Institute for Quantitative and Computational Biosciences

W25: Population Genetics Modeling
2025-11-18 13:30 - 2025-11-20 16:30 (America/Los_Angeles) | 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.

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

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

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.

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.

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”

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: 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: 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: 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: 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”

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: 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”

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”

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: 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”

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: 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”

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: Xuebing Wu, PhD, Assistant Professor of Medical Sciences - Columbia University
2025-04-14 12:00 - 13:00 | 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: Adam Yala, PhD, Assistant Professor of Computational Precision Heath, Statistics and EECS - UC Berkeley and UCSF
2025-04-07 12:00 - 13:00 | Boyer Hall 159
TITLE: “AI for personalized cancer care”
https://qcb.ucla.edu/wp-content/uploads/sites/14/2025/03/Yala_Adam_Edited-Recording-1.mp4

Frontiers in Computational Biosciences Seminar Series: Brenna Henn, PhD, Associate Professor, Department of Anthropology, Co-Director: Northern Cape Tuberculosis Project - UC Davis
2025-03-31 12:00 - 13:00 | Boyer Hall 159
TITLE: “Why study human genomic diversity in African populations?”

QCBio's New Quarterly Faculty Research Forum
2025-03-18 10:30 - 13:30 | Hershey Hall
We are excited to launch a quarterly QCBio Faculty Research Forum—a new initiative to spark innovation and collaboration, and shape the future of UCLA computational biosciences.
We invite you to join us for the inaugural event on March 18, 2025, from 10:30 AM to 1:30 PM in Hershey Hall Grand Salon.
We have terrific line-up of Faculty speakers:

Chongyuan Luo
Roy Wollman
Jamie Lloyd-Smith
Elisa Franco
Alan Garfinkel

If interested, fill out the registration form. Please make sure you respond by March 10, 2025.

Frontiers in Computational Biosciences Seminar Series: Christian Huber, PhD, Assistant Professor of Biology, Penn State University
2025-03-10 12:00 - 13:00 | Boyer Hall 159

Frontiers in Computational Biosciences Seminar Series: Jianzhi "George" Zhang, PhD, Marshall W. Nirenberg Collegiate Professor, University of Michigan
2025-03-03 12:00 - 13:00 | Boyer Hall 159

Frontiers in Computational Biosciences Seminar Series: Aik Choon Tan, PhD, Senior Director of Data Science, Huntsman Cancer Institute: Jon M. and Karen Huntsman Endowed Chair in Cancer Data Science and Professor, University of Utah
2025-02-24 12:00 - 13:00 | Boyer Hall 159

Computational Pathology Faculty Candidate Presentation - Dr. Matthew Jones
2025-02-20 08:00 - 09:00 | AS-260
Matthew Jones, PhD
Computational Pathology Faculty Candidate
Postdoctoral Fellow, Department of Dermatology, Stanford University School of Medicine
TITLE: “Unraveling The Evolutionary Principles of Cancer”

W11: Metagenomics Analysis with Python and R
2025-02-18 09:00 - 2025-02-20 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop provides an introduction to the microbiome analyses from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the microbiome data beyond QIIME, including statistical analyses and functional analyses.

Frontiers in Computational Biosciences Seminar Series: Karthik Sarma, MD, PhD, Chief Technology Officer, SimX; Computational Medical Scientist and Clinical Psychiatrist, UCSF
2025-02-10 12:00 - 13:00 | Boyer Hall 159

Frontiers in Computational Biosciences Seminar Series: Katie Hoadley, PhD, Associate Professor, Genetics, UNC-Chapel Hill
2025-02-03 12:00 - 13:00 | Boyer Hall 159
