Veli Mäkinen

Professor Veli Mäkinen works in the areas of algorithmic bioinformatics and succinct data structures.

Most recently prof. Mäkinen has focused on extending sequence analysis to different pan-genome representations such as directed acyclic graphs. Frequently used techniques include dynamic programming, reductions, stringology, and data compression.

Professor Veli Mäkinen

I am Professor of Computer Science at the Department of Computer Science of the University of Helsinki and Vice Head of Department. I mostly teach advanced computer science courses on algorithms and on bioinformatics. I am leading a research team on Genome-Scale Algorithmics. The team is part of Algorithmic Bioinformatics group and also contributes to the Foundations of Computational Health (FCHealth) programme of the Helsinki Institute of Information Technology (HIIT).


Recent publications from the university database:

I publish mainly in bioinformatics venues. Some algorithmic results of more general flavor are offered to theoretical computer science venues. Occasionally the tools developed enable new ways of analysis of biological measurement data, and then a molecular biology venue will be primary choice.


My courses typically follow a weekly schedule of lecture, study group, and exercise session. I prefer blackboard demonstration lectures that give extra insights on top of (self-study) lecture material.  Study groups often are about guided online problem solving. Exercises are independent homework and on small courses I use them as mini-exams. I'm happy to supervise Master's theses and discuss PhD study opportunities on the topics of my courses and seminars: algorithms and data structures, algorithmic bioinformatics, data compression, string processing, etc. 


Activities from the university database:

Contact and biography

Veli Mäkinen is Professor of Computer Science at the University of Helsinki and Vice Head of Department. He heads the Genome-scale algorithmics team at the Algorithmic Bioinformatics research group. He has supervised five PhD theses and over forty Master's theses. He is currently supervising three PhD students. 

Veli Mäkinen started his career in string algorithms and compressed data structures. As of 2022, he has  116 peer-reviewed publications on these and related topics, with the focus being shifted towards algorithmic bioinformatics, where different high-throughput sequencing data analysis scenarios make near-linear time algorithms that work in small space an appealing target of study. Inspired by this new angle to bioinformatics algorithms, Veli Mäkinen co-authored a textbook on Genome-scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing, published by Cambridge University Press, 2015.

The new textbook works as the main material for algorithmic bioinformatics courses taught frequently by Veli Mäkinen. He also teaches the general algorithms courses Design and Analysis of Algorithms, String Processing Algorithms, Data Compression Techniques, and projects and seminars related to these topics.

Some current research interests include studying algorithms and computational complexity when moving from sequences to variation graphs in (pan-)genomics, and studying applications of different index structures related to the variants of the Burrows-Wheeler transform.

Besides research and teaching, Veli Mäkinen has an active role in the research community. Some recent activities include co-chairing IWOCA 2016 and guest editing a special issue for Theory of Computing Systems, program committee memberships (CPM 2019, LATIN 2020, WABI 2021, RECOMB 2022), and keynote/invited talks e.g. at the ECCB 2016 workshop on Computational Pan-Genomics and SPIRE 2019.