Summer Bioinformatics Program 2020

June 8 - August 14, 2020


Due to the current COVID-19 situation, this summer program is designed to remotely teach a bioinformatics approach to the analysis of biological research data.  Researchers are increasingly expected to have the bioinformatics skills necessary to effectively process, manage and utilize complex sets of data. This program will provide students with the skillset and tools that are a vital component for advanced degrees and careers in any STEM field.

Students will learn the basics of a UNIX operating system, how to manage data on a high performance computer (HPC) cluster, coding with the data and visualization program R and the analysis of next-generation sequencing data. Using these skills, students will tackle projects using large biological datasets related to the most common form of muscular dystrophy and COVID-19 data sets as well as other ongoing research programs at the RNA Institute. Throughout this process, students will learn the computational pipelines used for bioinformatics and how to present these large data sets in figures and graphs.

This program is based on previously successful programs launched at the University of Oregon and the University of Florida.

Program Structure

In the first week, summer research students will attend mandatory remote classroom sessions in the mornings taught by course leaders and RNA Institute faculty.  During these morning sessions, students will learn the basics of UNIX operating system, the R programming language and bioinformatics pipeline. During the remainder of the day, students will research and learn independently with remote assistance provided by RNA Institute co-leaders. Students will meet up again remotely as a group at the end of the day for a Question and Answer session and for instructors to check in on their learning and research progress during the day.

In the following weeks (2-10), summer research students will maintain this schedule of shorter mandatory remote morning classroom sessions, independent study and end of the day Q&A and check-in session. The schedule of topics for each week (see attached document) are designed to take student through the fundamentals of RNA science and the bioinformatics pipeline.

Students in the summer program must commit to attending these twice daily sessions and to performing independent learning and research during the rest of the day.

Course Materials

Daily lectures are posted on the SLACK Channel


Introduction to Ubuntu/Terminal, R and RStudio

Sign in for your free access to: Code Academy

Project #3 Schedule and Zoom Recordings

9 Presentations on Thursday Afternoon (August 13th) (3 PM EST to ~5 PM EST)

Amber Altreith (Larsen Lab) – Endothelial Cell Gene Expression in Ductal Ligation Induced Fibrosis
Areej Chisthi (Larsen Lab) – A Look Into Salivary Gland Development in Mice
JD Dufflart (Larsen Lab) – Salivary Gland Development in Mice
Kamana Devkota (Larsen Lab) – Differential Gene Expression Analysis of Salivary Gland at Various Developing Time Point
Melissa Hinman (Berglund Lab) – Genome-wide analysis of alternative splicing changes in zebrafish myotonic dystrophy models
Rico Amato (Berglund Lab) – Differential Gene Expression in MBNL Mutant Zebrafish
Noah LeFever (Berglund Lab) – Potential Changes in Expression of Elongation Factor Genes as a Result of Furamidine
Emmanuella Owusu Ampaw (Fuchs Lab) – Differential Gene Analysis on Glycogen Synthase
Afrooz Golestanian (Fuchs Lab) – RACK1 RNA-seq Data Analysis
Click to watch Zoom Recording of above talks Password: Y.USfX37

10 Presentations on Friday Morning (August 14th) (10 AM to ~12PM EST)

Victoria Demeo (Dey Lab) – Differential Gene Expression and Alternative Splicing Analysis of Spinocerebellar ataxia type 1
Cristina Demeo (Berglund Lab) – A Differential Gene Expression and Alternative Splicing Analysis of ALS-Causing Gene Mutations
Subodh Mishra (Berglund Lab) – Differential gene expression analysis in colchicine treated HSALR DM1 mice compared to healthy control (Non-DM1) Mice
Eva Clervoyant (Berglund Lab) – Analyzing Small molecules to determine differences in splicing and gene expression
Jacob Shroader (Reddy Lab) – Alterations in the transcriptome due to ITPase deficiency in embryonic mouse tissues
Phenoah Badu (Pager Lab) – ATF3-driven transcriptional changes in chemically stressed cells
Gillian Berglund (Pager Lab) – Global transcriptome and alternative splicing analysis of Chikungunya virus
Courtney VanWormer (Pager Lab) – Differential Gene Expression and Alternative Splicing Analysis of ZIKV and DENV Infections in Human Neural Progenitor Cells (hNPCS)
Levi Doyle (Pager Lab) – Global transcriptome and alternative splicing analysis of Zika virus infections in pediatric patients
Cassidy Hawley (Larsen Lab) – Gene Expression Analysis of Salivary Gland Development in Mice and Orthotopically Functional Salivary Glands Generated with Mouse Embryonic Stem Cells
Click to watch Zoom Recording of above talks Password: HjPh%fm0

10 Presentations on Friday Afternoon (August 14th) (1:30 PM EST to ~3:30 PM EST)

JR Matthews (Forni / Rangan Lab) – scRNA Seq Peripheral Blood Mononucleate Cells (PBMCs)
Esperanza Rosas (Rangan Lab) – The role Kdm5 in Drosophila oogenesis
Katie O’Neill-Knasick (Forni Lab) – Gli3 and Cellular Differentiation Regulation
Alex Lai (Belfort Lab) – Computational modelling of the regulatory network for the response regulator LlrA in Lactococcus lactis
William Rice (Sheng Lab) – Phylogenetic Study of COVID-19 in New York
Abby McCann (Berglund Lab) – Effects of the combination of Erythromycin and Furamidine on mis-splicing in DM1
Tyler Dion (Berglund Lab) – A look into the expression of Apoptosis Genes in individuals with CDM
Megan Barber (Berglund Lab) – Differential gene expression in the Hippocampus and Frontal Cortex of DM1 and DM2 patients
Maria Rybakov (Berglund Lab) – Analysis of differential gene expression between males and females with myotonic dystrophy in cardiac tissue
Emily Davey (Berglund Lab) – Differential Gene Expression of RNA Modifications in the Central Nervous System of DM1 and DM2 Patients
Click to watch Zoom Recording of above talks Password: ?7c=Z+*0

In the News