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Parag Mallick, PhD
Research Assistant Professor of Medicine (Part Time)
CSC 240 Health Sciences Campus Los Angeles
+1 323 442 2839


Dr. Mallick's primary appointment is as Director of Clinical Proteomics at the CAMM. In addition, he is an Assistant Professor of Chemistry and Biochemistry at the University of California, Los Angeles. Dr. Mallick received his undergraduate degree in Computer Science and Biochemistry from Washington University in St. Louis, and his graduate degree with David Eisenberg at UCLA. His postdoctoral research, with Ruedi Aebersold at the Institute for Systems Biology, focused on quantitative and clinical proteomics. His current research interests focus on development of tools for quantitative, proteome-scale analyses of protein structure and function and on the application of those tools to global profiling for predictive, personalized cancer diagnosis and prognosis. His research bridges the interface between experimental studies and analytic computational challenges.


NIH-NIGMS: Biotechnology Fellowship, 1999

NSF IGERT: Fellowship, 2000-2002

University of California, Los Angeles: Chemistry Graduate Teaching Excellence Award, 1998

Leadershape Institute: Scholarship, 1996


Park SM, Lee JY, Hong S, Lee SH, Dimov IK, Lee H, Suh S, Pan Q, Li K, Wu AM, Mumenthaler SM, Mallick P, Lee LP. Dual transcript and protein quantification in a massive single cell array. Lab Chip. 2016 Oct 7; 16(19):3682-8. View in: PubMed

Garvey CM, Spiller E, Lindsay D, Chiang CT, Choi NC, Agus DB, Mallick P, Foo J, Mumenthaler SM. A high-content image-based method for quantitatively studying context-dependent cell population dynamics. Sci Rep. 2016; 6:29752. View in: PubMed

Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M. Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Med. 2016; 8(1):54. View in: PubMed

Li K, Zettlitz KA, Lipianskaya J, Zhou Y, Marks JD, Mallick P, Reiter RE, Wu AM. A fully human scFv phage display library for rapid antibody fragment reformatting. Protein Eng Des Sel. 2015 Oct; 28(10):307-16. View in: PubMed

Frieboes HB, Curtis LT, Wu M, Kani K, Mallick P. Simulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor. Cancer Inform. 2015; 14:163-75. View in: PubMed

Frieboes HB, Smith BR, Wang Z, Kotsuma M, Ito K, Day A, Cahill B, Flinders C, Mumenthaler SM, Mallick P, Simbawa E, Al-Fhaid AS, Mahmoud SR, Gambhir SS, Cristini V. Predictive Modeling of Drug Response in Non-Hodgkin's Lymphoma. PLoS One. 2015; 10(6):e0129433. View in: PubMed

Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P. The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells. Cancer Inform. 2015; 14(Suppl 4):19-31. View in: PubMed

Li K, Tavaré R, Zettlitz KA, Mumenthaler SM, Mallick P, Zhou Y, Marks JD, Wu AM. Anti-MET ImmunoPET for Non-Small Cell Lung Cancer Using Novel Fully Human Antibody Fragments. Mol Cancer Ther. 2014 Nov; 13(11):2607-17. View in: PubMed

Byun S, Son S, Amodei D, Cermak N, Shaw J, Kang JH, Hecht VC, Winslow MM, Jacks T, Mallick P, Manalis SR. Characterizing deformability and surface friction of cancer cells. Proc Natl Acad Sci U S A. 2013 May 7; 110(19):7580-5. View in: PubMed

Kani K, Malihi PD, Jiang Y, Wang H, Wang Y, Ruderman DL, Agus DB, Mallick P, Gross ME. Anterior gradient 2 (AGR2): blood-based biomarker elevated in metastatic prostate cancer associated with the neuroendocrine phenotype. Prostate. 2013 Feb 15; 73(3):306-15. View in: PubMed

A physical sciences network characterization of non-tumorigenic and metastatic cells. Sci Rep. 2013; 3:1449. View in: PubMed

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 MY, 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 10; 30(10):918-20. View in: PubMed

Kani K, Faca VM, Hughes LD, Zhang W, Fang Q, Shahbaba B, Luethy R, Erde J, Schmidt J, Pitteri SJ, Zhang Q, Katz JE, Gross ME, Plevritis SK, McIntosh MW, Jain A, Hanash S, Agus DB, Mallick P. Quantitative Proteomic Profiling Identifies Protein Correlates to EGFR Kinase Inhibition. Mol Cancer Ther. 2012 May; 11(5):1071-81. View in: PubMed

Kani K, Sordella R, Mallick P. Investigation of acquired resistance to EGFR-targeted therapies in lung cancer using cDNA microarrays. Methods Mol Biol. 2012; 795:233-53. View in: PubMed

Mumenthaler SM, Foo J, Leder K, Choi NC, Agus DB, Pao W, Mallick P, Michor F. Evolutionary modeling of combination treatment strategies to overcome resistance to tyrosine kinase inhibitors in non-small cell lung cancer. Mol Pharm. 2011 Dec 5; 8(6):2069-79. View in: PubMed

Eckels J, Hussey P, Nelson EK, Myers T, Rauch A, Bellew M, Connolly B, Law W, Eng JK, Katz J, McIntosh M, Mallick P, Igra M. Installation and Use of LabKey Server for Proteomics. Curr Protoc Bioinformatics. 2011 Dec; Chapter 13:Unit13. 5. View in: PubMed

Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmström J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics. 2011 Sep; 10(9):M110. 006353. View in: PubMed

Vogelsang MS, Kani K, Katz JE, Mallick P. Model-based discovery of circulating biomarkers. Methods Mol Biol. 2011; 728:87-107. View in: PubMed

Fang Q, Kani K, Faca VM, Zhang W, Zhang Q, Jain A, Hanash S, Agus DB, McIntosh MW, Mallick P. Impact of protein stability, cellular localization, and abundance on proteomic detection of tumor-derived proteins in plasma. PLoS One. 2011; 6(7):e23090. View in: PubMed

Mallick P, Kuster B. Proteomics: a pragmatic perspective. Nat Biotechnol. 2010 Jul; 28(7):695-709. View in: PubMed

Wang J, Pérez-Santiago J, Katz JE, Mallick P, Bandeira N. Peptide identification from mixture tandem mass spectra. Mol Cell Proteomics. 2010 Jul; 9(7):1476-85. View in: PubMed

Kessner D, Chambers M, Burke R, Agus D, Mallick P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics. 2008 Nov 1; 24(21):2534-6. View in: PubMed

Luethy R, Kessner DE, Katz JE, Maclean B, Grothe R, Kani K, Faça V, Pitteri S, Hanash S, Agus DB, Mallick P. Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J Proteome Res. 2008 Sep; 7(9):4031-9. View in: PubMed

Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res. 2008 Jan; 7(1):96-103. View in: PubMed

Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 2007 Jan; 25(1):125-31. View in: PubMed

Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Morris DR, Aebersold R. Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics. 2006 Dec; 6(23):6146-57. View in: PubMed

Souter I, Munir I, Mallick P, Weitsman SR, Geller DH, Magoffin DA. Mutagenesis of putative serine-threonine phosphorylation sites proximal to Arg255 of human cytochrome P450c17 does not selectively promote its 17,20-lyase activity. Fertil Steril. 2006 Apr; 85 Suppl 1:1290-9. View in: PubMed

Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B. Signal maps for mass spectrometry-based comparative proteomics. Mol Cell Proteomics. 2006 Mar; 5(3):423-32. View in: PubMed

Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D655-8. View in: PubMed

Katz JE, Mallick P, Agus DB. A perspective on protein profiling of blood. BJU Int. 2005 Sep; 96(4):477-82. View in: PubMed

Kuster B, Schirle M, Mallick P, Aebersold R. Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol. 2005 Jul; 6(7):577-83. View in: PubMed

Zhang H, Yi EC, Li XJ, Mallick P, Kelly-Spratt KS, Masselon CD, Camp DG, Smith RD, Kemp CJ, Aebersold R. High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol Cell Proteomics. 2005 Feb; 4(2):144-55. View in: PubMed

Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 2005; 6(1):R9. View in: PubMed

Kleiger G, Panina EM, Mallick P, Eisenberg D. PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence. Protein Sci. 2004 Jan; 13(1):221-9. View in: PubMed

Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 2003; 4(9):R59. View in: PubMed

Mallick P, Weiss R, Eisenberg D. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc Natl Acad Sci U S A. 2002 Dec 10; 99(25):16041-6. View in: PubMed

Mallick P, Boutz DR, Eisenberg D, Yeates TO. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc Natl Acad Sci U S A. 2002 Jul 23; 99(15):9679-84. View in: PubMed

French SW, Shen RR, Koh PJ, Malone CS, Mallick P, Teitell MA. A modeled hydrophobic domain on the TCL1 oncoprotein mediates association with AKT at the cytoplasmic membrane. Biochemistry. 2002 May 21; 41(20):6376-82. View in: PubMed

Kleiger G, Grothe R, Mallick P, Eisenberg D. GXXXG and AXXXA: common alpha-helical interaction motifs in proteins, particularly in extremophiles. Biochemistry. 2002 May 14; 41(19):5990-7. View in: PubMed

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