Ay F - Search Results

1

Measuring the reproducibility and quality of Hi-C data.

Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS. Yardımcı GG, et al. Among authors: ay f. Genome Biol. 2019 Mar 19;20(1):57. doi: 10.1186/s13059-019-1658-7. Genome Biol. 2019. PMID: 30890172 Free PMC article.

2

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.

3

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. Update in: Bioinformatics. 2025 Jan 12:btaf015. doi: 10.1093/bioinformatics/btaf015 PMID: 38915554 Free PMC article. Updated. Preprint.

4

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.

5

Genomic interaction profiles in breast cancer reveal altered chromatin architecture.

Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, Hoffman AR. Zeitz MJ, et al. Among authors: ay f. PLoS One. 2013 Sep 3;8(9):e73974. doi: 10.1371/journal.pone.0073974. eCollection 2013. PLoS One. 2013. PMID: 24019942 Free PMC article.

6

Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome.

Zeitz MJ, Lerner PP, Ay F, Van Nostrand E, Heidmann JD, Noble WS, Hoffman AR. Zeitz MJ, et al. Among authors: ay f. Nucleus. 2013 Nov-Dec;4(6):487-93. doi: 10.4161/nucl.27364. Epub 2013 Dec 5. Nucleus. 2013. PMID: 24448439 Free PMC article.

7

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.

Ay F, Bailey TL, Noble WS. Ay F, et al. Genome Res. 2014 Jun;24(6):999-1011. doi: 10.1101/gr.160374.113. Epub 2014 Feb 5. Genome Res. 2014. PMID: 24501021 Free PMC article.

8

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.

Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG. Ay F, et al. Genome Res. 2014 Jun;24(6):974-88. doi: 10.1101/gr.169417.113. Epub 2014 Mar 26. Genome Res. 2014. PMID: 24671853 Free PMC article.

9

A statistical approach for inferring the 3D structure of the genome.

Varoquaux N, Ay F, Noble WS, Vert JP. Varoquaux N, et al. Among authors: ay f. Bioinformatics. 2014 Jun 15;30(12):i26-33. doi: 10.1093/bioinformatics/btu268. Bioinformatics. 2014. PMID: 24931992 Free PMC article.

10

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum.

Ay F, Bunnik EM, Varoquaux N, Vert JP, Noble WS, Le Roch KG. Ay F, et al. Bioessays. 2015 Feb;37(2):182-94. doi: 10.1002/bies.201400145. Epub 2014 Nov 13. Bioessays. 2015. PMID: 25394267 Free PMC article.

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