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Graduate Students Postdoctoral Fellows Researchers / Staff Principal Investigator

Graduate Students

Jonathan Cooper – Cancer Biology

Jonathan Cooper

Education B.S. – Biology, 2010, Dallas Baptist University

Research Interests: Exploring the intersection between cellular growth and renewal signaling pathways and their dysregulation in cancer. Specifically, I am interested in investigating the key players in cellular responses to nutrient availability and probing for selective vulnerabilities in cancers harboring aberrant nutrient sensing.


Cooper, J. M., Bodemann, B. O., and White, M. A. (2013). The RalGEF/Ral pathway: evaluating an intervention opportunity for Ras cancers. The Enzymes 34, 137-157.

Thomas, J.C., Cooper, J.M., Clayton, N.S., Wang, C., White, M.A., Abell, C., Owen, D., and Mott, H.R. 2016. Inhibition of Ral GTPases Using a Stapled Peptide Approach. Journal of Biological Chemistry, in press.

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Elizabeth McMillan – Cell Regulation with Supplemental Curricula in Computational, Systems Biology

Elizabeth McMillan

Education: B.A. – Biology, B.A. – Mathematics, 2011, New York University College of Arts and Sciences/New York University Courant Institute of Mathematical Sciences

Research Interests: Oncogenic lesions arising during cancer progression provide an attractive target for chemical intervention strategies. The extreme molecular heterogeneity of tumors, however, makes it difficult to identify authentic intervention targets and to link patients to the most appropriate treatment. To confront this challenge, we launched a full scale investigation to identify the genetic lesions that arise during cancer progression together with a computational approach to link novel compounds to these lesions. A panel of 103 non-small cell lung cancer cell lines was screened with over 200,000 uncharacterized synthetic chemical compounds and natural products fractions in a tiered HTS approach. Statistical and machine learning procedures were then used to link drug activity to the complexity of cancer genomes by systematically assigning enrollment biomarkers to each compound from measures of gene expression, gene mutation, gene copy number, protein expression, and metabolomics datasets. Using this approach, we have found that genetic vulnerabilities that are not currently actionable can be linked to novel chemicals. Experimental mechanism of action hypotheses can be derived from these chemical/biomarker relationships and were validated for a subset. Notably, we are able to parse KRAS mutant cancers into multiple, distinct molecular subtypes defined by co-occurring mutations. This indicates that KRAS lung cancers are representative of diverse mechanistic subtypes, and we are able to identify putative novel compounds that may target each subtype. Collectively, we are using this approach as a data driven way to parse mechanistic cancer subtypes and identify a diverse cohort of therapies capable of contending with cancer heterogeneity together with enrollment biomarkers that can specify sensitivity.


Ekas, L. A., T. J. Cardozo, M. S. Flaherty, E. A. McMillan, F. C. Gonsalves and E. A. Bach (2010). "Characterization of a dominant-active STAT that promotes tumorigenesis in Drosophila." Dev Biol 344(2): 621-636.

Kim, H. S., S. Mendiratta, J. Kim, C. V. Pecot, J. E. Larsen, I. Zubovych, B. Y. Seo, J. Kim, B. Eskiocak, H. Chung, E. McMillan, S. Wu, J. De Brabander, K. Komurov, J. E. Toombs, S. Wei, M. Peyton, N. Williams, A. F. Gazdar, B. A. Posner, R. A. Brekken, A. K. Sood, R. J. Deberardinis, M. G. Roth, J. D. Minna and M. A. White (2013). "Systematic identification of molecular subtype-selective vulnerabilities in non-small-cell lung cancer." Cell 155(3): 552-566.

Osborne, J. K., M. L. Guerra, J. X. Gonzales, E. A. McMillan, J. D. Minna and M. H. Cobb (2014). "NeuroD1 mediates nicotine-induced migration and invasion via regulation of the nicotinic acetylcholine receptor subunits in a subset of neural and neuroendocrine carcinomas." Mol Biol Cell 25(11): 1782-1792

Borkowski, R., Du, L., Zhao, Z., McMillan, E., Kosti, A., Yang, C., Suraokar, M., Wistuba, I., Gazdar, A., Minna, J., White, M.A.* and Pertsemlidis, A.*. 2014. Genetic mutation of p53 and suppression of the miR17~92 cluster are synthetic lethal in non-small cell lung cancer due to upregulation of vitamin D signaling. Cancer Research in press. *co-corresponding authors.

Witkiewicz, A.K., McMillan, E.A., Balaji, U., Baek, H., Lin, W., Mansour, J., Mollaee, M., Wagner, K., Koduru, P., Yopp, A., Choti, M., Yeo, C.J., McCue, P., White, M.A., and Knudsen, E.S. 2015. Whole exome sequencing of pancreatic ductal adenocarcinoma reveals hallmarks of disease etiology, prognosis, and targets for therapeutic intervention. Nature Communications 6:6744.

Potts, M.B., McMillan, E.A., Rosales, T. I., Kim, H.S., Ou, Y.H., Tooms, J.E., Brekken, R.A., Minden, M.D., MacMillan, J.B., and White, M.A. 2015. Exceptional responders to dedemnin B illuminate the mechanism of action and pharmacogenomics biomarkers for antineoplastic activity. Nature Chemical Biology

McNamara, R.P., Reeder, J.E., McMillan, E.A., Bacon, C.W., McCann, J.L., and D’Orso, I.D. KAP1 recruitment of the 7SK snRNP complex to promoters enables transcription elongation by RNA Polymerase II. (2015) Molecular Cell (in press)

Shields, B.B., Pecot, C.V., Gao, H., McMillan, E., Potts, M., Nagel, C., Purinton, S., Wang, Y., Ivan, C., Kim, H.S., Borkowski, R. J., Khan, S., Rodriguez-Aguayo, C., Lopez-Berestein, G., Lea, J., Gazdar, A., Baggerly, K.A. Sood, A.K., and White, M.A. 2015. A genome-scale screen reveals context-dependent ovarian cancer sensitivity to miRNA overexpression. Molecular Systems Biology, 11: 842.

Young, J. H., Peyton, M., Kim, H., McMillan, E., Minna, J. D., White, M. A., and Marcotte, E. M. 2016. Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer. Bioinformatics, in press.

Hensley, C.T., Yuan, Q.Y., Lev-Cohain, H., Kim, J., Liang, L., Eunsook, J., Skelton, R., Loudat, L., Wodzak, M., Cai, L., Klimko, C., McMillan, E.A., Butt, Y., Torrealba, J., Malloy, C., Kernstine, K., Leninski, R.E., and Deberardinis, R.J., (2015). “Heterogeneous glucose metabolism within and between human non-small cell lung tumors”. Cell (in press)

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Chensu Wang – Biomedical Engineering

Chensu Wang

Education: B.S. – Biomedical Engineering, 2011, Southeast University, Nanjing, China

Research Interests: The interface between engineering and biology; in particular the design and development of nanotechnology tools that illuminate dynamic cell biological processes in space and time. My current project is the application of novel pH-responsive nanoprobes for analysis of autophagosome biogenesis at single organelle resolution. (Joint student with Professor Jinming Gao)


Wang, C., Wang, Y., Li, Y., Bodemann, B., Zhao, T., Ma, X., Huang, G., Hu, Z., DeBerardinis, R.J., White, M.A.* and Gao, J.* (2015). A nanobuffer reporter library for fine-scale imaging and perturbation of endocytic organelles. Nat Commun 6, 8524. *Co-corresponding authors

Dutchak, P.A., Laxman, S., Estill, S.J., Wang, C., Wang, Y., Wang, Y., Bulut, G.B., Gao, J., Huang, L.J., and Tu, B.P. (2015). Regulation of Hematopoiesis and Methionine Homeostasis by mTORC1 Inhibitor NPRL2. Cell Rep 12, 371-379.

Wang, C., Li, J., Amatore, C., Chen, Y., Jiang, H., and Wang, X.M. (2011). Gold nanoclusters and graphene nanocomposites for drug delivery and imaging of cancer cells. Angew Chem, Int Ed 50, 11644-11648.

Thomas, J.C., Cooper, J.M., Clayton, N.S., Wang, C., White, M.A., Abell, C., Owen, D., and Mott, H.R. 2016. Inhibition of Ral GTPases Using a Stapled Peptide Approach. Journal of Biological Chemistry, in press.

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Aubhishek Zaman– Cancer Biology

Aubhishek Zaman

Education: M.S. – Genetic Engineering and Biotechnology, University of Dhaka, Bangladesh

Research Interests: Cancer therapeutics and its mode of actions; key players in cellular growth, vesicular traffic and cellular responses to nutrient availability,.

Publications (selected):

Zaman A* and Razzaque S  ‘Designing Novel Antibacterials: Application of Omics Science’ Klimik Dergisi. 2013; 26; 2-8

Islam MR, Zaman A, Jahan I, Chakravorty R, Chakraborty S*. ‘In silico QSAR analysis of quercetin reveals its potential as therapeutic drug for Alzheimer's disease.’J Young Pharm. 2013 Dec;5(4):173-9.

Islam MR*, Hosen MI, Zaman A, Islam MO. ‘Structural, functional and molecular docking study to characterize GMI1 from Arabidopsis thaliana.’ Interdiscip Sci. 2013 Mar;5(1):13-22.

Zaman A*, Rahaman MH, Razzaque S. ‘Kaposi's sarcoma: a computational approach through protein-protein interaction and gene regulatory networks analysis.’ Virus Genes. 2013 Apr;46(2):242-54. doi: 10.1007/s11262-012-0865-z. Epub 2012 Dec 25.

Zaman A*, Fancy NN. ‘A computational prediction of structure and function of novel homologue of Arabidopsis thaliana Vps51/Vps67 subunit in Corchorus olitorius.’ Interdiscip Sci. 2012 Dec;4(4):256-67.

Zaman A*.Docking studies and network analyses reveal capacity of compounds from Kandelia rheedii to strengthen cellular immunity by interacting with host proteins during tuberculosis infection.’ Bioinformation. 2012;8(21):1012-20.

Islam R, Sakib M S, and Zaman A* ‘A Computational Assay to Design an Epitope-based Peptide Vaccine against Chikungunya Virus.’ Future Virology. 2012; 7 (10):1029–1042.

Zaman A* (2012) ‘Characterization of Coilin protein nucleotide binding region in Homo sapiens’ Online Journal of Bioinformatics, 13(2):314-330.

Zaman A* ‘Drug Designing Approaches Using In-Silico Techniques’ Lambert Academic Press (LAP). 2012; ISBN: 978-3-659-15283-2

*Corresponding author

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Postdoctoral Fellows

Rachel Vaden, Ph.D. – Chemistry

Rachel Vaden

Education: B.S. – Chemistry, 2008, University of West Georgia; PhD – Chemistry, 2015, University of Utah

Research interest: The use of molecular tools to probe biological systems can provide insight into complex cellular processes and disease states.  My research is focused on understanding how genetic mutations acquired during tumor progression can confer sensitivity to novel bioactive compounds.  Not only can these studies facilitate clinical therapeutic development by identifying patient populations that are likely to be sensitive a specific treatment, but they can also provide direct mechanistic information about cancer signaling pathways that may be used to inform additional treatment design strategies.


Vaden RM, Gligorich KM, Jana R, Sigman MS, & Welm BE (2014) The small molecule C-6 is selectively cytotoxic against breast cancer cells and its biological action is characterized by mitochondrial defects and endoplasmic reticulum stress. Breast Cancer Res 16(6):472.

Gligorich KM*, Vaden RM*, Shelton DN, Wang G, Matsen CB, Looper RE, Sigman, MS, & Welm BE (2013) Development of a screen to identify selective small molecules active against patient-derived metastatic and chemoresistant breast cancer cells. Breast Cancer Res 15(4):R58.

Pathak TP, Osiak JG, Vaden RM, Welm BE, Sigman MS (2012) Synthesis and Preliminary Biological Study of Bisindolylmethanes Accessed by an Acid-Catalyzed Hydroarylation of Vinylindoles. Tetrahedron 68(26):5203.

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Suzie Hight, Ph.D. – Cancer Biology

Suzie Hight, Ph.D.

Education: B.S. – Biochemistry 2002, University of Iowa; M.S. – Biochemistry and Molecular Biology 2006, Purdue University; Ph.D. – Cancer Biology 2015, University of Texas Southwestern Medical Center.

Research interest: Leveraging the power of functional genomics for identification of new therapeutic strategies to treat cancer. Using functional signature ontology (FuSiOn) mapping, we are elucidating mechanisms of action for bioactive natural products, and thus accelerating the discovery of new therapeutic agents. Also: The role of genetic instability and heterogeneity in tumorigenesis, and strategies for targeting genetic instability in tumors; Identification of synthetic lethal relationships that can be exploited as tumor-specific acquired vulnerabilities.

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Caroline Diep, Ph.D. – Cancer Biology

Caroline Diep

Education: B.A. – Art History 2003, University of Arizona; B.S. – Molecular Cellular Biology 2005, University of Arizona; Ph.D. – Microbiology, Immunology, and Cancer Biology 2015, University of Minnesota.

Research interest: I am interested in identifying and understanding the master molecular drivers and/or regulators of squamous lung carcinoma biology. Insights gained will be leveraged into novel and efficacious therapeutic strategies to precisely treat tumors.


Diep CH, Knutson TP, Lange CA. Active FOXO1 is a Key Determinant of Isoform-Specific Progesterone Receptor Transactivation and Senescence Programming. Mol Cancer Res. Nov 17, 2015. PMID: 26577046

Whatcott CJ, Diep CH, Jiang P, Watanabe A, Lobello J, Sima C, Hostetter G, Shepard M, Von Hoff DD, Han H. Desmoplasia in primary tumors and metastatic lesions of pancreatic cancer. Clin Cancer Res. 2015 Aug 1;21(15):3561-8. PMID: 25695692

Diep CH, Daniel AR, Mauro LJ, Knutson TP, Lange CA. Progesterone action in breast, uterine, and ovarian cancers. J Mol Endocrinol. 2015; 54(2):R31-53. PMID: 25587053

Dressing GE, Knutson TP, Schiewer MJ, Daniel AR, Hagan CR, Diep CH, Knudsen KE, Lange CA. Progesterone receptor-cyclin D1 complexes induce cell cycle-dependent transcriptional programs in breast cancer cells. Mol Endocrinol. 2014; 28(4):442-57. PMID: 24606123

Diep CH, Charles NJ, Gilks CB, Kalloger SE, Argenta PA, Lange CA. Progesterone receptors induce FOXO1-dependent senescence in ovarian cancer cells. Cell Cycle. 2013; 12(9):1433-49. PMID: 23574718

Diep CH, Zucker K, Hostetter G, Watanabe A, Hu C, Munoz RM, Von Hoff DD, Han H. Down-regulation of Yes-Associated Protein 1 (YAP1) expression reduces cell proliferation and clonogenicity of pancreatic cancer cells. PLoS One. 2012; 7(3):e32783. PMID: 22396793

Diep CH, Munoz RM, Choudhary A, Von Hoff DD, Han H. Synergistic effect between erlotinib and MEK inhibitors in K-Ras wildtype human pancreatic cancer cells. Clin Cancer Res. 2011; 17(9):2744-56. PMID: 21385921

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Jeon Lee, Ph.D. – Computational Biology

Jeon Lee

Education:  Ph.D. – Biomedical Engineering, 2006, Yonsei University, South Korea; Postdoctoral Fellow, 2013-2014, Johns Hopkins University School of Medicine

Research Interests:  Data fusion for anti-cancer drug response prediction, machine learning algorithms for cancer biology and biomedical image and signals, physiological signal analytics, arrhythmia diagnosis and prognosis algorithms, finding links between sleep apnea and arrhythmia, scientific approaches to traditional Korean/Chinese medicine, and clinical trials.


Lee, C. H, Park, K. H, Nam, J. H, Lee, J., Choi, Y. J., Kong, E. J. Son, J. W., Kim, U., Park, J. S., Kim, Y. J., and Shin, D. G (2015). Increased Variability of the Coupling Interval of Premature Ventricular Contractions as a Predictor of Cardiac Mortality in Patients with Left Ventricular Dysfunction. Circulation Journal, 79(11), 2360-2366.

Lee, J., Kim, S. J., Chen, R., and Herskovits, E. H. (2015, August). Brain tumor image segmentation using kernel dictionary learning. In Engineering in Medicine and Biology Society (EMBC), 2015 37th Annual International Conference of the IEEE (pp. 658-661). IEEE.

Kim, J. U., Lee, Y. J., Lee, J., and Kim, J. Y. (2015). Differences in the Properties of the Radial Artery between Cun, Guan, Chi, and Nearby Segments Using Ultrasonographic Imaging: A Pilot Study on Arterial Depth, Diameter, and Blood Flow. Evidence-Based Complementary and Alternative Medicine.

Lee, J., & Finkelstein, J. (2014). Evaluation of a portable stress management device. Studies in health technology and informatics, 208, 248-252.

Lee, J., and Finkelstein, J. (2014). Consumer sleep tracking devices: a critical review. Studies in health technology and informatics, 210, 458-460.

Choi, Y. J., Park, K. H., Lee, C. H., Lee, S. H., Park, J. S., Kim, U., Son, J. W., Lee, J., Kim, J. R., and Shin, D. G. (2014). “Optimal” cutoff value of heart rate; appraisal based on heart rate variability and C-reactive protein. International journal of cardiology, 176(2), 497-499.

Lee, H. K., Lee, J., Kim, H., Ha, J. Y., and Lee, K. J. (2013). Snoring detection using a piezo snoring sensor based on hidden Markov models. Physiological measurement, 34(5), N41.

Lee, J., Song, M. H., Shin, D. G., and Lee, K. J. (2012). Event synchronous adaptive filter based atrial activity estimation in single-lead atrial fibrillation electrocardiograms. Medical & biological engineering & computing, 50(8), 801-811.

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Researchers / Staff

Kiran Kaur, Ph.D. – Adjunct Instructor / Lab Manager

Kiran Kaur, Ph.D.

Education: M.S., 1982, University of Kentucky; Ph.D. 1994, Southern Methodist University


Saurabh Mendiratta – Research Scientist

Saurabh Mendiratta

Education: M.S. – Biotechnology, 2003, MS University, Baroda, India; M.S. – Cell and Molecular Biology, 2006, University of Texas at Dallas

Research Interests: High throughput SiRNA and chemical compound screening to identify gene targets selectively required for cancer cell survival.


Kim, H. S., Mendiratta S., J. Kim, C. V. Pecot, J. E. Larsen, I. Zubovych, B. Y. Seo, J. Kim, B. Eskiocak, H. Chung, E. McMillan, S. Wu, J. De Brabander, K. Komurov, J. E. Toombs, S. Wei, M. Peyton, N. Williams, A. F. Gazdar, B. A. Posner, R. A. Brekken, A. K. Sood, R. J. Deberardinis, M. G. Roth, J. D. Minna and M. A. White (2013). "Systematic identification of molecular subtype-selective vulnerabilities in non-small-cell lung cancer." Cell 155(3): 552-566.

Potts, M.B., Kim, H.S., Fisher, K.W., Hu, Y., Carrasco, Y., Bulut, G.B., Ou, Y.-H., Herrera-Herrera, M.L., Cubillos, F., Mendiratta, S., Xiao, G., Hofree, M., Ideker, T., Xie, Y., Huang, L.J.-S., Lewis, R.E., MacMillan, J.B., and White, M.A. (2013).  Using Functional Signature Ontology (FUSION) to identify mechanisms of action for natural products.  Sci. Signal., 6(297), ra90.

Ward S.E., Kim H.S., Komurov K. Mendiratta S., Tsai P.L, Schmolke M., Satterly N., Manicassamy B., Forst C.V., Roth M.G., García-Sastre A., Blazewska K.M., McKenna C.E., Fontoura B.M., White M.A., "Host Modulators of H1N1 Cytopathogenicity," PLoS One, 2012;7(8):e39284. Epub 2012 Aug 2.

Goldsmith E.J., Mendiratta S., Akella R., Dahlgren K., "Natural language query in the biochemistry and molecular biology domains based on cognition search™," Summit on Translat Bioinforma, 2009 Mar 1;2009:32-7.

Garcia-Rodriguez J., Mendiratta, S., White, M. A., Xie, X.-S., and De Brabander, J. K. 2015. Synthesis and structure-activity studies of the V-ATPase inhibitor saliphenylhalamide (SaliPhe) and simplified analogs. Bioorganic and Medical Chemistry Letters, 25:4393-4398.

Li, Y., Mendiratta, S., Ehrhardt, K., Kashyap, N., White, M. A., Bleris, L. 2015. Exploiting the CRSPR/Cas9 PAM constraint for single-nucleotide resolution interventions. Plos One, 11:e0144970.

Jean René Clemenceau - Research Assistant I

Jean Clemenceau

Education: B.S. - Informatics, 2013, Baylor University

Role: I am the administrator for the lab's databases and servers. I also develop and mantain the lab's different software tools. These include web user interfaces used to access and analyze the data produced and gathered by the lab and fellow contributors within our different projects. I strive to create user-friendly tools that can increase the efficiency of drug discovery out of massive amounts of data.

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Principal Investigator

Michael A. White, Ph.D. – Professor, Cell Biology

Michael A. White, Principal Investigator

Grant A. Dove Chair for Research in Oncology
The Sherry Wigley Crow Cancer Research Endowed Chair in Honor of Robert Lewis Kirby, M.D.

Education: University of Iowa (1986), Undergraduate; University of North Carolina at Chapel Hill (1992), Graduate

Research Interests: Cancer, molecular architecture of growth regulatory signal transduction cascades, oncogenes, signal transduction and tumor suppressors

Publications: 1992 – 2015

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