<commit_before>---
layout: page
title: Research
permalink: /research/
modified: 2015-02-05
tags: [about]
image: 
  feature: Tess_w_MSEAS.jpg 
---

My dissertation is focused on investigating the biological impacts of climate change in the ecologially and economically important California market squid, *Doryteuthis opalescens*.


#### Doryteuthis opalescens

The California opalescent (market) squid is a primary forage species for fish, sharks, mammals, and seabirds in the California Current and also is one of California’s largest fishery species. These squid lay eggs that are attached to the seafloor for the duration of development (~1 month at 11˚C), where they are exposed to variations in temperature, pH, and oxygen as a result of upwelling and longer-term events such as El Nino/La Nina events (ENSO). Investigating the transcriptional
and signaling mechanisms that allow these squid to thrive and develop at lower oxygen and pH conditions may provide insight to understand and predict future acclimation or adaptation to climate change in the ocean. In collaboration with <NAME> and the Levin lab, we exposed squid embryos to constant low-pH, low-oxygen conditions during development. We are currently investigating the gene expression response of these squid, with particular attention to pathways that regulate
development. For a cartoon depiction of the "super" market squid life cycle and fishery, check out this [squidtoons comic](http://www.squidtoons.com/the-super-market-squid.html/), created by collaborator [<NAME>](https://scripps.ucsd.edu/labs/mtresguerres/members/garfield/).

The adult and developmental transcriptomes are nearing completion and data will be shared soon. [Contact me](mailto:<EMAIL>) for more details. 

#### De novo transcriptomics 

Along the way to my main project on market squid, I developed a python framework for automated de novo transcriptome assemblies, MakeMyTranscriptome. This pipeline leverages popular quality control, assembly, annotation, and expression tools to produce high-quality *de novo* reference assemblies with minimal user input. The goal here is to help biologists just getting into transcriptomics produce high quality references from their data, which can then be used for additional downstream analyses. The framework operates as a "black box" for those unfamilar with python and coding, but offers complete flexibility and customization for advanced users. Coming soon.

#### Mantis Shrimp

If you don't know anything about mantis shrimp, check out this [Oatmeal comic](http://theoatmeal.com/comics/mantis_shrimp/) for a fun introduction.

In collaboration with [<NAME>](http://scrippsscholars.ucsd.edu/mdevries/biocv/) and [<NAME>](http://scrippsscholars.ucsd.edu/j3taylor/biocv/), I am investigating the transcriptome response of *Neogonodactylus bredini* to high temperature and low pH conditions. Their larger project is focused on impacts of warming and ocean acidification on the carapace and smashing appendage. [Contact me](mailto:<EMAIL>) for more details.

#### Funding

I was fortunate to be funded by an NSF IGERT to SIO for Global Change, Ecosystems and Society, an NSF GRFP, and the San Diego Diversity Fellowship for six years during my PhD, including a small research grant of $12k from a network of [local donors](https://scripps.ucsd.edu/giving/impacts/fellowship-donors-recognized). Many thanks to all who have made it possible for me to work on such interesting questions.




<commit_msg>upd to include postdoc research<commit_after>---
layout: page
title: Research
permalink: /research/
modified: 2015-02-05
tags: [about]
image: 
  feature: Tess_w_MSEAS.jpg 
---

### Postdoc work

I am very fortunate to be funded by an [NSF Postdoctoral Research Fellowship in Biology](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1711984&HistoricalAwards=false), and advised by [<NAME>](https://biology.ucdavis.edu/people/c-titus-brown) at UC Davis.

My project focuses on improving RNA-Seq through graph-based analysis and computational indexing. The overarching goal of this project is to improve RNA sequencing analysis by both improving tools for rapid and accurate analysis of newly sequenced data, and by developing methods for comparative analysis with existing reference data. Specifically, the focus is on 1) developing open-source best practices pipelines for improved assembly, annotation, and expression analysis of RNA-Seq data, 2) leveraging computational indexing methods to allow rapid comparative analysis of new data with large existing reference data, and 3) extending these indexing methods to include expression information and enable comparative expression analyses with reference data. Each of these advancements will be tested via computational experiments using data from the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP). Alongside these scientific goals, we are committed to developing and conducting data science training and outreach to expose a wide array of students to bioinformatics research to build a larger base for the development of an equitable, diverse, and inclusive academe.

#### Facilitating de novo transcriptomics

Building off a project from my PhD work and a previously-existing workflow at the dib-lab, I constructed an automated de novo transcriptome assemblies, [eelpond](https://github.com/dib-lab/eelpond). Eelpond leverages the snakemake workflow management system to run popular quality control, assembly, annotation, and expression tools to produce high-quality *de novo* reference assemblies with minimal user input. The framework operates as a "black box" for those unfamilar with python and coding, but offers complete flexibility and customization for advanced users. Quick-Start [here](https://dib-lab.github.io/eelpond/).


### PhD Work

#### Doryteuthis opalescens

The California opalescent (market) squid is a primary forage species for fish, sharks, mammals, and seabirds in the California Current and also is one of California’s largest fishery species. These squid lay eggs that are attached to the seafloor for the duration of development (~1 month at 11˚C), where they are exposed to variations in temperature, pH, and oxygen as a result of upwelling and longer-term events such as El Nino/La Nina events (ENSO). Investigating the transcriptional and signaling mechanisms that allow these squid to thrive and develop at lower oxygen and pH conditions may provide insight to understand and predict future acclimation or adaptation to climate change in the ocean. In collaboration with <NAME> and the Levin lab, we exposed squid embryos to constant low-pH, low-oxygen conditions during development. We are currently investigating the gene expression response of these squid, with particular attention to pathways that regulate
development. For a cartoon depiction of the "super" market squid life cycle and fishery, check out this [squidtoons comic](http://www.squidtoons.com/the-super-market-squid.html/), created by collaborator [<NAME>](https://scripps.ucsd.edu/labs/mtresguerres/members/garfield/).

The adult and developmental transcriptomes are nearing completion and data will be available soon. [Contact me](mailto:<EMAIL>) for more details. 


#### <NAME>

If you don't know anything about mantis shrimp, check out this [Oatmeal comic](http://theoatmeal.com/comics/mantis_shrimp/) for a fun introduction.

In collaboration with [<NAME>](http://scrippsscholars.ucsd.edu/mdevries/biocv/) and [<NAME>](http://scrippsscholars.ucsd.edu/j3taylor/biocv/), I am investigating the transcriptome response of *Neogonodactylus bredini* to high temperature and low pH conditions. Their larger project is focused on impacts of warming and ocean acidification on the carapace and smashing appendage. [Contact me](mailto:<EMAIL>) for more details.

#### PhD Funding

I was fortunate to be funded by an NSF IGERT to SIO for Global Change, Ecosystems and Society, an NSF GRFP, and the San Diego Diversity Fellowship for six years during my PhD, including a small research grant of $12k from a network of [local donors](https://scripps.ucsd.edu/giving/impacts/fellowship-donors-recognized). Many thanks to all who have made it possible for me to work on such interesting questions.





{'fraction_non_alphanumeric': 0.06092538759689922, 'fraction_numerical': 0.004602713178294574, 'mean_word_length': 5.189655172413793, 'pattern_counts': {'":': 0, '<': 17, '<?xml version=': 0, '>': 17, 'https://': 8, 'lorem ipsum': 0, 'www.': 3, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7441021', 'n_tokens_mistral': 2225, 'n_tokens_neox': 1984, 'n_words': 1068}