Institute for Quantitative and Computational Biosciences

Frontiers in Computational Biosciences Seminar Series: Casey Overby Taylor, PhD, Associate Professor, Medicine (General Internal Medicine and Clinical Pharmacology) and Biomedical Engineering, Johns Hopkins University
2026-01-12 12:00 - 13:00 (America/Los_Angeles) | Boyer Hall 159
“Real-World Evidence for Guideline-Directed Genomic Medicine”

W3: Intro to R and Data Visualization
2026-01-13 13:30 - 2026-01-15 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
R (www.r-project.org) is a free software environment for statistical computing and graphics. First, this workshop introduces basic concepts, syntax, and usage in R programming, statistical analysis, and visualization techniques. We will conduct hands-on tutorials throughout the session, giving attendees a chance to see R in action. This course is a pre-requisite for several other Collaboratory workshops.
This workshop is geared towards researchers who have little or no experience with R who want to get started with importing data into R and visualize it. This workshop will provide resources for data wrangling, visualization and cover principles and best-practices for robust and reproducible data visualization. If you are interested in any particular R/Data Visualization tool, please contact the instructor in advance and effort will be made to cover topics of community interest.

W2: Using NGS Analysis Tools
2026-01-20 09:00 - 2026-01-22 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. First, this workshop introduces the more “universal” aspects of high-throughput sequence analysis—from experimental design to sequencing and alignment methods. Next, this workshop covers common file formats for sequence data and limitations of sequencing technologies.
We will explore a hands-on exercise using the Hoffman2 cluster and will use programs designed to analyze read data, clean artifact and low-quality sequences, and align short reads to a reference genome. At the end of this workshop, students will better understand the logic behind how many of these steps work.
Students who are comfortable working with the command line will find this course significantly easier than those who are inexperienced in command-line interface. While Workshop 1 is not an absolute requirement, it is highly recommended for any student who is not already experienced working in a command line environment. A student who takes this workshop at the same time as Workshop 1 should not find any problems with timing of material between these two classes.

W18: Advanced Python
2026-01-20 13:30 - 2026-01-22 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop will cover some more advanced topics in python including an overview of object-oriented python (this will not be an in-depth course on object-oriented programming), use of the numpy and pandas libraries (python libraries for efficient handling of large numeric and heterogenous datasets, and matplotlib for plotting results. At the end of this workshop, students will better understand the python data structures for handling large datasets and will have some knowledge of how to manipulate these data and plot them for presentation.

Frontiers in Computational Biosciences Seminar Series: Nasa Sinnott-Armstrong, PhD, Assistant Professor, Computational Biology, Fred Hutchinson Cancer Center
2026-01-26 12:00 - 13:00 | Boyer Hall 159
“Building a framework to integrate genetics, environment, and society”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W17: Machine Learning with Python
2026-01-27 09:00 - 2026-01-29 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop will cover the basic principles involved in the applications mentioned above, such as pattern recognition, linear and non-linear regression and cluster analysis. The workshop will be oriented towards hands-on activities, starting from the basics of how to load and prepare biological datasets in a Python environment.

W14: Intro to Modern Statistics with R
2026-01-27 13:30 - 2026-01-29 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
Through this seminar, attendees will walk away knowing when and how to run modern versions of traditional statistical analysis. These tests and the underlying bioinformatical lesson about resampling will be of use to most scientific disciplines. The course makes no assumptions about familiarity with traditional statistics – we will simply go through relatable experimental examples and ask how to test various hypotheses, introducing the relevant methods along the way. There will be homework assignments each night to solidify the concepts from class. These are short and optional, but will allow advanced students to gain more of the class.

Frontiers in Computational Biosciences Seminar Series: Melissa Gymrek, PhD, Associate Professor, Division Chief of Genetics, Department of Pediatrics, Department of Computer Science and Engineering, UCSD
2026-02-02 12:00 - 13:00 | Boyer Hall 159
“Leveraging multi-ancestry biobanks to understand shared and ancestry-specific factors driving disease risk”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W16: Library Prep for NGS
2026-02-03 09:00 - 2026-02-05 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq, ChIP-seq, RNA-seq, Methyl-seq) are explained the first and second day in class. The third day, Quality Control steps of the starting input material and final libraries are performed in the Lab (TapeStation). Purification from Primer Dimers (using AMPure beads) and Library Submission is also performed on the same day. The third day is optional, sign-up is required.

W28: Advanced Data Visualization w/ ggplot2
2026-02-03 09:00 - 2026-02-05 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States

Frontiers in Computational Biosciences Seminar Series: Victoria Yao, PhD, Assistant Professor, Department of Computer Science, Rice University
2026-02-09 12:00 - 13:00 | Boyer Hall 159
“Embedding strategies for understanding genes, pathways, and phenotypes”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W21: Image Processing for Microscopy
2026-02-10 09:00 - 2026-02-12 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
The analysis of imaging datasets is both exciting and challenging. New and increasingly powerful techniques try to maximize the information derived from multi-dimensional imaging datasets. Yet, every dataset can be a unique analysis challenge, and packages may not always work out-of-the-box. In this workshop, we will explore some popular computational tools to extract quantitative information from imaging data. Our focus will be to first grasp the principles underlying image analysis, and see how they can be logically applied to different kinds of imaging datasets. We will cover image generation, filtering, object identification, measurement of object properties, and the basics of object tracking. Through a series of stepwise hands-on exercises for each concept, we will build up to the goal of designing a full image analysis pipeline. Some programming experience in Python is highly recommended (but optional). Participants are also welcome to bring their own images and videos for discussion.

W26: Protein Structure with AlphaFold
2026-02-10 13:30 - 2026-02-12 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
The goal of the workshop is to enable the participants to submit
and rationally evaluate results of the AlphaFold protein structure
predictions. The class will cover the basic principles of the
structural biology of proteins, protein structure visualization
(in pymol) and protein structure prediction. The participants will
have opportunity to generate AlphaFold predictions for a protein
sequence/sequences of their choice and interpret the results
(provided these will be meaningful)
Note: Depending on interest, there might be a limit on the number
of predictions generated for workshop participants; Workshop
participants interested in generating novel AlphaFold predictions
are encouraged to provide the protein sequence(s) of interest
and a short (on or two sentences) description of each protein.

W31: Spatial Transcriptomics
2026-02-17 09:00 - 2026-02-19 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
Spatial transcriptomics is an emerging field that bridges molecular biology and anatomy. Over the last decade, a battery of assays have been developed that profile gene expression in-situ, i.e, measuring the abundances of mRNA molecules in cells and tissues while retaining information about their spatial locations. This workshop will introduce the basic concepts, major techniques, and typical analysis workflows in spatial transcriptomics. It will also offer guided hands-on coding exercises for the analysis of public spatial transcriptomic datasets.
Given the field’s rapid development, this workshop will try not to position itself as an authoritative guide of the subject. Rather, it will serve as a means of encouragement and support. It aims to help people jump into the field, plan experiments, play with data analysis, and contemplate about the future potential of this powerful technology.

W37: Applications of Large Language Models
2026-02-17 13:30 - 2026-02-19 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This 3-day interactive workshop introduces the overarching principles guiding generative modeling and specifically Large-Scale Language Models (LLM), their application in Python for inference, and specific use-cases in Genomics. Experience with Python is necessary, and basic knowledge about ML workflows is preferred.
At the end of this workshop, you WILL be comfortable with loading, inferencing and experimenting with state-of-the-art LLMs in Python, and making small changes to suit your research interests in Genomics. You WILL NOT be exposed to the internal architecture of LLMs and training your own models.

Frontiers in Computational Biosciences Seminar Series: Jian Ma, PhD, Ray and Stephanie Lane Professor of Computational Biology, School of Computer Science, Carnegie Mellon University
2026-02-23 12:00 - 13:00 | Boyer Hall 159
“Learning cellular organization and function across scales”

W5a: RNA-seq I Analysis
2026-02-24 13:30 - 2026-02-26 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
RNA-seq I aims to provide an introduction and the basics tools to process raw RNA-seq data on a cluster machine (Hoffman2). The workshop can serve also as a starting point to develop a gene expression project. This workshop is divided in three days that will cover major steps of processing RNA-seq.
To facilitate learning, the workshop will be centered on hands-on tutorial that will guide students in processing the data from raw reads through read counts using a real case study based approach appropriate for Illumina read data.

W5b: RNA-Seq II Analysis
2026-03-02 09:00 - 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
RNA-seq II aims to provide tools for analysis of gene expression data from read counts to biology using R. To facilitate learning, the workshop will use a real case study based approach appropriate for Illumina read data (same as RNA-seq I).

Frontiers in Computational Biosciences Seminar Series: Yuan Luo, PhD, Chief AI Officer and Professor, Northwestern University
2026-03-02 12:00 - 13:00 | Boyer Hall 159
“EPIC Multi-modal AI for Health Care”

Frontiers in Computational Biosciences Seminar Series: William Stafford Noble, PhD, Professor, Department of Genome Sciences, University of Washington, Seattle
2026-03-09 12:00 - 13:00 | Boyer Hall 159
“Foundation models for chromatin 3D architecture and proteomics mass spectrometry”

W20: Single-Cell RNA-Seq Analysis with R
2026-03-10 09:00 - 2026-03-12 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop aims to introduce the basic concepts and algorithms for single-cell RNA-seq analysis. It will help participants obtain a better idea of how to use scRNA-seq technology, from considerations in experimental design to data analysis and interpretation. This workshop can serve researchers who are interested in designing an scRNA-seq study or who have acquired scRNA-seq data and would like to learn about different analytical approaches.

15th Annual Southern California Systems Biology Symposium
2026-04-25 09:30 - 19:00 | Geffen Hall, 885 Tiverton Drive, Los Angeles, CA, 90095, United States
