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Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools.
Altenbuchinger M, Weihs A, Quackenbush J, Grabe HJ, Zacharias HU. Altenbuchinger M, et al. Biochim Biophys Acta Gene Regul Mech. 2020 Jun;1863(6):194418. doi: 10.1016/j.bbagrm.2019.194418. Epub 2019 Oct 19. Biochim Biophys Acta Gene Regul Mech. 2020. PMID: 31639475 Free PMC article. Review.
BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52.
Hatchi E, Goehring L, Landini S, Skourti-Stathaki K, DeConti DK, Abderazzaq FO, Banerjee P, Demers TM, Wang YE, Quackenbush J, Livingston DM. Hatchi E, et al. Nature. 2021 Mar;591(7851):665-670. doi: 10.1038/s41586-020-03150-2. Epub 2021 Feb 3. Nature. 2021. PMID: 33536619 Free PMC article.
PUMA: PANDA Using MicroRNA Associations.
Kuijjer ML, Fagny M, Marin A, Quackenbush J, Glass K. Kuijjer ML, et al. Bioinformatics. 2020 Sep 15;36(18):4765-4773. doi: 10.1093/bioinformatics/btaa571. Bioinformatics. 2020. PMID: 32860050 Free PMC article.
Bayesian inference of sample-specific coexpression networks.
Saha E, Fanfani V, Mandros P, Ben Guebila M, Fischer J, Shutta KH, DeMeo DL, Lopes-Ramos CM, Quackenbush J. Saha E, et al. Genome Res. 2024 Oct 11;34(9):1397-1410. doi: 10.1101/gr.279117.124. Genome Res. 2024. PMID: 39134413 Free PMC article.
Spatial Cellular Networks from omics data with SpaCeNet.
Schrod S, Lück N, Lohmayer R, Solbrig S, Völkl D, Wipfler T, Shutta KH, Ben Guebila M, Schäfer A, Beißbarth T, Zacharias HU, Oefner PJ, Quackenbush J, Altenbuchinger M. Schrod S, et al. Genome Res. 2024 Oct 11;34(9):1371-1383. doi: 10.1101/gr.279125.124. Genome Res. 2024. PMID: 39231609
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.
Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta KH, Sonawane AR, Lim J, Calderer G, van IJzendoorn DGP, Morgan D, Marin A, Chen CY, Song Q, Saha E, DeMeo DL, Padi M, Platig J, Kuijjer ML, Glass K, Quackenbush J. Ben Guebila M, et al. Genome Biol. 2023 Mar 9;24(1):45. doi: 10.1186/s13059-023-02877-1. Genome Biol. 2023. PMID: 36894939 Free PMC article.
33 results