Workshop overview

This intensive, interactive workshop explores evolution through the lens of stochastic processes and dynamical systems. Conducted in English the workshop spans 2.5 days with limited number of participants and moves from gene cellular expression dynamics to population genetics and the evolution of complex phenotypes governed by gene regulatory networks. In the afternoon sessions, participants will gain hands-on experience bridging theory and data by developing numerical simulations.

Approximate Key Times (can be updated later on)

• Start: ~14:00 on July 4th (Saturday)
• End: ~18:00 on July 6th (Monday)

Core Curriculum

• Systems Biology: Modeling gene circuits with non-linear ODEs (bistability and limit cycles), the Chemical Master Equation, and Gillespie simulations to construct complex genotype-phenotype maps and fitness landscapes.
• Population Genetics: The Wright-Fisher Model. Diffusion approximations and analytical solutions using the Backward Kolmogorov Equation to determine fixation times and stationary state distributions.
• Hands-on Evolutionary Systems Biology: Investigating selection on networks (robustness, evolvability, and modularity) through active, code-based simulation sessions.

Who Should Attend

This workshop is designed for mathematically inclined university students, postdocs, or researchers (from Physics, Biology, or Mathematics backgrounds) who want to:

• Acquire a solid, quantitative understanding of evolutionary principles, population modeling, and systems biology.
• Master tools like diffusion approximations, Fokker-Planck equations, and stochastic simulations.
• Gain hands-on skills combining classic mathematical theory with modern computational modeling using their preferred programming and prompt/AI languages.

Please Note

• While participation in the main EEBST symposium is not mandatory, it is highly recommended, and priority for the workshop is given to registered symposium individuals.
• A strong motivation to work on mathematical derivations (blackboard lectures) and numerical simulations is essential. Participants should have completed at least university-level coursework in Calculus and Ordinary Differential Equations (ODEs).

Venue, Accommodation, and Costs

• Venue: The workshop will take place at the Yenişehir campus of Mersin University.
• Accommodation: Lodging will be at Mersin University’s Guesthouse, within walking distance of the lecture rooms. Participants are expected to stay in this guesthouse. Exceptions may be made for local participants or in special cases (please clearly state your reasons in the application). The total cost for 2 nights of accommodation is expected to be around 4000 TL including breakfasts (price to be fixed in early June). This rate is based on a 2-person shared room. Currently, we do not have any budget to cover students’ lodging costs. However, depending on availability, costs may be reduced for participants who require support (please describe your situation during the application).
• There is no additional cost for workshop attendance.

How to Apply

Workshop overview

This one-day workshop will provide both theoretical background and hands-on training in evolutionary bioinformatics using the DAMBE (Data Analysis in Molecular Biology and Evolution) software which is widely used in research and teaching in Molecular Biology and Evolution. Participants will gain practical experience in computational approaches commonly applied in molecular evolution, transcriptomics, and sequence analysis.

Topics

The workshop would include the following topics:

• Position weight matrix in Identification and characterization of signal motifs in sequences, quantification of motif signal strength, and detection of differential natural selection shaping the signal motifs and their decoders (Application scenario: What are the most efficient splicing 5′ and 3′ splice sites and branchpoint sites? What is the opposite, and why would nature allow the existence of the opposite?)
• Gibbs sampler in de novo discovery of sequence motifs (Application scenario: Given an intron, what does a branchpoint look like, and where is it? Alternatively, given a set of sequences from ChIP-Seq, what and where is the protein-binding site? How does the protein binding motif and the DNA binding site coevolve?)
• Signal motifs and their decoders in optimization of RNA splicing and translation efficiency (Application scenario: How to help the industry to increase protein production? How to optimize an mRNA vaccine? Different viral proteins are needed in very different amounts to assemble a virion. How do viruses achieve approximate stoichiometric production of proteins?)
• Transcriptomic data analysis: read quality evaluation and quantification of differential gene expression (Application scenario: How to characterize gene expression in multicellular Eukaryotes with numerous paralogous genes in their genomes? Highly expressed genes, such as ribosomal protein genes, need to be spliced and translated efficiently. How does natural selection shape the splicing signals and translation signals for efficiency in highly and lowly expressed genes?)
• Ordination of signal motifs through multivariate statistics and self-organizing map (Signal motifs often cannot be ranked in one dimension from the most efficient to the least efficient.)
• The iterative algorithm for characterizing protein isoelectric point, electrostatic interactions among proteins, and identification of proteins that have undergone post-translational modifications.

Format & Schedule

The workshop will combine theoretical lectures, practical demonstrations, and hands-on computational exercises using DAMBE. The schedule consists of a 3-hour session in the morning and another in the afternoon, followed by an optional free interaction session in the evening where participants can ask questions or seek clarifications.

Participants are encouraged to bring their own laptops for the practical sessions. A Windows computer is ideal, as program installation is a bit more complicated with Mac computers. It would be ideal if participants could install DAMBE (freely available at https://dambe.bio.uottawa.ca/) before coming to the workshop.

Lecturer

Professor Xuhua Xia is an internationally recognized researcher in evolutionary bioinformatics, molecular evolution, and computational biology, and the developer of DAMBE (Data Analysis in Molecular Biology and Evolution). His work focuses on the molecular evolution of genes and their interactions through proteins and RNAs, combining computational approaches with wet-lab collaborations. His research sheds light on the evolution and coevolution of biological systems, cellular interactions and regulation, optimization of biological processes, and applications in animal and human forensics and disease.