UPCOMING SEMINAR:
REGISTER HERE: https://events.uchicago.edu/event/282147-cri-bioinformatics-workshop-series-beyond-the
Beyond the Expression Matrix: Turning RNA-seq Data into Biological Insight
Monday, November 9th | 2:00pm – 4:00pm
Donnelley (BSLC) Room #218 or via Zoom
Hosted by: Yan Li, Associate Director of Bioinformatics
Once you have a gene expression matrix, what comes next? This workshop starts with the underlying concepts — differential expression, over-representation, and gene set enrichment — then puts them into practice with DEApp and FeaVis, two internally hosted web applications developed by our group that make these analyses accessible without writing a line of code. FeaVis also offers AI-assisted interpretation to help you make sense of your enrichment results. Point, click, interpret.
Prerequisites:
- An active UChicago CNetID (required for one application access)
- No programming experience necessary
Topics Covered:
- Differential expression (DE) analysis: concepts and interpretation
- Gene set over-representation analysis (ORA)
- Gene set enrichment analysis (GSEA)
- Hands-on: running DE analysis in DEApp
- Hands-on: running functional enrichment analysis in FeaVis
This seminar will take place at Donnelley (BSLC) Classroom #218. 924 E 57th, Chicago, IL. also, via Zoom. Registration is required for all attendees, whether you plan to attend in person or via Zoom. Zoom meeting information will be emailed to registrants one day prior to the session. Please note that due to limited capacity, registration may close early if capacity is reached. Participation is open to University of Chicago, UCM, and Pritzker School of Medicine faculty, staff, and students.
About the speaker: Yan received her PhD in Bioinformatics (December 2013) and dual MS degrees in Statistics and Plant Pathology (August 2009) from the University of Georgia. Prior to joining the CRI in 2014, she worked on multidisciplinary projects using advanced computational tools, statistical methods, and mathematical modeling to address a variety of questions across the biological sciences. Currently, she is focused on developing and applying bioinformatics computational software and pipelines to facilitate the analysis of Next Generation Sequencing (NGS) data. She works closely with faculty and researchers to explore genomics-associated biomedical questions, including the NGS data analysis of RNA-Seq, ChIP-Seq, small RNA-Seq, and exome sequencing.
About the series: Since 2012, the Center for Research Informatics has offered free training sessions for the University of Chicago community in informatics research tools and techniques. Topics include REDCap, clinical data, bioinformatics analysis, data visualization, high performance computing, grant preparation, and more. To hear about upcoming seminars, sign up for our email list at https://cri.uchicago.edu/seminar-series.
Questions? Please contact Janaya Lee at janayalee@bsd.uchicago.edu or Cody Lasenby at Cody.Lasenby@bsd.uchicago.edu
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PAST SEMINARS
We archive our past training seminars here, including links to the content if it is available.
| Date | Topic | Seminar Title | Content |
|---|---|---|---|
| October 2026 | Bioinformatics | Single-Cell RNA-seq Visualization Shiny Application | Single-Cell RNA-seq Visualization Shiny Application |
| October 2026 | CRI/UCM/EPIC | 2026 Epic Cosmos Datathon | |
| May 2026 | Bioinformatics | 10X Spatial Transcriptomics | Spatial Transcriptomics: Visium and Xenium |
| April 2026 | Bioinformatics | Bruker Spatial Transcriptomics: GeoMx and CosMx | Bruker Spatial Transcriptomics: GeoMx and CosMx Slides Recording of Bruker Spatial Transcriptomics: GeoMx and CosMx |
| March 2026 | Bioinformatics | AI-Assisted scRNA-seq Analysis Explorations, Use Cases and Pitfalls | AI-Assisted scRNA-seq Analysis Explorations, Use Cases and Pitfalls |
| January 2026 | AI & Data Science | Enhancing Clinical Data Science: Machine Learning and Advanced Techniques for Novel Insights in Clinical Research | Enhancing Clinical Data Science: Machine Learning and Advanced Techniques for Novel Insights in Clinical Research |
| November 2025 | Bioinformatics | Functional Enrichment Analysis | Functional Enrichment Data Analysis |
| October 2025 | Bioinformatics | Practical Workshop on Bulk RNA-seq Bioinformatics Pipelines | Bulk-RNAseq Pipeline Hands-on Training |
| June 2025 | Bioinformatics | scRNA-seq Data Integration | |
| April 2025 | Bioinformatics | Spatial Transcriptome Analysis | Spatial Transcriptomics Workshop |
| February 2025 | Bioinformatics | Bulk-RNAseq Pipeline | Bulk-RNAseq Pipeline Hands-on Training |
| October 2024 | CRI/BSDIS | Overview of CRI and BSDIS | CRI/BSDIS IT Expo Session |
| August 2024 | Bioinformatics | Using R Bioconductor packages for bulk RNA-seq DE analysis | Using R Bioconductor packages for bulk RNA-seq DE analysis |
| January 2024 | Bioinformatics | Introduction to Linux Command Line for Bioinformatics | |
| November 2023 | Data Analytics | Showcase of Reseach Project: NLP to Identify Mental Illness and Substance Use Factors in Clinical Notes | Case Illustration of NLP in a Research Project |
| November 2023 | Bioinformatics | Workshop Series: Part One Introduction to 10x Genomics Sequencing Protocols | Single Cell RNA-seq Data Analysis |
| February 2023 | REDCap | Introduction to REDCap | Introduction to REDCap |
| January 2021 | Data Analytics | Case Illustrations of NLP in Clinical Research | |
| May 2020 | HPC | Introduction to NVIDIA Parabricks | |
| April 2020 | REDCap | Making the Most of REDCap: All About Surveys | All About REDCap Surveys |
| February 2020 | REDCap | Making the Most of REDCap: Beyond the Basics | REDCap Beyond the Basics |
| January 2020 | HPC | Overview of CRI Computing Infrastructure | Overview of CRI Computing Infrastructure |
| May 2019 | Bioinformatics | Advanced Interactive Data Visualizations with Python | |
| March 2019 | Data Analytics | Using Natural Language Processing in Clinical Data Analytics | Using NLP in Clinical Data Analytics |
| February 2019 | Bioinformatics | Introduction to Reproducible Research via R Markdown | |
| December 2018 | Grant Preparation | Including Informatics in Grant Applications | Including Informatics in Grant Applications |
| November 2018 | Clinical Data | Using the CRDW and Cohort Discovery Tools | CRDW and Cohort Discovery |
| October 2018 | Guest Talk | Introduction to the Human Imaging Research Office | Introduction to HIRO |
| September 2018 | HPC | Parallel Computing 101 | Parallel Computing 101 |
| August 2018 | Grant Preparation | Including Informatics in Grant Applications | Including Informatics in Grant Applications |
| May 2018 | Clinical Data | Using the CRDW and Cohort Discovery Tools | CRDW and Cohort Discovery |
| April 2018 | HPC | CRI Infrastructure and New Parallel Storage | CRI Infrastructure and New Storage |
| March 2018 | Bioinformatics | Introduction to IPython and Pandas for Bioinformatics | iPython and Pandas |
| February 2018 | Clinical Data | Statistical Modeling with Clinical Data | Statistical Modeling - Methods Statistical Modeling - CRDW |
| December 2017 | Grant Preparation | Including Informatics in Grant Applications | Including Informatics in Grant Applications |
| November 2017 | HPC | Computing with the CRI: Storage, HPC, and Virtual Servers | Computing with the CRI |
| October 2017 | Bioinformatics | Biological Interpretation of Gene, Transcript, and Protein Expression Data with IPA | Biological Interpretation with IPA |
| September 2017 | Data Analytics | Using NLP in Clinical Data Analytics | NLP in Clinical Research |
| August 2017 | Grant Preparation | Including Informatics in Grant Applications | Informatics in Grants, Part 1 Informatics in Grants, Part 2 |
| May 2017 | Bioinformatics | Genomics Data Visualization | Genomics Data Visualization |
| April 2017 | HPC | HPC Workshop: Advanced | HPC: Advanced |
| April 2017 | HPC | HPC Workshop: Beginner | HPC: Beginner |
| November 2016 | Bioinformatics | Biological Interpretation of Gene, Transcript, and Protein Expression Data with IPA | -- |
| November 2016 | Clinical Data | Optimizing Data Requests for the CRDW | Optimizing CRDW Requests |
| October 2016 | HPC | Introduction to Gardner: The CRI's New HPC Cluster | Introduction to Gardner |
| April 2016 | Bioinformatics | Biological Interpretation of Gene, Transcript, and Protein Expression Data with IPA | -- |
| December 2015 | Bioinformatics | Annual Workshop: Bioinformatics Analysis of Integrative -Omics Data | Workshop Recap |
| October 2015 | Bioinformatics | Introductory Statistics with R | Introductory Statistics with R |
| September 2015 | Bioinformatics | Introduction to iPython and Pandas, Part II | iPython and Pandas, Part II |
| June and July 2015 | Bioinformatics | Introduction to iPython and Pandas, Part I | iPython and Pandas, Part I |
| May 2015 | Bioinformatics | Introduction to Python Programming, Part II | Introduction to Python, Part II |
| April 2015 | Bioinformatics | Introduction to Python Programming, Part I | Introduction to Python, Part I |
| March 2015 | Bioinformatics | Analysis of Affymetrix Microarray Data with R and Bioconductor | Analysis of Affymetrix Microarray Data |
| February 2015 | Bioinformatics, HPC | Introduction to CRI’s HPC Cluster for Bioinformatics Computing | Introduction to CRI's HPC Cluster |
| January 2015 | Bioinformatics | R Graphics for Bioinformatics | R Graphics for Bioinformatics |
| December 2014 | Bioinformatics | Annual Workshop: Bioinformatics Analysis of High-Throughput Genomics Data | Workshop Recap |
| October 2014 | Bioinformatics | Visual Exploration of Data with the Advanced R Graphics Library: ggplot2 | -- |
| September 2014 | Bioinformatics | Introduction to R Programming, Part II | Introduction to R Programming, Part II |
| August 2014 | Bioinformatics | Introduction to R Programming, Part I | Introduction to R Programming, Part I |
| July 2014 | Bioinformatics | Introduction to Python Programming, Part II | Introduction to Python, Part II |
| June 2014 | Bioinformatics | Introduction to Python Programming, Part I | Introduction to Python, Part I |
| May 2014 | Bioinformatics | Introduction to Linux Command Line for Bioinformatics | Introduction to Linux for Bioinformatics |
| April 2014 | Bioinformatics | Analyzing Illumina RNA-Seq Data with the CRI | Analyzing Illumina RNA-Seq Data with the CRI |
| March 2014 | Bioinformatics | Overview and Tutorial of Lynx: An Integrated Systems Biology Platform for Analysis of Multi-Gene Disorders | -- |
| February 2014 | Bioinformatics | Analysis of Illumina Microarray Data with R and Bioconductor | Analysis of Microarrays with R and Bioconductor |
| January 2014 | Bioinformatics | How to Use the CRI’s Computational Infrastructure for Bioinformatics Analysis | CRI Infrastructure for Bioinformatics, Part I and Part II |
| November 2013 | Bioinformatics | Introduction to Perl: Learning by Example | Introduction to Perl |
| October 2013 | Bioinformatics | Maximizing the Biological Interpretation of Gene, Transcript, & Protein Expression Data with IPA | -- |
| September 2013 | Bioinformatics | Introduction to Python Programming | Introduction to Python Programming |
| August 2013 | Bioinformatics | Introduction to R Programming | Introduction to R Programming |
| June and July 2013 | Bioinformatics | Introduction to Linux Command Line for Bioinformatics | Introduction to Linux Command Line for Bioinformatics |
| May 2013 | Bioinformatics | Analyzing Illumina ChIP-Seq Data with the CRI | Analyzing Illumina ChIP-Seq Data with the CRI |
| April 2013 | Bioinformatics, HPC | Introduction to CRI’s HPC Cluster for Bioinformatics Computing | Introduction to CRI's HPC for Bioinformatics |
| March 2013 | Bioinformatics | Analysis of Illumina Microarray Data with R and Bioconductor | Analysis of Microarrays with R and Bioconductor |
| February 2013 | Bioinformatics | Analyzing Illumina RNA-Seq Data with the CRI | Analyzing Illumina RNA-Seq Data |
| January 2013 | Bioinformatics | Analysis of Microarrays with R and Bioconductor | Analysis of Microarrays with R and Bioconductor |
| November 2012 | Bioinformatics | Analyzing Illumina Whole Exome Data with the CRI | Analyzing Illumina Whole Exome Data with the CRI |
| September 2012 | Bioinformatics | Galaxy: Web-based Bioinformatics Analysis & RNA-Seq Workflow Management | Galaxy: Web-Based Bioinformatics Analysis |
| August 2012 | Bioinformatics | Analyzing Illumina RNA-Seq Data with the CRI | Analyzing Illumina RNA-seq Data |
| July 2012 | Bioinformatics | Analysis of Microarray Data with R and Bioconductor | Analysis of Microarrays with R and Bioconductor |
