Stephen Altschul, Ph.D.

Senior Investigator

Stephen Altschul's Research Group


Building 38A, Room 6N605
8600 Rockville Pike
Bethesda, MD 20894


Research Topics

Dr. Altschul's research has focused on the development of algorithms and measures for the comparison and analysis of DNA and protein molecules. He helped develop the MSA program for global multiple sequence alignment, the MACAW and Gibbs sampling programs for local multiple alignment, and the BLAST suite of programs for database similarity search. He has helped develop the statistical theory for ungapped local alignments and for the assessment of multiple distinct alignments, as well as methods for estimating statistical parameters for gapped alignments. Dr. Altschul's research has had a particular focus on the construction of appropriate measures for sequence comparison. This has included the development of sequences weighting methods, the description of an information theoretic perspective on substitution matrices, the development of gap costs for pairwise and multiple sequence alignment, and methods for the compositional scaling and adjustment of substitution matrices. Most recently, his work has focussed on a variety of theoretical and practical issues stemming from the Dirichlet mixture model for describing positional amino acid frequencies within families of related proteins.


Dr. Altschul received his A.B. in mathematics from Harvard College in 1979, and his Ph.D. in the same field from M.I.T in 1987, under the supervision of Profs. Daniel Kleitman and Bruce Erickson. He came to the NIDDK in 1987 to do postdoctoral work with Dr. David Lipman, and moved with him to the NCBI/NLM in 1989, shortly after its establishment. There, he has served as Staff Fellow, Senior Staff Fellow and Senior Investigator.

Selected Publications

  1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-402.

  2. Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A. 1990;87(6):2264-8.

  3. Altschul SF, Wootton JC, Zaslavsky E, Yu YK. The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput Biol. 2010;6(7):e1000852.

  4. Yu YK, Wootton JC, Altschul SF. The compositional adjustment of amino acid substitution matrices. Proc Natl Acad Sci U S A. 2003;100(26):15688-93.

  5. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993;262(5131):208-14.

Related Scientific Focus Areas

This page was last updated on May 10th, 2013