Transcriptomics Bioinformatics for Precision Medicine
BIOL-X404.11
Unlock the power of the post-genomic era with this advanced course at UC San Diego. Building upon the foundations of Processing Actionable Data in Genomics, this course provides students with the technical expertise to navigate the complexities of transcriptomics, a driving force in modern precision medicine.
Since the completion of the human genome sequence, the scientific community has shifted toward understanding genomic variation and annotating protein-coding gene sequences. Because the annotation of genes relies heavily on transcript identification, mastering transcriptomics is essential for anyone looking to contribute to the fields of genomics and personalized healthcare.
Students will gain hands-on experience with industry-standard bioinformatics pipelines, learning to process both short-read datasets (Illumina) and long-read datasets (PacBio and Oxford Nanopore Technologies) to keep pace with current technological trends.
Learning Outcomes By the end of this course, students will be able to:
- Implement up-to-date bioinformatics pipelines to process complex transcriptomics data.
- Distinguish between and process short-read (Illumina) and long-read (PacBio/Oxford Nanopore) datasets.
- Execute splice-aware alignment to accurately map RNA-seq data.
- Perform transcript assembly and quantification.
- Conduct differential transcript level comparisons to identify significant biological variations.
Course Information
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This course is entirely web-based and to be completed asynchronously between the published course start and end dates. Synchronous attendance is NOT required.
You will have access to your online course on the published start date OR 1 business day after your enrollment is confirmed if you enroll on or after the published start date.
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All course materials are included unless otherwise stated.
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Instructor:
Genaro Pimienta
After obtaining a PhD degree in structural biology (EMBL-Heidelberg, Germany), Genaro pursued post-doctoral training in proteomics and transcriptomics (Hopkins University and Yale University). Heralding the value of computational biology, Dr. Pimienta has, for the past 20 years, explored various ways of combining proteomics, transcriptomics and genomics data, to answer biomedical questions.
In his spare time, Genaro finds piece spending time with his family, gardening, or reading and writing fiction. A most recent joy of his, is to (pen in hand) spot the predictions of a world welded by artificial intelligence technologies, made by science fiction writers of last century, like Isaac Asimov, Phillip K. Dick, and William Gibson.
