Frontiers in Computational Biosciences Seminar Series: Xuebing Wu, PhD, Assistant Professor of Medical Sciences - Columbia University
2025-04-14 12:00 - 13:00 (America/Los_Angeles) | Boyer Hall 159
TITLE: “Illuminating the Twilight Zone: The Noncoding Genome Lost in Translation”

https://qcb.ucla.edu/wp-content/uploads/sites/14/2025/03/Wu_Xuebing_Edited.mp4

Frontiers in Computational Biosciences Seminar Series: Justin Sonnenburg, PhD, Alex and Susie Algard Endowed Professor, Microbiology & Immunology - Stanford University
2025-04-21 12:30 - 13:00 | Boyer Hall 159
TITLE: “The Predicament of the Industrialized Gut Microbiome”

Frontiers in Computational Biosciences Seminar Series: Tiffani Bright, PhD, Co-Director, Center for Artificial Intelligence Research and Education; Assistant Professor, Department of Computational Biomedicine - Cedars-Sinai Medical Center
2025-04-28 12:00 - 17:00 | ZOOM, CA, United States
TITLE: “Fair AI for Health: Reducing Bias in Predictive Models”

W21: Image Processing for Microscopy
2025-04-29 09:00 - 2025-05-01 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.

Webinar: Big data for novel diagnostics and therapeutics
2025-04-29 17:30 - 18:30 | ZOOM, CA, United States
Fueled by technological innovations, online databases and algorithmic developments, biomedical research is rapidly becoming a data science. In this webinar, three of the most innovative UCLA faculty will share their perspectives on how biological big data are enabling their research. We will hear about robotic instrumentation that generate big data about drugs and genes, how diverse datasets can be integrated to identify patterns that inform novel diagnostics, and how shared databases can be leveraged to identify new disease insights from existing drugs.
Big Data for Novel Diagnostics and Therapeutics
a conversation featuring
Xia Yang
Professor, Integrative Biology and Physiology
Professor, Molecular and Medical Pharmacology
Robert D. Damoiseaux
Professor, Molecular and Medical Pharmacology
Professor, Bioengineering
Jennifer L. Wilson
Assistant Professor, Bioengineering
moderated by
Alexander Hoffmann
Director, Institute for Quantitative and Computational Biosciences
Asher Professor of Microbiology, Department of Microbiology, Immunology and Molecular Genetics

Frontiers in Computational Biosciences Seminar Series: Mark Gerstein, PhD, Albert L Williams Professor of Biomedical Informatics and Professor of Molecular Biophysics & Biochemistry, of Computer Science, and of Statistics & Data Science - Yale
2025-05-05 12:00 - 13:00 | Boyer Hall 159
TITLE: “TBD”

W6: BS-DNA Methylation Analysis with Hoffman2 and R
2025-05-06 09:00 - 2025-05-08 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop will introduce the basic principles of DNA methylation and briefly describe available methods for DNA methylation assessment, focusing on bisulfite sequencing (BS-Seq). We will cover the principles of BSseq preprocessing, alignment and methylation calling, differential methylation analysis, annotation and visualization. Attendees will have the opportunity to work on real DNA methylation data provided by the instructor and run the analysis on Hoffman2 and locally. Attendees need to have a basic knowledge in UNIX commands and R programming for this workshop. No previous experience with NGS or DNA methylation analysis is necessary.

Frontiers in Computational Biosciences Seminar Series: Roy Wollman, PhD, Professor, Biochemistry, Structural and Computational Biology, Systems Biology and Biological Regulation - UCLA
2025-05-12 12:00 - 13:00 | Boyer Hall 159
TITLE: “Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains”

W1c: Intro to Unix command line III
2025-05-13 13:30 - 2025-05-15 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States

Frontiers in Computational Biosciences Seminar Series: Carl Veller, PhD, Assistant Professor of Ecology & Evolution - University of Chicago
2025-05-19 12:00 - 13:00 | Boyer Hall 159
TITLE: “Chromosome-scale drift under stabilizing selection, with evolutionary implications”

W36: Mergeomics for Multiomics Integration
2025-05-20 09:00 - 2025-05-22 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
Mergeomics is a computational tool designed to elucidate the underlying pathways, networks, and key regulators of complex diseases by integrating multi-omics data (genomics, transcriptomics, epigenomics, proteomics, etc). With use of integrative omics concepts and network modeling methods, this tool can uncover disease-associated gene sets and biological pathways across omics layers and can identify key drivers within gene regulatory networks or protein-protein interaction networks. In this workshop, we will first discuss the background, omics integration concepts, and capabilities of Mergeomics as well as the key analytical functions and various inputs that are commonly used. Next, we will demonstrate how this web tool can be used to analyze a complex disease by walking participants through each step within the Mergeomics web server and explain how to interpret the results.

Frontiers in Computational Biosciences Seminar Series: Lixing Yang, PhD, Assistant Professor of Ben May Department of Cancer Research - University of Chicago
2025-06-02 12:00 - 13:00 | Boyer Hall 159
TITLE: “The Causes and Consequences of Somatic Structural Variations in Human Cancer”

W20: Single-Cell RNA-Seq Analysis with R
2025-06-03 09:00 - 2025-06-05 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.

W9: Intro to Python
2025-09-30 09:00 - 2025-10-02 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop will cover the basic concepts of Python programming. The course is supplemented with many hands-on exercises with emphasis given towards computational biology use cases.

W1A: Unix command line I
2025-09-30 13:30 - 2025-10-02 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
Unix is a command-line-based platform that is a highly powerful and flexible tool for data management and analysis. First, this workshop introduces the basic concepts of UNIX operating system and shell scripting. We will explore essential hands-on skills to confidently use the command line interface on either a local (laptop) or a remote (hoffman2 cluster) computer running the Unix system. Next, this workshop covers how to navigate around the Unix file system from the command line and use a number of basic, common Unix commands. The course is supplemented with many hands-on examples. No prior knowledge of Unix or programming is required.

Frontiers in Computational Biosciences Seminar Series: Genevieve Konopka, PhD, Professor & Chair, Department of Neurobiology, UCLA David Geffen School of Medicine
2025-10-06 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Cell type-specific transcriptional networks in brain evolution and disease”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W2: Using NGS Analysis Tools
2025-10-07 09:00 - 2025-10-09 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
2025-10-07 13:30 - 2025-10-09 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: Yuzhe Yang, PhD, Assistant Professor, Computational Medicine & Computer Science, UCLA
2025-10-13 12:00 - 13:00 | ZOOM, CA, United States
TITLE: “Multisensory AI for Personalized Healthcare”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W3: Intro to R and Data Visualization
2025-10-14 09:00 - 2025-10-16 12:00 | 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.

W17: Machine Learning with Python
2025-10-14 09:00 - 2025-10-16 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.

Frontiers in Computational Biosciences Seminar Series: Amy Goldberg, PhD, Associate Professor, Human Genetics, UCLA
2025-10-20 12:00 - 13:00 | Boyer Hall 159
TITLE: “Evolutionary perspectives on malaria”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W16: Library Prep for NGS
2025-10-21 09:00 - 2025-10-23 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.

W14: Intro to Modern Statistics with R
2025-10-21 13:30 - 2025-10-23 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: Yosuke Tanigawa, PhD, Assistant Professor, UCLA Engineering
2025-10-27 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Enhancing polygenic prediction with flexible models on individual-level data”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W31: Spatial Transcriptomics
2025-10-28 09:00 - 2025-10-30 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.

W26: Protein Structure with AlphaFold
2025-10-28 13:30 - 2025-10-30 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.

Frontiers in Computational Biosciences Seminar Series: Hooman Allayee, PhD, Professor-in-residence, Medicine, UCLA
2025-11-03 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “System Genetics Studies of Coronary Artery Disease”

W28: Advanced Data Visualization w/ ggplot2
2025-11-04 09:00 - 2025-11-06 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States

W24: Cancer Genomics
2025-11-04 13:30 - 2025-11-06 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
As we step into the era of precision medicine, the need for extensive genomic data analysis is more pressing than ever. With the advent of high-throughput technologies, a plethora of genomic, transcriptomic, and epigenomic datasets from cancer patients have been sequenced, providing a wealth of data for systematic bioinformatics analysis. This workshop is tailored to assist cancer bioinformaticians, postdoc researchers, and graduate students who are interested in incorporating expansive cancer genomic datasets from an open-source platform – The Cancer Genome Atlas (TCGA) – into their research.
Enrolled participants will gain insights into the fundamental principles of TCGA, including the different data categories and structures, methods for downloading data, and basic pipelines for data analysis within the TCGA platform. The workshop will also provide a versatile R script scaffold for mining TCGA datasets, empowering attendees to analyze their own unique cohorts of cancer genomic datasets.
