Bioinformatics research group

We develop computational methods for faster and more reliable analysis of genomic sequences. Some examples of such methods are:
* prediction of antibiotic resistance and plasmid content of bacterial isolate from its genomic sequence [1,2];
* detection of microbial pathogens from human cell-free DNA, from wastewater samples and from other relevant metagenomic samples;
* detection of rare variants in personal human genomes [3,4];
* surveillance of food composition and food origin, based on traces of DNA detected from food [5].

Our future plan is to develop a large set of DNA sequence-based predictive models and software for surveillance of bacterial pathogens (virulence, resistance to drugs or cleaning agents), microbiome and food composition.


Oselin K, Kaplinski L, Jääger A, Valter A, Puurand T, et al. (2023). Comparative Genomic Analysis to Distinguish Triple Metachronous Lung Carcinoma from Metastatic Recurrence: Brief Report on First Case Treated with Three Consecutive VATS Lobectomies. Annals of Medical and Clinical Oncology 5 (145)

Pajuste FD, Remm M. (2023). GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads. Scientific Reports, 13 (17765)

Kaplinski L, Möls M, Puurand T, Remm M. (2023). DOCEST—fast and accurate estimator of human NGS sequencing depth and error rate. Bioinformatics Advances, 3 (1)

Kaplinski L, Möls M, Puurand T, Pajuste FD, Remm M. (2021). KATK: Fast genotyping of rare variants directly from unmapped sequencing reads. Human Mutation, 42(6):777-786

Raime K, Krjutškov K and Remm M. (2020). Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin. Front. Plant Sci., 11:646

Kaplinski L, Möls M, Puurand T, Pajuste FD, Remm M (2021). KATK: Fast genotyping of rare variants directly from unmapped sequencing reads. Human Mutation, 42(6):777-786

Puurand T, Kukuškina V, Pajuste FD and Remm M. (2019). AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mobile DNA, 10:31

Roosaare M, Puustusmaa M, Möls M, Vaher M, and Remm M. (2018). PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads. PeerJ, 6: e4588

Aun E, Brauer A, Kisand V, Tenson T and Remm M. (2018). A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria. PLoS Computational Biology, 14(10):e1006434