Institute for Quantitative and Computational Biosciences

W6: BS-DNA Methylation Analysis with Hoffman2 and R
2025-05-06 09:00 - 2025-05-08 12:00 (America/Los_Angeles) | 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”

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”

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

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

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

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

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”

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.

W27: Systems biology of metabolism – workflows and resources for multi-omics data integration
2025-11-10 09:00 - 2025-11-13 12:00 | ZOOM, CA, United States
The application of omics (i.e., metabolomics, proteomics, transcriptomics, genomics) has become greatly popular in the life sciences. These technologies unlock the investigation of metabolism across thousands of genes, proteins, and metabolites, and provide a holistic perspective on the system of interest. However, to gather a systems-level understanding of biological functions in health and disease, omics data must be integrated in the relevant metabolic networks, in the context of allosteric, signaling and other regulatory layers. Metabolites can be regarded as a functional readout for the activity of a biological system. Therefore, their measured abundances can be leveraged to guide the interpretation of other omics layers of information. In this workshop, we provide an introduction and hands-on practical exercises on state-of-the art workflows and tools for the integration and interpretation of metabolomics data sets in the context of transcriptomics, proteomics, and genomics data. We will first introduce tools for processing metabolomics data at high throughput, such as the XCMS, MetaboAnalyst, METLIN, LIPID MAPS, The Human Metabolome Database, and the GNPS. We will further present tools for multi-omics integration and interpretation, including PathView, Reactome, MixOmics, PARADIGM, among others. The objective of this workshop is to i) provide a comprehensive overview on tools and resources for metabolomics data analysis and multi-omics interpretation, ii) provide hands-on training on open-source tools for systems biology of metabolism. This workshop is addressed to empirical biologists and computational biologists interested in metabolism.

Frontiers in Computational Biosciences Seminar Series: Jian Zeng, PhD, Group Leader - Centre for Population and Disease Genomics - Institute for Molecular Bioscience The University of Queensland - Australia
2025-11-10 12:00 - 13:00 | ZOOM, CA, United States
TITLE: “Leveraging functional annotations to enhance trait prediction and biological discovery”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

Frontiers in Computational Biosciences Seminar Series: Kalli Kappel, PhD, Assistant Professor, Department of Chemistry & Biochemistry, UCLA
2025-11-17 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Decoding RNA and protein sequence-organization-function relationships”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W25: Population Genetics Modeling
2025-11-18 13:30 - 2025-11-20 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
In order to make inferences based on genomic data, it is useful to understand the evolutionary forces that underlie observed genetic variation. The field of population genetics offers theoretical tools to test predictions, gain intuition, and even generate training data for statistical and deep learning models. However, population genetics simulations have historically been slow and complex, making effective usage of such tools difficult. Recently, the evolutionary simulation framework SLiM (Selection on Linked Mutations) has revolutionized the field, making the capability to model complex evolutionary scenarios more accessible. In this workshop, participants will be introduced to the population genetics theory underlying SLiM, learn how to model complex scenarios, and practice interpreting the results of their simulations to make predictions about real-world data. Participants will also be given the opportunity to bring in their own data to analyze and use as inspiration to generate models. By learning about the fundamental forces that shape genomic data and how to model them, participants will gain a combination of both theoretical insights into evolutionary genetics and practical insights into relevant computational tools.

QCBio Special Seminar: Thomas Kammertöns, PhD, Institute for Cancer Immunology, Charité, Universitätsmedizin Berlin
2025-11-20 12:00 - 13:00 | Boyer Hall 554
TITLE: ““The role of IFN-γ in Tumor Immunity – Mechanisms and TCR Gene Therapy”

Frontiers in Computational Biosciences Seminar Series: Yi Zhang, PhD, Assistant Professor, Neurosurgery and Biostatistics & Bioinformatics, Duke University
2025-11-24 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Interpretable machine learning methods to understand tissue heterogeneity using large-scale single-cell genomics and high-definition spatial transcriptomics”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

Frontiers in Computational Biosciences Seminar Series: Eric Deeds, Professor, Integrative Biology and Physiology, UCLA
2025-12-01 12:00 - 13:00 | Boyer Hall 130
TITLE: TBD
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

QCBio Faculty Research Forum
2025-12-09 13:00 - 16:00 | Boyer Hall 159
Join us for a series of talks featuring QCBio faculty as they share ideas that excite them
Mehdi Bouhaddou
Assistant Professor, Microbiology, Immunology & Molecular Genetics
The Bouhaddou Lab dissects the biochemical regulatory circuits that control fate decisions using latest proteomic-mass spec technologies and quantitative analysis. They are specifically interested in understanding virus host interactions. While it is well appreciated that viruses hijack the cell’s core machineries for their replication, we have found that they also exquisitely sense cellular signaling activities to inform their own decision-making.
Aaron Meyer
Associate Professor, Bioengineering
The Meyer lab integrates experimental and computational strategies to measure, model, and therapeutically manipulate cell-to-cell communication, with applications in the development of immune and cancer therapies. They currently focus this integrated approach on the immune system, specifically on the mechanisms of selective cytokine and antibody Fc signaling. They also develop tensor-based data modeling approaches that have found wide applicability in the analysis of high dimensional clinical datasets.
Van Savage
Professor, Departments of Computational Medicine, and Ecology and Evolutionary Biology
Biological systems display extraordinary diversity in form and function. By understanding this diversity, we can discover mechanisms that provide critical new insights into biomedical problems. My overall research goal is to combine novel mathematical models with newly collected or analyzed empirical data to understand how biological systems are organized, constrained, and controlled across multiple levels of organization.
Grace Xiao
Professor, Integrative Biology and Physiology
The Xiao lab combines the latest computational and experimental methods in RNA biology to elucidate molecular mechanisms underlying disease. The overarching goals of our research are to understand how the transcriptome and epitranscriptome are controlled by the intricate network of genetic factors, RNA elements, and RNA-binding proteins, and how such regulation contributes to neurological diseases and cancer.
Jason Zhang
Assistant Professor, Bioengineering
The newly established Zhang lab focuses on AI-driven molecular engineering to study cellular signaling. One focus is the development of biosensors that reveal cellular activities in real time in living cells and tissues. His research leverages the latest AI structure prediction tools combined with principles from biophysics and cell biology.

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 | Boyer Hall 159
“Real-World Evidence for Guideline-Directed Genomic Medicine”

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

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 13:30 - 2026-02-05 16:30 | 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.

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

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”

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”
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

Jeff Saucerman (University of Virginia) - Frontiers in Computational Biosciences Seminar Series
2026-03-30 12:00 - 13:00 | Boyer Hall 159
Jeff Saucerman, Professor, Biomedical Engineering, University of Virginia
Network drivers of cardiac inflammation-fibrosis coupling
Watch recording on YouTube: https://www.youtube.com/channel/UCokAYrjf_TaziPtmn6l4-5A

W9: Intro to Python
2026-03-31 09:00 - 2026-04-02 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: Intro to Unix & the Hoffman2 Cluster
2026-03-31 13:30 - 2026-04-02 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.
