| Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes JN Alanko, J Vuohtoniemi, T Mäklin, SJ Puglisi Bioinformatics 39 (Supplement_1), i260–i269, 2023 | 44 | 2023 |
| Strong pathogen competition in neonatal gut colonisation T Mäklin, HA Thorpe, AK Pöntinen, RA Gladstone, Y Shao, A McNally, ... Nature Communications 13 (7417), 2022 | 38 | 2022 |
| Bacterial genomic epidemiology with mixed samples T Mäklin, T Kallonen, J Alanko, Ø Samuelsen, K Hegstad, V Mäkinen, ... Microbial Genomics 7 (11), 000691, 2021 | 36* | 2021 |
| High-resolution sweep metagenomics using fast probabilistic inference T Mäklin, T Kallonen, S David, CJ Boinett, B Pascoe, G Méric, ... Wellcome open research, 2021 | 33 | 2021 |
| Genomic and phenotypic characterization of Clostridium botulinum isolates from an infant botulism case suggests adaptation signatures to the gut FP Douillard, Y Derman, C Woudstra, K Selby, T Mäklin, MB Dorner, ... MBio 13 (3), e02384-21, 2022 | 11 | 2022 |
| Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis R Derelle, J von Wachsmann, T Mäklin, J Hellewell, T Russell, A Lalvani, ... Genome research 34 (10), 1661-1673, 2024 | 7 | 2024 |
| Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan T Khawaja, T Mäklin, T Kallonen, RA Gladstone, AK Pöntinen, S Mero, ... Nature Communications 15 (1), 5196, 2024 | 4 | 2024 |
| Closing Clostridium botulinum Group III Genomes Using Long-Read Sequencing C Woudstra, T Mäklin, Y Derman, L Bano, H Skarin, C Mazuet, A Honkela, ... Microbiology resource announcements 10 (22), 10.1128/mra. 01364-20, 2021 | 4 | 2021 |
| Enhanced metagenomics-enabled transmission inference with TRACS G Tonkin-Hill, Y Shao, AE Zarebski, S Mallawaarachchi, O Xie, T Mäklin, ... bioRxiv, 2024.08. 19.608527, 2024 | 2 | 2024 |
| Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli T Mäklin, A Taira, S Arredondo-Alonso, Y Shao, MR Stratton, TD Lawley, ... The Lancet Microbe, 2024 | 1 | 2024 |
| Group 2 and 3 ABC-transporter dependant capsular K-loci contribute significantly to variation in the invasive potential of Escherichia coli RA Gladstone, M Pesonen, AK Pöntinen, T Mäklin, N MacAlasdair, ... medRxiv, 2024.11. 22.24317484, 2024 | 1 | 2024 |
| A Novel Prophage-like Insertion Element within yabG Triggers Early Entry into Sporulation in Clostridium botulinum FP Douillard, IM Portinha, Y Derman, C Woudstra, T Mäklin, MB Dorner, ... Viruses 15 (12), 2431, 2023 | 1 | 2023 |
| Probabilistic Methods for High-Resolution Metagenomics T Mäklin Doctoral dissertation, University of Helsinki, 2022 | 1 | 2022 |
| Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study HA Thorpe, M Pesonen, M Corbella, H Pesonen, S Gaiarsa, CJ Boinett, ... The Lancet Microbe 5 (10), 2024 | | 2024 |
| Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing S Pol, T Kallonen, T Mäklin, P Sar, J Hopkins, S Soeng, T Miliya, CL Ling, ... Mbio 15 (6), e00784-24, 2024 | | 2024 |
| Basic reproduction number for pandemic Escherichia coli clones is comparable to typical pandemic viruses F Ojala, H Pesonen, RA Gladstone, T Mäklin, G Tonkin-Hill, P Marttinen, ... bioRxiv, 2024.05. 08.593267, 2024 | | 2024 |
| A longitudinal genomic and functional analysis of Clostridium botulinum isolated from an infant botulism case FP Douillard, Y Derman, C Woudstra, K Selby, T Mäklin, A Honkela, ... Toxicon 190, S17-S17, 2021 | | 2021 |
| Identifying Bacterial Strains from Sequencing Data T Mäklin, J Corander, A Honkela Data Mining for Systems Biology: Methods and Protocols, 1-7, 2018 | | 2018 |
| Probabilistic quantification of bacterial strain mixtures T Mäklin Master's thesis, University of Helsinki, 2017 | | 2017 |
