Mallick Lab

~ translating multi-omic discovery into precision diagnostics ~
meaningful AI
meaningful AI

building new approaches to AI that require less input data and generate more accurate explanations

integrated omics
integrated omics

approaches to rationally integrate diverse types of high-throughput data.

multi-scale models
multi-scale models

modeling the non-linear, multi-scale processes that govern how cells behave and misbehave.

biomarker discovery
biomarker discovery

understanding the processes that give rise to biomarkers and govern their potential utility.

tumor evolution
tumor evolution

characterizing how evolutionary forces (e.g. microenvironment, or drug treatment) impact tumor composition.

proteomics technology
proteomics technology

experimental and computational approaches to improve the throughput and sensitivity of proteomics technologies

proteoWizard
proteoWizard

a platform to accelerate the development of proteomics analysis tools.

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meaningful AI meaningful AI
integrated omics integrated omics
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overview

The Mallick lab focuses on translating multi-omic discovery into precision diagnostics. We use integrative, multi-omic approaches to model the processes that govern proteome dynamics and then use those models to discover cancer biomarkers and mechanisms.

 

 

Canary Center @ Stanford

news

check out our latest papers on

- ProteoWizard (Nature Biotech)

- Cell Squishyness & Sliminess & Metastatic Potential (PNAS)

- Drug Resistance as Mediated by Epigenetics (Genome Medicine)

- SWATH MS Libraries (Nature Protocols)

Publications2

  • Building high-quality assay libraries for targeted analysis of SWATH MS data. Nature protocolsSchubert, O. T., Gillet, L. C., Collins, B. C., Navarro, P., Rosenberger, G., Wolski, W. E., Lam, H., Amodei, D., Mallick, P., MacLean, B., Aebersold, R.2015; 10 (3): 426-441More
     
  • The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells. Cancer informaticsMumenthaler, S. M., Foo, J., Choi, N. C., Heise, N., Leder, K., Agus, D. B., Pao, W., Michor, F., Mallick, P.2015; 14 (Suppl 4): 19-31More
     
  • A cross-platform toolkit for mass spectrometry and proteomics NATURE BIOTECHNOLOGYChambers, M. C., MacLean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T. A., Brusniak, M., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S. L., Nuwaysir, L. M., 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, E. W., Moritz, R. L., Katz, J. E., Agus, D. B., MacCoss, M., Tabb, D. L., Mallick, P.2012; 30 (10): 918-920More
     
  • Quantitative Proteomic Profiling Identifies Protein Correlates to EGFR Kinase InhibitionMOLECULAR CANCER THERAPEUTICSKani, K., Faca, V. M., Hughes, L. D., Zhang, W., Fang, Q., Shahbaba, B., Luethy, R., Erde, J., Schmidt, J., Pitteri, S. J., Zhang, Q., Katz, J. E., Gross, M. E., Plevritis, S. K., McIntosh, M. W., Jain, A., Hanash, S., Agus, D. B., Mallick, P.2012; 11 (5): 1071-1081More
     
  • Impact of Protein Stability, Cellular Localization, and Abundance on Proteomic Detection of Tumor-Derived Proteins in Plasma PLOS ONEFang, Q., Kani, K., Faca, V. M., Zhang, W., Zhang, Q., Jain, A., Hanash, S., Agus, D. B., McIntosh, M. W., Mallick, P.2011; 6 (7)More
     
  • Proteomics: a pragmatic perspective NATURE BIOTECHNOLOGYMallick, P., Kuster, B.2010; 28 (7): 695-709More
     
  • Computational prediction of proteotypic peptides for quantitative proteomics. Nature biotechnologyMallick, P., Schirle, M., Chen, S. S., Flory, M. R., Lee, H., Martin, D., Ranish, J., Raught, B., Schmitt, R., Werner, T., Kuster, B., Aebersold, R.2007; 25 (1): 125-131More
     
  • Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments. Bioinformatics Bemis, K. D., Harry, A., Eberlin, L. S., Ferreira, C., van de Ven, S. M., Mallick, P., Stolowitz, M., Vitek, O.2015; 31 (14): 2418-2420More
     
  • Predictive Modeling of Drug Response in Non-Hodgkin's Lymphoma PLOS ONEFrieboes, H. B., Smith, B. R., Wang, Z., Kotsuma, M., Ito, K., Day, A., Cahill, B., Flinders, C., Mumenthaler, S. M., Mallick, P., Simbawa, E., Al-Fhaid, A. S., Mahmoud, S. R., Gambhir, S. S., Cristini, V.2015; 10 (6)More
     
  • Neuronal Activity Promotes Glioma Growth through Neuroligin-3 Secretion CELLVenkatesh, H. S., Johung, T. B., Caretti, V., Noll, A., Tang, Y., Nagaraja, S., Gibson, E. M., Mount, C. W., Polepalli, J., Mitra, S. S., Woo, P. J., Malenka, R. C., Vogel, H., Bredel, M., Mallick, P., Monje, M.2015; 161 (4): 803-816More
     
  • A fully human scFv phage display library for rapid antibody fragment reformatting. Protein engineering, design & selection : PEDSLi, K., Zettlitz, K. A., Lipianskaya, J., Zhou, Y., Marks, J. D., Mallick, P., Reiter, R. E., Wu, A. M.2015More
     
  • Anti-MET ImmunoPET for Non-Small Cell Lung Cancer Using Novel Fully Human Antibody Fragments MOLECULAR CANCER THERAPEUTICSLi, K., Tavare, R., Zettlitz, K. A., Mumenthaler, S. M., Mallick, P., Zhou, Y., Marks, J. D., Wu, A. M.2014; 13 (11): 2607-2617More
     
  • Employing ProteoWizard to Convert Raw Mass Spectrometry Data. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]Holman, J. D., Tabb, D. L., Mallick, P.2014; 46: 13 24 1-9More
     
  • Characterizing deformability and surface friction of cancer cells. Proceedings of the National Academy of Sciences of the United States of AmericaByun, S., Son, S., Amodei, D., Cermak, N., Shaw, J., Kang, J. H., Hecht, V. C., Winslow, M. M., Jacks, T., Mallick, P., Manalis, S. R.2013; 110 (19): 7580-7585More
     
  • A physical sciences network characterization of non-tumorigenic and metastatic cellsSCIENTIFIC REPORTSAgus, D. B., Alexander, J. F., Arap, W., Ashili, S., Aslan, J. E., Austin, R. H., Backman, V., Bethel, K. J., Bonneau, R., Chen, W., Chen-Tanyolac, C., Choi, N. C., Curley, S. A., Dallas, M., Damania, D., Davies, P. C., Decuzzi, P., Dickinson, L., Estevez-Salmeron, L., Estrella, V., Ferrari, M., Fischbach, C., Foo, J., Fraley, S. I., Frantz, C., Fuhrmann, A., Gascard, P., Gatenby, R. A., Geng, Y., Gerecht, S., Gillies, R. J., Godin, B., Grady, W. M., Greenfield, A., Hemphill, C., Hempstead, B. L., Hielscher, A., Hillis, W. D., Holland, E. C., Ibrahim-Hashim, A., Jacks, T., Johnson, R. H., Joo, A., Katz, J. E., Kelbauskas, L., Kesselman, C., King, M. R., Konstantopoulos, K., Kraning-Rush, C. M., Kuhn, P., Kung, K., Kwee, B., Lakins, J. N., Lambert, G., Liao, D., Licht, J. D., Liphardt, J. T., Liu, L., Lloyd, M. C., Lyubimova, A., Mallick, P., Marko, J., McCarty, O. J., Meldrum, D. R., Michor, F., Mumenthaler, S. M., Nandakumar, V., O'Halloran, T. V., Oh, S., Pasqualini, R., Paszek, M. J., Philips, K. G., Poultney, C. S., Rana, K., Reinhart-King, C. A., Ros, R., Semenza, G. L., Senechal, P., Shuler, M. L., Srinivasan, S., Staunton, J. R., Stypula, Y., Subramanian, H., Tlsty, T. D., Tormoen, G. W., Tseng, Y., van Oudenaarden, A., Verbridge, S. S., Wan, J. C., Weaver, V. M., Widom, J., Will, C., Wirtz, D., Wojtkowiak, J., Wu, P.2013; 3More
     
  • Anterior gradient 2 (AGR2): Blood-based biomarker elevated in metastatic prostate cancer associated with the neuroendocrine phenotype PROSTATEKani, K., Malihi, P. D., Jiang, Y., Wang, H., Wang, Y., Ruderman, D. L., Agus, D. B., Mallick, P., Gross, M. E.2013; 73 (3): 306-315More
     
  • Unexpected Dissemination Patterns in Lymphoma Progression Revealed by Serial Imaging within a Murine Lymph Node CANCER RESEARCHIto, K., Smith, B. R., Parashurama, N., Yoon, J., Song, S. Y., Miething, C., Mallick, P., Lowe, S., Gambhir, S. S.2012; 72 (23): 6111-6118More
     
  • Investigation of acquired resistance to EGFR-targeted therapies in lung cancer using cDNA microarrays. Methods in molecular biology (Clifton, N.J.)Kani, K., Sordella, R., Mallick, P.2012; 795: 233-253More
     
  • Cancer as a Multi-scale Complex Adaptive System Assessment Of Physical Sciences And Engineering Advances In Life Sciences And Oncology (Aphelion) In EuropeParag Mallick2012: 4-21
  • Installation and use of LabKey Server for proteomics. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]Eckels, J., Hussey, P., Nelson, E. K., Myers, T., Rauch, A., Bellew, M., Connolly, B., Law, W., Eng, J. K., Katz, J., McIntosh, M., Mallick, P., Igra, M.2011; Chapter 13: Unit 13 5-?More
     
  • Evolutionary Modeling of Combination Treatment Strategies To Overcome Resistance to Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancer MOLECULAR PHARMACEUTICSMumenthaler, S. M., Foo, J., Leder, K., Choi, N. C., Agus, D. B., Pao, W., Mallick, P., Michor, F.2011; 8 (6): 2069-2079More
     
  • A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas MOLECULAR & CELLULAR PROTEOMICSFarrah, T., Deutsch, E. W., Omenn, G. S., Campbell, D. S., Sun, Z., Bletz, J. A., Mallick, P., Katz, J. E., Malmstroem, J., Ossola, R., Watts, J. D., Lin, B., Zhang, H., Moritz, R. L., Aebersold, R.2011; 10 (9)More
     
  • Applying Multi-Agent Techniques to Cancer Modeling Proceedings of the Sixth Workshop on Multiagent Sequential Decision Making in Uncertain DomainsBrown M, Bowring Epstein S, Maheswaran R, Mallick P, Tambe M.2011
  • Interactively Mapping Data Sources into the Semantic Web Proceedings of The First International Symposium on Linked ScienceKnoblock C, Szekely P, Ambite JL, Gupta S, Aman Goel, Muslea M, Lerman K, Mallick P2011; 783
  • Model-based discovery of circulating biomarkers. Methods in molecular biology (Clifton, N.J.)Vogelsang, M. S., Kani, K., Katz, J. E., Mallick, P.2011; 728: 87-107More
     
  • Peptide Identification from Mixture Tandem Mass Spectra MOLECULAR & CELLULAR PROTEOMICSWang, J., Perez-Santiago, J., Katz, J. E., Mallick, P., Bandeira, N.2010; 9 (7): 1476-1485More
     
  • Mass spectrometry based proteomics in cancer research Modern Molecular Biology: Approaches for Unbiased Discovery in Cancer ResearchAbbani M, Mallick P, Vogelsang M2010: 117-156
  • Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles JOURNAL OF PROTEOME RESEARCHRodriguez, H., Snyder, M., Uhlen, M., Andrews, P., Beavis, R., Borchers, C., Chalkley, R. J., Cho, S. Y., Cottingham, K., Dunn, M., Dylag, T., Edgar, R., Hare, P., Heck, A. J., Hirsch, R. F., Kennedy, K., Kolar, P., Kraus, H., Mallick, P., Nesvizhskii, A., Ping, P., Ponten, F., Yang, L., Yates, J. R., Stein, S. E., Hermjakob, H., Kinsinger, C. R., Apweiler, R.2009; 8 (7): 3689-3692More
     
  • ProteoWizard: open source software for rapid proteomics tools development BIOINFORMATICSKessner, D., Chambers, M., Burke, R., Agusand, D., Mallick, P.2008; 24 (21): 2534-2536More
     
  • Halobacterium salinarum NRC-1 PeptideAtlas: Toward strategies for targeted proteomics and improved proteome coverage JOURNAL OF PROTEOME RESEARCHVan, P. T., Schmid, A. K., King, N. L., Kaur, A., Pan, M., Whitehead, K., Koide, T., Facciotti, M. T., Goo, Y. A., Deutsch, E. W., Reiss, D. J., Mallick, P., Baliga, N. S.2008; 7 (9): 3755-3764More
     
  • Precursor-ion mass re-estimation improves peptide identification on hybrid instrumentsJOURNAL OF PROTEOME RESEARCHLuethy, R., Kessner, D. E., Katz, J. E., McLean, B., Grothe, R., Kani, K., Faca, V., Pitteri, S., Hanash, S., Agus, D. B., Mallick, P.2008; 7 (9): 4031-4039More
     
  • The standard protein mix database: A diverse data set to assist in the production of improved peptide and protein identification software tools JOURNAL OF PROTEOME RESEARCHKlimek, J., Eddes, J. S., Hohmann, L., Jackson, J., Peterson, A., Letarte, S., Gafken, P. R., Katz, J. E., Mallick, P., Lee, H., Schmidt, A., Ossola, R., Eng, J. K., Aebersold, R., Martin, D. B.2008; 7 (1): 96-103More
     
  • Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents PROTEOMICSFlory, M. R., Lee, H., Bonneau, R., Mallick, P., Serikawa, K., Morris, D. R., Aebersold, R.2006; 6 (23): 6146-6157More
     
  • Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing JOURNAL OF PROTEOME RESEARCHSeebacher, J., Mallick, P., Zhang, N., Eddes, J. S., Aebersold, R., Gelb, M. H.2006; 5 (9): 2270-2282More
     
  • Mutagenesis of putative serine-threonine phosphorylation sites proximal to Arg255 of human cytochrome P450c17 does not selectively promote its 17,20-lyase activity FERTILITY AND STERILITYSouter, I., Munir, I., Mallick, P., Weitsman, S. R., Geller, D. H., Magoffin, D. A.2006; 85: 1290-1299More
     
  • Signal maps for mass spectrometry-based comparative proteomics MOLECULAR & CELLULAR PROTEOMICSPrakash, A., Mallick, P., Whiteaker, J., Zhang, H. D., Paulovich, A., Flory, M., LEE, H., Aebersold, R., Schwikowski, B.2006; 5 (3): 423-432More
     
  • Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas GENOME BIOLOGYKing, N. L., Deutsch, E. W., Ranish, J. A., Nesvizhskii, A. I., Eddes, J. S., Mallick, P., Eng, J., Desiere, F., Flory, M., Martin, D. B., Kim, B., Lee, H., Raught, B., Aebersold, R.2006; 7 (11)More
     
  • The PeptideAtlas project NUCLEIC ACIDS RESEARCHDesiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I., Mallick, P., Eng, J., Chen, S., Eddes, J., Loevenich, S. N., Aebersold, R.2006; 34: D655-D658More
     
  • A perspective on protein profiling of blood BJU INTERNATIONALKatz, J. E., Mallick, P., Agus, D. B.2005; 96 (4): 477-482More
     
  • Scoring proteomes with proteotypic peptide probes NATURE REVIEWS MOLECULAR CELL BIOLOGYKuster, B., Schirle, M., Mallick, P., Aebersold, R.2005; 6 (7): 577-583More
     
  • High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry MOLECULAR & CELLULAR PROTEOMICSZhang, H., Yi, E. C., Li, X. J., Mallick, P., Kelly-Spratt, K. S., Masselon, C. D., Camp, D. G., Smith, R. D., Kemp, C. J., Aebersold, R.2005; 4 (2): 144-155More
     
  • Finding protein domain boundaries: an automated, non-homology-based method IEEE Intelligent SystemsGurbaxani BM, Mallick P2005; Nov-Dec (6): 26-33
  • Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry GENOME BIOLOGYDesiere, F., Deutsch, E. W., Nesvizhskii, A. I., Mallick, P., King, N. L., Eng, J. K., Aderem, A., Boyle, R., Brunner, E., Donohoe, S., Fausto, N., Hafen, E., Hood, L., Katze, M. G., Kennedy, K. A., Kregenow, F., Lee, H. K., Lin, B. Y., Martin, D., Ranish, J. A., Rawlings, D. J., Samelson, L. E., Shiio, Y., Watts, J. D., Wollscheid, B., Wright, M. E., Yan, W., Yang, L. H., Yi, E. C., Zhang, H., Aebersold, R.2005; 6 (1)More
     
  • PFIT and PFRIT: Bioinformatic algorithms for detecting glycosidase function from structure and sequence PROTEIN SCIENCEKleiger, G., Panina, E. M., Mallick, P., Eisenberg, D.2004; 13 (1): 221-229More
     
  • Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach GENOME BIOLOGYStrong, M., Mallick, P., Pellegrini, M., Thompson, M. J., Eisenberg, D.2003; 4 (9)More
     
  • The directional atomic solvation energy: An atom-based potential for the assignment of protein sequences to known folds PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICAMallick, P., Weiss, R., Eisenberg, D.2002; 99 (25): 16041-16046More
     
  • Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bondsPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICAMallick, P., Boutz, D. R., Eisenberg, D., Yeates, T. O.2002; 99 (15): 9679-9684More
     
  • A modeled hydrophobic domain on the TCL1 oncoprotein mediates association with AKT at the cytoplasmic membrane BIOCHEMISTRYFrench, S. W., Shen, R. R., Koh, P. J., Malone, C. S., Mallick, P., Teitell, M. A.2002; 41 (20): 6376-6382More
     
  • GXXXG and AXXXA: Common alpha-helical interaction motifs in proteins, particularly in extremophiles BIOCHEMISTRYKleiger, G., Grothe, R., Mallick, P., Eisenberg, D.2002; 41 (19): 5990-5997More
     
  • Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions and interactions. Proteins and Proteomics: A Laboratory Manual. Cold Spring Harbor Laboratory Press:Parag Mallick, Edward Marcotte2002: Chapter 11
  • The 1.7 angstrom crystal structure of BPI: A study of how two dissimilar amino acid sequences can adopt the same fold JOURNAL OF MOLECULAR BIOLOGYKleiger, G., Beamer, L. J., Grothe, R., Mallick, P., Eisenberg, D.2000; 299 (4): 1019-1034More
     
  • Selecting protein targets for structural genomics of Pyrobaculum aerophilum: Validating automated fold assignment methods by using binary hypothesis testing PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICAMallick, P., Goodwill, K. E., Fitz-Gibbon, S., Miller, J. H., Eisenberg, D.2000; 97 (6): 2450-2455More
     
  • The accidental bioinformaticist JOURNAL OF CELLULAR BIOCHEMISTRYMallick, P.2000; 80 (2): 208-209More

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