Samuel H. Payne, Ph.D. - Publications

Affiliations: 
2008 Bioinformatics University of California, San Diego, La Jolla, CA 
Area:
chemotactic motility in developed Dictyostelium

40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, et al. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nature Microbiology. 1: 16065. PMID 27573103 DOI: 10.1038/nmicrobiol.2016.65  1
2016 Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, et al. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. PMID 27372738 DOI: 10.1016/j.cell.2016.05.069  1
2015 Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, ... ... Payne SH, et al. Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts. Journal of Proteome Research. PMID 26653538 DOI: 10.1021/acs.jproteome.5b00859  1
2015 Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, ... ... Payne S, et al. An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer. Molecular & Cellular Proteomics : McP. PMID 26631509 DOI: 10.1074/mcp.M115.056226  1
2015 Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, Smith RD. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. Scientific Data. 2: 150041. PMID 26306205 DOI: 10.1038/sdata.2015.41  1
2015 Gibbons BC, Chambers MC, Monroe ME, Tabb DL, Payne SH. Correcting systematic bias and instrument measurement drift with mzRefinery. Bioinformatics (Oxford, England). PMID 26243018 DOI: 10.1093/bioinformatics/btv437  1
2015 Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold RH, Smith RD, Noble WS, MacCoss MJ. Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Molecular & Cellular Proteomics : McP. PMID 26217018 DOI: 10.1074/mcp.O114.047035  1
2015 Wu C, Monroe ME, Xu Z, Slysz GW, Payne SH, Rodland KD, Liu T, Smith RD. An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics. Journal of the American Society For Mass Spectrometry. PMID 26015166 DOI: 10.1007/s13361-015-1169-z  1
2015 Payne SH. The utility of protein and mRNA correlation. Trends in Biochemical Sciences. 40: 1-3. PMID 25467744 DOI: 10.1016/j.tibs.2014.10.010  1
2015 Xu Z, Wu C, Xie F, Slysz GW, Tolic N, Monroe ME, Petyuk VA, Payne SH, Fujimoto GM, Moore RJ, Fillmore TL, Schepmoes AA, Levine DA, Townsend RR, Davies SR, et al. Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes. Journal of Proteome Research. 14: 422-33. PMID 25350482 DOI: 10.1021/pr500840w  1
2014 Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM. Bayesian proteoform modeling improves protein quantification of global proteomic measurements. Molecular & Cellular Proteomics : McP. 13: 3639-46. PMID 25433089 DOI: 10.1074/mcp.M113.030932  1
2014 Woo S, Cha SW, Na S, Guest C, Liu T, Smith RD, Rodland KD, Payne S, Bafna V. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data. Proteomics. 14: 2719-30. PMID 25263569 DOI: 10.1002/pmic.201400206  1
2014 Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, et al. Proteogenomic characterization of human colon and rectal cancer. Nature. 513: 382-7. PMID 25043054 DOI: 10.1038/nature13438  1
2014 Kronewitter SR, Slysz GW, Marginean I, Hagler CD, LaMarche BL, Zhao R, Harris MY, Monroe ME, Polyukh CA, Crowell KL, Fillmore TL, Carlson TS, Camp DG, Moore RJ, Payne SH, et al. GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization. Analytical Chemistry. 86: 6268-76. PMID 24881670 DOI: 10.1021/ac501492f  1
2014 Prost SA, Crowell KL, Baker ES, Ibrahim YM, Clowers BH, Monroe ME, Anderson GA, Smith RD, Payne SH. Detecting and removing data artifacts in Hadamard transform ion mobility-mass spectrometry measurements. Journal of the American Society For Mass Spectrometry. 25: 2020-7. PMID 24796262 DOI: 10.1007/s13361-014-0895-y  1
2014 Amidan BG, Orton DJ, Lamarche BL, Monroe ME, Moore RJ, Venzin AM, Smith RD, Sego LH, Tardiff MF, Payne SH. Signatures for mass spectrometry data quality. Journal of Proteome Research. 13: 2215-22. PMID 24611607 DOI: 10.1021/pr401143e  1
2014 Ryu SY, Payne SH, Schaab C, Xiao W. Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013. Bioinformatics (Oxford, England). 30: 2089-90. PMID 24590439 DOI: 10.1093/bioinformatics/btu116  1
2014 Tovchigrechko A, Venepally P, Payne SH. PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. Bioinformatics (Oxford, England). 30: 1469-70. PMID 24470574 DOI: 10.1093/bioinformatics/btu051  1
2014 Slysz GW, Steinke L, Ward DM, Klatt CG, Clauss TR, Purvine SO, Payne SH, Anderson GA, Smith RD, Lipton MS. Automated data extraction from in situ protein-stable isotope probing studies. Journal of Proteome Research. 13: 1200-10. PMID 24467184 DOI: 10.1021/pr400633j  1
2014 Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH. Accounting for population variation in targeted proteomics. Journal of Proteome Research. 13: 321-3. PMID 24320210 DOI: 10.1021/pr4011052  1
2013 Crowell KL, Baker ES, Payne SH, Ibrahim YM, Monroe ME, Slysz GW, LaMarche BL, Petyuk VA, Piehowski PD, Danielson WF, Anderson GA, Smith RD. Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry. International Journal of Mass Spectrometry. 354: 312-317. PMID 25089116 DOI: 10.1016/j.ijms.2013.06.028  1
2013 Crowell KL, Slysz GW, Baker ES, LaMarche BL, Monroe ME, Ibrahim YM, Payne SH, Anderson GA, Smith RD. LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. Bioinformatics (Oxford, England). 29: 2804-5. PMID 24008421 DOI: 10.1093/bioinformatics/btt465  1
2013 Abdul Halim MF, Pfeiffer F, Zou J, Frisch A, Haft D, Wu S, Tolić N, Brewer H, Payne SH, Paša-Tolić L, Pohlschroder M. Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein. Molecular Microbiology. 88: 1164-75. PMID 23651326 DOI: 10.1111/mmi.12248  1
2013 Ivankov DN, Payne SH, Galperin MY, Bonissone S, Pevzner PA, Frishman D. How many signal peptides are there in bacteria? Environmental Microbiology. 15: 983-90. PMID 23556536 DOI: 10.1111/1462-2920.12105  1
2013 Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, Smith RD, Adkins JN, Grundner C, Wright AT. Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Chemistry & Biology. 20: 123-33. PMID 23352146 DOI: 10.1016/j.chembiol.2012.11.008  1
2012 Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolić L, Smith RD, Pevzner PA. Unexpected diversity of signal peptides in prokaryotes. Mbio. 3. PMID 23169999 DOI: 10.1128/mBio.00339-12  1
2012 Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. Bmc Genomics. 13: 131. PMID 22480257 DOI: 10.1186/1471-2164-13-131  1
2012 Schrimpe-Rutledge AC, Jones MB, Chauhan S, Purvine SO, Sanford JA, Monroe ME, Brewer HM, Payne SH, Ansong C, Frank BC, Smith RD, Peterson SN, Motin VL, Adkins JN. Comparative omics-driven genome annotation refinement: application across Yersiniae. Plos One. 7: e33903. PMID 22479471 DOI: 10.1371/journal.pone.0033903  1
2012 Haft DH, Payne SH, Selengut JD. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. Journal of Bacteriology. 194: 36-48. PMID 22037399 DOI: 10.1128/JB.06026-11  1
2011 Venter E, Smith RD, Payne SH. Proteogenomic analysis of bacteria and archaea: a 46 organism case study. Plos One. 6: e27587. PMID 22114679 DOI: 10.1371/journal.pone.0027587  1
2011 Pieper R, Zhang Q, Clark DJ, Huang ST, Suh MJ, Braisted JC, Payne SH, Fleischmann RD, Peterson SN, Tzipori S. Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies. Plos One. 6: e26554. PMID 22087229 DOI: 10.1371/journal.pone.0026554  1
2011 Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, et al. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. Bmc Genomics. 12: 433. PMID 21867535 DOI: 10.1186/1471-2164-12-433  1
2010 Payne SH, Huang ST, Pieper R. A proteogenomic update to Yersinia: enhancing genome annotation. Bmc Genomics. 11: 460. PMID 20687929 DOI: 10.1186/1471-2164-11-460  1
2008 Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. Discovery and revision of Arabidopsis genes by proteogenomics. Proceedings of the National Academy of Sciences of the United States of America. 105: 21034-8. PMID 19098097 DOI: 10.1073/pnas.0811066106  1
2008 Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. Journal of Proteome Research. 7: 3373-81. PMID 18563926 DOI: 10.1021/pr800129m  1
2008 Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Molecular & Cellular Proteomics : McP. 7: 1389-96. PMID 18407956 DOI: 10.1074/mcp.M700468-MCP200  1
2008 Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V. Accurate annotation of peptide modifications through unrestrictive database search. Journal of Proteome Research. 7: 170-81. PMID 18034453 DOI: 10.1021/pr070444v  1
2007 Rana BK, Insel PA, Payne SH, Abel K, Beutler E, Ziegler MG, Schork NJ, O'Connor DT. Population-based sample reveals gene-gender interactions in blood pressure in White Americans. Hypertension. 49: 96-106. PMID 17159089 DOI: 10.1161/01.HYP.0000252029.35106.67  1
2006 Hirose S, Payne SH, Loomis WF. cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum. Eukaryotic Cell. 5: 1104-10. PMID 16835454 DOI: 10.1128/EC.00047-06  1
2006 Payne SH, Loomis WF. Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences. Eukaryotic Cell. 5: 272-6. PMID 16467468 DOI: 10.1128/EC.5.2.272-276.2006  1
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