Spring 2026
Surviving your PhD Qualifying Exam
Hosted by Dr. Grace Brannigan. This is a two-part workshop. Participants are expected to attend both sessions.
Feb 4, 11:00am-1:00pm | JHSC 104BC
Apr 1, 11:00pm-1:00pm | JHSC 104BC
Workshop Description
This two-hour workshop will present “survival tips”, cover expectations for the overall format, Q&A panels with students who recently qualified, give you a glimpse into the conversation when the student is out of the room, provide tips on answering questions, and help you construct your own checklist and timeline for the months leading up to the qualifying exam.
Who Should Attend
Strongly recommended for anyone who will take their CCIB PhD qualifying exam in the next six months
Detecting Natural Selection
Hosted by Anthony Geneva
Dates and Times
- April 22, 2026 In person workshop
Workshop Description
One of the core aims of evolutionary genomics is to identify and understand the impact of natural selection on genome evolution. Theory, drawn from population genetics and phylogenetics, makes straightforward predictions regarding the impacts natural selection is expected to have on genomes. These, in turn, have been used to develop analyses to rigorously test for historical evidence of natural selection in genomic sequences. In this lecture-based workshop, students will be guided through the underlying theory and be introduced to analyses designed to identify the molecular signatures of natural selection from DNA sequence data.
Learning Goals
- After participating in this workshop, students will have learned:
- The theoretical underpinnings of modern natural selection analyses
- How genomes are expected to change in response to different forms of natural selection
- A general understanding of how analysis tools identify genome regions putatively under selection
Who Should Attend
This workshop is suitable for any STEM Graduate Student. Please bring a laptop to the workshop.
Clustering (unsupervised learning) of Lung Cancer samples using both somatic mutation and gene expression
Hosted by Iman Dehzangi
Dates and Times
- May 6, 2026 11:00 AM- 1:00 PM In person or Hybrid
Workshop Description
Cancer is a heterogeneous disease, with numerous subtypes differing in molecular profiles, risk factors, clinical outcomes, and tumor locations. Lung cancer, the third most diagnosed cancer in the United States, is driven by a complex combination of molecular alterations, which influence tumor behavior and patient outcomes. Large-scale consortia such as The Cancer Genome Atlas (TCGA) have generated comprehensive data sets encompassing genomic, transcriptomic, proteomic, and clinical data that present a unique opportunity to uncover novel subtypes through multi-omics integration. While clustering methods have been used to identify subtypes in lung cancer, many integrations and avenues remain underexplored. To address this issue, in this workshop, we study an analytical pipeline that combines autoencoder-based feature extraction with unsupervised clustering to integrate publicly available gene expression data and somatic mutation data in lung cancer to identify distinct molecular subtypes.
Learning Goals
- How to use supervised learning from the beginning to interpretation of the results.
Who Should Attend
Open to STEM graduate students preparing to present their research in short formats.
Code Review
Hosted by Sunil Shende
Dates and Times: March 4
Workshop Description:
This workshop focuses on reviewing Python (or similar programming language) code to encourage best practices for documentation, linting, and refactoring. Students will submit code samples with specific questions for critique, and in the second session, they will incorporate feedback to improve their code.
In the first session, students are asked to submit code samples along with specific questions they may have about the readability or efficiency of their code. This code is reviewed and critiqued by me and to the extent that time allows, by students attending the workshop. The critiques provide an opportunity to discussing general aspects of
best practices for code organization, documentation and layout. Students are given specific feedback for improving their code with the understanding that they will make those changes before the second session. These suggestions can include learning to use tools for documenting and testing the code.
In the second session, students return having incorporate the suggested corrections to their earlier code. The code is reviewed again and any additional suggestions for implementing good STEM-specific software engineering principles are reiterated and reframed based on the quality of the code.
Learning Goals:
- Learn to document code properly and use a linter to detect errors.
- Implement best practices in code organization, refactoring, and testing.
Open to any STEM graduate student.
Materials must be submitted to Dr. Shende at least 1 week prior to workshop date
Open to STEM graduate students preparing to present their research in short formats.
A Hands-On Introduction to Deep Learning
Hosted by Sunil Shende
Dates and Times: March 11 and 25 (two part workshop) 2026 11:00 AM- 1:00 PM JHSC 104BC
Workshop Description:
TBA
Individual Development Plan (IDP)Workshop
Hosted by Guillaume Lamoureux
Dates and Times: April 28 11:00 AM – 1:00 PM JHSC 104BC
Workshop Description:
Workshop designed for students who must complete an IDP. This is a new requirement for NSF grants. Workshop will utilized the MyIDP platform. https://myidp.sciencecareers.org/
Jobs in Contract Research Organizations
Hosted by iJobs (Janet Alder)
Dates and Times: April 8 11:00 AM – 1:00 PM JHSC 104BC
Workshop Description:
A group of panelists will discuss jobs in contract research organization. More details on panelist to come.