Samuel H Payne, PhD
Senior Informatics Scientist, Pacific Northwest National Lab
3335 Q Ave. | Richland, WA99354
509-371-6513 |
Education
Doctor of Philosophy, Bioinformatics, University of California, San Diego (2008)
Advisor: Vineet Bafna
Co-Advisor: William F Loomis
Thesis: Advances in Computational Mass Spectrometry: Phosphoproteomics and Proteogenomics
Bachelor of Science, Computer Science, Brigham Young University (2002)
Phi Kappa Phi Honors Society
Specialization: Image Processing
FUNDING
Automated Proteogenomic Annotation for Prokaryotic Genomes
P.I.: Payne NSF (EF-0949047)
September 2009- August 2012 $707,345
Improved Sensitivity and Utility of Metaproteomics Analyses
P.I.: PayneDOE (Early Career)
August 2012 – July 2017$2,500,000
Research Experience
Senior Informatics Scientist Pacific Northwest National Laboratory
Meta-proteomics, proteogenomics, pan-omics
Data Visualization and collaboration
Assistant Professor of InformaticsJ Craig Venter Institute
Proteogenomic, comparative genomics and multi-genome annotation
Graduate Researcher: Computational Mass Spectrometry, Systems Biology
University of California, San Diego
Algorithms for improved sensitivity and specificity in proteomics
Discovered conservation pattern of metabolic pathways using comparative genomics.
Undergraduate Researcher: Image Processing and Pattern Recognition
National Institutes of Health and Brigham Young University
Implemented hybrid algorithm for 3D data storage reducing disk space by 95%. (BYU)
Streamlined data flow with new methods for particle recognition and image registration. (NIH)
Publications (from 45 total)
Payne SH. (2015) The utility of protein and mRNA correlation. Trends Biochem Sci. 40:1-3.
Payne SH, Monroe ME, Overall CC, Kiebel GR, et al., Smith RD. (2015) The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.Sci Data. 2:150041.
Prost SA, Crowell KL, Baker ES, Ibrahim YM, Clowers BH, Monroe ME, Anderson GA, Smith RD, Payne SH.(2014) Detecting and removing data artifacts in Hadamard transform ion mobility-mass spectrometry measurements.J Am Soc Mass Spectrom. 25(12):2020-7.
A Tovchigrechko, P Venepally, SH Payne. (2014) PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. Bioinformatics 30(10):1469-70.
Ansong C, Ortega C, Payne SH, Haft DH, et al., Wright AT. (2013) Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium tuberculosis.Chem Biol. 20(1):123-33.
Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolic L, Smith RD, Pevzner PA. (2012)Unexpected diversity of signal peptides in prokaryotes. mBio 3(6):e00339-12.
Haft DH, Payne SH, Selengut JD. (2012) Archaeosortases and exosortases: widely distributed systems linking membrane transit with posttranslational modification. J Bacteriol. 194(1):36-48.
Venter E, Smith RD, Payne SH. (2011) Proteogenomic analysis of bacteria and archaea: a 46 organism case study.PLoS One. 2011;6(11):e27587.
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP (2008) Discovery and revision of Arabidopsis genes by proteogenomics.. Proc Natl Acad Sci U S A. 105(52):21034-8
Payne SH, Yau M, Smolka MB, Zhou H, Bafna V (2008) Phosphorylation specific MS/MS scoring for rapid and accurate phospho-peptide analysis. J Proteome Res. 7:3373-81
Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth P, David L, Loomis WF, Briggs SP, Bafna V (2008) Accurate Annotation of Peptide Modifications through Unrestrictive Database Search. J Proteome Res 7:170-181
Payne SH and Loomis WF (2006) Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences. Eukaryot Cell 5(2):272-6.
Payne SH (2005) Metabolic pathways, p. 41-57. In W. F. Loomis and A. Kuspa (ed.), Dictyostelium genomics. Horizon Press, Far Hills, N.J.
Honors and Awards
National Science Foundation Plant Systems Biology IGERT Grant (2007-2008)
National Institutes of Health Bioinformatics Training Grant (2002-2005)
Research and Creative Activities Award (Brigham Young University, 2001)
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