Research in the Sheffield lab

# Research in the Sheffield lab

Nathan Sheffield

<span style="font-size:0.6em"><a href="http://www.databio.org/slides">www.databio.org/slides</a></span>

</section>
---

# Mission statement

We develop and apply computational methods<br/>
to organize, analyze, and understand large epigenomic data.<br/><br/>
<img src="/_modules/mission-statement/understand.svg" width="695">
<br> <img src="/_modules/mission-statement/logo_databio.svg" width="195">
</section>
---

## Keywords

### BIOLOGICAL QUESTIONS

Gene regulation<br/>
Epigenetics<br/>
Cancer<br/>

</div>

### COMPUTATIONAL ANSWERS

High-performance computing<br/>
Machine learning<br/>
Data science<br/>

</div>

---

## Biological motivation

<div class="col2">
<img src="/slides/research-overview/one_genome.svg" width="250" style="align:center"><br/>
Each cell's genome is the same
</div>

<div class="col2">
<img src="/slides/research-overview/cellTypes.jpg" width="370"><br/>
...yet the cells are diverse
</div>

<br clear="all">How can one set of instructions<br>give rise to a multicellular being?

---

## Biological motivation

<div class="col2">
<img src="/slides/research-overview/division.svg" width="300"><br clear="all"/>
In development, cells differentiate into roles...
</div>

<div class="col2">
<br><br>
<img src="/slides/research-overview/dna_folding_diversity.svg" width="400"><br/>
...by folding DNA differently to use a different subset. <br>
</div>

---

## Biological motivation

<img src="/slides/research-overview/differentation_gone_awry.svg" width="500"><br/>
...but when it breaks down, disease can result

---

<img src="https://www.genome.gov/sites/default/files/inline-images/costpermb_2017.jpg" width="650"><br clear="all"/>
We can measure DNA folding by sequencing

---

<img src="/slides/research-overview/IGV_DNase.png" width="550" style="float:left">
<br><br><br><br><br>But huge, diverse datasets lead to computational challenges.

---

# Full-stack bioinformatics

---

# Full-stack bioinformatics

---

# Full-stack bioinformatics

---

# Full-stack bioinformatics

<div class="col2">
<img src="/_modules/full-stack-bioinformatics/pyramid_algorithms.svg" width="500"><br>
</div>
<div class="col2">
Augmented Interval List
<img src="/_modules/full-stack-bioinformatics/ailist_summary.svg" width="450"><br>
</div>

---

# Full-stack bioinformatics

---

# Full-stack bioinformatics

<div class="col2">
<img src="/_modules/full-stack-bioinformatics/pyramid_analysis.svg" width="500"><br>
</div>
<div class="col2">
Analysis of DNA methylation  
in Ewing sarcoma<br/>
<img src="/_modules/full-stack-bioinformatics/analysis_ews.svg" height="450"><br>
</div>

---

# Full-stack bioinformatics

<div class="col2">
<img src="/_modules/full-stack-bioinformatics/pyramid_yellow.svg" width="500"><br>
</div>
<div class="col2">
<img src="/_modules/full-stack-bioinformatics/integration.svg" width="500"><br>
</div>
---

## Thanks for listening!

<span class="small bullet"><img src="/images/external/github_bug_black.svg" height="20" class="bullet"><a href="http://github.com/nsheff">nsheff</a></span> &middot;
<span class="small bullet"><img src="/images/icons/web.svg" height="25" class="bullet"><a href="http://databio.org">databio.org</a></span> &middot;
<span class="small bullet"><img src="/images/icons/letter.svg" height="25" class="bullet"><a href="mailto:nsheffield@virginia.edu">nsheffield@virginia.edu</a></span>

---

# Thank You

</section>