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Mathematical and Computational Biology In Drug Discovery

University of Basel/ Spring Semester 2021/ Fridays 12:15-14:00

Welcome to the web page for Mathematical and Computational Biology in Drug Discovery, the course series running at the Department of Mathematics and Computer Science, University of Basel in the spring semester 2021.

The course is open to all students who wish to learn about principles and techniques of mathematical and computational biology as well as their applications in drug discovery.

Table of content

Preparation

To prepare for the course, please (1) check that you have acquired required prior knowledge, (2) make sure that you can commit enough time to the course, (3) be aware that the lecture will take place virtually on Zoom, and (4) fill the pre-course survey.

You should foremost be familiar with the content covered by the course series Introduction to Applied Mathematics and Informatics In Drug Discovery that run in fall semesters.

The MCBDD course on average requires about 4-6 hours’ time each week for reading assignments or programming tasks.

Due to the coronavirus pandemic, the MCBDD course in 2021 will take place online with Zoom. The meeting link is shared with registered participants via Email.

Finally, to make the course useful and valuable for you, I invite you to fill the pre-course survey. Your opinions help to shape the course.

Logistics

Time

Lectures take place on Fridays between 12:15 and 14:00 on Zoom. See Syllabus for the topics we plan to cover.

Course material and licensing

Course material, including lecture notes, slides, and reading material, is shared on the course’s web site, https://www.MCBDD.ch, under the Creative Commons Attribution-ShareAlike 4.0 Interactional License unless otherwise specified.

All Zoom sessions are recorded and distributed among attendees.

Assessment

The final note is given by offline activities (50%) and project work (50%).

For end-term project work, participants will form teams of two, and work on either option of the project work:

Once the project report is submitted, it will peer-reviewed by another group, which give comments and suggestions.

Timelines:

Notes for the course are given when both project report and peer review are submitted.

Syllabus

Module Zero: Introduction

Module I is an introduction to mathematical and computational biology in drug discovery on 05.03.2021.

Module I: What are drug targets and where to find them?

This module consists of two lectures: (1) what makes a good drug target (12.03.2021), and (2) how to identify, assess, and validate drug targets? (19.03.2021).

Prior to attending the courses, you can refresh your knowledge in the central dogma of molecular biology and in the human genome by watching the animation film From DNA to protein - 3D by yourgenome, and the film mRNA processing and the spliceosome by WEHI that combines an artist’s impression and simulation.

Module II: What can we do if there are no good targets?

Module II discusses about alternatives to target-based drug discovery, in particular phenotypic drug discovery. It includes two lectures: (1) phenotypic screening with chemogenomic libraries (26.03.2021), and (2) molecular phenotypic screening based on gene expression (09.04.2021). We will have no lecture on 02.04.2021, the Good Friday.

Module III: What kind of drug should we develop?

Module III considers modality selection from a computational point of view. It includes two lectures: (1) novel small molecules and antisense oligonucleotides (16.04.2021), and (2) antibodies, multi-target drugs, and gene- and cell-therapies (23.04.2021).

Module IV: What efficacy and safety profiles can we expect?

Module IV focuses on MoA inference for safety and efficacy profiles of drug candidates. We will mainly computational analysis and impact of single-cell omics data (30.04.2021), and explore the potential of proteomics to infer mode of action (21.05.2021).

The offline activities of Module IV is to do single-cell RNA-seq analysis yourself with either Python or R. This activity is optional: it does not count to the final grade. I recommend you doing it because you can get first-hand experience analysing high-dimensional, sparse, and noisy biological data. See slides for links to tutorials and courses.

Module V: For which patients will the drug work and how does it work, really?

We consider the problem of biomarker identification and causal inference in Module V. We will learn about how mathematical and computational biology contributes to biomarker identification (28.05.2021), and consider how to model disease progression and drug’s action using integrated modelling with knowledge, data, and software (04.06.2021).

Topics that we shall discuss

We mainly discuss following topics from biology

We mainly discuss applications of following mathematical and computational topics:

Contact

In case you have further questions, comments, and suggestions about the course, please contact the lecturer, Jitao David Zhang, at jitao-david.zhang@unibas.ch.