Ari Löytynoja, PhD

Senior bioinformatician working on sequence analysis and evolutionary genomics

Experienced in

Algorithmics, software development - creating missing tools for sequence analysis and comparative genomics.

Leading academic research collaborations, managing multi-year scientific projects, writing funding grants, leading a software team.

Managing & processing massive whole-genome sequencing data, leading & performing population genetic and evolutionary genomic analyses.

Authoring top-ranking publications, developing novel visualization methods for data and mechanisms.

Teaching masters-level courses in scientific computing and computational data analysis, developing self-learning material.

Professional Experience

2026 - now University researcher, Department of Computer Science, University of Helsinki
lead a software team developing an application for clinical diagnostics
set development targets, design test protocols, and select test materials
set a publication strategy and work as a lead-author
establish academic collaborations
supervise MSc students, grade theses

2023 - 2025 University lecturer, Department of Organismal and Evolutionary Biology, University of Helsinki
teach masters-level course in population genomic data analysis
develop self-learning material for masters-level course in scientific computing
supervise MSc and PhD students, grade theses
win 300,000€ grant to develop research findings to clinical diagnostics
hire and establish a software team for the development work author top-ranking publication in Current Biology

2011 - 2023 Group leader, Institute of Biotechnology, University of Helsinki
hire and establish a research team to work on evolutionary sequence analysis
redesign and reimplement the phylogeny alignment algorithm with sequence graphs
join genome sequencing projects and implement & lead processing and analyses of massive WGS data
develop masters-level course for population genomic data analysis
supervise MSc and PhD students, grade theses co-organize international research symposia, organize & host seminar series
member in working groups for bioinformatics teaching, graduate-student/postdoc education, masters program development
write funding grants, obtain 650,00€+ of funding
author top-ranking publications in PNAS, Bioinformatics, Genome Research, Molecular Biology and Evolution

2003 - 2011 Post-doc researcher (staff), EMBL-European Bioinformatics Institute, UK
create algorithm for phylogeny-aware alignment of multiple sequence
develop alignment algorithm considering both phylogeny and structural constraints
author top-ranking publications in Science, PNAS, Bioinformatics participate in the ENCODE pilot phase project
host and supervise visiting students
establish & participate in postdoc association work

Education

2003 Ph.D., Bioinformatics, Université Libre de Bruxelles, Belgium
Department of Molecular and Cell Biology
Thesis: Molecular sequence alignment and character homology

1999 M.Sc., Population genetics, University of Oulu, Finland
Department of Biology Thesis: Itämeren lohen (Salmo salar L.) mitokondrion ND1-geenin muuntelu.
(“Variation of the mitochondrial gene ND1 in the Baltic salmon”)

2023 Title of Docent in Bioinformatics, University of Helsinki, Finland

Computing

Linux, bash, awk, git
R - ggplot2, dplyr, Gviz
Nextflow/Seqera, Python, Perl, C++
Conda, Quarto, LaTeX
HPC (SLURM), cloud (AWS), containers (Docker/Apptainer)
Ensembl, NCBI

Research Output

Authored in total 45 peer-reviewed publications (12,130 citations, h-index 28), e.g. in: Science, Nature, PNAS, Current Biology, Bioinformatics, Genome Research
Authored four book chapters on sequence alignment and alignment methods
Publications on alignment programs PRANK and PAGAN cited over 3,000 times

Supervision and Leadership

Head of Research Council of Finland Proof of Concept project (#365249; 300,000€) in 2025-2026
-Supervising software engineer, research assistant; two M.Sc. students
Head of Research Council of Finland project (#322681; 496,000€) in 2019-2023
-Supervised one postdoc, three Ph.D. students, M.Sc. students and research assistants

Teaching Merits

20 ECTS of university pedagogy studies, University of Helsinki
Taught advanced courses on scientific computing and population genomic data analysis
-Scientific Computing (2 ECTS): http://loytynojalab.biocenter.helsinki.fi/teaching/intscicom
-Population Genomics (5 ECTS): http://loytynojalab.biocenter.helsinki.fi/teaching/popgeno

Societal Impact

Popularising my research by preparing news articles and press releases for national and international distribution. Our studies on Saimaa ringed seals received visibility in Finnish media and the study on Greenlandic fjord seals was picked up by the BBC. Participated in PNAS podcast and YLE podcast (in Finnish) on seal studies.
The Finnish Association for Nature Conservation selected our study, eventually leading to the species status of the endangered Saimaa ringed seal, as the environmental act of the year 2025.