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 Prof. David L Tabb

Position: Professor Extraordinary in Biotechnology
Department: Department of Biotechnology
Faculty: Faculty of Natural Science
Qualifications: BSc (1996 University of Arkansas—Fayetteville),
PhD (2003 University of Washington—Seattle)
Tel:  
Fax:  
Email: dtabb@sun.ac.za 
Research:
 
 
 
 

Biography

 An American by birth, I learned to program computers while in primary school, and I gained a love for biology while in high school.  I chose to major in biology with a minor in computer science while studying for my Bachelor of Science, and so attending a Molecular Biotechnology graduate program for my Ph.D. helped combine these two interests into one discipline.  I served as a post-doctoral fellow in the Genomes to Life program at the Oak Ridge National Laboratory (2003—2005).  For ten years I served as an assistant professor and then an associate professor at the Department of Biomedical Informatics at Vanderbilt University, teaching a semester-long course introducing bioinformatics and conducting research as part of the NCI Clinical Proteomic Technology Assessment for Cancer program.  In 2015, I decided to leave Vanderbilt University to come to Stellenbosch University, here in South Africa.  The unique combination of significant public health threats in infectious disease and a powerful research infrastructure made me feel that Cape Town would be a place where my career could have the most beneficial impact.

Research:
My group conducts research in bioinformatics, with a particular emphasis on mass spectrometry-based proteomics.  We are part of the South African Tuberculosis Bioinformatics Initiative at Stellenbosch University Faculty of Medicine and Health Sciences (Tygerberg Hospital).

Publications

1.            Tabb DL, Saraf A, Yates JR. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem. 2003 Dec 1;75(23):6415–6421. PMCID: PMC2915448



2.            Tabb DL, Ma Z-Q, Martin DB, Ham A-JL, Chambers MC. DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res. 2008 Sep;7(9):3838–3846. PMCID: PMC2810657


3.            Dasari S, Chambers MC, Slebos RJ, Zimmerman LJ, Ham A-JL, Tabb DL. TagRecon: high-throughput mutation identification through sequence tagging. J Proteome Res. 2010 Apr 5;9(4):1716–1726. PMCID: PMC2859315


4.            Dasari S, Chambers MC, Codreanu SG, Liebler DC, Collins BC, Pennington SR, Gallagher WM, Tabb DL. Sequence tagging reveals unexpected modifications in toxicoproteomics. Chem Res Toxicol. 2011 Feb 18;24(2):204–216. PMCID: PMC3042045


5.            Tabb DL, Fernando CG, Chambers MC. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res. 2007 Feb;6(2):654–661. PMCID: PMC2525619


6.            Dasari S, Chambers MC, Martinez MA, Carpenter KL, Ham A-JL, Vega-Montoto LJ, Tabb DL. Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment. J Proteome Res. 2012 Mar 2;11(3):1686–1695. PMCID: PMC3292681


7.            Zhang B, Chambers MC, Tabb DL. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res. 2007 Sep;6(9):3549–3557. PMCID: PMC2810678


8.            Ma Z-Q, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL. IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. J Proteome Res. 2009 Aug;8(8):3872–3881. PMCID: PMC2810655


9.            Tabb DL, Vega-Montoto L, Rudnick PA, Variyath AM, Ham A-JL, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski KA, Neubert TA, Regnier FE, Schilling B, Tegeler TJ, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Fisher SJ, Gibson BW, Kinsinger CR, Mesri M, Rodriguez H, Stein SE, Tempst P, Paulovich AG, Liebler DC, Spiegelman C. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res. 2010 Feb 5;9(2):761–776. PMCID: PMC2818771


10.          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 MJC, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou J-Y, Liebler DC. Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts. J Proteome Res. 2015 Dec 22; PMID: 26653538


11.          Wang X, Chambers MC, Vega-Montoto LJ, Bunk DM, Stein SE, Tabb DL. QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics. Anal Chem. 2014 Mar 4;86(5):2497–2509. PMCID: PMC3982976


12.          Bennett KL, Wang X, Bystrom CE, Chambers MC, Andacht TM, Dangott LJ, Elortza F, Leszyk J, Molina H, Moritz RL, Phinney BS, Thompson JW, Bunger MK, Tabb DL. The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses. Mol Cell Proteomics. 2015 Dec;14(12):3299–3309. PMID: 26435129


13.          Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak M-Y, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P. A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol. 2012 Oct;30(10):918–920. PMCID: PMC3471674


14.          French WR, Zimmerman LJ, Schilling B, Gibson BW, Miller CA, Townsend RR, Sherrod SD, Goodwin CR, McLean JA, Tabb DL. Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard’s msConvert. J Proteome Res. 2015 Feb 6;14(2):1299–1307. PMCID: PMC4324452


15.          Seymour SL, Farrah T, Binz P-A, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR. A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics. 2014 Nov;14(21–22):2389–2399. PMCID: PMC4384534

 

Networks

 American Society of Mass Spectrometry
Association of Biomolecular Resource Facilities
Human Proteomics Organization—Proteomics Standards Initiative

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