Research

I'm currently a Bioengineering PhD candidate in the Cremins Lab at the University of Pennsylvania. My research revolves around developing analysis techniques for studying the three dimensional structure of the mammalian genome. In particular, I analyze maps of genome folding obtained using techniques like 5C or Hi-C and integrate them with other epigenetic datasets to understand how genome folding plays a role in development and disease.

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

First author and co-led projects

Cell Systems 2019 | DOI | Pubmed | PDF




3DeFDR: Identifying cell type-specific looping interactions with empirical false discovery rate guided thresholding

Lindsey Fernandez*, Thomas G. Gilgenast*, and Jennifer E. Phillips-Cremins

Manuscript under revision | bioRxiv

Collaborative projects in which I played a lead/major role in data analysis

Cell Stem Cell 2016 | DOI | Pubmed | PDF

Molecular Cell 2016 | DOI | Pubmed | PDF

Nature 2019 | DOI | Pubmed | PDF

Projects to which I provided assistance in the form of code and technical scientific advice

Genome Research 2017 | DOI | Pubmed | PDF

Methods 2018 | DOI | Pubmed | PDF

Cell 2018 | DOI | Pubmed | PDF
Nature Methods 2019 | DOI | Pubmed | PDF



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Di Zhang, Peng Huang, Cheryl Keller, Belinda Giardine, Haoyue Zhang, Thomas Gilgenast, Jennifer Phillips-Cremins, Ross Hardison, and Gerd A. Blobel

Manuscript under revision