2023 RNA Institute Summer Fellowship Program

June 12th - August 11th, 2023

Overview

The RNA Institute is offering a competitive Summer fellowship program with in-person laboratory research track and a bioinformatics track this year. Students can participate in either track or both depending on their Institute mentor and availability. The structure of each track is outlined below along with the specific requirements. This program will provide students with the skillset and tools that are a vital component for advanced degrees and careers in any STEM field.

 

Program Structure

Overview of both tracks of The RNA Institute Summer Fellowship program.

 

Laboratory Research

Bioinformatics Program

In-person

Remote

You must identify and contact mentor before applying to the program

Do not need to contact a mentor before applying to the program

Partial funding support by RNA Institute

Competitive stipend available based on successful completion of the program

Research topic based on mentor research

Research topics by program and your interests

No laboratory experience necessary

No bioinformatics experience necessary

Both tracks must attend weekly general interest science lectures, research seminars and professional development workshops. Must also present their research at the Fellowship Symposium in August.

 

Laboratory Research (2023)

Below is a summary of the summer laboratory research.

  • You must be a citizen of the United States, or on an F1 or J1 Visa, to participate and receive the stipend
  • You must contact and have a mentor prior to applying to the fellowship
  • The length of the program and weekly hours depends upon your mentor but is typically June to August
  • Students will receive financial support based on the agreement with your mentor.
  • Students will receive a packet of information, including administrative paperwork, by the end of May
  • From June 12th to July 7th there will be weekly general interest science lectures. Participants must attend these lectures.
  • From July 10th to August 11th there will be weekly research seminars or professional development workshops. Participants must attend these workshops.
  • All participants will present their Research at the Summer Fellowship Symposium on August 10-12th

 

Bioinformatics Program (2023)

Below is a summary of the summer bioinformatics program.

  • You must be a citizen of the United States, or on an F1 or J1 Visa, to participate and receive the stipend. If you don't meet this requirement you are still able to audit the course without receiving the stipend
  • You do not need to have a mentor decided prior to applying to the fellowship
  • 9 weeks in length, starts June 12th, ends Aug 12th
  • Competitive stipends will be available based on the successful completion of the program
  • Students will receive 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 13th
  • Participants are expected to be available at 11am for morning lectures and 4pm for 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 8th
    • 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 Summer Fellowship Symposium on August 10-12th 

 

Course Resources
Schedule for Bioinformatics Program

Week of 

Bioinformatics Track

May 23rd  

  • Students receive information packet with pre-work outlined

June 6th 

  • Complete administrative paperwork 
  • Introductory meeting will be held on June 9th 

June 13th  

  • Introduction to myotonic dystrophy  
  • Introduction to the sequencing pipeline 
  • Students gain access to the HPCC 

June 20th  

  • RNA-Seq Alignment with STAR (using command line skills and bash scripts) 

* In observance of Juneteenth holiday, there won't be any classes on June 20, 2022

June 27th  

  • Differential gene expression (using DESeq2 R package) and alternative splicing analysis (using rMATS) 

July 4th 

  • Figure generation (with R using DESeq2 and maser packages) 
  • Gene Ontology enrichment analysis 
  • Introduction to different sequencing technologies 
  • Project 1 presentations in small groups 

* In observance of Independence day, there won't be any classes on July 4, 2022

July 11th 

  • Planning and preparation for Project 2 
  • Students present plan for Project 2 on July 14th and 15th (students must have access to data and plan for analysis by this time) 

July 11th to August 10th  

  • Weekly research seminars or professional development workshops 

August 10th to August 12th  

  • All students present at Summer Fellowship Program Symposium 

 

Bioinformatics Program Groups

Summer Bioinformatics Program Groups

Groups

Leaders

Participants

Group 1

Emily Davey

Claudia Lennon

Berglund Lab:

Cécilia Légaré

Alexa Mascorro

Kristina Karamchand

Mireille Caton-Darby

Julia Hartman

Ali Gaynor

Jose Velez

Emmanuel Nwade

Mark Joseph Remucal

 

Lee Lab:

Nimmy John

Pavithra N

 

Larsen Lab:

Joey Tavarez

Samuel Apooyin

Group 2

Gillian Berglund

Cristina DeMeo

Berglund Lab:

Michelle Brose

 

Pager Lab:

Damilola Gbore

Ridwan Adesola

Kevin Zou

Angelo Agosto

 

Yigit Lab:

Mahera Kachwala

 

Begley Lab:

Katherine Urner

Ryan Swick

Jatin Mukerji

 

Pata Lab:

Ariella Kornfeld

Group 3

Jacob Schroader

Reddy Lab:

Ty Hamel

Marufa Kasham

 

Fuchs Lab:

Shu Jun Lin

Shane Breznak

Eduards Norkvests

Esperanza Rosas

Haley MacNeil

Stephanie Fischer

John (Jack) Geary

Matthew Long

Emmanuel Adedokum

Daniel Samuel

 

NSCI:

Swapna Nandakumar

Akinsola Akinyemi

Boluwatife Adewale

Meysam Yazdankhah

 

Ware Lab:

James Muldowney

Caroline Pritchard

Sara Aden

Stephen Mensah

Group 4

Jhos Dufflart

Rico Amato

Sammons Lab:

Tobi Olanipekun

Rizwan Ahmad

Avery Willis

Mason Salonic

Sahil Adil

 

Forni Lab:

Alliana Charles

Sarthak Srivatsava

Patricia Kamanda

Muskaan Gupta

Group 5

Teddy Garcia Aroca

Nicole Traver

Andam Lab:

Kelley Martinez

Dorentina Humolli

Hafeez Akinniyi

Sefiyat Adebiyi

 

Valm Lab:

Mir-Mammad Javad-zada

Colin Henneberry

Hasan Mehdi

Molly Bogardus

Meghan Stern

Group 6

Noah LeFever

Dr. Sweta Vangaveti

Gerdes Lab:

AJ Bergamo

 

AMC Postdocs:

Shreya Das

Saugata Majumder

Mohd Saqib

 

SUNY Poly:

Maria Belen Paredes-Espinosa

Fernando Pesantez

 

Chen Lab:

Isabel Dengos

Waqas Awan

Shaima Hussaini

 

Vangaveti Lab:

Hadassah Grimaldi

Aaditya Ojha

Lauren Fox

Annabel Anyang

 

Laboratory Research Group
In-person Program Groups
Participant Name Lab Name
Victoria DeMeo Berglund Lab
Hannah Talbot Chandrasekaran Lab
Arlin Rodríguez Chandrasekaran Lab
Hiba Faheem Chen Lab and Chandrasekaran Lab
Miranda Porter Conklin Lab
Avik Paul Dey Lab
Olivia Tassone Ghosh Lab
Sakthi Muthukrishnan Herschkowitz Lab
Ahmed Al Zaydan Herschkowitz Lab
Matthew Brockley Paczkowski Lab
Lia Prager Paczkowski Lab
Celeste Danso Pager Lab
Briana Kano Pata Lab
Chengze Wu Sheng Lab
Ricky Dartawan Sheng Lab

 

Summer Program Virtual Symposium Schedule

Wednesday, August 10 & Thursday, August 11, 2022

Zoom link

https://albany.zoom.us/j/94449519054

Meeting ID: 944 4951 9054

 

Wednesday, August 10, 2022

9:00AM-9:05AM

Introduction to Symposium

9:05AM-10:35AM

Virtual Presentations

Ryan Swick – Begley lab

Jatin Mukerji – Begley lab

Kevin Zou – Pager lab

Damilola Gbore – Pager lab

Ridwan Adesola – Pager lab

Angelo Agosto – Pager lab

Matthew Long – Fuchs lab

Emmanuel Adedokun – Fuchs lab

Daniel Samuel – Fuchs lab

11:00AM-12:00PM

Berkshire Sterile Manufacturing: Careers in Science

12:45PM-3:05PM

Virtual Presentations

Sarthak Srivastava – Forni lab

Alliana Charles – Forni lab

Patricia Kamanda – Forni lab

Muskaan Gupta – Forni lab

Avery Willis – Sammons lab

10 minute break

Mason Salonic – Sammons lab

Sahil Adil – Sammons lab

Rizwan Ahmad – Sammons lab

Tobi Olanipekun – Sammons lab

Samuel Apooyin – Larsen lab

Waqas Awan – Chen lab

 

Thursday, August 11, 2022

9:00AM-10:30AM

Virtual Presentations

AJ Bergamo - Gerdes Lab

Mark Joseph Remucal – Berglund lab

Alison Gaynor – Berglund lab

Kristina Karamchand – Berglund lab

Pavithra Nagendran - Lee Lab

Boluwatife Adewale – NSCI

Marufa Kasham – Reddy lab

Briana Kano - Pata Lab

Mahera Kachwala – Yigit lab

11:00AM-12:30PM

Virtual Presentations

Kelley Martinez – Andam lab

Dorentina Humolli – Andam lab

Hafeez Akinniyi – Andam lab

Sefiyat Adebiyi – Andam lab

Colin Henneberry – Valm lab

Meghan Stern – Valm lab

Hasan Mehdi – Valm lab

Molly Bogardus – Valm lab

1:00PM-2:40PM

Virtual Presentations

James Muldowney – Ware lab

Sara Aden – Ware lab

Stephen Mensah – Ware lab

Lauren Fox – Vangaveti lab

Hadassah Grimaldi – Vangaveti lab

Aaditya Ojha – Vangaveti lab

Annabel Anyang – Vangaveti lab

Shreya Das – AMC

Saugata Majumder – AMC

Mohd Saqib – AMC

2:40PM-2:45PM

Closing Remarks

Summer Program Poster Session Information

2022 RNA Institute Summer Fellowship Program

Poster Session

August 9, 2022, 5PM - 7PM

 
Poster Number Name of the Presenter Lab Name
1 Cecilia Legare Berglund Lab
2 Isabel Dengos Chen Lab
3 Shu Jun Lin Fuchs Lab
4 Esperanza Rosas Fuchs Lab
5 Haley MacNeil Fuchs Lab
6 Ed Norkvests Fuchs Lab
7 Stephanie Fischer Fuchs Lab
8 Shane Breznak Fuchs Lab
9 Joey Tavarez Larsen Lab
10 Mimi Caton-Darby Berglund Lab
11 Maria Belen Paredes-Espinosa SUNY Poly
12 Fernando Pesantez SUNY Poly
13 Cristina DeMeo Berglund Lab
14 Gillian Berglund Pager Lab
15 Michelle Brose Berglund Lab
16 Caroline Pritchard Ware Lab
17 Katherine Urner Begley Lab
18 Shaima Hussaini Chen Lab
19 John Geary Fuchs Lab
20 Ariella Kornfeld Pata Lab
21 Ty Hamel Reddy Lab
22 Mir-Mammad Javad-zada Valm Lab
23 Celeste Danso Pager Lab
24 Victoria DeMeo Berglund Lab
25 Hannah Talbot Chandrasekaran Lab
26 Arlin Rodriguez Chandrasekaran Lab
27 Hiba Faheem Chen/Chandrasekaran Lab
28 Miranda Porter Conklin Lab
29 Avik Paul Dey Lab
30 Noah Hake Forni Lab
31 Olivia Tassone Ghosh Lab
32 Sakthi Muthukrishnan Herschkowitz Lab
33 Ahmed Al Zaydan Herschkowitz Lab
34 Matthew Brockley Paczkowski Lab
35 Lia Prager Paczkowski Lab
36 Chengze Wu Sheng Lab
37 Ricky Dartawan Sheng Lab