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Education

 
University of Helsinki, Helsinki, Finland
PhD, Computer science, 2022
Thesis: Probabilistic methods for high-resolution metagenomics

University of Helsinki, Helsinki, Finland
MSc, Statistical machine learning, 2017
Major studies in statistics

University of Helsinki, Helsinki, Finland
BSc, Statistics, 2016
Minor studies in mathematics and computer science


Research experience

 
University of Oslo, Oslo, Norway
Researcher, 2025–ongoing
I study the ecology, evolution, and epidemiology of cancer-associated bacteria by developing and applying methods for longitudinal metagenomics data.

University of Helsinki, Helsinki, Finland
Postdoctoral researcher, 2023–2024
I worked on developing and applying statistical methods for studying the ecology and epidemiology of E. coli in the human gut microbiome.

EMBL-EBI, Hinxton, Cambridgeshire, UK
Visiting postdoctoral fellow, Feb 2023–July 2023
I visited the Pathogen Informatics and Modelling group led by Dr John Lees on a Theory@EMBL grant.

University of Helsinki, Helsinki, Finland
Doctoral researcher, 2018–2022
My PhD developed and implemented statistical models for strain-level metagenomics.

Helsinki Institute for Information Technology, Helsinki, Finland
Research assistant, 2016–2017
I designed and implemented a statistical model for identifying bacterial strains in DNA sequencing data.


Other employment

 
Heldata oy, Helsinki, Finland
Part-time entrepreneur, 2018–2022
Planned, organised, and hosted a 250-person data science networking and recruiting event in 2019 and 2021 together with others.

Stokastiko oy, Helsinki, Finland
Independent consultant, 2016–2018
I designed and taught a 3-day statistics introductory course for the Finnish Tax Administration and consulted small organizations.


Publications

 
Preprints

Sequence alignment with k-bounded matching statistics
Mäklin, Alanko, Biagi, and Puglisi
preprint (2025), available at bioRxiv: 10.1101/2025.05.19.654936
software in GitHub: kbo

Group 2 and 3 ABC-transporter dependant capsular K-loci contribute significantly to variation in the invasive potential of Escherichia coli
Gladstone, Pesonen, Pöntinen, Mäklin, MacAlasdair, Thorpe, Shao, Mallawaarachchi, Arredondo-Alonso, Parcell, Turnbull, Tonkin-Hill, Johnsen, Samuelsen, Thomson, Lawley, and Corander
preprint (2024), available at medRxiv: 10.1101/2024.11.22.24317484

Enhanced metagenomics-enabled transmission inference with TRACS
Tonkin-Hill, Shao, Zarebski, Mallawaarachchi, Xie, Mäklin, Thorpe, Davies, Bentley, Lawley, and Corander
preprint (2024), available at bioRxiv: 10.1101/2024.08.19.608527
software in GitHub: TRACS

Basic reproduction number for pandemic Escherichia coli clones is comparable to typical pandemic viruses
Ojala, Pesonen, Gladstone, Mäklin, Tonkin-Hill, Marttinen, and Corander
preprint (2024), available at bioRxiv: 10.1101/2024.05.08.593267


Peer-reviewed journal articles

Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli
Mäklin, Taira, Arredondo-Alonso, Shao, Stratton, Lawley, Aaltonen, and Corander
The Lancet Microbe (2025), doi: 10.1016/j.lanmic.2024.101015

Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
Derelle, von Wachsmann, Mäklin, Hellewell, Russell, Lalvani, Chindelevitch, Croucher, Harris, and Lees
Genome Research (2024), doi: 10.1101/gr.279449.124

Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in Spring 2020: a prospective cohort study
Thorpe, Pesonen, Corbella, Pesonen, Gaiarsa, Boinett, Tonkin-Hill, Mäklin, Pöntinen, MacAlasdair, Gladstone, Arredondo-Alonso, Kallonen, Jamrozy, Lo, Chaguza, Blackwell, Honkela, Schürch, Willems, Merla, Petazzoni, Feil, Cambieri, Thomson, Bentley, Sassera, and Corander
The Lancet Microbe (2024), doi: 10.1016/S2666-5247(24)00113-7

Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan
Khawaja°, Mäklin°, Kallonen°, Gladstone, Pöntinen, Mero, Thorpe, Samuelsen, Parkhill, Izhar, Akhtar, Corander, and Kantele
° joint first authors
Nature Communications (2024), doi: 10.1038/s41467-024-49591-5

Exploring the paediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing
Sreymom, Kallonen, Mäklin, Sar, Hopkins, Soeng, Miliya, Ling, Bentley, Corander, and Turner
mBio (2024), doi: 10.1128/mbio.00784-24

A novel prophage-like insertion element within yabG triggers early entry into sporulation in Clostridium botulinum
Douillard, Martins Portinha, Derman, Woudstra, Mäklin, Dorner, Korkeala, Henriques, and Lindström
Viruses (2023), doi: 10.3390/v15122431

Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes
Alanko, Vuohtoniemi, Mäklin, and Puglisi
Bioinformatics (2023), doi: 10.1093/bioinformatics/btad233
software in GitHub: Themisto

Strong pathogen competition in neonatal gut colonisation
Mäklin, Thorpe, Pöntinen, Gladstone, Shao, Pesonen, McNally, Johnsen, Samuelsen, Lawley, Honkela, and Corander
Nature communications (2022), doi: 10.1038/s41467-022-35178-5

Genomic and phenotypic characterization of Clostridium botulinum isolates from an infant botulism case suggests adaptation signatures to the gut
Douillard, Derman, Woudstra, Selby, Mäklin, Dorner, Saxén, Dorner, Korkeala, and Lindström
mBio (2022), doi: 10.1128/mbio.02384-21

Bacterial genomic epidemiology with mixed samples
Mäklin, Kallonen, Alanko, Samuelsen, Hegstad, Mäkinen, Corander, Heinz, and Honkela
Microbial genomics (2021), doi: 10.1099/mgen.0.000691

High-resolution sweep metagenomics using ultrafast read mapping and inference
Mäklin, Kallonen, David, Boinett, Pascoe, Méric, Aanensen, Feil, Baker, Parkhill, Sheppard, Corander, and Honkela
Wellcome open research (2021), doi: 10.12688/wellcomeopenres.15639.2
software in GitHub: mSWEEP

Closing Clostridium botulinum Group III genomes using long-read sequencing
Woudstra, Mäklin, Derman, Bano, Skarin, Mazuet, Honkela, and Lindström
Microbiology resource announcements (2021), doi: 10.1128/MRA.01364-20


Grants

 
Theory@EMBL visitor fellowship
For visit costs, approx. £5 000, 2023

DONASCI thesis finalization grant
Covered six months salary, approx. €20 000, 2021


Research visits

 
Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
Visitor, May 2024

European Bioinformatics Institute, Hinxton, Cambridge, UK
Visiting postdoctoral fellow, Feb 2023–July 2023


External affiliations

 
Wellcome Sanger Institute, Hinxton, Cambridge, UK
Visiting worker, Pathogens and microbes programme, 2022-2025

Positions of trust

 
University of Helsinki, Helsinki, Finland
Union representative (shop steward), 2023–2024

Volunteer experience

 
Finnish union of university researchers and teachers
Board member, 2024 ∘ Deputy board member, 2023 and 2025

Helsinki university researchers and teachers association
Vice chair, 2023–2024 ∘ Board member, 2022–2025 ∘ Deputy board member 2020–2021

Finnish statistical society
Secretary, 2017–2022 ∘ Deputy board member 2022–2023


Service

 
Boards and committees

Doctoral school in natural sciences, University of Helsinki
Board member, 2020–2021

Doctoral programme in computer science, University of Helsinki
Board member, 2020–2021

Peer review

2025 Microbial genomics, Scientific reports
2024 ECML PKDD, Journal of open source software, Microbiome
2023 Genome biology, Nature communications, Microbiome, Scientific reports
2022 BMC microbiology
2021 International conference on machine learning (ICML)
2019 International conference on machine learning (ICML)


Research software

 
kbo
With Jarno N Alanko & others
Sequence-to-sequence aligner and variant caller, tmaklin/kbo

mGEMS
Main contributor
Taxonomic binner with lineage-level resolution, PROBIC/mGEMS

mSWEEP
Main contributor
Taxonomic profiler with lineage-level resolution, PROBIC/mSWEEP

Themisto
With Jarno N Alanko & others
Pseudoaligner and k-mer index for short-read sequencing data, algbio/Themisto

SKA2
With John A Lees & others
Split k-mer analysis of closely related genomic sequences, bacpop/ska.rust

cpprate
Main contributor
Variable selection in Bayesian regression models with relative centrality, tmaklin/cpprate


Media coverage

 
Outlets with national reach

Jopa puolet suolistosyövistä johtuu bakteeritartunnasta – tuore tutkimus antaa toivoa myös rokotteesta syöpään
Yle, Finland, 5 December 2024
https://yle.fi/a/74-20129530

Vaccine targeting common gut bacteria E. coli could help prevent cancer, scientists suggest
The Independent, UK, 4 December 2024
https://www.independent.co.uk/news/health/cancer-vaccine-e-coli-gut-health-b2658131.html

Sairaalabakteeri ei tartu terveisiin vastasyntyneisiin, kertoo tutkimus
Helsingin Sanomat, Finland, 8 February 2023
https://www.hs.fi/helsinki/art-2000009380665.html


Presentations and conference activity

 
Session chair

Probabilistic modelling in microbial ecology workshop
Kellogg College, University of Oxford, Oxford, UK, March 2023

Invited talks

Computational methods in AMR research
University of Turku, Turku, Finland, October 2023

Lawley group meeting
Wellcome Sanger Institute, Hinxton, Cambridge, UK, June 2023

Theory@EMBL seminar
European Molecular Biology Laboratory EMBL, Hinxton, Cambridge, UK, June 2023

Heinz group meeting
Liverpool school of tropical medicine, Liverpool, UK, February 2023

Lahti group meeting
University of Turku, Turku, Finland, January 2023

AMR-bridge annual meeting
AMR-bridge consortium, Tromsø, Norway, June 2022

Thomson group meeting
Wellcome Sanger Institute, Hinxton, Cambridge, UK, June 2020

CompLifeSci 4th annual meeting
Åbo Akademi, Turku, Finland, November 2019

Contributed talks

SMBE Satellite workshop on pathogen pangenome evolution between and within their hosts
Tokyo, Japan, November 2024

Microbial (gen)omics meeting
Wellcome Sanger Institute, Hinxton, Cambridge, UK, July 2023

EBI research retreat
European Bioinformatics Institute, Hinxton, Cambridge, UK, July 2023

ISMB/ECCB 2019
Basel, Switzerland, July 2019

Bioinformatics research and education workshop
Max Planck Institute for Molecular Genetics, Berlin, Germany, May 2019

Mathematical and statistical aspects of molecular biology workshop
European Bioinformatics Institute, Hinxton, Cambridge, UK, April 2019

Probabilistic modelling in genomics
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, US, November 2018

Regional workshop of European young researchers in Statistics
Henri Poincaré Institute, Paris, France, November 2018

Mathematical and statistical aspects of molecular biology workshop
University of St Andrews, St Andrews, Scotland, UK, March 2018


Tommi Mäklin –