Publications


Journal Articles

paper Nafshi R and Lezon TR. Predicting the Effects of Drug Combinations Using Probabilistic Matrix Factorization. Front Bioinform 1:708815 (2021).
paper Erdem C, Lee AV, Taylor DL, Lezon TR. Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells. PLoS Computational Biology 17: e1009125 (2021). PMID: 34191793
paper Pei F, Li H, Henderson MH, Titus SA, Jadhav A, Simeonov A, Cobanoglu MC, Mousavi SH, Shun T, McDermott L, Iyer P, Fioravanti M, Carlisle D, Friedlander RM, Bahar I, Taylor DL, Lezon TR, Stern AM, Schurdak, ME. Connecting neuronal cell protective pathways and drug combinations in a Huntington’s disease model through the application of quantitative systems pharmacology. Scientific Reports 7:17803 (2017). PMID: 29259176
paper Suofu Y, Li W, Jean-Alphonse FG, Jiao J, Khattar NK, Li J, Baranov SV, Leronni D, Mihalik AC, He Y, Cecon E, Wehbi V, Kim J, Heath BE, Baranova OV, Wang X, Gable M, Kretz E, Di Benedetto G, Lezon TR, Ferrando L, Larkin TM, Sullivan MLG, Yablonska S, Wang J, Minnigh MB, Guillaumet G, Suzenet F, Richardson RM, Poloyac S, Stolz DB, Jockers R, Witt-Enderby P, Carlisle DL, Vilardaga J-P, Friedlander RM. Dual role of mitochondria in producing melatonin and driving GPCR signaling to block cytochrome c release. Proc Natl Acad Sci USA 114:E7997-E8006 (2017). PMID: 28874589
paper Spagnolo DM, Al-Kofahi Y, Zhu P, Lezon TR, Gough A, Stern AM, Lee AV, Ginty F, Sarachan B, Taylor DL, Chennubholta C. Platform for quantitative evaluation of spatial intratumoral heterogeneity in multiplexed fluorescence images. Cancer Research 77:e71–74 (2017).
paper Bergman S and Lezon TR. Modeling global changes induced by local perturbations to the HIV-1 capsid. J Mol Graphics Modelling 71:218-226 (2017). PMID: 27951510
paper Gough A, Stern AM, Maier J, Lezon T, Shun T-Y, Chennubhotla C, Schurdak ME, Haney SA and Taylor DL. Biologically relevant heterogeneity: Metrics and practical insights. SLAS Discovery 22:213-227 (2017). PMID: 28231035
paper Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor DL, Chennubhotla SC. Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers. J Pathol Inform 7:47 (2016). PMID: 27994939
paper Erdem C, Nagle AM, Casa AJ, Litzenburger BC, Wang Y, Taylor DL, Lee AV and Lezon TR. Proteomic screening and lasso regression reveal differential signaling in insulin and insulin-like growth factor I pathways. Mol Cell Proteomics 15:3045-3057 (2016). PMID: 27364358
paper Gough A, Chen N, Schurdak M, Shun TY, Lezon T, Boltz R, Reese C, Wagner J, Vernetti L, Grandis J, Lee A and Taylor DL. Identifying and Quantifying Heterogeneity in High Content Analysis: Application of Heterogeneity Indices to Drug Discovery. PLoS ONE 9:e102678 (2014). PMID: 4103836
paper Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR and Bahar I. Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics 30:2681-2683 (2014). PMID: 24849577
paper Bahar I, Lezon TR, Yang L-W and Eyal E. Global dynamics of proteins: Bridging between structure and function. Ann Rev Biophys 39:23-32 (2010). PMID: 20192781
paper Lezon TR, Banavar JR, Cieplak M, Maritan A and Fedoroff NV. Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc Natl Acad Sci USA 103:19033-19038 (2006). PMID: 17138668
paper Lezon TR, Banavar JR and Maritan A. The origami of life. J Phys: Condens Matter 18:847-888 (2006).
paper Banavar JR, Cieplak M, Flammini A, Hoang TX, Kamien RD, Lezon TR, Marenduzzo D, Maritan A, Seno F, Snir Y and Trovato A. Geometry of proteins: hydrogen bonding, sterics and marginally compact tubes. Phys Rev E. 73:031921 (2006). PMID: 16605572
paper Lezon TR, Banavar JR, Lesk AM and Maritan A. What determines the spectrum of protein native state structures? Proteins 63:273-277 (2006). PMID: 16470841
paper Lezon T, Banavar JR and Maritan A. Recognition of coarse-grained protein tertiary structure. Proteins 55:536-547 (2004). PMID: 15103618

Book Chapters

paper Taylor DL, Gough A, Schurdak ME, Vernetti L, Chennubhotla CS, Lefever D, Pei F, Faeder JR, Lezon TR, Stern AM and Bahar I. Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology, in Handbook of Experimental Pharmacology. Springer, Berlin, Heidelberg, 2019.
paper Schurdak ME, Pei F, Lezon TR, Carlisle D, Friedlander R, Taylor DL, Stern AM. A Quantitative Systems Pharmacology Approach to Infer Pathways Involved in Complex Disease Phenotypes, in Phenotypic Screening. Methods in Molecular Biology, vol 1787. Edited by Wagner B. Humana Press, New York, NY, 2018. PMID: 29736721
paper Gough A, Lezon T, Faeder JR, Chennubhotla C, Murphy RF, Critchley-Thorne R and Taylor DL. High-content analysis with cellular and tissue systems biology: A bridge between cancer cell biology and tissue-based diagnostics, in The Molecular Basis of Cancer. Edited by Mendelsohn J, Gray JW, Howley PM, Israel MA and Thompson CB. Elsevier, 2014.
paper Zomot E, Bakan A, Shrivastava IH, DeChancie J, Lezon TR and Bahar I. Sodium-coupled secondary transporters: insights from structure-based computations, in Molecular Machines. Edited by Roux B. World Scientific, 2011.
paper Lezon TR, Shrivastava IH, Yang Z and Bahar I. Elastic network models for biomolecular dynamics: Theory and application to membrane proteins and viruses, in Handbook on Biological Networks. Edited by Boccaletti S, Latora V and Moreno Y. World Scientific, 2009.
paper Lezon TR, Banavar JR, Cieplak M, Fedoroff NV and Maritan A. The most probable genetic interaction networks inferred from gene expression patterns, in Analysis of Microarray Data: A Network-Based Approach. Edited by Dehmer M and Emmert-Streib F. Wiley, 2008.

Fiction, not peer-reviewed

novel It's like Frankenstein meets Little Shop of Horrors, but with fewer musical numbers, more drugs, and a phenomenal bakery.