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

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 will provide an overview of how deep learning can be used to learn the regulatory code of the genome, discuss specific models and applications, and get hands-on experience implementing them.

• In the first lecture, we will introduce the elements and questions in regulatory genomics, classical methods for analysis of DNA sequences, and deep learning algorithms.
• In the second lecture, we will focus on specific deep learning methods and applications in different genomics problems, including CNNs, transformers and LLMs.
• In the hands-on session, we will train and interpret models to predict regulatory activities and gene expression from DNA sequences. The practical session will use Python.

A laptop with internet access is required for the practical session, and basic familiarity with Python is beneficial. Limited to 30 participants. All materials will be available to the participants before the course.

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

Registration is free but mandatory for organizational purposes. Please register here until April 16, 2023: https://docs.google.com/forms/d/e/1FAIpQLScrXTYYSfv4m6GptMZFOAYH8XtVxU4FzvGJHtHGXkY8-RWGFA/viewform