Biomedical Research Education & Training
Faculty Member

Friedman, David B., Ph.D.
Adjunct Research Associate Professor of Biochemistry

Lab Url:

Phone Number: 343-7333

Email Address: david.friedman@Vanderbilt.Edu

Friedman, David's picture
Academic history
Ph.D., University of Washington, Seattle
B.S., University of California

Office Address   Mailing Address

9114C Medical Research Building III

9160 MRB III 465 21st Ave. S. 37232-8575

Research Specialty
Proteomics; differential protein expression and protein/peptide mass spectrometry.

Research Description
Proteomics is the study of the dynamic protein expression of a tissue, cell type or organism. As an Associate Director of the Proteomics Laboratory in the Mass Spectrometry Research Center from 2001-2012, I directed research and technology that targets differential protein expression upon various experimental treatments/conditions (2-dimensional difference gel electrophoresis; 2D DIGE), protein identification using tandem mass spectrometry from proteins isolated from polyacrylamide gels or in complex mixtures, characterize and map sites of protein post-translational modification using tandem mass spectrometry, and quantify relative protein abundance by selected/multiple reaction monitoring tandem mass spectrometry.

Betke, KM, Rose, KL, Friedman, DB, Baucum, AJ, Hyde, K, Schey, KL, Hamm, HE. Differential localization of G protein ???? subunits. Biochemistry, 53(14), 2329-43, 2014

Grabowska, MM, Elliott, AD, DeGraff, DJ, Anderson, PD, Anumanthan, G, Yamashita, H, Sun, Q, Friedman, DB, Hachey, DL, Yu, X, Sheehan, JH, Ahn, JM, Raj, GV, Piston, DW, Gronostajski, RM, Matusik, RJ. NFI transcription factors interact with FOXA1 to regulate prostate-specific gene expression. Mol Endocrinol, 28(6), 949-64, 2014

Ocak, S, Friedman, DB, Chen, H, Ausborn, JA, Hassanein, M, Detry, B, Weynand, B, Aboubakar, F, Pilette, C, Sibille, Y, Massion, PP. Discovery of new membrane-associated proteins overexpressed in small-cell lung cancer. J Thorac Oncol, 9(3), 324-36, 2014

Hill, MF, Patel, AV, Murphy, A, Smith, HM, Galindo, CL, Pentassuglia, L, Peng, X, Lenneman, CG, Odiete, O, Friedman, DB, Kronenberg, MW, Zheng, S, Zhao, Z, Song, Y, Harrell, FE, Srinivas, M, Ganguly, A, Iaci, J, Parry, TJ, Caggiano, AO, Sawyer, DB. Intravenous glial growth factor 2 (GGF2) isoform of neuregulin-1?? improves left ventricular function, gene and protein expression in rats after myocardial infarction. PLoS One, 8(2), e55741, 2013

McClain, CM, Friedman, DB, Hajri, T, Coffin, CM, Cates, JM. Predicting dedifferentiation in liposarcoma: a proteomic approach. Virchows Arch, 463(1), 85-92, 2013

Noto, JM, Gaddy, JA, Lee, JY, Piazuelo, MB, Friedman, DB, Colvin, DC, Romero-Gallo, J, Suarez, G, Loh, J, Slaughter, JC, Tan, S, Morgan, DR, Wilson, KT, Bravo, LE, Correa, P, Cover, TL, Amieva, MR, Peek, RM. Iron deficiency accelerates Helicobacter pylori-induced carcinogenesis in rodents and humans. J Clin Invest, 123(1), 479-92, 2013

Shi, J, Friedman, DB, Aiken, C. Retrovirus restriction by TRIM5 proteins requires recognition of only a small fraction of viral capsid subunits. J Virol, 87(16), 9271-8, 2013

Friedman, DB. Assessing signal-to-noise in quantitative proteomics: multivariate statistical analysis in DIGE experiments. Methods Mol Biol, 854, 31-45, 2012

Loh, JT, Friedman, DB, Piazuelo, MB, Bravo, LE, Wilson, KT, Peek, RM, Correa, P, Cover, TL. Analysis of Helicobacter pylori cagA promoter elements required for salt-induced upregulation of CagA expression. Infect Immun, 80(9), 3094-106, 2012

Pruitt, RN, Chumbler, NM, Rutherford, SA, Farrow, MA, Friedman, DB, Spiller, B, Lacy, DB. Structural determinants of Clostridium difficile toxin A glucosyltransferase activity. J Biol Chem, 287(11), 8013-20, 2012

Takahashi, K, Mernaugh, RL, Friedman, DB, Weller, R, Tsuboi, N, Yamashita, H, Quaranta, V, Takahashi, T. Thrombospondin-1 acts as a ligand for CD148 tyrosine phosphatase. Proc Natl Acad Sci U S A, 109(6), 1985-90, 2012

Venkateswaran, A, Friedman, DB, Walsh, AJ, Skala, MC, Sasi, S, Rachakonda, G, Crooks, PA, Freeman, ML, Sekhar, KR. The novel antiangiogenic VJ115 inhibits the NADH oxidase ENOX1 and cytoskeleton-remodeling proteins. Invest New Drugs, 2012

Viquez, OM, Caito, SW, McDonald, WH, Friedman, DB, Valentine, WM. Electrophilic adduction of ubiquitin activating enzyme E1 by N,N-diethyldithiocarbamate inhibits ubiquitin activation and is accompanied by striatal injury in the rat. Chem Res Toxicol, 25(11), 2310-21, 2012

Wegrzynowicz, M, Holt, HK, Friedman, DB, Bowman, AB. Changes in the striatal proteome of YAC128Q mice exhibit gene-environment interactions between mutant huntingtin and manganese. J Proteome Res, 11(2), 1118-32, 2012

Boutt??, AM, Friedman, DB, Bogyo, M, Min, Y, Yang, L, Lin, PC. Identification of a myeloid-derived suppressor cell cystatin-like protein that inhibits metastasis. FASEB J, 25(8), 2626-37, 2011

Friedman, DB, Andacht, TM, Bunger, MK, Chien, AS, Hawke, DH, Krijgsveld, J, Lane, WS, Lilley, KS, MacCoss, MJ, Moritz, RL, Settlage, RE, Sherman, NE, Weintraub, ST, Witkowska, HE, Yates, NA, Turck, CW. The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Proteomics, 11(8), 1371-81, 2011

Nam, EA, Zhao, R, Glick, GG, Bansbach, CE, Friedman, DB, Cortez, D. Thr-1989 phosphorylation is a marker of active ataxia telangiectasia-mutated and Rad3-related (ATR) kinase. J Biol Chem, 286(33), 28707-14, 2011

Rauth, TP, Slone, J, Crane, G, Correa, H, Friedman, DL, Lovvorn, HN. Laparoscopic nephron-sparing resection of synchronous Wilms tumors in a case of hyperplastic perilobar nephroblastomatosis. J Pediatr Surg, 46(5), 983-8, 2011

Smith, AL, Friedman, DB, Yu, H, Carnahan, RH, Reynolds, AB. ReCLIP (reversible cross-link immuno-precipitation): an efficient method for interrogation of labile protein complexes. PLoS One, 6(1), e16206, 2011

Cates, JM, Friedman, DB, Seeley, EH, Dupont, WD, Schwartz, HS, Holt, GE, Caprioli, RM, Young, PP. Proteomic analysis of osteogenic sarcoma: association of tumour necrosis factor with poor prognosis. Int J Exp Pathol, 91(4), 335-49, 2010

Dimitrova, YN, Li, J, Lee, YT, Rios-Esteves, J, Friedman, DB, Choi, HJ, Weis, WI, Wang, CY, Chazin, WJ. Direct ubiquitination of beta-catenin by Siah-1 and regulation by the exchange factor TBL1. J Biol Chem, 285(18), 13507-16, 2010

Loh, JT, Gupta, SS, Friedman, DB, Krezel, AM, Cover, TL. Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system. J Bacteriol, 192(8), 2034-43, 2010 PMCID:2849440

Sarilla, S, Habib, SY, Tollefsen, DM, Friedman, DB, Arnett, DR, Verhamme, IM. Glycosaminoglycan-binding properties and kinetic characterization of human heparin cofactor II expressed in Escherichia coli. Anal Biochem, 406(2), 166-75, 2010

Torres, VJ, Attia, AS, Mason, WJ, Hood, MI, Corbin, BD, Beasley, FC, Anderson, KL, Stauff, DL, McDonald, WH, Zimmerman, LJ, Friedman, DB, Heinrichs, DE, Dunman, PM, Skaar, EP. Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia. Infect Immun, 78(4), 1618-28, 2010 PMCID:2849423

Franco, AT, Friedman, DB, Nagy, TA, Romero-Gallo, J, Krishna, U, Kendall, A, Israel, DA, Tegtmeyer, N, Washington, MK, Peek, RM. Delineation of a carcinogenic Helicobacter pylori proteome. Mol Cell Proteomics, 8(8), 1947-58, 2009

Friedman, DB, Hoving, S, Westermeier, R. Isoelectric focusing and two-dimensional gel electrophoresis. Methods Enzymol, 463, 515-40, 2009

Wang, Y, Azuma, Y, Friedman, DB, Coffey, RJ, Neufeld, KL. Novel association of APC with intermediate filaments identified using a new versatile APC antibody. BMC Cell Biol, 10, 75, 2009 PMCID:2774295

Friedman, DB, Lilley, KS. Optimizing the difference gel electrophoresis (DIGE) technology. Methods Mol Biol, 428, 93-124, 2008

Gibson, F, Anderson, L, Babnigg, G, Baker, M, Berth, M, Binz, PA, Borthwick, A, Cash, P, Day, BW, Friedman, DB, Garland, D, Gutstein, HB, Hoogland, C, Jones, NA, Khan, A, Klose, J, Lamond, AI, Lemkin, PF, Lilley, KS, Minden, J, Morris, NJ, Paton, NW, Pisano, MR, Prime, JE, Rabilloud, T, Stead, DA, Taylor, CF, Voshol, H, Wipat, A, Jones, AR. Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol, 26(8), 863-4, 2008

Meyrick, BO, Friedman, DB, Billheimer, DD, Cogan, JD, Prince, MA, Phillips, JA, Loyd, JE. Proteomics of transformed lymphocytes from a family with familial pulmonary arterial hypertension. Am J Respir Crit Care Med, 177(1), 99-107, 2008 PMCID:2176118

Friedman, DB. Quantitative proteomics for two-dimensional gels using difference gel electrophoresis. Methods Mol Biol, 367, 219-39, 2007

Friedman, DB, Wang, SE, Whitwell, CW, Caprioli, RM, Arteaga, CL. Multivariable difference gel electrophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2 signaling. Mol Cell Proteomics, 6(1), 150-69, 2007

Haas, KF, Miller, SL, Friedman, DB, Broadie, K. The ubiquitin-proteasome system postsynaptically regulates glutamatergic synaptic function. Mol Cell Neurosci, 35(1), 64-75, 2007 PMCID:1936977

Hamblin, M, Friedman, DB, Hill, S, Caprioli, RM, Smith, HM, Hill, MF. Alterations in the diabetic myocardial proteome coupled with increased myocardial oxidative stress underlies diabetic cardiomyopathy. J Mol Cell Cardiol, 42(4), 884-95, 2007 PMCID:2677446

Keller, JW, Franklin, JL, Graves-Deal, R, Friedman, DB, Whitwell, CW, Coffey, RJ. Oncogenic KRAS provides a uniquely powerful and variable oncogenic contribution among RAS family members in the colonic epithelium. J Cell Physiol, 210(3), 740-9, 2007

Khoshnoodi, J, Hill, S, Tryggvason, K, Hudson, B, Friedman, DB. Identification of N-linked glycosylation sites in human nephrin using mass spectrometry. J Mass Spectrom, 42(3), 370-379, 2007

Pollins, AC, Friedman, DB, Nanney, LB. Proteomic Investigation of Human Burn Wounds by 2D-Difference Gel Electrophoresis and Mass Spectrometry. J Surg Res, 2007 PMCID:2696121

Robertson, PD, Warren, EM, Zhang, H, Friedman, DB, Lary, JW, Cole, JL, Tutter, AV, Walter, JC, Fanning, E, Eichman, BF. Domain architecture and biochemical characterization of vertebrate MCM10. J Biol Chem, 2007 PMCID:2753450

Viquez, OM, Valentine, HL, Friedman, DB, Olson, SJ, Valentine, WM. Peripheral Nerve Protein Expression and Carbonyl Content in N,N-Diethlydithiocarbamate Myelinopathy. Chem Res Toxicol, 2007 PMCID:2525616

Wang, SE, Narasanna, A, Whitell, CW, Wu, FY, Friedman, DB, Arteaga, CL. Convergence of p53 and Transforming Growth Factor beta (TGFbeta) Signaling on Activating Expression of the Tumor Suppressor Gene maspin in Mammary Epithelial Cells. J Biol Chem, 282(8), 5661-9, 2007

Anumanthan, G, Halder, SK, Friedman, DB, Datta, PK. Oncogenic serine-threonine kinase receptor-associated protein modulates the function of Ewing sarcoma protein through a novel mechanism. Cancer Res, 66(22), 10824-32, 2006

Busler, VJ, Torres, VJ, McClain, MS, Tirado, O, Friedman, DB, Cover, TL. Protein-protein interactions among Helicobacter pylori cag proteins. J Bacteriol, 188(13), 4787-800, 2006 PMCID:1482994

Friedman, DB, Stauff, DL, Pishchany, G, Whitwell, CW, Torres, VJ, Skaar, EP. Staphylococcus aureus redirects central metabolism to increase iron availability. PLoS Pathog, 2(8), e87, 2006 PMCID:1557832

Tabb, DL, Friedman, DB, Ham, AJ. Verification of automated peptide identifications from proteomic tandem mass spectra. Nat Protoc, 1(5), 2213-22, 2006

Wang, SE, Shin, I, Wu, FY, Friedman, DB, Arteaga, CL. HER2/Neu (ErbB2) signaling to Rac1-Pak1 is temporally and spatially modulated by transforming growth factor beta. Cancer Res, 66(19), 9591-600, 2006

Tian, C, Breyer, RM, Kim, HJ, Karra, MD, Friedman, DB, Karpay, A, Sanders, CR. Solution NMR spectroscopy of the human vasopressin V2 receptor, a G protein-coupled receptor. J Am Chem Soc, 127(22), 8010-1, 2005

Vanacore, RM, Friedman, DB, Ham, AJ, Sundaramoorthy, M, Hudson, BG. Identification of S-hydroxylysyl211-methionine93 as the covalent crosslink of the noncollagenous (NC1) hexamer of the alpha 1alpha 1alpha 2 collagen IV network: A role for the posttranslational modification of lysine211 to hydroxylysine211 in hexamer assembly. J Biol Chem, 2005

Zhang, Yong Q, Friedman, David B, Wang, Zhe, Woodruff, Elvin, Pan, Luyuan, O''donnell, Janis, Broadie, Kendal. Protein expression profiling of the drosophila fragile X mutant brain reveals upregulation of monoamine synthesis. Mol Cell Proteomics, 2005

Chytil, Anna, Waltner-Law, Mary, West, Robert, Friedman, David, Aakre, Mary, Barker, Dana, Law, Brian. Construction of a cyclin D1-Cdk2 fusion protein to model the biological functions of cyclin D1-Cdk2 complexes. J Biol Chem, 279(46), 47688-98, 2004

Daikoku, Takiko, Tranguch, Susanne, Friedman, David B, Das, Sanjoy K, Smith, David F, Dey, Sudhansu K. Proteomic analysis identifies immunophilin FKBP52 as a downstream target of Hoxa10 in the periimplantation mouse uterus. Mol Endocrinol, 2004

Friedman, DB, Hill, S, Keller, JW, Merchant, NB, Levy, SE, Coffey, RJ, Caprioli, RM. Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics, 4(3), 793-811, 2004

Gerbasi, Vincent R, Weaver, Connie M, Hill, Salisha, Friedman, David B, Link, Andrew J. Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression. Mol Cell Biol, 24(18), 8276-87, 2004 PMCID:515043

Lilley, KS, Friedman, DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics, 1(4), 401-9, 2004

Vanacore, Roberto M., Shanmugasundararaj, Sivananthaperumal, Friedman, David B., Bondar, Olga, Hudson, Billy G., Sundaramoorthy, Munirathinam. The a1.a2-network of collagen IV: Reinforced stabilization of the noncollagenous domain-1 by noncovalent forces and the absence of Met-Lys crosslinks. J Biol Chem, 2004

Zhang, YQ, Matthies, HJ, Mancuso, J, Andrews, HK, Woodruff, E, Friedman, D, Broadie, K. The Drosophila fragile X-related gene regulates axoneme differentiation during spermatogenesis. Dev Biol, 270(2), 290-307, 2004

Low, RL, Orton, S, Friedman, DB. A truncated form of DNA topoisomerase IIbeta associates with the mtDNA genome in mammalian mitochondria. Eur J Biochem, 270(20), 4173-86, 2003

Matsuoka, TA, Zhao, L, Artner, I, Jarrett, HW, Friedman, D, Means, A, Stein, R. Members of the large Maf transcription family regulate insulin gene transcription in islet beta cells. Mol Cell Biol, 23(17), 6049-62, 2003 PMCID:180917

Sekhar, KR, Crooks, PA, Sonar, VN, Friedman, DB, Chan, JY, Meredith, MJ, Starnes, JH, Kelton, KR, Summar, SR, Sasi, S, Freeman, ML. NADPH oxidase activity is essential for Keap1/Nrf2-mediated induction of GCLC in response to 2-indol-3-yl-methylenequinuclidin-3-ols. Cancer Res, 63(17), 5636-45, 2003

Friedman, DB, Kern, JW, Huneycutt, BJ, Vinh, DB, Crawford, DK, Steiner, E, Scheiltz, D, Yates, J, Resing, KA, Ahn, NG, Winey, M, Davis, TN. Yeast Mps1p phosphorylates the spindle pole component Spc110p in the N-terminal domain. J Biol Chem, 276(21), 17958-67, 2001

Kironmai, KM, Muniyappa, K, Friedman, DB, Hollingsworth, NM, Byers, B. DNA-binding activities of Hop1 protein, a synaptonemal complex component from Saccharomyces cerevisiae. Mol Cell Biol, 18(3), 1424-35, 1998 PMCID:108856

Friedman, DB, Sundberg, HA, Huang, EY, Davis, TN. The 110-kD spindle pole body component of Saccharomyces cerevisiae is a phosphoprotein that is modified in a cell cycle-dependent manner. J Cell Biol, 132(5), 903-14, 1996 PMCID:2120732

Friedman, DB, Hollingsworth, NM, Byers, B. Insertional mutations in the yeast HOP1 gene: evidence for multimeric assembly in meiosis. Genetics, 136(2), 449-64, 1994 PMCID:1205800

Friedman, DB, Johnson, TE. A mutation in the age-1 gene in Caenorhabditis elegans lengthens life and reduces hermaphrodite fertility. Genetics, 118(1), 75-86, 1988 PMCID:1203268

Friedman, DB, Johnson, TE. Three mutants that extend both mean and maximum life span of the nematode, Caenorhabditis elegans, define the age-1 gene. J Gerontol, 43(4), B102-9, 1988

Johnson, TE, Friedman, DB, Fitzpatrick, PA, Conley, WL. Mutant genes that extend life span. Basic Life Sci, 42, 91-100, 1987

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