Ay F - Search Results

1

TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer.

Lio CJ, Shukla V, Samaniego-Castruita D, González-Avalos E, Chakraborty A, Yue X, Schatz DG, Ay F, Rao A. Lio CJ, et al. Among authors: ay f. Sci Immunol. 2019 Apr 26;4(34):eaau7523. doi: 10.1126/sciimmunol.aau7523. Sci Immunol. 2019. PMID: 31028100 Free PMC article.

2

Loop Catalog: a comprehensive HiChIP database of human and mouse samples.

Reyna J, Fetter K, Ignacio R, Marandi CCA, Rao N, Jiang Z, Figueroa DS, Bhattacharyya S, Ay F. Reyna J, et al. Among authors: ay f. bioRxiv [Preprint]. 2024 Apr 29:2024.04.26.591349. doi: 10.1101/2024.04.26.591349. bioRxiv. 2024. PMID: 38746164 Free PMC article. Preprint.

3

Brd2 is dispensable for genome compartmentalization and replication timing.

Hinojosa-Gonzalez L, Turner JL, Sasaki T, Ay F, Gilbert DM. Hinojosa-Gonzalez L, et al. Among authors: ay f. bioRxiv [Preprint]. 2023 Nov 19:2023.11.17.567572. doi: 10.1101/2023.11.17.567572. bioRxiv. 2023. PMID: 38249518 Free PMC article. Preprint.

4

nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Non-linear Iterative Partial Least Squares.

Mattessich M, Reyna J, Aron E, Ay F, Kilmer M, Kleinstein SH, Konstorum A. Mattessich M, et al. Among authors: ay f. bioRxiv [Preprint]. 2024 Jun 10:2024.06.07.597819. doi: 10.1101/2024.06.07.597819. bioRxiv. 2024. PMID: 38915554 Free PMC article. Preprint.

5

17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells.

Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P. Schmiedel BJ, et al. Among authors: ay f. Nat Commun. 2016 Nov 16;7:13426. doi: 10.1038/ncomms13426. Nat Commun. 2016. PMID: 27848966 Free PMC article.

6

Identification of copy number variations and translocations in cancer cells from Hi-C data.

Chakraborty A, Ay F. Chakraborty A, et al. Among authors: ay f. Bioinformatics. 2018 Jan 15;34(2):338-345. doi: 10.1093/bioinformatics/btx664. Bioinformatics. 2018. PMID: 29048467 Free PMC article.

7

The role of 3D genome organization in disease: From compartments to single nucleotides.

Chakraborty A, Ay F. Chakraborty A, et al. Among authors: ay f. Semin Cell Dev Biol. 2019 Jun;90:104-113. doi: 10.1016/j.semcdb.2018.07.005. Epub 2018 Jul 17. Semin Cell Dev Biol. 2019. PMID: 30017907 Free PMC article. Review.

8

The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain.

Cajigas I, Chakraborty A, Swyter KR, Luo H, Bastidas M, Nigro M, Morris ER, Chen S, VanGompel MJW, Leib D, Kohtz SJ, Martina M, Koh S, Ay F, Kohtz JD. Cajigas I, et al. Among authors: ay f. Mol Cell. 2018 Sep 20;71(6):956-972.e9. doi: 10.1016/j.molcel.2018.07.024. Epub 2018 Aug 23. Mol Cell. 2018. PMID: 30146317 Free PMC article.

9

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.

Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Sima J, et al. Among authors: ay f. Cell. 2019 Feb 7;176(4):816-830.e18. doi: 10.1016/j.cell.2018.11.036. Epub 2018 Dec 27. Cell. 2019. PMID: 30595451 Free PMC article.

10

Replication timing networks reveal a link between transcription regulatory circuits and replication timing control.

Rivera-Mulia JC, Kim S, Gabr H, Chakraborty A, Ay F, Kahveci T, Gilbert DM. Rivera-Mulia JC, et al. Among authors: ay f. Genome Res. 2019 Sep;29(9):1415-1428. doi: 10.1101/gr.247049.118. Epub 2019 Aug 21. Genome Res. 2019. PMID: 31434679 Free PMC article.

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