Danielle Denisko

I’m a PhD candidate in the Bioinformatics and Integrative Genomics program at Harvard. Previously, I completed my undergraduate and Master’s studies at the University of Toronto in Canada. My research interests include transposable elements, alternative splicing, 3D chromatin architecture, and epigenomics.

selected publications

Motif elucidation in ChIP-seq datasets with a knockout control

Danielle Denisko, Coby Viner, and Michael M Hoffman

Bioinformatics Advances, 2023

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Chromatin immunoprecipitation-sequencing is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout (KO) experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO—a computational method to automatically optimize motif analyses with KO controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of KO controls, which far outperform input controls.PeaKO is freely available at https://peako.hoffmanlab.org.michael.hoffman@utoronto.ca
@article{peaKO, author = {Denisko, Danielle and Viner, Coby and Hoffman, Michael M}, title = {{Motif elucidation in ChIP-seq datasets with a knockout control}}, journal = {Bioinformatics Advances}, volume = {3}, number = {1}, pages = {vbad031}, year = {2023}, issn = {2635-0041}, doi = {10.1093/bioadv/vbad031}, url = {https://doi.org/10.1093/bioadv/vbad031}, eprint = {https://academic.oup.com/bioinformaticsadvances/article-pdf/3/1/vbad031/49761827/vbad031.pdf}, }

Classification and interaction in random forests

Danielle Denisko, and Michael M Hoffman

Proceedings of the National Academy of Sciences, 2018

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@article{Denisko2018,
  author = {Denisko, Danielle and Hoffman, Michael M},
  doi = {10.1073/pnas.1800256115},
  issn = {0027-8424},
  journal = {Proceedings of the National Academy of Sciences},
  mendeley-groups = {Commentary},
  number = {8},
  pages = {1690--1692},
  pmid = {29440440},
  title = {{Classification and interaction in random forests}},
  url = {http://www.pnas.org/content/115/8/1690.abstract},
  volume = {115},
  year = {2018},
}