Carlos Lopez
Faculty Member
Last active: 3/14/2018

  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. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  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. 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)