Institute for Quantitative and Computational Biosciences

W7: ChIP-seq Analysis
2024-11-05 13:30 - 2024-11-07 15:30 (America/Los_Angeles) | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop aims to provide skills needed to address principles of the assay, quality assessment, sequencing depth, data processing and functional downstream analyses of ChIP-seq datasets. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.

Frontiers in Computational Biosciences Seminar Series: Julia Salzman, PhD, Associate Professor, Department of Biomedical Data Science and of Biochemistry, Stanford University
2024-11-04 12:00 - 13:00 | Boyer Hall 159
TITLE: TBD
Hosted by Nandita Garud for Bioinformatics

W12: Intro to MATLAB
2024-10-29 09:00 - 2024-10-31 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
MATLAB is a powerful, high-level programing language for numerical computation, visualization, and application development. This workshop will start by introducing the MATLAB environment and then cover working with arrays and matrices, loops and conditional statements, writing your own functions, working with files and visualizing your data. The final day will briefly introduce utilizing MATLAB to solve differential equations and the basics of computational systems biology modeling using MATLAB. The course is supplemented with many hands-on exercises. The workshop is suitable for those with or without coding experience in other languages. No computational knowledge is assumed and no prerequisite workshops are required, however the Unix workshop (workshop 1) may be a useful foundation.

Frontiers in Computational Biosciences Seminar Series: Jayashree Kalpathy-Cramer, PhD, Professor, Ophthalmology; Chief, Division of Artificial Medical Intelligence, Ophtalmology; Director, Health Informatics, CCTSI; University of Colorado - Anschutz Medical Center
2024-10-28 12:00 - 13:00 | Boyer Hall 159
TITLE: TBD
Hosted by William Hsu for Medical Informatics

QCBio Research Seminar: Rizal Hariadi, Associate Professor, Department of Physics and Biodesign Institute, Arizona State University
2024-10-22 12:30 - 13:30 | Boyer Hall 159
TITLE: Sensing and applying multi-axial tension to biomolecules using molecular devices built from DNA.
ABSTRACT: DNA nanotechnology enables the construction of molecular devices for diverse biomedical applications. By leveraging DNA’s exquisite positional control, researchers can engineer sophisticated nanostructures that execute a range of tasks. In this talk, I will present 2 DNA-based devices: an amphiphilic double-stranded DNA sensor for non-destructive detection of cytosolic biomarkers and a DNA origami platform for multi-axial mechanical manipulation of biomolecules. In the first part of my talk, I will show synthetic transmembrane devices inspired by G protein-coupled receptors (GPCRs) that transduce signals across cell membranes. These amphiphilic DNA nanodevices detect specific intracellular oligonucleotides, generating fluorescent signals without cell lysis and genetic engineering. In the second half of the talk, I will present some recent results on a Holliday junction, a model system in biophysics, under multi-axial tension using the Multi-Axial Entropic Spring Tweezer along Rigid Origami (MAESTRO). This molecular tool, which exploits the entropic elasticity of single-stranded DNA, uncovers the non-ergodicity of Holliday junction dynamics. The talk concludes with a discussion on the potential applications of these devices, including their use in high-throughput single-molecule biophysics of integrin signaling, cryo-EM structural studies of integrins under tension, and live-cell isolation targeting RNA markers.

Frontiers in Computational Biosciences Seminar Series: Yin Yi, PhD, Assistant Professor, UCLA
2024-10-21 12:00 - 13:00 | Boyer Hall 159
TITLE: TBD
Hosted by Kirk Lohmueller for Bioinformatics

Frontiers in Computational Biosciences Seminar Series: Ludmil Alexandrov, Phd, Professor, Cellular and Molecular Medicine, UC San Diego
2024-10-14 12:00 - 13:00 | Boyer Hall 159
TITLE: TBD
Hosted by Paul Spellman for Genetics & Genomics

Frontiers in Computational Biosciences Seminar Series: Erik Andersen, PhD, Professor, Johns Hopkins University
2024-10-07 12:00 - 13:00 | Boyer Hall 159
TITLE: “Mechanisms of differences in gene expression and organismal traits caused by structural variation (both real and imagined)”
Hosted by Leonid Kruglyak for Genetics & Genomics

Frontiers in Computational Biosciences Seminar Series: Armita Nourmohammad, PhD, Associate Professor, University of Washington
2024-09-30 12:00 - 13:00 | Boyer Hall 159
TITLE: TBD
Hosted by Alexander Hoffmann for Bioinformatics

Research-in-Progress (RIP) Seminar: Raag Agrawal (Boutros), Graduate Student in Genetics & Genomics, UCLA/Caltech MSTP
2024-06-05 11:30 - 12:00 | Boyer Hall 159
TITLE: “Discovering biomarkers for predicting response to neo-adjuvant ADT and radionuclide treatment in high-risk prostate cancer”
ABSTRACT: Prostate cancer is the number one cause of cancer death in non-smoking American men. Next generation treatments for prostate cancer include androgen deprivation therapy (ADT) drugs such as Enzalutamide and radionuclide treatments like Lu-PSMA-617. While both of these treatment approaches are initially effective, prostate cancer almost always recurs. We use multimodal genomic data to discover clinically useful prostate cancer subtypes to determine mechanisms of treatment resistance. We further explore how these subtypes relate to the dearth of model systems in prostate cancer research – and whether we are ignoring clinically relevant genetic diversity in our drug development pipeline.

Research-in-Progress (RIP) Seminar: Jonathan Mah (Garud-Lohmueller), Graduate Student in Bioinformatics Interdepartmental Program
2024-06-05 11:00 - 11:30 | Boyer Hall 159
TITLE: “Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history”
ABSTRACT: Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their demographic histories and distributions of fitness effects (DFE) of mutations. Here, we infer the demographic histories and DFEs for amino-acid changing mutations of 27 of the most prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations. We find reductions in genetic variation in North American versus African rural microbiomes. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Together, these findings suggest that gut microbes have distinct evolutionary histories, possibly reflecting their unique roles.

QCBio Special Evening Lecture: Dr. Michael Elowitz, Assistant Adjunct Professor, Biological Chemistry, UCLA
2024-05-30 17:30 - 19:00 | Boyer Hall 159
TITLE: “Designing synthetic circuits for biological understanding and therapeutic applications”

W13: Genetic Analysis (VCF-Plink)
2024-05-21 09:00 - 2024-05-23 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
High-throughput sequencing technologies have allowed researchers to extract DNA at the individual, population, and species levels. In this workshop, students will learn how to analyze and interpret population-level genetic information with PLINK and R. Students will also be exposed to the literature on the different topics, followed by hands-on exercises and paper discussion.

Career Workshop for PhDs and Postdocs
2024-05-20 14:00 - 17:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
Join us for a tailored workshop designed to empower you with the skills and knowledge needed to excel in the competitive landscape of academia, industry, and beyond.
Learn from experienced professionals, gain valuable insights, and expand your network.
Guest Speakers:
• Kathrin Burch, Associate Manager, Statistical Genetics, Regeneron
• Max Shokhirev, Head of Bioinformatics at Tally Health
• Tiffany Hsu, Scientist at Genentech
• Darren Kessner, Bioinformatics Software Engineer & Math and Computer Science Teacher
Register here: https://docs.google.com/forms/d/1ECWkASxZ95SEVKaDXzPCub-WOj5bHqX1mUvsxpHGhNo/edit

Frontiers in Computational Biosciences Seminar Series: Jana Lipkova, PhD, Assistant Professor of Pathology, UC Irvine
2024-05-20 12:00 - 13:00 | Boyer Hall 159
TITLE: “AI-based multimodal data fusion in oncology”
Hosted by William Hsu for Medical Informatics and UCLA JCCC

Frontiers in Computational Biosciences Seminar Series: Ghayda Mirzaa, MD, Associate Professor, Pediatrics and Medical Genetics, Seattle Children's Hospital
2024-05-13 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “The genetics of pediatric surgical epilepsy disorders: successes, challenges and future avenues”
Hosted by Saitta Sulagna for Genetics & Genomics

Frontiers in Computational Biosciences Seminar Series: Angela Brooks, PhD, Professor, Department of Biomolecular Engineering, UC Santa Cruz
2024-05-06 12:00 - 13:00 | Boyer 159
TITLE: TBD
Hosted by Grace Xiao for Bioinformatics

Frontiers in Computational Biosciences Seminar Series: Omolola Ogunyemi, PhD, FACMI, Director, Center for Biomedical Informatics, Professor, Preventive & Social Medicine Charles Drew University
2024-04-29 14:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
TITLE: “AI and the Healthcare Safety Net”
Hosted by William Hsu for Medical Informatics

Webinar: Age - Just a Number?
2024-04-25 17:30 - 18:30 | ZOOM, CA, United States

Frontiers in Computational Biosciences Seminar Series: Mia Levine, PhD, Associate Professor, University of Pennsylvania
2024-04-22 12:00 - 13:00 | Boyer 159
TITLE: “Intra-genomic conflict and the evolution of genome integrity”
Hosted by Kirk Lohmueller for Genetics & Genomics

Frontiers in Computational Biosciences Seminar Series: Chongzhi Zang, PhD, Associate Professor, University of Virginia
2024-04-15 12:00 - 13:00 | Boyer 159
TITLE: “Computational Methods for Trancriptional Regulation”
Hosted by Jingyi Jessica Li for Bioinformatics

Frontiers in Computational Biosciences Seminar Series: Barbara Cheifet, PhD, Editor in Chief, Nature Biotechnology
2024-04-08 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Publishing for Impact”
Hosted by Jingyi Jessica Li for Bioinformatics

Frontiers in Computational Biosciences Seminar Series: Alexis Battle, PhD, Professor, Biomedical Engineering, Computer Science and Genetics Medicine Director, Malone Center for Engineering in Healthcare, Johns Hopkins University
2024-04-01 12:00 - 13:00 | Boyer 159
TITLE: “Multi-omic and temporal data for rare and common genetic variation”

Frontiers in Computational Biosciences Seminar Series: Alkes Price, PhD, Professor, Harvard School of Public Health
2024-03-11 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Functional architectures of complex disease”
Hosted by Noah Zaitlen for Genetics & Genomics

Frontiers in Computational Biosciences Seminar Series: Katherine L. Nathanson, MD, Deputy Director Penn Cancer Center, University of Pennsylvania
2024-03-04 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “The evolving landscape of hereditary breast cancer”
Hosted by Paul Spellman for Genetics & Genomics and UCLA JCCC

W8: Variant Calling with GATK
2024-02-27 09:00 - 2024-02-29 12:00 | 529 Boyer Hall, 611 Charles E Young Dr E,, Los Angeles, CA, 90095, United States
This workshop uses materials developed by the Broad Institute to teach Variant Discovery with GATK. Attendees with no prior experience in variant calling are recommended to review all of the materials below before coming to the workshop. This early preparation will allow a focus on the specific issues of running GATK on the UCLA hoffman2 cluster rather than introducing the GATK variant calling pipeline. There will also be a focus on post variant discovery quality control steps as time allows.

Frontiers in Computational Biosciences Seminar Series: Chongyi Chen, PhD, Stadtman Investigator, NCI
2024-02-26 12:00 - 13:00 | Boyer 159
TITLE: “Quantitative mapping of DNA supercoiling tension throughout the human genome”
Hosted by Yi Yin for Genetics & Genomics

Frontiers in Computational Biosciences Seminar Series: Nancy Zhang, PhD, Ge Li and Ning Zhao Professor, University of Pennsylvania
2024-02-12 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Signal recovery in single cell data integration”
Hosted Jingyi Jessica Li for Bioinformatics

Frontiers in Computational Biosciences Seminar Series: Xuanyao Liu, PhD, Assistant Professor, University of Chicago
2024-02-05 12:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Linking variants to function with powerful multivariate approaches”
Hosted by Brunilda Balliu for Bioinformatics

Frontiers in Computational Biosciences Seminar Series: Heidi Rehm, PhD, Co-Director, Population and Medical Genetics, Broad Institute; Chief Genomics Officer, Mass General Hospital; Professor of Pathology, Harvard Medical School
2024-01-29 00:00 - 13:00 | Boyer 159, 611 Charles E. Young Dr. E., Los Angeles, CA, 90095, United States
TITLE: “Advancing Genomic Medicine through Global Collaboration”
Hosted by Sulagna Saitta for Genetics & Genomics
