Lopez CF - Search Results

1

Programming biological models in Python using PySB.

Lopez CF, Muhlich JL, Bachman JA, Sorger PK. Lopez CF, et al. Mol Syst Biol. 2013;9:646. doi: 10.1038/msb.2013.1. Mol Syst Biol. 2013. PMID: 23423320 Free PMC article.

2

GPU-powered model analysis with PySB/cupSODA.

Harris LA, Nobile MS, Pino JC, Lubbock ALR, Besozzi D, Mauri G, Cazzaniga P, Lopez CF. Harris LA, et al. Among authors: lopez cf. Bioinformatics. 2017 Nov 1;33(21):3492-3494. doi: 10.1093/bioinformatics/btx420. Bioinformatics. 2017. PMID: 28666314 Free PMC article.

3

Programmatic modeling for biological systems.

Lubbock ALR, Lopez CF. Lubbock ALR, et al. Among authors: lopez cf. Curr Opin Syst Biol. 2021 Sep;27:100343. doi: 10.1016/j.coisb.2021.05.004. Epub 2021 May 24. Curr Opin Syst Biol. 2021. PMID: 34485764 Free PMC article.

4

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. Chylek LA, et al. Among authors: lopez cf. Wiley Interdiscip Rev Syst Biol Med. 2014 Jan-Feb;6(1):13-36. doi: 10.1002/wsbm.1245. Epub 2013 Sep 30. Wiley Interdiscip Rev Syst Biol Med. 2014. PMID: 24123887 Free PMC article. Review.

5

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

Shockley EM, Vrugt JA, Lopez CF. Shockley EM, et al. Among authors: lopez cf. Bioinformatics. 2018 Feb 15;34(4):695-697. doi: 10.1093/bioinformatics/btx626. Bioinformatics. 2018. PMID: 29028896 Free PMC article.

6

Signal integration and information transfer in an allosterically regulated network.

Shockley EM, Rouzer CA, Marnett LJ, Deeds EJ, Lopez CF. Shockley EM, et al. Among authors: lopez cf. NPJ Syst Biol Appl. 2019 Jul 18;5:23. doi: 10.1038/s41540-019-0100-9. eCollection 2019. NPJ Syst Biol Appl. 2019. PMID: 31341635 Free PMC article.

7

Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python.

Lubbock ALR, Lopez CF. Lubbock ALR, et al. Among authors: lopez cf. Bioinformatics. 2022 Oct 14;38(20):4823-4825. doi: 10.1093/bioinformatics/btac580. Bioinformatics. 2022. PMID: 36000837 Free PMC article.

8

Data-driven structural analysis of small cell lung cancer transcription factor network suggests potential subtype regulators and transition pathways.

Ozen M, Lopez CF. Ozen M, et al. Among authors: lopez cf. NPJ Syst Biol Appl. 2023 Oct 31;9(1):55. doi: 10.1038/s41540-023-00316-2. NPJ Syst Biol Appl. 2023. PMID: 37907529 Free PMC article.

9

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. Chifman J, et al. Among authors: lopez cf. PLoS Comput Biol. 2017 Feb 6;13(2):e1005352. doi: 10.1371/journal.pcbi.1005352. eCollection 2017 Feb. PLoS Comput Biol. 2017. PMID: 28166223 Free PMC article.

10

Interactive Multiresolution Visualization of Cellular Network Processes.

Ortega OO, Lopez CF. Ortega OO, et al. Among authors: lopez cf. iScience. 2020 Jan 24;23(1):100748. doi: 10.1016/j.isci.2019.100748. Epub 2019 Nov 29. iScience. 2020. PMID: 31884165 Free PMC article.

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