Carlos F. Lopez, Ph.D.

Assistant Professor

Visit Lab Site

Faculty Appointments
Assistant Professor of Biochemistry Assistant Professor of Biomedical InformaticsAssistant Professor of Pharmacology
Ph.D., Chemistry, University of Pennsylvania, Philadelphia, PennsylvaniaB.S., University of Miami, Coral Gables, Florida
Office Address
Vanderbilt University, Dept. of Biochemistry
2215 Garland Ave, 639 LH
Nashville, TN 37232
Research Description
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 molecular cancer cell 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 ( 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.
Research Keywords
modeling, simulation, kinetics, molecular simulation, molecular dynamics, multi scale, computation, computational, signaling, cancer. ORCID:
Shockley EM, Vrugt JA, Lopez CF. PyDREAM: High-dimensional parameter inference for biological models in Python. Bioinformatics [print-electronic]. 2017 Oct 10/4/2017; PMID: 29028896, PII: 4345643, DOI: 10.1093/bioinformatics/btx626, ISSN: 1367-4811.

Harris LA, Nobile MS, Pino JC, Lubbock ALR, Besozzi D, Mauri G, Cazzaniga P, Lopez CF. GPU-powered model analysis with PySB/cupSODA. Bioinformatics [print-electronic]. 2017 Jun 6/28/2017; PMID: 28666314, PII: 3896987, DOI: 10.1093/bioinformatics/btx420, ISSN: 1367-4811.

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. Integrated, High-Throughput, Multiomics Platform Enables Data-Driven Construction of Cellular Responses and Reveals Global Drug Mechanisms of Action. J. Proteome Res [print-electronic]. 2017 Mar 3/3/2017; 16(3): 1364-75. PMID: 28088864, DOI: 10.1021/acs.jproteome.6b01004, ISSN: 1535-3907.

Chifman J, Arat S, Deng Z, Lemler E, Pino JC, Harris LA, Kochen MA, Lopez CF, Akman SA, Torti FM, Torti SV, Laubenbacher R. Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective. PLoS Comput. Biol. 2017 Feb; 13(2): e1005352. PMID: 28166223, PMCID: PMC5293201, PII: PCOMPBIOL-D-16-00797, DOI: 10.1371/journal.pcbi.1005352, ISSN: 1553-7358.

Harris LA, Frick PL, Garbett SP, Hardeman KN, Paudel BB, Lopez CF, Quaranta V, Tyson DR. An unbiased metric of antiproliferative drug effect in vitro. Nat. Methods [print-electronic]. 2016 May 5/2/2016; PMID: 27135974, PII: nmeth.3852, DOI: 10.1038/nmeth.3852, ISSN: 1548-7105.

Fischer AW, Heinze S, Putnam DK, Li B, Pino JC, Xia Y, Lopez CF, Meiler J. CASP11 - An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline. PLoS ONE. 2016; 11(4): e0152517. PMID: 27046050, PMCID: PMC4821492, PII: PONE-D-15-54006, DOI: 10.1371/journal.pone.0152517, ISSN: 1932-6203.

Mitchener MM, Hermanson DJ, Shockley EM, Brown HA, Lindsley CW, Reese J, Rouzer CA, Lopez CF, Marnett LJ. Competition and allostery govern substrate selectivity of cyclooxygenase-2. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2015 Oct 10/6/2015; 112(40): 12366-71. PMID: 26392530, PMCID: PMC4603459, PII: 1507307112, DOI: 10.1073/pnas.1507307112, ISSN: 1091-6490.

Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med [print-electronic]. 2014 Jan; 6(1): 13-36. PMID: 24123887, PMCID: PMC3947470, DOI: 10.1002/wsbm.1245, ISSN: 1939-005X.

Lopez CF, Muhlich JL, Bachman JA, Sorger PK. Programming biological models in Python using PySB. Mol. Syst. Biol. 2013; 9: 646. PMID: 23423320, PMCID: PMC3588907, PII: msb20131, DOI: 10.1038/msb.2013.1, ISSN: 1744-4292.

Lopez CF, Darst RK, Rossky PJ. Mechanistic elements of protein cold denaturation. J Phys Chem B [print-electronic]. 2008 May 5/15/2008; 112(19): 5961-7. PMID: 18181599, DOI: 10.1021/jp075928t, ISSN: 1520-6106.

Giovambattista N, Lopez CF, Rossky PJ, Debenedetti PG. Hydrophobicity of protein surfaces: Separating geometry from chemistry. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2008 Feb 2/19/2008; 105(7): 2274-9. PMID: 18268339, PMCID: PMC2268126, PII: 0708088105, DOI: 10.1073/pnas.0708088105, ISSN: 1091-6490.

Lopez CF, Nielsen SO, Srinivas G, Degrado WF, Klein ML. Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics. J Chem Theory Comput. 2006 May; 2(3): 649-55. PMID: 18985168, PMCID: PMC2577386, DOI: 10.1021/ct050298p, ISSN: 1549-9626.

Nielsen SO, Srinivas G, Lopez CF, Klein ML. Modeling surfactant adsorption on hydrophobic surfaces. Phys. Rev. Lett [print-electronic]. 2005 Jun 6/10/2005; 94(22): 228301. PMID: 16090439, DOI: 10.1103/PhysRevLett.94.228301, ISSN: 0031-9007.

Lopez CF, Nielsen SO, Ensing B, Moore PB, Klein ML. Structure and dynamics of model pore insertion into a membrane. Biophys. J [print-electronic]. 2005 May; 88(5): 3083-94. PMID: 15722425, PMCID: PMC1305460, PII: S0006-3495(05)73362-2, DOI: 10.1529/biophysj.104.053769, ISSN: 0006-3495.

Nielsen SO, Lopez CF, Ivanov I, Moore PB, Shelley JC, Klein ML. Transmembrane peptide-induced lipid sorting and mechanism of Lalpha-to-inverted phase transition using coarse-grain molecular dynamics. Biophys. J. 2004 Oct; 87(4): 2107-15. PMID: 15454415, PMCID: PMC1304638, PII: S0006-3495(04)73690-5, DOI: 10.1529/biophysj.104.040311, ISSN: 0006-3495.

Lopez CF, Nielsen SO, Moore PB, Klein ML. Understanding nature's design for a nanosyringe. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2004 Mar 3/30/2004; 101(13): 4431-4. PMID: 15070735, PMCID: PMC384764, PII: 0400352101, DOI: 10.1073/pnas.0400352101, ISSN: 0027-8424.

Lopez CF, Montal M, Blasie JK, Klein ML, Moore PB. Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the human immunodeficiency virus HIV-1. Biophys. J. 2002 Sep; 83(3): 1259-67. PMID: 12202353, PMCID: PMC1302226, PII: S0006-3495(02)73898-8, DOI: 10.1016/S0006-3495(02)73898-8, ISSN: 0006-3495.

Moore PB, Lopez CF, Klein ML. Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation. Biophys. J. 2001 Nov; 81(5): 2484-94. PMID: 11606264, PMCID: PMC1301718, PII: S0006-3495(01)75894-8, DOI: 10.1016/S0006-3495(01)75894-8, ISSN: 0006-3495.