Frontiers in Computational Biosciences Seminar Series: Gary Bader, PhD, Professor, The Donnelly Centre, University of Toronto
2025-01-27 12:00 - 13:00 (America/Los_Angeles) | Boyer Hall 159
TITLE: “TBD”

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

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

W1B: Intro to Unix command line II
2025-02-11 13:30 - 2025-02-13 16:30 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop (UNIX Command Line II) continues Workshop W1: UNIX Command Line I and uses the Hoffman2 campus computing cluster. The focus is on features that make dealing with large files or large numbers of files or repetitive tasks easier. These include shell variables, substitutions, redirections, pipes, loops, conditionals, subshells, shell functions, and shell scripts. There will be illustrations of how to run modest numbers of multiple commands at the same time — both within a single node/one computer, and (using the Hoffman2 queue system) across multiple nodes of the cluster.

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.

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”

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

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: Christian Huber, PhD, Assistant Professor of Biology, Penn State University
2025-03-10 12:00 - 13:00 | Boyer Hall 159

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: 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?”

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: 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: 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”

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

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”

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.
