work on database algorithms one day and then solve the statistical problems the next. I can use my quantitative skills and I don’t have to define myself just as a biostatistician or computer scientist and thereby limit what kinds of quantitative things I can do for my chosen field. I can actually be much broader. I am also a member of the American Statistical Association. Some of my work at AMIA would not be well understood at ASA, but I think most of the work I present at ASA would be received and understood at AMIA as well.
What are your ambitions? At the end of your career, what do you hope to have accomplished?
It’s evolving. I envision that I will be in this field for another 30-40 years, and I don’t have a definite vision for that far ahead quite yet. But if I look forward to the next 10-20 years, I see my goal as being able to use information about the microbes that live on and inside your body to design treatments and create lifestyle recommendations for people to better their health. That’s what I want to do. That’s part of my passion.
Who or what are your “key sources” in the informatics field?
One of the professors who established the biomathematics training program at UCLA was one of the first fellows of ACMI, Carol Newton. She was a trained physician who had a passion for math and who worked in developing informatics systems and I view her as one particular source of inspiration. She has been gone for a couple of years now, but there is an endowment in her name back at UCLA, my alma mater. In addition, I now look up to people like Marc Suchard, Constantin Aliferis, Greg Cooper, Mike Becich, people who are quantitatively solid, but who also have the leadership and organizational skills to make complex informatics possible by embedding it into the bloodstream of larger organizations.
Articles that spotlight my research interest
- Alekseyenko, AV. “Multivariate Welch t-test on distances.” Bioinformatics. 2016 Dec 1;32(23):3552-3558.
- Statnikov, A., Henaff, M., Narendra, V., Konganti, K., Li, Z., Yang, L., Pei, Z., Blaser, MJ., Aliferis, CF., Alekseyenko, AV. “A comprehensive evaluation of multicategory classification methods for microbiomicdata.” Microbiome 2013 Apr 5;1(1):11.
- Baele, G., Lemey, P., Bedford, T., Rambaut, A., Suchard, MA., Alekseyenko, AV. “Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty”. Mol Biol Evol. 2012 Sep;29(9):2157-67.
- Cho, I., Meth ́e, BA., Nondorf, L., Li, K., Alekseyenko, AV., Blaser, MJ. “Subtherapeutic antibiotics alter the colonic microbiome and early life adiposity in mice”. Nature. 2012 Aug 30;488(7413):621-6.
- Alekseyenko, AV., Lytkin, NI., Ai, J., Padyukov, L., Aliferis, CF., Statnikov, A. “Causal Graph-Based Predictive Modelling of Rheumatoid Arthritis from Genome-Wide Association Data”. Biology Direct 2011 May 18;6(1):25.
- Alekseyenko, AV., Lee, CJ., Suchard, MA. “Wagner and Dollo: a stochastic duet by composing two parsimonious solos”. Systematic Biology 2008 57(5): 772 – 784.
- Alekseyenko, AV., Kim, N., Lee, CJ, “Global analysis of exon creation vs. loss, and the role of alternative splicing, in 17 vertebrate genomes.” RNA 2007, 13:661 - 670.
Hobbies/Interests outside AMIA
Deep sea fishing. I can go for 24 hours, leave on a Friday night and come back on Saturday night. It’s a very absorbing hobby, I don’t have much time but I make a point of finding it at least twice a year.
AMIA is important to me because
It gives me a community that understands what I do and the significance of it.
I am involved with AMIA
For the last two years, I have run three panels on microbiomes, both at the Annual Symposium and at the AMIA Informatics Summit meeting, bringing experts, mostly from outside of AMIA, to talk about microbiomes and to show what role informaticists can play. Whenever I go to AMIA meetings, I try to organize ‘Probiotic breakfast’ to discuss informatics issues in microbiome research. I think I’ve created a small community inside of AMIA of people who are interested in microbiomes and wish to explore how their skills could help further knowledge of microbiomes and help with disease. Hopefully, this is turning into a small interest group inside of AMIA.
It may surprise people to know
I supported myself through college by selling computers, both new and used, at computer shows and on eBay. A well-washed computer is almost like new! I used to do small sailboat racing in Hudson River off Manhattan, back when I was a junior faculty at NYU. I have even won a second place (after tie breaker) trophy at a regatta one year.