Gunawardena J - Search Results

1

A mathematical model clarifies the ABC Score formula used in enhancer-gene prediction.

Nasser J, Nam KM, Gunawardena J. Nasser J, et al. Among authors: gunawardena j. bioRxiv [Preprint]. 2024 Dec 3:2024.11.29.626072. doi: 10.1101/2024.11.29.626072. bioRxiv. 2024. PMID: 39677755 Free PMC article. Preprint.

2

The Hill function is the universal Hopfield barrier for sharpness of input-output responses.

Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. Martinez-Corral R, et al. Among authors: gunawardena j. bioRxiv [Preprint]. 2024 Mar 28:2024.03.27.587054. doi: 10.1101/2024.03.27.587054. bioRxiv. 2024. Update in: Proc Natl Acad Sci U S A. 2024 May 28;121(22):e2318329121. doi: 10.1073/pnas.2318329121 PMID: 38585761 Free PMC article. Updated. Preprint.

3

The linear framework II: using graph theory to analyse the transient regime of Markov processes.

Nam KM, Gunawardena J. Nam KM, et al. Among authors: gunawardena j. Front Cell Dev Biol. 2023 Nov 3;11:1233808. doi: 10.3389/fcell.2023.1233808. eCollection 2023. Front Cell Dev Biol. 2023. PMID: 38020901 Free PMC article.

4

The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems.

Nam KM, Martinez-Corral R, Gunawardena J. Nam KM, et al. Among authors: gunawardena j. Interface Focus. 2022 Jun 10;12(4):20220013. doi: 10.1098/rsfs.2022.0013. eCollection 2022 Aug 6. Interface Focus. 2022. PMID: 35860006 Free PMC article. Review.

5

The Hill function is the universal Hopfield barrier for sharpness of input-output responses.

Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. Martinez-Corral R, et al. Among authors: gunawardena j. Proc Natl Acad Sci U S A. 2024 May 28;121(22):e2318329121. doi: 10.1073/pnas.2318329121. Epub 2024 May 24. Proc Natl Acad Sci U S A. 2024. PMID: 38787881 Free PMC article.

6

Robustness and parameter geography in post-translational modification systems.

Nam KM, Gyori BM, Amethyst SV, Bates DJ, Gunawardena J. Nam KM, et al. Among authors: gunawardena j. PLoS Comput Biol. 2020 May 4;16(5):e1007573. doi: 10.1371/journal.pcbi.1007573. eCollection 2020 May. PLoS Comput Biol. 2020. PMID: 32365103 Free PMC article.

7

Emergence of activation or repression in transcriptional control under a fixed molecular context.

Martinez-Corral R, Friedrich D, Frömel R, Velten L, Gunawardena J, DePace AH. Martinez-Corral R, et al. Among authors: gunawardena j. bioRxiv [Preprint]. 2024 Jun 2:2024.05.29.596388. doi: 10.1101/2024.05.29.596388. bioRxiv. 2024. PMID: 38854049 Free PMC article. Preprint.

8

Gene Regulation in and out of Equilibrium.

Wong F, Gunawardena J. Wong F, et al. Among authors: gunawardena j. Annu Rev Biophys. 2020 May 6;49:199-226. doi: 10.1146/annurev-biophys-121219-081542. Annu Rev Biophys. 2020. PMID: 32375018 Review.

9

A framework for modelling gene regulation which accommodates non-equilibrium mechanisms.

Ahsendorf T, Wong F, Eils R, Gunawardena J. Ahsendorf T, et al. Among authors: gunawardena j. BMC Biol. 2014 Dec 5;12:102. doi: 10.1186/s12915-014-0102-4. BMC Biol. 2014. PMID: 25475875 Free PMC article.

10

Biochemically plausible models of habituation for single-cell learning.

Eckert L, Vidal-Saez MS, Zhao Z, Garcia-Ojalvo J, Martinez-Corral R, Gunawardena J. Eckert L, et al. Among authors: gunawardena j. Curr Biol. 2024 Dec 16;34(24):5646-5658.e3. doi: 10.1016/j.cub.2024.10.041. Epub 2024 Nov 19. Curr Biol. 2024. PMID: 39566497 Free article.

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