Intriguing Computational Biologists & Genomic Scientists: Part 2
Stephen Frank Altschul
Dr. Altschul is a prominent mathematician who has pioneered the ubiquitous BLAST algorithm as well as the Karlin-Altschul algorithm in the field of bioinformatics [3]. Notably, the BLAST (Basic Local Alignment Search Tool) platform is used by many scientists to analyze protein and nucleotide sequences [4]. I’ve personally used this resource numerous times to confirm DNA sequences, analyze genealogy, and more evolutionary-related tasks. These algorithms examine sequence alignment, and Dr. Altschul’s work expands on the statistics of sequence compassion and sequence similarity. The Karlin-Altschul algorithm provides a methodology to compute the probability that local alignment of a certain score will be present between two random sequences with similar lengths a the query and database sequence [1]. The probability term is expressed as an expectation value, or E-value. Before developing this tool, Dr. Altschul received his Ph.D. in mathematics from MIT.
Serafim Batzoglou
Dr. Batzoglou was previously the Vice President of computational genomics at Illumina, and he received his Ph.D. in mathematics and computer science at MIT [8]. Dr. Batzoglou has founded various companies at the intersection of ML and genomics such as Seer and DNAnexus. He has also served as a professor of biomedical data science at Stanford. Interestingly, Dr. Batzoglou’s advisor is Dr. Bonnie Berger, a respected bioinformatician who explored deterministic algorithms (a topic I’ve briefly explored). Dr. Btazolgou has also worked with the Human Genome Project that determined the DNA base pairs in humans and The Encyclopedia of DNA Elements (ENCODE) which identified functional elements in the human genome [5] [6]. One of his seminal papers was on the initial sequencing and analysis of the human genome, in coordination with a plethora of scientists from around the world. This work was supplementing the Human Genome Project’s efforts and served to provide initial observation about sequencing and decoding the information present in the human genome [7].
Wolfgang Huber
Dr. Huber is a computational biologist who leads the Huber Group at the European Molecular Biology Laboratory (EMBL), a research institution that aims to promote molecular biology research in Europe [9]. The Huber group conducts large-scale statistical modeling and integrated genomic and molecular information from people with varying phenotypes in health and disease to understand differences between individuals. Dr. Huber works to develop ways to translate biological discoveries into clinical research and works to enable new, computation-based studies [9]. What I found interesting was that Dr. Huber gained his Ph.D. in theoretical physics, from which the transition to computational biology would be intriguing, yet possible as both require a strong mathematical and computational background. Dr. Huber has worked at the German Cancer Research Centre in cancer genomics and microarray analysis! He leads the Molecular Medicine Partnership Unit that aims to understand the response heterogeneity to anticancer drugs. This research is especially relevant in the personalized medicine revolution as well as in drug and treatment development as cancer and other diseases (such as Rheumatoid Arthritis) exhibit clinical variation which can be difficult to target and alleviate. Dr. Huber is also a founding member of Bioconductor, one of the largest bioinformatics projects that focus on analyzing and comprehending high-throughput genomic data using R programming [2]. Bioconductor is open source and open development.
Works Cited
- Karlin-Altschul Statistics, drive5.com/usearch/manual/karlin_altschul.html.
2. “AboutBioconductor.” Bioconductor, bioconductor.org/.
3 Altschul, Stephen F., et al. “Basic Local Alignment Search Tool.” Journal of Molecular Biology, vol. 215, no. 3, 1990, pp. 403–410., doi:10.1016/s0022–2836(05)80360–2.
4. “BLAST: Basic Local Alignment Search Tool.” National Center for Biotechnology Information, U.S. National Library of Medicine, blast.ncbi.nlm.nih.gov/Blast.cgi.
5. “Encyclopedia of DNA Elements.” ENCODE, www.encodeproject.org/.
6. “Human Genome Project Information Archive1990–2003.” Human Genome Project Information, web.ornl.gov/sci/techresources/Human_Genome/index.shtml#:~:text=The Human Genome Project (HGP) was an international 13-,bases in the human genome.
7. Lander, Eric S., et al. “Initial Sequencing and Analysis of the Human Genome.” Nature, vol. 409, no. 6822, 2001, pp. 860–921., doi:10.1038/35057062.
8. “People.” Serafim’s Lab, www.serafimb.org/people.html.
9. “Wolfgang Huber.” Huber Group, www.huber.embl.de/people/wolfgang-huber/.
