Genomics Cohort Training—2025-2026

Summer 2025

Students who needed preparation for their fall matriculation into the program took a summer bridging course DSCC 162: Data Structures in Python with Andrea Cogliatti.

At the end of the summer, students were invited to participate in the annual biomedical hackathon.

Fall 2025

Students participated in 13 credits of coursework. Based on previous feedback, BIO 457: Applied Genomics course is being taken now in the first semester and DSCC 461: Database Systems course has been moved to the third semester of study. During the first semester the students took the following courses:

  • BIO 457: Applied Genomics, Professor Amanda Larracuente
  • DSCC 462: Computational Introduction to Statistics, Professor Anson Kahng
  • DSCC 440: Data Mining, Professor Monika Polak
  • IND 501: SMD Research Ethics, Professor Jonathan Herrington

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.

Other events that happened during the semester included:

  • Attending poster presentations by the previous cohort during Meliora Weekend.
  • Connecting with mentors at a mentor meetup.
  • Attending a biotech career panel organized by Professor Justin Fay with panelists from Charles River Laboratories, GenScript, Novo Nordisk, and Calvery Holdings.
  • Attending a bioinformatics career session hosted by the bioinformatics core staff at the Genomics Research Center.

Winter 2026

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 Monday, January 12 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:

  • Tuesday, January 13: 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).
  • Wednesday, January 14: Bulk RNAseq. This workshop introduces quality control in bulk RNA sequencing experiments and best practices in RNA seq analysis.
  • Thursday, January 15: Single cell sequencing. This workshop introduces single cell RNAseq and ATACseq data generation and analysis.

Spring 2026

Students returned to studies with 12 credits of coursework taking:

  • 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 2026

Students engage full-time in their internships and lab’s research assignments.

Professor Fay will lead the Summer Seminar Series—a weekly venue to learn and engage in applied problems in genomics. The series includes short presentations from students, trainees and faculty on current research problems with an emphasis on pragmatic solutions. Presentations will be followed by a discussion to enhance practical understanding and assessment of genomics approaches, methods and computational analyses. The seminar series will be 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 will 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 TBA)

At the end of the summer, students will participate in the annual Biomedical Data Science Hackathon.

Fall 2026

Students enroll in:

  • DSCC 483: Practicum Project, Professors Ajay Anand and Cantay Caliskan
  • DSCC 461: Database Systems, Professor Eustrat Zhupa

Conference Travel

The cohort is considering attending one of the following conferences: TBD

Practicum Project

Fall presentations will be posted as they become available.

Genomics Cohort 2025-2026

Headshot of Tasmia Almagir.

TASMIA ALMAGIR

HOMETOWN: Dhaka, BANGLADESH (currently Rochester, NY)

UNDERGRAD DEGREE: BS Software Engineering, Shahjalal University of Science and Technology (BANGLADESH), 2020

WHY ROCHESTER: The University of Rochester is a leading institution in multidisciplinary research. In particular, the GIDS-REM curriculum provides a unique opportunity, combining strong support, resources, and mentorship to develop future data scientists. I believe pursuing the Genomics track within Data Science will enable me to build on my current skills and contribute to this dynamic, diverse field.

PREVIOUS EXPERIENCES: Before moving to the U.S., I worked for three years as a software engineer at Pathao, an on-demand digital platform operating in Bangladesh & Nepal. As a software engineer, I’ve seen how data is used to transform business operations and user experiences.

SELECTED MENTORS:

  • Ajay Anand: Data analytics, machine learning, and deep learning for healthcare; Biomedical/ultrasound signal processing, biomedical instrumentation, predictive modeling, time-series analysis
  • Juilee Thakar: Bioinformatics; Systems biology; Dynamic Modeling Tools

FUTURE PLANS: My long-term goal is to become a data science professional specializing in optimizing software systems and developing intelligent solutions, primarily in the healthcare sector. I look forward to applying my technical skills in a new direction within the health sciences.

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Headshot of Matthew Goldman.

MATTHEW (MATEO) GOLDMAN

HOMETOWN: Miami, Florida


UNDERGRAD DEGREE: BS Biological Sciences from Florida International University, December 2024.

WHY ROCHESTER: This program had made clear its dedication to building an academic environment that makes genomics accessible to students from diverse backgrounds. I wanted to be part of a community that combines not only has rigorous training and research opportunities but also is complete with a culture that equally prioritizes mentorship and equity.

PREVIOUS EXPERIENCES: I was an undergraduate researcher in the Laboratory of Tropical Genetics to investigate the role of transposable elements in the Aedis aegypti genome, focusing on the domestication of Gypsy-Ty3 Long Terminal Repeat (LTR) retrotransposons.

SELECTED MENTORS:

  • Caitlin Dreisbach: Use of quantitative methods to make better clinical assessments during pregnancy
  • Tim Dye: Applied public health, particularly within marginalized, isolated, and global; Social and cultural determinants of health

FUTURE PLANS: I plan to build the foundational technical and research skills necessary to pursue a doctoral program. My broad research interest is in studying human genomic diversity to address inequities in healthcare, and I am looking forward to the mentorship and research experiences this program provides, helping me sharpen this interest.

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Headshot of Gabrielle Nemer.

GABRIELLE (GABBY) NEMER

HOMETOWN: Albuquerque, NM

UNDERGRADUATE DEGREE: BS in Biology: Computational Biology from the University of Rochester, Phi Beta Kappa, 2025

WHY ROCHESTER: As someone with a biological science background, the GIDS-REM curriculum blends my interests in genomics while improving my technical skills. The close mentorship and focus on research provide the support I need to grow professionally and explore diverse research areas.

PREVIOUS EXPERIENCES: Besides my undergraduate degree, I’ve done research experience in neuroscience and biology at UNM Health Sciences Center as well as at the University of Rochester with Professor Larracuente. My volunteer experiences at the hospital and as an EMT taught me the importance of medicine and biomedical research. Despite advances in medicine, many genetic and epigenetically influenced conditions remain unmanaged.

MENTORS:

  • Paul Boutz: Implement a multi-disciplinary approach that includes molecular biology, genomics, bioinformatics, and state-of-the-art genome engineering to understand the essential roles of RNA processing in normal and tumor cell physiology, and to uncover the molecular mechanisms by which drugs alter gene expression.
  • Seong-Hwan Jun: Bayesian models and computation; Probabilistic machine learning; Graphical models; Statistical inference for combinatorial problems; Statistical methods for analysis of single cell transcriptomics data; Multi-omics data integration; Cancer genomics; Cancer-immune interaction; Phylogenetics

FUTURE PLANS: I want to pursue more education to contribute to research in genomics related to the health sciences. In the future, I want to work on genomics research that focuses on disease risk assessment or tailored treatments.

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Headshot of Abigail Waryanka.

ABIGAIL WARYANKA

HOMETOWN: Pittsburgh, PA

UNDERGRAD DEGREE: BS Biology with honors; BS Computer Science; Allegheny College, Magna Cum Laude, 2023

WHY ROCHESTER: I chose Rochester because of its curated curriculum aimed at building the tools necessary to work in the genomics field. Additionally, the research and personal mentorship qualities provide invaluable support for future career development.

PREVIOUS EXPERIENCES: I graduated from Allegheny College in 2023 with a degree in Biology and Computer Science. My senior honors thesis was titled: DEG-PI, A Computational Tool that Identifies Differently Expressed Genes and Enriched Pathways in Cancer Tissues.

MENTORS:

  • John Ashton: Cancer biology, specifically leukemia stem cell (LSC) biology
  • Darren Carpizo: Cancer biology with an emphasis on developmental therapeutics. Employ a variety of experimental systems including mouse cancer models, patient derived tissues as well as therapeutic clinical protocols.

FUTURE PLANS: Pursue a career studying genetic mutations. I believe that data science plays a critical role in understanding how mutations disrupt biological pathways and contribute to the development of complex diseases. By analyzing large-scale genomic data, I hope to uncover patterns that reveal the molecular mechanisms behind breakdowns.

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Previous Genomics Cohorts