Payne, Samuel


Email: 2ucowgnaRc{pgBd{w0gfw  (Email Form)


4029  LSB
Provo, UT 84602
(801) 422-6652

Associate Professor

Curriculum Vitae

Dr. Payne received a B.S. of computer science at Brigham Young University and a Ph.D. in Bioinformatics from UC, San Diego working. His current research focuses on cancer biology, algorithm design and data integration.
 Teaching Interests
Algorithms in bioinformatics, bioethics, research methodology, undergraduate training
 Research Interests
Bioinformatics, cancer biology, proteomics, protein function
  • Doctor of Philosophy, Bioinformatics, UC San Diego, 2008
  • Bachelor of Science, Computer Science, Brigham Young University, 2002

  • Senior Bioinformatics Scientist, Pacific Northwest National Library, 2010-2018
  • Bioinformatics Engineer - Principle Investigator, J Craig Venter Institute, 2008-2010

 Courses Taught

Fall 2018
  • BIO 494R: Mentored Research Section 028

Selected Publications

Journal Articles

Jarman KH, Heller NC, Jenson SC, Hutchison JR, Payne SH, Wunschel DS, Merkley ED. 2018. Proteomics Goes to Court: A Statistical Foundation for Forensic Toxin/Organism Identification Using Bottom-Up Proteomics.  doi:10.1021/acs.jproteome.8b00212

Lee JY, Fujimoto GM, Wilson R, Wiley HS, Payne SH. 2018. Blazing Signature Filter: a library for fast pairwise similarity comparisons. 19(1):221.  doi:10.1186/s12859-018-2210-6

The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. 2018. A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms. Journal of proteome research. 17(5):1879-1886.  doi:10.1021/acs.jproteome.7b00899

Nakayasu ES, Burnet MC, Walukiewicz HE, Wilkins CS, Shukla AK, Brooks S, Plutz MJ, Lee BD, Schilling B, Wolfe AJ, et al. 2017. Ancient Regulatory Role of Lysine Acetylation in Central Metabolism. 8(6).  doi:10.1128/mBio.01894-17

Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, et al. 2017. Informed-Proteomics: open-source software package for top-down proteomics. 14(9):909-914.  doi:10.1038/nmeth.4388

Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ. 2017. PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data. 14(9):903-908.  doi:10.1038/nmeth.4390

Kyle JE, Crowell KL, Casey CP, Fujimoto GM, Kim S, Dautel SE, Smith RD, Payne SH, Metz TO. 2017. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. 33(11):1744-1746.  doi:10.1093/bioinformatics/btx046

Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. 2017. Methods, Tools and Current Perspectives in Proteogenomics. 16(6):959-981.  doi:10.1074/mcp.MR117.000024

Na S, Payne SH, Bandeira N. 2016. Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks. 15(11):3501-3512.  doi:10.1074/mcp.O116.060913

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, et al. 2016. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. 166(3):755-765.  doi:10.1016/j.cell.2016.05.069

Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, et al. 2016. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. 1(8):16065.  doi:10.1038/nmicrobiol.2016.65

Gibbons BC, Chambers MC, Monroe ME, Tabb DL, Payne SH. 2015. Correcting systematic bias and instrument measurement drift with mzRefinery. 31(23):3838-40.  doi:10.1093/bioinformatics/btv437

Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, et al. 2015. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. 2:150041.  doi:10.1038/sdata.2015.41

Tripp HJ, Sutton G, White O, Wortman J, Pati A, Mikhailova N, Ovchinnikova G, Payne SH, Kyrpides NC, Ivanova N. 2015. Toward a standard in structural genome annotation for prokaryotes. 10:45.  doi:10.1186/s40793-015-0034-9

Payne SH. 2015. The utility of protein and mRNA correlation. 40(1):1-3.  doi:10.1016/j.tibs.2014.10.010

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. 25(12):2020-2027.  doi:10.1007/s13361-014-0895-y

Amidan BG, Orton DJ, Lamarche BL, Monroe ME, Moore RJ, Venzin AM, Smith RD, Sego LH, Tardiff MF, Payne SH. 2014. Signatures for mass spectrometry data quality. 13(4):2215-22.  doi:10.1021/pr401143e

Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH. 2014. Accounting for population variation in targeted proteomics. 13(1):321-3.  doi:10.1021/pr4011052

Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, et al. 2013. Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. 20(1):123-33.  doi:10.1016/j.chembiol.2012.11.008

Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolić L, Smith RD, Pevzner PA. 2012. Unexpected diversity of signal peptides in prokaryotes. 3(6).  doi:10.1128/mBio.00339-12

Haft DH, Payne SH, Selengut JD. 2012. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. 194(1):36-48.  doi:10.1128/JB.06026-11

Venter E, Smith RD, Payne SH. 2011. Proteogenomic analysis of bacteria and archaea: a 46 organism case study. 6(11):e27587.  doi:10.1371/journal.pone.0027587

Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. 2008. Discovery and revision of Arabidopsis genes by proteogenomics. 105(52):21034-8.  doi:10.1073/pnas.0811066106

Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. 2008. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. 7(8):3373-81.  doi:10.1021/pr800129m


Oliphant AE, Hoskins EL, Adams DW, Beecroft SJ, Payne SH. Effects of TP53 Mutation on Protein Expression and Function in Endometrial Cancer. Rocky Mountain Bioinformatics conference. Snowmass CO. 2018 .

Adams DW, Beecroft SJ, Hoskins EL, Oliphant AE, Payne SH. Facilitating CPTAC Data for Data Scientists. Rocky Mountain Bioinformatics conference. Snowmass CO. 2018 .

Payne SH. Proteomics of natural bacterial isolates via deep learning-based de novo identification. Rocky Mountain Bioinformatics conference. Snowmass CO. 2018 .

Payne SH. Proteomics of natural bacterial isolates via deep learning-based de novo identification. Rocky Mountain Bioinformatics conference. Snowmass CO. 2018 .

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