Stephen Will Tanner

Bioinformatics Scientist 2 at Illumina in San Diego

Ph.D. from UCSD Bioinformatics program
Advisor: Vineet Bafna
Co-advisor: Julian Schroeder
 Stephen Tanner has been known to sit on couches

Research

I work at Illumina on algorithms for the design and manufacture of bead arrays. Researchers use bead arrays to genotype people (and mice, and cows, etc.) Bead arrays are also useful for measuring gene expression, for studying DNA methylation, and for studying copy number variation. A paper related to this work is "Decoding Randomly Ordered DNA Arrays" by Gunderson et al in Genome Research 2004.

My graduate research focused on mass spectrometry. I worked on Inspect and MS-Alignment, software tools for identification of peptides from tandem mass spectra. Inspect annotates tandem mass spectra efficiently by using a peptide sequence tags to filter the protein database. These tags are analogous to the short seeds used by BLAST, when searching for a sequence match. The tools are now available online to proteomics researchers. For the curious, here are my dissertation defense presentation slides and the dissertation itself. I wrote up a few notes on life in graduate school. Much more thorough guide for new and prospective grad students would be Ronald Azmua's guide to graduate school (from a CS perspective).

Personal Interests

  • I co-authored the Python 2.1 Bible, published by Hungry Minds (now Wiley). Python is a superb high-level programming language; I highly recommend it.

  • I enjoy making and listening to music.

  • I enjoy making and playing video games.

  • Here are some pictures I took or made.

    Publications (newest first)

    Stephen Tanner, Pankaj Agarwal. Gene Vector Analysis (Geneva). BMC Bioinformatics, in press.

    Jianyin Shao, Stephen W. Tanner, Nephi Thompson, and Thomas E. Cheatham, III. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. Journal of Chemical Theory and Computation, 06-Oct-2007; (Article) DOI: 10.1021/ct700119m

    Stephen W. Tanner, "Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry" (PhD Dissertation, University of California, San Diego, 2007)

    Clustering Tandem Mass Spectra: From Spectral Libraries to Spectral Archives. Ari M. Frank, Nuno Bandeira, Zhouxin Shen, Stephen Tanner, Steven P. Briggs, Richard D. Smith, Pavel A. Pevzner. In preparation.

    Accurate Annotation of Peptide Modifications through Unrestrictive Database Search. Stephen Tanner, Samuel H. Payne, Surendra Dasari, Zhouxin Shen, Phillip Wilmarth, Larry David, William F. Loomis, Steven P. Briggs and Vineet Bafna 2007. Journal of Proteome Research, In press.

    Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Nitin Gupta, Stephen Tanner, Navdeep Jaitly, Joshua Adkins, Mary Lipton, Robert Edwards, Margaret Romine, Andrei Osterman, Vineet Bafna, Richard D. Smith, Pavel Pevzner, 2007. Genome Research 2007 Sep;17(9):1362-77. Epub 2007 Aug 9.

    Patricelli, M.P., Szardenings, A.K., Liyanage, M., Nomanbhoy, T.K., Wu, M., Weissig, H., Aban, A., Chun, D., Tanner, S., Kozarich, J.W., 2007. Functional Interrogation of the Kinome Using Nucleotide Acyl Phosphates. Biochemistry 46: 350-358.

    Improving gene annotation using peptide mass spectrometry. Stephen Tanner, Pavel A. Pevzner, Liliana Florea, Steve Briggs, Zhouxin Chen, Julio Ng, Roderic Guigo, and Vineet Bafna, 2007. Genome Research 17(2):231-239.

    Annotation of peptide mass spectra with a genomic exon graph. Stephen Tanner, Vineet Bafna. Poster presented at the 2006 ASMS conference in Seattle.

    Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Stephen Tanner, Pavel A. Pevzner, Vineet Bafna, 2006. Nature Protocols 1(1),67-72.

    Age-Related Changes in Human Crystallins Determined from Comparative Analysis of Post-Translational Modifications in Young and Aged Lens: Does Deamidation Contribute to Crystallin Insolubility? P.A. Wilmarth1, S. Tanner, S. Dasari, M.A. Riviere, V. Bafna, P.A. Pevzner, and L.L David, 2006. Journal of Proteome Research 5(10), 2554--2566.

    Identification of Post-translational Modifications via Blind Search of Mass-Spectra. Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner. Nature Biotechnology 23, 1562-2567 (01 Dec 2005).

    Identification of Post-translational Modifications via Blind Search of Mass-Spectra. Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, and Pavel A. Pevzner IEEE Computer Society Bioinformatics Conference (CSB) 2005.

    S. Tanner, H. Shu, A. Frank, L.Wang, E. Zandi, M. Mumby, P.A. Pevzner, and V. Bafna. Inspect: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra. Anal. Chem., 77(14):4626–4639, 2005.

    Peptide Sequence Tags for Fast Database Search in Mass Spectrometry. Ari Frank, Stephen Tanner, and Pavel Pevzner. Conference on Research in Computational Molecular Biology (RECOMB) 2005.

    Frank A, Tanner S, Bafna V, Pevzner P. Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res. 2005 Jul-Aug;4(4):1287-95.