Background:

I am a post-graduate scholar at the department of Computer Science and Engineering at the University of California, San Diego. My research interests involve machine learning, algorithms and bioinformatics. I am a member of the Computational Mass Spectrometry research group, where I work on various aspects of computational analysis of mass spectrometry data: de novo sequencing (the PepNovo algorithm), peptide tag generation, spectral clustering and filtering, interpretation of top-down mass spectra, and more.

Education:

2003-2008	Ph.D. in Computer Science, the University of California, San Diego Advisor: Prof. Pavel Pevzner
1999-2002	M.Sc. in Computer Science, Technion-Israel Institute of Technology Advisors: Prof. Dan Geiger and Dr. Zohar Yakhini
1999-2001	B.A. in Biology, Technion-Israel Institute of Technology
1996-1999	B.A. in Computer Science, Technion-Israel Institute of Technology

Publications:

Interpreting Top-Down Mass Spectra Using Spectral Alignment
Frank, A.M., Pesavento, J.J., Mizzen, C.A., Kelleher, N.L., Pevzner, P.A.
Analytical Chemistry, 80: 2499-2505, 2008. PubMed

 

Clustering Tandem Mass Spectra: From Spectral Libraries to Spectral Archives
Frank, A.M., Bandeira, N., Shen, Z., Tanner, S., Briggs, S.P., Smith, R.D. and Pevzner, P.A.

J. Proteome Research, 7:113-122, 2008 . PubMed

Protein Identification by Spectral Networks Analysis

Bandeira, N., Tsur, D., Frank, A., and Pevzner, P.A.

PNAS, 104:6140-6145, 2007. PubMed

Sequence similarity-driven proteomics in organisms with unknown genomes

by LC-MS/MS and automated de novo sequencing.

Waridel, P., Frank, A., Thomas, H., Surendranath, V., Sunyaev, S., Pevzner, P., Shevchenko A.

Proteomics. 7:2318-2329, 2007. PubMed

De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry
Frank, A.M., Savitski, M.M., Nielsen, M.L., Zubarev, R.A. and Pevzner, P.A.
J. Proteome Research, 6:114-123, 2007. PubMed

Rapid validation of protein identifications with the borderline statistical

confidence via de novo sequencing and MS BLAST searches.

Wielsch, N., Thomas, H., Surendranath, V., Waridel, P., Frank, A., Pevzner, P., Shevchenko A.

J. Proteome Research, 5:2448-2456, 2006. PubMed

Inspect: Fast and Accurate Identification of Post-Translationally Modified

Peptides from Tandem Mass Spectra

Tanner, S., Shu, H., Frank, A., Wang, L., Zandi, E., Mumby, M., Pevzner, P.A., and Bafna., V.

Anal. Chem., 77:4626–4639, 2005. PubMed

Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry

Frank, A., Tanner, S., Bafna, V. and Pevzner,  P.

J. Proteome Research, 4:1287-95, 2005. PubMed

PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling

Frank, A. and Pevzner, P.

Analytical Chemistry, 77:964-973, 2005. PubMed

 

A Distance-Based Branch and Bound Feature Selection Algorithm

Frank, A., Geiger, D. and Yakhini, Z.

Proceedings of the 19th Annual Conference on Uncertainty in Artificial Intelligence (UAI-03),
241-248, 2003. CiteSeer

 

 

 

Ari M. Frank

Computer Science and Engineering