Genomics Cohort Training—2023-2024
Summer 2023
Students took a summer bridging course of data structures in Python as preparation for their fall matriculation into the program.
Fall 2023
Students participated in 13 credits of coursework. During the first semester the students took the following courses:
- DSCC 462: Computational Introduction to Statistics, Professor Anson Kahng
- DSCC 461: Introduction to Databases, Professor Eustrat Zhupa
- DSCC 440: Data Mining, Professor Jiebo Luo
A pre-program survey was done by Cathy Cerosaletti to assess the cohort’s understanding and experiences and competency with research, ethics, equity and inclusion, genomics and career development skills.
Winter 2024
A sequence of three extra-curricular, hands-on workshops aimed at building core competencies in genomic data analysis were offered by the Genomics Research Center (GRC) in conjunction with the Goergen Institute for Data Science GIDS-REM fellowship program and the Center for Integrated Research Computing (CIRC). These workshops covered nine core competencies were required for GIDS-REM fellows were open to any researchers in the University of Rochester and Medical Center communities.
An introductory session on Tuesday, January 9 from 10 a.m.-3:30 p.m. by Professor Brendan Mort and staff of CIRC at the Vista Collaboratory in Carlson Library was required for those who needed Blue Hive access or basic knowledge of Linux clusters, running Jobs and Slurm, Modules, Software, and Jupyter.
The workshops were two hours each and led by John Ashton and staff of GRC:
- Wednesday, January 10: Experimental Design and GRC deliverables. This workshop introduces experimental design considerations in the generation of high throughput sequencing data including RNAseq, ChIP-seq (and related -seq technologies).
- Thursday, January 11: Bulk RNAseq. This workshop introduces quality control in bulk RNA sequencing experiments and best practices in RNA seq analysis.
- Friday, January 12: Single cell sequencing. This workshop introduces single cell RNAseq and ATACseq data generation and analysis.
Spring 2024
Students returned to studies with 12 credits of coursework to take:
- DSCC 465: Introduction to Statistical Machine Learning, Professor Cantay Caliskan
- BST 434: Genomic Data Analysis, Professor Matthew McCall
- BIOL 453: Computational Biology, Professor Justin Fay
Mentor Meetings were used to start discussions about summer internship placements.
Summer 2024
Students engaged full-time in their lab’s research assignments. Professor Fay initiated the Summer Seminar series—a weekly venue to learn and engage in applied problems in genomics. The series included short presentations from students, trainees and faculty on current research problems with an emphasis on pragmatic solutions. Presentations were followed by a discussion to enhance practical understanding and assessment of genomics approaches, methods and computational analyses. The seminar series was run as part of the Goergen Institute for Data Science MS program in applied genomics and open to students and faculty interested in application of genomics and genome technologies to problems in biology.
The seminar series also included a professional development component for students in the GIDS-REM training program. For this component students learn and assess presentation strategies and research communication skills to enhance their career goals in either academics or industry.
Seminar schedule:
- Session 1: 5/29 Discussion Topic: Population genomics with Tuuli Lappalainen, Assistant Professor in the Department of Systems Biology at Columbia University.
- Session 2: 6/5 PostDoc talk: Elsie Shogren, Biology Post-doc at University of Rochester
- Session 3: 6/12 PI Talk: Juilee Thakar, an associate professor of microbiology and immunology, biomedical genetics, and biostatistics and computational biology
- Break: 6/19 (Juneteenth holiday)
- Session 4: 6/26 PI talk: Hongbo Liu, Assistant Professor of Department of Biomedical Genetics at University of Rochester
- Break: July 3-10
- Session 5: 7/17 Graduate Student talk: Eric Cefaloni, Biology PhD candidate studying epigenetic mechanisms in breast cancer under Dr. Paula Vertino. Molecular, Cellular and Developmental Biology Program
- Session 6: 7/24 Graduate Student talk: Eric Moeller, PhD student (Dr. Juliee Thakar Lab), Molecular, Cellular and Developmental Biology Program
- Session 7: 7/31 Discussion Topic: Single cell genomics with Rahul Satija, Associate Professor of Biology, Center for Genomics and Systems Biology at New York University
- Session 8: 8/7 Professional development: Transition to Industry with Lucas Hemmer, Invaio Sciences
- Session 9: 8/14 Professional development: Data Ethics with Danielle Presgraves, Director, Data Science Training at The Jackson Laboratory
Fall 2024
Students enrolled in:
- DSCC 483: Practicum Project, Professor Ajay Anand
- DSCC 457: Applied Genomics, Professor Amanda Larracuente
Presentations of summer research were given during Meliora Weekend and the Fall Graduate Research Symposium.
Conference Travel
The cohort is considering attending one of the following conferences:
- National Diversity in STEM Conference for the Society for Advancement of Chicanos/Hispancis and Native Americans in Science (NDiSTEM SACNAS 2024)
- Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS 2024)
Practicum Project
Fall presentations will be posted as they become available.