Bussemaker HJ - Search Results

1

Predicting the DNA binding specificity of mutated transcription factors using family-level biophysically interpretable machine learning.

Liu S, Gomez-Alcala P, Leemans C, Glassford WJ, Mann RS, Bussemaker HJ. Liu S, et al. Among authors: bussemaker hj. bioRxiv [Preprint]. 2024 Jan 29:2024.01.24.577115. doi: 10.1101/2024.01.24.577115. bioRxiv. 2024. PMID: 38352411 Free PMC article. Preprint.

2

Benchmarking DNA binding affinity models using allele-specific transcription factor binding data.

Li X, Melo LAN, Bussemaker HJ. Li X, et al. Among authors: bussemaker hj. bioRxiv [Preprint]. 2023 Dec 15:2023.12.15.571887. doi: 10.1101/2023.12.15.571887. bioRxiv. 2023. PMID: 38168434 Free PMC article. Preprint.

3

Identifying genetic regulatory variants that affect transcription factor activity.

Li X, Lappalainen T, Bussemaker HJ. Li X, et al. Among authors: bussemaker hj. Cell Genom. 2023 Aug 18;3(9):100382. doi: 10.1016/j.xgen.2023.100382. eCollection 2023 Sep 13. Cell Genom. 2023. PMID: 37719147 Free PMC article.

4

Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements.

Trauernicht M, Rastogi C, Manzo SG, Bussemaker HJ, van Steensel B. Trauernicht M, et al. Among authors: bussemaker hj. Nucleic Acids Res. 2023 Oct 13;51(18):9690-9702. doi: 10.1093/nar/gkad718. Nucleic Acids Res. 2023. PMID: 37650627 Free PMC article.

5

Emerging questions in transcriptional regulation.

Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Nora EP, et al. Among authors: bussemaker hj. Cell Syst. 2023 Apr 19;14(4):247-251. doi: 10.1016/j.cels.2023.03.005. Cell Syst. 2023. PMID: 37080160 Free article.

6

Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR.

FitzPatrick VD, Leemans C, van Arensbergen J, van Steensel B, Bussemaker HJ. FitzPatrick VD, et al. Among authors: bussemaker hj. Nucleic Acids Res. 2023 Jun 23;51(11):5499-5511. doi: 10.1093/nar/gkad232. Nucleic Acids Res. 2023. PMID: 37013986 Free PMC article.

7

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors.

Feng S, Rastogi C, Loker R, Glassford WJ, Tomas Rube H, Bussemaker HJ, Mann RS. Feng S, et al. Among authors: bussemaker hj. Nat Commun. 2022 Jul 1;13(1):3808. doi: 10.1038/s41467-022-31501-2. Nat Commun. 2022. PMID: 35778382 Free PMC article.

8

Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning.

Rube HT, Rastogi C, Feng S, Kribelbauer JF, Li A, Becerra B, Melo LAN, Do BV, Li X, Adam HH, Shah NH, Mann RS, Bussemaker HJ. Rube HT, et al. Among authors: bussemaker hj. Nat Biotechnol. 2022 Oct;40(10):1520-1527. doi: 10.1038/s41587-022-01307-0. Epub 2022 May 23. Nat Biotechnol. 2022. PMID: 35606422 Free PMC article.

9

Transcription factor regulation of eQTL activity across individuals and tissues.

Flynn ED, Tsu AL, Kasela S, Kim-Hellmuth S, Aguet F, Ardlie KG, Bussemaker HJ, Mohammadi P, Lappalainen T. Flynn ED, et al. Among authors: bussemaker hj. PLoS Genet. 2022 Jan 31;18(1):e1009719. doi: 10.1371/journal.pgen.1009719. eCollection 2022 Jan. PLoS Genet. 2022. PMID: 35100260 Free PMC article.

10

Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes.

Zhang L, Rube HT, Vakulskas CA, Behlke MA, Bussemaker HJ, Pufall MA. Zhang L, et al. Among authors: bussemaker hj. Nucleic Acids Res. 2020 May 21;48(9):5037-5053. doi: 10.1093/nar/gkaa231. Nucleic Acids Res. 2020. PMID: 32315032 Free PMC article.

Save citations to file

Email citations

Send citations to clipboard

Add to Collections

Add to My Bibliography

Create a file for external citation management software

Your saved search

Your RSS Feed

My NCBI Filters

Text availability

Article attribute

Article type

Publication date

81 results

Search Page