2024 RNA Institute Summer Bioinformatics Program
June 24 - August 2, 2024
Overview
The RNA Institute Summer Bioinformatics Program is a competitive summer training program held virtually for high school and undergraduate students. The bioinformatics program delivers training in bioinformatic analysis of RNA-Seq data followed by independent bioinformatic research supervised by an RNA Institute faculty member.
2024 Bioinformatics Program Information
2024 Summer Program Schedule
Date | Lecture Topics & Small Group Session (SGS) Topics Lecture time: Noon - 1 p.m. EDT; SGS time: 3 - 4 p.m. EDT |
|---|---|
| 17-Jun | Welcome Meeting |
Project 1Week 1 | |
| 24-Jun | Lecture 1: Intro biology, history of sequencing, & intro to RNASeq SGS 1: Intro to small groups & pre-program material check in |
| 25-Jun | Lecture 2: DM1 Lecture SGS 2: Install GlobalProtect VPN, get on HPCC, & map network drive |
| 26-Jun | Lecture 3: FASTQ files, DMSeq.org, intro bioinformatics, & the HPCC (Quiz #1 Assigned) SGS 3: Download miniconda3 & STAR aligner |
| 27-Jun | Lecture 4: The command line, submitting jobs to HPCC, & FastQC No SGS Other events: DM Family Q&A @ 1:30 p.m. EDT |
| 28-Jun | Lecture 5: Submit first HPCC job & STAR alignment (Quiz #1 Due, Quiz #2 Assigned) SGS 4: Submit STAR job & troubleshoot for success Other events: Research Spotlights Seminar (Ryan Treen, Michelle Urman, & Sawyer Hicks) @9:30AM EDT |
Week 2 | |
| 1-Jul | Lecture 6: Differential gene expression analysis & figure generation SGS 5: Configure RStudio to run DESeq2 & troubleshoot any errors |
| 2-Jul | Lecture 7: DGE figure generation (continued), intro to rMATS, & alternative splicing analysis (Quiz #2 Due, Quiz #3 Assigned) SGS 6: DGE figure code breakdown, download rMATS, & submit rMATS job |
| 3-Jul | Lecture 8: rMATS output & AS figure generation SGS 7: Configure RStudio to run maser, AS figure code breakdown, & troubleshoot any errors |
| 4-Jul | No lecture No SGS |
| 5-Jul | Lecture 9: Tips & tricks for the command line (optional attendance with recording available) SGS 8: Checkpoint for Project 1 (optional attendance) |
Week 3 | |
| 8-Jul | Lecture 10: Questions from Project 1 & expectation for Project 2 (Quiz #3 Due) SGS 9: Checkpoint for finalizing Project 1 |
| 9-Jul | Lecture 11: Gene ontology enrichment analysis SGS 10: Project 1 Presentations |
| 10-Jul | Lecture 12: Alternative sequencing methods: Nanopore & single-cell sequencing (Assignment #1-2 Assigned) SGS 11: Project 1 Presentations (if needed) |
| 11-Jul | No lecture SGS 12: Check students have access to data for Project 2, help plan research question and tools/pipeline to use |
| 12-Jul | No lecture SGS 13: Check students have access to data for Project 2, help plan research question and tools/pipeline to use Other events: DEI in STEM Seminar (Lakia Green) @11 a.m. EDT |
Project 2Week 4 | |
| 15-Jul | Lecture & SGS: Presentations on Project 2 Plans |
| 16-Jul | Lecture & SGS: Presentations on Project 2 Plans |
| 17-Jul | No lectures & SGS 2x per week depending on Group Leaders’ schedules (Project 2 questions & help)
Other events: 19 July - Research Seminar (Dr. Craig Martin) @2 p.m. EDT |
| 18-Jul | |
| 19-Jul | |
Week 5 | |
22-Jul to 26- Jul | No lectures & SGS 2x per week depending on Group Leaders’ schedules (Project 2 questions & help)
Other events: 26 July - Research Spotlights Seminar (Gregory Theopall, Asmer Aliyeva, & Jacob Schroader) @ 9:30 a.m. EDT |
Week 6 | |
| 29-Jul to 31-Jul | No lectures & SGS 2x per week depending on Group Leaders’ schedules (Finalize Project 2)
Other events: 30 July - Interview/CV prep Seimar (Tammy Reid) @9:30 a.m. EDT |
| 1-Aug | RNA Institute’s 2024 RNA Day Celebration (Remote summer bioinformatics students local to Albany, NY area or able to travel to campus can present Project 2 in person as poster presentations) |
| 2-Aug | 2024 Summer Bioinformatics Program Virtual Symposium (All other remote students will present Project 2 as virtual presentations to entire cohort) |
2024 Bioinformatics Program Groups
| Groups | Group Leaders | Trainee list and affiliated labs |
|---|---|---|
Group 1 Virology & Neurodegenerative diseases | Claudia Lennon (Berglund Lab) Tehreem Fatima (Berglund Lab) | Pager Lab: Serafina Parvattan Paige Charlesworth Patricia Bazwell Banda Lily Joseph Fatmata Marah
Reddy Lab - ITPase group: Pierce Douglas Qiuguo Tang Navid Khosrojerdi |
Group 2 Muscular Dystrophies | Cécilia Légaré (Berglund/Duchesne Lab) Lori Planco (Berglund Lab) | Reddy Lab - DM1 group: Preeti Kumari Kaitlin Levy Delaney Baratka
Berglund Lab: Faizan Fayaz Lone Luis Villacreses Laken Bergin Mihir Kulkarni |
Group 3 Muscular Dystrophies & Developmental Biology | Liv Ransiear (Dey Lab) Eric Jestel (Vangaveti Lab) | Dey Lab: Melissa Zambrano García Senbahavalli Ramasamy Akira Morishita
Larsen Lab: Anya Vedhathiri Riddhi Narsapuram Emiko Tonachel Cherron Griffith |
Group 4 Neurodegenerative diseases & Mechanisms of protein translation | Brianna Nelthrope (Berglund Lab) Asmer Aliyeva (Berglund Lab) | Shorrock Lab: Santoshi Yadagiri Dancan Oruko
Fuchs Lab: Riana Patel Sarah Kornfeld Benjamin Rappel Mosopefoluwa John
Begley Lab: Suzanna Amirbekian |
Group 5 Microbiology & Muscular dystrophies | Odion Ikhimiukor (Andam Lab) Carter Wilkins (Berglund Lab) | Andam Lab: Carol Wang Johan Kavanal Max Paul Massa Masri
Berglund Lab: Grace DeMaria Divyansh Pramanick Sophia Levy |
Group 6 Developmental biology | Gaby Baniulyte (Sammons Lab) Clara Yeboah (Berglund Lab) | Sammons Lab: Maitaishe Mangundhla Shashank Boosa Kristie Benel Mahitha Jonnalagadda Nathaniel Boateng
Farnsworth Lab: Shreeya Gillela Ahmad Osmani |
Group 7 Computational modeling, Neurodegenerative diseases, & Developmental biology
| Sweta Vangaveti (PI) Caroline Pritchard (Berglund Lab) | Vangaveti Lab: Chinonyelum Agbo Ananyaa Srivatsan Mubasshir Mumtaz Young Xu
Shorrock Lab: Amina Bhatti
Turner Lab: Nyla Barrow Gertrude Hattoh
Dash Lab: Favour Aina |
Eligibility
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Highschool students: Only Rising Seniors are eligible and must have GPA above 3.2
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Only High school students and undergraduate students who are US citizen, permanent resident or on F1/J1 visa are eligible to receive stipend on successful completion of the program
Summary of Bioinformatics Program
Bioinformatics Program (2024)
Below is a summary of the summer bioinformatics program.
6 weeks in length, starts June 24th, ends Aug 1st
After being selected to the program, students will receive a packet of information, including some pre-course work and administrative paperwork, by the end of May
The pre-course work develops basic programming skills, and these short online courses should be completed prior to the start date of June 24th
Participants are expected to be available for lectures and small group meetings (small group meeting times may be adjusted depending on group leaders)
The summer bioinformatics program is separated into two projects:
Project 1 is the same for all students and is used to teach a pipeline for analysis of RNA sequencing data
Participants will complete Project 1 by July 7th
Project 2 is based on data from or relevant to research in their mentor’s lab
Participants are expected to have a plan for Project 2 and access to data for Project 2 by July 14th
All participants will present their Project 2 at the RNA Day Summer celebration on August 1, or during the virtual summer symposium on August 2.
Stipends will be available based on the successful completion of the program
Application Deadline: March 31, 2024
Required Materials
For the Bioinformatics program, a computer with access to high-speed internet is required.