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Items: 20

1.

Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Simulations.

Wilson BA, Ramanathan A, Lopez CF.

Biophys J. 2019 Aug 6;117(3):429-444. doi: 10.1016/j.bpj.2019.06.023. Epub 2019 Jul 2.

2.

Signal integration and information transfer in an allosterically regulated network.

Shockley EM, Rouzer CA, Marnett LJ, Deeds EJ, Lopez CF.

NPJ Syst Biol Appl. 2019 Jul 18;5:23. doi: 10.1038/s41540-019-0100-9. eCollection 2019.

3.

Arrestin-3 scaffolding of the JNK3 cascade suggests a mechanism for signal amplification.

Perry NA, Kaoud TS, Ortega OO, Kaya AI, Marcus DJ, Pleinis JM, Berndt S, Chen Q, Zhan X, Dalby KN, Lopez CF, Iverson TM, Gurevich VV.

Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):810-815. doi: 10.1073/pnas.1819230116. Epub 2018 Dec 27.

4.

PyDREAM: high-dimensional parameter inference for biological models in python.

Shockley EM, Vrugt JA, Lopez CF.

Bioinformatics. 2018 Feb 15;34(4):695-697. doi: 10.1093/bioinformatics/btx626.

5.

GPU-powered model analysis with PySB/cupSODA.

Harris LA, Nobile MS, Pino JC, Lubbock ALR, Besozzi D, Mauri G, Cazzaniga P, Lopez CF.

Bioinformatics. 2017 Nov 1;33(21):3492-3494. doi: 10.1093/bioinformatics/btx420.

6.

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.

PLoS Comput Biol. 2017 Feb 6;13(2):e1005352. doi: 10.1371/journal.pcbi.1005352. eCollection 2017 Feb.

7.

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.

J Proteome Res. 2017 Mar 3;16(3):1364-1375. doi: 10.1021/acs.jproteome.6b01004. Epub 2017 Feb 9.

PMID:
28088864
8.

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.

Nat Methods. 2016 Jun;13(6):497-500. doi: 10.1038/nmeth.3852. Epub 2016 May 2.

9.

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.

PLoS One. 2016 Apr 5;11(4):e0152517. doi: 10.1371/journal.pone.0152517. eCollection 2016.

10.

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.

Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):12366-71. doi: 10.1073/pnas.1507307112. Epub 2015 Sep 21. Erratum in: Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):E1413.

11.

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.

Wiley Interdiscip Rev Syst Biol Med. 2014 Jan-Feb;6(1):13-36. doi: 10.1002/wsbm.1245. Epub 2013 Sep 30. Review.

12.

Programming biological models in Python using PySB.

Lopez CF, Muhlich JL, Bachman JA, Sorger PK.

Mol Syst Biol. 2013;9:646. doi: 10.1038/msb.2013.1.

13.

Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics.

Lopez CF, Nielsen SO, Srinivas G, Degrado WF, Klein ML.

J Chem Theory Comput. 2006 May;2(3):649-655.

14.

Hydrophobicity of protein surfaces: Separating geometry from chemistry.

Giovambattista N, Lopez CF, Rossky PJ, Debenedetti PG.

Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2274-9. doi: 10.1073/pnas.0708088105. Epub 2008 Feb 11.

15.

Mechanistic elements of protein cold denaturation.

Lopez CF, Darst RK, Rossky PJ.

J Phys Chem B. 2008 May 15;112(19):5961-7. doi: 10.1021/jp075928t. Epub 2008 Jan 9.

PMID:
18181599
16.

Modeling surfactant adsorption on hydrophobic surfaces.

Nielsen SO, Srinivas G, Lopez CF, Klein ML.

Phys Rev Lett. 2005 Jun 10;94(22):228301. Epub 2005 Jun 8.

PMID:
16090439
17.

Structure and dynamics of model pore insertion into a membrane.

Lopez CF, Nielsen SO, Ensing B, Moore PB, Klein ML.

Biophys J. 2005 May;88(5):3083-94. Epub 2005 Feb 18.

18.

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.

Biophys J. 2004 Oct;87(4):2107-15.

19.

Understanding nature's design for a nanosyringe.

Lopez CF, Nielsen SO, Moore PB, Klein ML.

Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4431-4. Epub 2004 Mar 12.

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