For the first time in several years, the DOE Joint Genome Institute hosted several UC Merced students this past summer. This year’s cohort for the JGI-UC Merced Internship Program was brimming with excitement and determination as they came onsite. From data carpentry to science communications, their schedules were filled with trainings that they later reported were incredibly valuable to their careers going forward. Watch this short video (above) to hear more about the summer from their own perspectives.
The interns from this cohort and their JGI mentors are listed below, along with their project focus areas:
- Andrew Lin and mentor Vy Duong, Understanding Key Genes in Photosynthesis
- Ravikiran Madichetty and mentors TBK Reddy and Dimitri Stamatis, Porting XML/Python Based Quality Control to Database/Java Based Process in Gold
- Sandra Hernandez Gonzalez and mentor Hualan Liu, Building Expression Host in Bacilli Class using CRAGE Technology
- Emerald Nash and mentor Jonelle Basso, Experimental Study of Root Colonization by Resident Phages of a Plant Growth Promoting Rhizobacterium
- Tahirah Williams and mentors Igor Grigoriev and Bishoy Kamel, A Comparative Analysis of Metabolic Pathways in Fungal Pathogens
- Shayna Bennett and mentor Robert Bowers, Mobile Genetic Elements and CRISPR Spacers in the Conifer Needle Microbiome
- Carlos Vazquez and mentor Bryce Foster, Benchmarking Bioinformatics Tools for Sequence Similarity Searching
- Morgan Lavenstein Bendall and mentor Juan C. Villada, Ecology & Evolution of Self-Catalytic Introns across Earth’s Microbiomes
- Sonia Vargas and mentors Tomas Tyml and Frederik Schulz, Eukaryotes in Extreme Environments
- Theo Loreaux and mentors Simon Roux and Frederik Schulz, Structure Prediction to Annotate Novel Viruses: the Case of Polintoviruses
- Josue Duque and mentor Miguel Romero, Classification and Analysis of Eukaryotic MAGs from Novel Taxa
- Christopher Bivins and mentor Satria Kautsar, Comparing BGC Detection Tools and Exploring Novel BGC Detection Techniques on Fungal Genomes
Emerald Nash: What I’m working on here is an experimental study of root colonization by resident phages of a plant growth promoting bacterium. And my mentor is Dr. Jonelle Basso.
Shayna Bennett: So while here at the JGI, I’ve been studying mobile genetic elements and CRISPR spacers in the conifer needle microbiome, and I’ve been working with Robert Bowers.
Andrew Lin: My mentor is Vy Duong, and we’re working together on predicting the level of photosynthesis in a model green alga called Chlamydomonas reinhardtii. We’re using an attentive deep learning model called Tabnet in order to perform regression on the level of photosynthesis giving gene expression values.
Sonia Vargas: I am working with Dr. Tomas Tyml and Dr. Frederik Schulz with the New Lineages of Life Group at JGI. And we’ve been working on isolating and cultivating and sequencing extremophile protists from a hypersaline alkaline lake in California.
Sandra Hernandez Gonzalez: Out of this internship, I hope to gain professional skills, advice skills, wet lab skills and overall connections.
Theo Loureaux: I wanted to first discover new methods with tools I wasn’t familiar with in terms of machine learning and new software I’d never been using before. I also wanted to improve my communication skills by being able to talk to people that are working at the lab, my coworkers and I also wanted to know what it’s like to work in the lab. You know, the kind of job that you have to perform, the kind of tasks you’re given and how this is going.
Tahirah Williams: I hope to gain experience working at a national lab as well as bioinformatics tools that I can use for my own PhD while at UC Merced
Christopher Bivins: So coming into this internship, I was really excited to have the opportunity to vastly improve my bioinformatics skills and work at the command line, manipulating huge amounts of data. I was excited to work on fungal genomics and the fact that I got to do a project involving over 12,000 fungal genomes was just really, really exciting for me and learning how to use the capabilities of the supercomputers here to work with that vast amount of data is something that has been really exciting to be able to learn how to do.
Ravikiran Madichetty: The best part of interning at JGI for me has been definitely the people. For example, my team, the GOLD team and my mentors are very helpful and very understanding, and I never felt that asking dumb questions would like undermine me or anything like that. So I feel really comfortable with them as well. And moreover, I was able to see their own experiences and understand what it takes to have a good and strong career as well.
Morgan Lavenstein Bendall: The best part about interning here is that I get to meet a lot of researchers that have been working on genomics data for a very long time, and it’s great to see how far the field has come from the early 2000s.
Josue Duque: One of the best parts about interning at the JGI has been the ability to sort of step back from my typical work and sort of jump feet first into this new subfield that I had limited experience with, and to do so with some of the top scientists in that subfield.
Byline: Graham Rutherford