Molecular biology has taught us a great deal about what is happening inside a cell, that is that pathways can get very complicated and life is not just independent pathways but networks. Fortunately, we can use computational tools to understand dynamics of complex networks. This workshop introduces the basic concepts of modeling cell signaling pathways. […]
Phylogenetics – the reconstruction of the evolutionary history of a the variety of species known to us, is among the most fundamental and traditional tasks in Biology. With the dramatic developments in molecuar biology and the exponential growth in annotated genetic sequences, novel directions and goals have been developed in this seemingly stagnant field. Phylogenetic […]
The workshop will mainly focus on teaching the fundamentals of bacterial genomics and basic bioinformatics analysis. As a sample data Vibrio cholerae genome will be used as the practice dataset, and workshop participants will try to reproduce the expected results. The workshop will start with detailed instructions on how to quality control the raw sequence […]
The workshop introduces Cytoscape (https://cytoscape.org/) – an open source platform for retrieval and visualization of complex biological interactions that are available from public interaction resources: The IMEx Consortium (https://www.imexconsortium.org/), STRING (https://string-db.org/) and BioGIRD (https://thebiogrid.org/). It covers querying for interactions data using built-in search interface, interaction data cleanup and visualization as well as overlying of the […]
Galaxy (https://usegalaxy.org/) is a web-based infrastructure for bioinformatics application. First, this workshop introduces participants to using Galaxy for analysis of Next-Generation Sequencing data. Next, this workshop covers the structure of Galaxy, data format and manipulation, obtaining and sharing data, and building and sharing workflows. We will use the tools installed on the UCLA galaxy to […]
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 […]
The workshop will cover experimental approaches to protein interaction determination; processing and presentation of interaction data available from online resources, and the role of interaction data in the interpretation of large scale datasets. Highly encourage: Students should working knowledge of python scripting.
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 […]
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 […]
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.
