Thompson D - Search Results

1

Comparative analysis of gene regulatory networks: from network reconstruction to evolution.

Thompson D, Regev A, Roy S. Thompson D, et al. Annu Rev Cell Dev Biol. 2015;31:399-428. doi: 10.1146/annurev-cellbio-100913-012908. Epub 2015 Sep 3. Annu Rev Cell Dev Biol. 2015. PMID: 26355593 Review.

2

Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.

Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A. Roy S, et al. Among authors: thompson d. Genome Res. 2013 Jun;23(6):1039-50. doi: 10.1101/gr.146233.112. Epub 2013 May 2. Genome Res. 2013. PMID: 23640720 Free PMC article.

3

Evolution of regulatory networks in Candida glabrata: learning to live with the human host.

Roy S, Thompson D. Roy S, et al. Among authors: thompson d. FEMS Yeast Res. 2015 Dec;15(8):fov087. doi: 10.1093/femsyr/fov087. Epub 2015 Oct 7. FEMS Yeast Res. 2015. PMID: 26449820 Review.

4

Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies.

Koch C, Konieczka J, Delorey T, Lyons A, Socha A, Davis K, Knaack SA, Thompson D, O'Shea EK, Regev A, Roy S. Koch C, et al. Among authors: thompson d. Cell Syst. 2017 May 24;4(5):543-558.e8. doi: 10.1016/j.cels.2017.04.010. Cell Syst. 2017. PMID: 28544882 Free PMC article.

5

Evolutionary principles of modular gene regulation in yeasts.

Thompson DA, Roy S, Chan M, Styczynsky MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A. Thompson DA, et al. Elife. 2013 Jun 18;2:e00603. doi: 10.7554/eLife.00603. Elife. 2013. PMID: 23795289 Free PMC article.

6

Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum.

Knaack SA, Thompson DA, Roy S. Knaack SA, et al. Methods Mol Biol. 2016;1361:375-89. doi: 10.1007/978-1-4939-3079-1_21. Methods Mol Biol. 2016. PMID: 26483033 Free PMC article.

7

The evolution, evolvability and engineering of gene regulatory DNA.

Vaishnav ED, de Boer CG, Molinet J, Yassour M, Fan L, Adiconis X, Thompson DA, Levin JZ, Cubillos FA, Regev A. Vaishnav ED, et al. Nature. 2022 Mar;603(7901):455-463. doi: 10.1038/s41586-022-04506-6. Epub 2022 Mar 9. Nature. 2022. PMID: 35264797 Free PMC article.

8

Fungal regulatory evolution: cis and trans in the balance.

Thompson DA, Regev A. Thompson DA, et al. FEBS Lett. 2009 Dec 17;583(24):3959-65. doi: 10.1016/j.febslet.2009.11.032. FEBS Lett. 2009. PMID: 19914250 Free PMC article. Review.

9

The role of nucleosome positioning in the evolution of gene regulation.

Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. Tsankov AM, et al. PLoS Biol. 2010 Jul 6;8(7):e1000414. doi: 10.1371/journal.pbio.1000414. PLoS Biol. 2010. PMID: 20625544 Free PMC article.

10

GeNets: a unified web platform for network-based genomic analyses.

Li T, Kim A, Rosenbluh J, Horn H, Greenfeld L, An D, Zimmer A, Liberzon A, Bistline J, Natoli T, Li Y, Tsherniak A, Narayan R, Subramanian A, Liefeld T, Wong B, Thompson D, Calvo S, Carr S, Boehm J, Jaffe J, Mesirov J, Hacohen N, Regev A, Lage K. Li T, et al. Among authors: thompson d. Nat Methods. 2018 Jul;15(7):543-546. doi: 10.1038/s41592-018-0039-6. Epub 2018 Jun 18. Nat Methods. 2018. PMID: 29915188 Free PMC article.

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