R01 GM121613/GM/NIGMS NIH HHS/United States[Grants and Funding] - Search Results

Year	Number of Results
2019	5
2020	5
2021	6
2022	2
2024	0

1

Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns.

Srivastava D, Mahony S. Srivastava D, et al. Biochim Biophys Acta Gene Regul Mech. 2020 Jun;1863(6):194443. doi: 10.1016/j.bbagrm.2019.194443. Epub 2019 Oct 19. Biochim Biophys Acta Gene Regul Mech. 2020. PMID: 31639474 Free PMC article. Review.

2

CTCF blocks antisense transcription initiation at divergent promoters.

Luan J, Vermunt MW, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA. Luan J, et al. Nat Struct Mol Biol. 2022 Nov;29(11):1136-1144. doi: 10.1038/s41594-022-00855-y. Epub 2022 Nov 11. Nat Struct Mol Biol. 2022. PMID: 36369346 Free PMC article.

3

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding.

Cochran K, Srivastava D, Shrikumar A, Balsubramani A, Hardison RC, Kundaje A, Mahony S. Cochran K, et al. Genome Res. 2022 Mar;32(3):512-523. doi: 10.1101/gr.275394.121. Epub 2022 Jan 18. Genome Res. 2022. PMID: 35042722 Free PMC article.

4

S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types.

Xiang G, Giardine BM, Mahony S, Zhang Y, Hardison RC. Xiang G, et al. Bioinformatics. 2021 Sep 29;37(18):3011-3013. doi: 10.1093/bioinformatics/btab148. Bioinformatics. 2021. PMID: 33681991 Free PMC article.

5

The changing mouse embryo transcriptome at whole tissue and single-cell resolution.

He P, Williams BA, Trout D, Marinov GK, Amrhein H, Berghella L, Goh ST, Plajzer-Frick I, Afzal V, Pennacchio LA, Dickel DE, Visel A, Ren B, Hardison RC, Zhang Y, Wold BJ. He P, et al. Nature. 2020 Jul;583(7818):760-767. doi: 10.1038/s41586-020-2536-x. Epub 2020 Jul 29. Nature. 2020. PMID: 32728245 Free PMC article.

6

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells.

Hardison RC, Zhang Y, Keller CA, Xiang G, Heuston EF, An L, Lichtenberg J, Giardine BM, Bodine D, Mahony S, Li Q, Yue F, Weiss MJ, Blobel GA, Taylor J, Hughes J, Higgs DR, Göttgens B. Hardison RC, et al. IUBMB Life. 2020 Jan;72(1):27-38. doi: 10.1002/iub.2195. Epub 2019 Nov 25. IUBMB Life. 2020. PMID: 31769130 Free PMC article. Review.

7

Direct prediction of regulatory elements from partial data without imputation.

Zhang Y, Mahony S. Zhang Y, et al. PLoS Comput Biol. 2019 Nov 4;15(11):e1007399. doi: 10.1371/journal.pcbi.1007399. eCollection 2019 Nov. PLoS Comput Biol. 2019. PMID: 31682602 Free PMC article.

8

Clinically relevant updates of the HbVar database of human hemoglobin variants and thalassemia mutations.

Giardine BM, Joly P, Pissard S, Wajcman H, K Chui DH, Hardison RC, Patrinos GP. Giardine BM, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1192-D1196. doi: 10.1093/nar/gkaa959. Nucleic Acids Res. 2021. PMID: 33125055 Free PMC article.

9

Distinct properties and functions of CTCF revealed by a rapidly inducible degron system.

Luan J, Xiang G, Gómez-García PA, Tome JM, Zhang Z, Vermunt MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA. Luan J, et al. Cell Rep. 2021 Feb 23;34(8):108783. doi: 10.1016/j.celrep.2021.108783. Cell Rep. 2021. PMID: 33626344 Free PMC article.

10

Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types.

Rieber L, Mahony S. Rieber L, et al. Epigenetics Chromatin. 2019 Oct 8;12(1):61. doi: 10.1186/s13072-019-0308-3. Epigenetics Chromatin. 2019. PMID: 31594535 Free PMC article.

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