Annika Jorgensen

Annika Jorgensen

Bioinformatics Programmer

Xin Sun Lab

Center for Epigenomics

Biography

I am a Bioinformatics programmer with a Master’s Degree in Computational Life Sciences. I work in the Pediatrics Department of University of California San Diego’s School of Medicine researching the lung using spatial epigenomics. We are developing the first open access dataset of single nucleus RNAseq and ATACseq normal human lung samples. Outside of work, my hobbies are reading, hiking, and rock climbing.

Interests
  • Computational Biology
  • Bioinformatics
  • Epigenomics
Education

  • Master's Computational Life Sciences, 2024

    Arizona State University

  • Honors Bachelor's Biophysics, 2023

    Arizona State University

Skills

Techniques
Sequence Alignment
Data Science
Variant Calling
Languages
R/Rstudio
Python
bash

Experience

 
 
 
 
 
Bioinformatics Programmer
Dr. Xin Sun Lab
July 2024 – Present San Diego, California
I research the lung using spatial epigenomics. We are developing the first open access dataset of single nucleus RNAseq and ATACseq normal human lung samples.
 
 
 
 
 
Research Assistant
Dr. Melissa Wilson Sex Chromosome Lab
November 2021 – May 2024 Tempe, Arizona
I researched sex differential gene expression in viral-mediated Hepatocellular Carcinoma. I also helped develop a CURE at ASU Online and analyzing the engagement of students in the course.
 
 
 
 
 
Teaching Assistant
Arizona State University
August 2022 – May 2024 Tempe, Arizona
I was the teaching assistant for the following courses, Computing for Research, Genomics Research Experience, and Functional Genomics. I educated students on writing bash scripts and logging onto a cluster through SSH. I taught students how to work with SAM and BAM files, run sequence alignment algorithms, and call variants. I helped students learn the basic molecular functions in genomics as well as interpreting common genomic data analysis, and how to access publically available genomic data.
 
 
 
 
 
Compliance Editor
American Preparatory Academy
August 2021 – May 2023 Draper, Utah

Responsibilities included:

  • Editing IEPs for special education students
  • Managing projects for special education services
  • Taking notes for IEP quality assurance
  • Converting special education files to a digital format
 
 
 
 
 
Research Aide
SciHub ASU
May 2020 – November 2021 Tempe, Arizona
Lead the Flourescence Spectroscopy Project where I aimed to create a portable flourescence spectrometer for consumer use. I learned how to operate spectorscopy equipment. I also drafted market studies for products and constructed electric circuits using reflow soldering.
 
 
 
 
 
Commercial Intern
Civica
May 2020 – March 2021 Lehi, Utah

Responsibilities included:

  • Querying, creating, and maintaing drug sales databases with Tableau and Excel
  • Drafting sales agreement for hospital partners
  • Creating government official datasheets

Featured Certificate

Nov 20, 2023
Data Analysis with Pandas
Data Analysis with Pandas

Data cleaning, plotting, linear regression, basic statistics, correlation coefficients
Code Certificate Zenva Academy

Certificates

*
All Pandas Turtle Medical Bot Object-Oriented
Data Analysis with Pandas

Data Analysis with Pandas

Data cleaning, plotting, linear regression, basic statistics, correlation coefficients

Code Certificate Zenva Academy
Build a Medical Diagnosis Bot with Python

Build a Medical Diagnosis Bot with Python

Created a script that diagnoses a patient’s state of dehydration based on a short questionnaire. The script stores a list of patients and their diagnoses and the user can retrieve the list of patients.

Code Certificate Zenva Academy
Data Manipulation with Pandas

Data Manipulation with Pandas

Dataframes, selecting data, sorting data, filtering data, grouping data

Code Certificate Zenva Academy
Intro to Object-Oriented Programming with Python

Intro to Object-Oriented Programming with Python

Data types, variables, operators, lists, tuples, dictionaries, control flow, functions, objects, classes, inheritence

Code Certificate Zenva Academy
Python Turtle Mini-Projects

Python Turtle Mini-Projects

Data manipulation and storage with variables, creating functions and conditions, randomness, loops

Code Certificate Zenva Academy
Intro to Coding with Python Turtle

Intro to Coding with Python Turtle

concept of programming, flowcharts, pseudocode, concept of Python Turtle, hexademical colors, moving and turning the turtle, filling in shapes, changing background color, lifting the pen

Code Certificate Zenva Academy

Featured Project

Oct 19, 2023
Viral-mediated Hepatocellular Carcinoma
Viral-mediated Hepatocellular Carcinoma

Detecting sex differential gene expression in viral-Mediated Hepatocelluar Carcinoma
Paper Slides

Projects

*
All Differential Expression Analysis Teaching Portfolio Python Projects
Python Projects

Python Projects

This is a compilation of all the projects I have done while obtaining my certificates

What is a Portfolio? What is a CURE? CIRTL's Core Ideas 21 Teaching Strategies
Teaching Portfolio

Teaching Portfolio

This is my teaching portfolio

What is a Portfolio? What is a CURE? CIRTL's Core Ideas 21 Teaching Strategies
Viral-mediated Hepatocellular Carcinoma

Viral-mediated Hepatocellular Carcinoma

Detecting sex differential gene expression in viral-Mediated Hepatocelluar Carcinoma

Paper Slides

Contact

Contact me with any questions or collaboration ideas