OLISSIPO was pleased to host the OLISSIPO Workshop on Decoding the genome with deep learning, held on April 27, 2023 at INESC-ID, Lisbon. The workshop was given by Bernardo Pereira de Almeida (IMP and University of Vienna, iMM alumni).

OLISSIPO Workshop on Decoding the genome with deep learning

April 27, 2023 | 09:15-16:30 (WEST – Lisbon)

Location: INESC-ID (Lisboa, Portugal), Room 9, Floor -1 (ask at the reception)

Abstract: The human genome sequence provides the underlying code for human biology. Understanding the sequence-code of the genome is vital for understanding how genetic variants affect human disease and traits, but it has remained one of the biggest challenges in biology. In an era of exponential growth of genomics and biomedical data, deep learning methods have emerged as powerful tools to aid this goal due to their capacity to identify highly complex patterns in large datasets. Can deep learning models that have revolutionized image recognition and natural language also help us decode the human genome and advance personalized medicine?
In this course, we provided an overview of how deep learning can be used to learn the regulatory code of the genome, discussed specific models and applications, and got hands-on experience implementing them.
• In the first lecture, we introduced the elements and questions in regulatory genomics, classical methods for analysis of DNA sequences, and deep learning algorithms.
• In the second lecture, we focused on specific deep learning methods and applications in different genomics problems, including CNNs, transformers and LLMs.
• In the hands-on session, we trained and interpreted models to predict regulatory activities and gene expression from DNA sequences. The practical session will use Python.

Programme:

9:15 – Welcome and Registration
9:30 – 10:30: Lecture 1 – Introduction to regulatory genomics, classical methods for analysis of DNA sequences, and deep learning
—Coffee-break—
11:00 – 12:00: Lecture 2 – Deep learning methods and applications in genomics
—Lunch—
13:30 – 15:00: Hands-on session 1 – Training CNNs to predict enhancer activities from DNA sequences
—Coffee-break—
15:30 – 16:30: Hands-on session 2 – Using attention and transformers to predict gene expression from sequence
16:30 – Closing