Carlos F Lopez, Ph.D

Profile

The goal of my work is the development and application of numerical methods to understand signal transduction cascades in cells and their dysregulation in cancer. My group efforts comprise a tri-partite approach to study cancer biology: (1) Development of modelling and simulation tools necessary to study signalling events across multiple spatiotemporal time-scales. To this end we use techniques of statistical mechanics, molecular simulation, mesoscale modelling, reaction kinetics, and cell-population modelling to develop a systems-level description of cellular environments. (2) Use developed tools to study signalling processes relevant to cancer phenotypes. (3) Collaborate with experimental and theoretical groups to test and expand our hypotheses to develop a fundamental understanding of the rules that govern functional genomics and systems biology. My group currently co-develops and contributes to the PySB(www.pysb.org) modelling platform, which uses a novel modelling-with-programs paradigm to biological signalling pathway simulations. With this approach, the biological knowledge is encoded into executable programs that enhance our capabilities to express, share, and revise our understanding of complex interactions at a large signalling network scale. We have employed a combination of this modelling framework along with in-house developed numerical methods to explore proposed mechanistic hypotheses in the literature about cell death regulation. With our work we were able to elucidate important aspects of signalling, identify gaps in our knowledge, and bring a consensus to the field about extrinsic apoptosis regulation. [Lopez et al. Submitted] My lab is located at the Vanderbilt-Ingram Cancer Center in Vanderbilt University School of Medicine; one of the leading institutions for cancer research in the world and consistently ranked in the top five for NIH funding in the USA. My work provides a theoretical perspective to experimental and clinical efforts in the department and university with the goal of developing a better understanding of cancer development and treatment

Publications

The following timeline graph is generated from all co-authored publications.

1. PyDREAM: high-dimensional parameter inference for biological models in python. Shockley EM, Vrugt JA, Lopez CF (2018) Bioinformatics 34(4): 695-697
   › Primary publication · 29028896 (PubMed) · PMC5860607 (PubMed Central)
2. GPU-powered model analysis with PySB/cupSODA. Harris LA, Nobile MS, Pino JC, Lubbock ALR, Besozzi D, Mauri G, Cazzaniga P, Lopez CF (2017) Bioinformatics 33(21): 3492-3494
   › Primary publication · 28666314 (PubMed) · PMC5860165 (PubMed Central)
3. Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective. Chifman J, Arat S, Deng Z, Lemler E, Pino JC, Harris LA, Kochen MA, Lopez CF, Akman SA, Torti FM, Torti SV, Laubenbacher R (2017) PLoS Comput Biol 13(2): e1005352
   › Primary publication · 28166223 (PubMed) · PMC5293201 (PubMed Central)
4. Integrated, High-Throughput, Multiomics Platform Enables Data-Driven Construction of Cellular Responses and Reveals Global Drug Mechanisms of Action. Norris JL, Farrow MA, Gutierrez DB, Palmer LD, Muszynski N, Sherrod SD, Pino JC, Allen JL, Spraggins JM, Lubbock AL, Jordan A, Burns W, Poland JC, Romer C, Manier ML, Nei YW, Prentice BM, Rose KL, Hill S, Van de Plas R, Tsui T, Braman NM, Keller MR, Rutherford SA, Lobdell N, Lopez CF, Lacy DB, McLean JA, Wikswo JP, Skaar EP, Caprioli RM (2017) J Proteome Res 16(3): 1364-1375
   › Primary publication · 28088864 (PubMed)
5. An unbiased metric of antiproliferative drug effect in vitro. Harris LA, Frick PL, Garbett SP, Hardeman KN, Paudel BB, Lopez CF, Quaranta V, Tyson DR (2016) Nat Methods 13(6): 497-500
   › Primary publication · 27135974 (PubMed) · PMC4887341 (PubMed Central)
6. CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline. Fischer AW, Heinze S, Putnam DK, Li B, Pino JC, Xia Y, Lopez CF, Meiler J (2016) PLoS One 11(4): e0152517
   › Primary publication · 27046050 (PubMed) · PMC4821492 (PubMed Central)
7. Competition and allostery govern substrate selectivity of cyclooxygenase-2. Mitchener MM, Hermanson DJ, Shockley EM, Brown HA, Lindsley CW, Reese J, Rouzer CA, Lopez CF, Marnett LJ (2015) Proc Natl Acad Sci U S A 112(40): 12366-71
   › Primary publication · 26392530 (PubMed) · PMC4603459 (PubMed Central)
8. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS (2014) Wiley Interdiscip Rev Syst Biol Med 6(1): 13-36
   › Primary publication · 24123887 (PubMed) · PMC3947470 (PubMed Central)
9. Programming biological models in Python using PySB. Lopez CF, Muhlich JL, Bachman JA, Sorger PK (2013) Mol Syst Biol : 646
   › Primary publication · 23423320 (PubMed) · PMC3588907 (PubMed Central)
10. Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics. Lopez CF, Nielsen SO, Srinivas G, Degrado WF, Klein ML (2006) J Chem Theory Comput 2(3): 649-655
    › Primary publication · 18985168 (PubMed) · PMC2577386 (PubMed Central)
11. Hydrophobicity of protein surfaces: Separating geometry from chemistry. Giovambattista N, Lopez CF, Rossky PJ, Debenedetti PG (2008) Proc Natl Acad Sci U S A 105(7): 2274-9
    › Primary publication · 18268339 (PubMed) · PMC2268126 (PubMed Central)
12. Mechanistic elements of protein cold denaturation. Lopez CF, Darst RK, Rossky PJ (2008) J Phys Chem B 112(19): 5961-7
    › Primary publication · 18181599 (PubMed)
13. Modeling surfactant adsorption on hydrophobic surfaces. Nielsen SO, Srinivas G, Lopez CF, Klein ML (2005) Phys Rev Lett 94(22): 228301
    › Primary publication · 16090439 (PubMed)
14. Structure and dynamics of model pore insertion into a membrane. Lopez CF, Nielsen SO, Ensing B, Moore PB, Klein ML (2005) Biophys J 88(5): 3083-94
    › Primary publication · 15722425 (PubMed) · PMC1305460 (PubMed Central)
15. Transmembrane peptide-induced lipid sorting and mechanism of Lalpha-to-inverted phase transition using coarse-grain molecular dynamics. Nielsen SO, Lopez CF, Ivanov I, Moore PB, Shelley JC, Klein ML (2004) Biophys J 87(4): 2107-15
    › Primary publication · 15454415 (PubMed) · PMC1304638 (PubMed Central)
16. Understanding nature's design for a nanosyringe. Lopez CF, Nielsen SO, Moore PB, Klein ML (2004) Proc Natl Acad Sci U S A 101(13): 4431-4
    › Primary publication · 15070735 (PubMed) · PMC384764 (PubMed Central)
17. Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the human immunodeficiency virus HIV-1. Lopez CF, Montal M, Blasie JK, Klein ML, Moore PB (2002) Biophys J 83(3): 1259-67
    › Primary publication · 12202353 (PubMed) · PMC1302226 (PubMed Central)
18. Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation. Moore PB, Lopez CF, Klein ML (2001) Biophys J 81(5): 2484-94
    › Primary publication · 11606264 (PubMed) · PMC1301718 (PubMed Central)

Keywords & MeSH Terms

MeSH terms are retrieved from PubMed records. Learn more.

Key: MeSH Term Keyword