https://github.com/mvinyard/mvinyard
PhD Student @ Harvard University
https://github.com/mvinyard/mvinyard
Last synced: 7 months ago
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PhD Student @ Harvard University
- Host: GitHub
- URL: https://github.com/mvinyard/mvinyard
- Owner: mvinyard
- Created: 2021-11-17T05:51:31.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2023-08-18T14:07:40.000Z (about 2 years ago)
- Last Synced: 2025-01-21T00:04:34.664Z (9 months ago)
- Size: 78.1 KB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
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I'm currently working on my PhD at Harvard University where I am developing methods for the analysis of single-cell genomics data. I also work on methods for CRISPR-Cas9-based genome-editing tools (like base-editing) to study cancer progression. My PhD work is funded by an NIH F31 award through the NCI and focuses on applying innovations in deep learning to analogous problems in the analysis of single-cell data. You can read more about me and my studies at my [website](https://www.michaelvinyard.com).
I am passionate about and interested in:
- 🧿 (single-cell) epigenomics and chromatin biology
- 🧬 Functional annotation of variation in the human genome
- 🧮 Deep learning
- ✂️ Functional CRISPR studies
- 🧠 Psychiatric disorders
- 🧫 Cancer biology
- 🐍 Implementing open-source tools for genomics in python.
- 🎨 Computer graphics art
### Links
### Repos and software libraries
---
#### Deep learning
#### Bioinformatics: CRISPR and other assays (single-cell and bulk)
#### Python developer utility packages and plotting
For tutorials and resources: [link](https://github.com/mvinyard/mvinyard/wiki)
### GitHub Stats
---
](https://github.com/mvinyard/)
### Selected Publications and preprints
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#### [CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML](https://www.nature.com/articles/s41589-019-0263-0)
* **Michael E. Vinyard**, et al. . *Nat. Chem. Biol.* DOI: 10.1038/s41589-019-0263-0 (**2019**).
#### [Assessement of computational methods for the analysis of single-cell ATAC-seq data](https://link.springer.com/article/10.1186/s13059-019-1854-5)
* Chen, H., Lareau, C.†, Andreani, T.†, **Michal E. Vinyard**†, et al. . *Genome Biol.* DOI: 10.1186/s13059-019-1854-5 (**2020**).
* [GitHub](https://github.com/pinellolab/scATAC-benchmarking/)
#### [SIMBA: SIngle-cell eMBedding Along with features](https://www.biorxiv.org/content/10.1101/2021.10.17.464750v2)
* Huidong Chen, Jayoung Ryu, **Michael E. Vinyard**, Adam Lerer, & Luca Pinello. . _bioRxiv_, DOI: 2021.2010.2017.464750 (**2021**).
* [GitHub](https://github.com/pinellolab/simba)
* [docs](https://simba-bio.readthedocs.io/en/latest/)
#### [Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate](https://www.sciencedirect.com/science/article/abs/pii/S2452310021000093)
* L. Wang†, Q. Zhang†, Q. Qin†, N. Trasanidis†, **Michael E. Vinyard**†, et al., . *Curr. Opin. in Syst. Biol.* ISSN 2452-3100. DOI: 10.1016/j.coisb.2021.03.006 (**2021**).
#### [singlecellVR: interactive visualization of single-cell data in virtual reality](https://www.frontiersin.org/articles/10.3389/fgene.2021.764170/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Genetics&id=764170)
* Stein, D.†, Chen, H.†, Vinyard, M.E.†, et al. . *Front. genet.* DOI: 10.1101/2020.07.30.229534 (**2021**).
* [GitHub](https://github.com/pinellolab/singlecellvr)
* [singlecellVR.com](https://singlecellvr.pinellolab.partners.org/)
---
[](http://commonmark.org)
[](https://GitHub.com/mvinyard/mvinyard)
[](https://GitHub.com/mvinyard/mvinyard)
*Dyanmically generated stats are implemented from [GitHub Readme Stats](https://github.com/anuraghazra/github-readme-stats)*
_† denotes equal contribution_