.. title: Research
.. slug: research
.. date: 2019-12-05
.. tags: 
.. category: 
.. link: 
.. description: 
.. type: text

I recently defended my PhD in Bioengineering, which I did in the [Cremins Lab](http://creminslab.com/)
at the University of Pennsylvania. My research revolved around developing
analysis techniques for studying the three dimensional structure of the
mammalian genome. In particular, I analyzed maps of genome folding obtained
using techniques like 5C or Hi-C and integrated them with other epigenetic
datasets to understand how genome folding plays a role in development and
disease.

Here's a list of publications I was a part of during my time in the lab:

First author and co-led projects
================================
<div class="container-fluid"><div class="row"><div class="col-md-6 col-xs-12">
![](/images/papers/cell-systems.png)

Cell Systems 2019 |
[DOI](https://doi.org/10.1016/j.cels.2019.02.006) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/30904376) |
[PDF](/papers/gilgenast-cell-systems-systematic-looping.pdf)
</div>
<div class="col-md-6 col-xs-12">
![](/images/papers/genome-biology.png)

Genome Biology 2020 |
[DOI](https://doi.org/10.1186/s13059-020-02061-9) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/32859248) |
[PDF](/papers/fernandez-genome-biology-3defdr.pdf)
</div></div></div>

Collaborative projects in which I played a lead/major role in data analysis
===========================================================================
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![](/images/papers/cell-stem-cell.png)

Cell Stem Cell 2016 |
[DOI](http://dx.doi.org/10.1016/j.stem.2016.04.004) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/27152443) |
[PDF](/papers/beagan-cell-stem-cell-incomplete-reprogramming.pdf)
</div>
<div class="col-md-6 col-xs-12">
![](/images/papers/mol-cell.png)

Molecular Cell 2016 |
[DOI](http://dx.doi.org/10.1016/j.molcel.2017.02.027) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/28388437) |
[PDF](/papers/hsu-mol-cell-brd2-ctcf.pdf)
</div>
<div class="col-md-6 col-xs-12">
![](/images/papers/nature.png)

Nature 2019 |
[DOI](https://doi.org/10.1038/s41586-019-1778-y) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/31776509) |
[PDF](/papers/zhang-nature-mitosis.pdf)
</div></div></div>

Projects to which I provided assistance in the form of code and technical scientific advice
===========================================================================================
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![](/images/papers/genome-research.png)

Genome Research 2017 |
[DOI](https://doi.org/10.1101/gr.215160.116) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/28536180) |
[PDF](/papers/beagan-genome-research-yy1.pdf)
</div>
<div class="col-md-6 col-xs-12">
![](/images/papers/methods.png)

Methods 2018 |
[DOI](https://doi.org/10.1016/j.ymeth.2018.05.005) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/29772275) |
[PDF](/papers/kim-methods-5c-id.pdf)
</div>
<div class="col-md-6 col-xs-12">
![](/images/papers/cell.png)

Cell 2018 |
[DOI](https://doi.org/10.1016/j.cell.2018.08.005) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/30173918) |
[PDF](/papers/sun-cell-tnr.pdf)
</div>
<div class="col-md-6 col-xs-12">
![](/images/papers/nat-methods.png)

Nature Methods 2019 |
[DOI](https://doi.org/10.1038/s41592-019-0436-5) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/31235883) |
[PDF](/papers/kim-nat-methods-ladl.pdf)
</div>
<div class="col-md-6 col-xs-12">
![](/images/papers/nature-genetics.png)

Nature Genetics 2020 |
[DOI](https://doi.org/10.1038/s41588-020-0680-8) |
[Pubmed](https://pubmed.ncbi.nlm.nih.gov/32868908) |
[PDF](/papers/nature-genetics.png)
</div></div></div>