Publications by topic
Template switch mutations and RNA evolution
Mönttinen, Frilander, Löytynoja 2023. Generation of de novo miRNAs from template switching during DNA replication. Proc. Natl. Acad. Sci. U. S. A. 120(49):e2310752120 (DOI)
Löytynoja 2022. Thousands of human mutation clusters are explained by short-range template switching. Genome Res. 32(8):1437–1447 (DOI)
Mönttinen, Löytynoja 2022. Template switching in DNA replication can create and maintain RNA hairpins. Proc. Natl. Acad. Sci. U. S. A. 119(4):e2107005119 (DOI)
Löytynoja, Goldman 2017. Short template switch events explain mutation clusters in the human genome. Genome Res. 27(6):1039–1049 (DOI)
Pinniped population genetics and speciation
Löytynoja et al. 2025. Deep origins, distinct adaptations, and species-level status indicated for a glacial relict seal. Proc. Natl. Acad. Sci. U. S. A. 122(25):e2503368122 (DOI)
Tange Olsen et al. 2025. Complex origins and history of the relict Fennoscandian ringed seals. Ecol. Evol. 15(3):e71067 (DOI)
Olkkonen, Löytynoja 2023. Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data. STAR Protoc. 4(4):102567 (DOI)
Rosing-Asvid et al. 2023. An evolutionarily distinct ringed seal in the Ilulissat Icefjord. Mol. Ecol. 32(22):5932–5943 (DOI)
Löytynoja et al. 2023. Fragmented habitat compensates for the adverse effects of genetic bottleneck. Curr. Biol. 33(6):1009–1018.e7 (DOI)
Savriama et al. 2018. Bracketing phenogenotypic limits of mammalian hybridization. Royal Soc. Open Sci. 5(11):180903 (DOI)
Stickleback population genetics and evolutionary mechanisms
Chen et al. 2025. Dynamics of deleterious mutations and purifying selection in small population isolates. Mol. Biol. Evol. 42(7):msaf110 (DOI)
Feng, Löytynoja, Merilä 2025. Estimating recent and historical effective population size of marine and freshwater sticklebacks. Mol. Ecol.:e17825 (DOI)
Yi et al. 2024. Sex chromosome turnover in hybridizing stickleback lineages. Evol. Lett. 8(5):658–668 (DOI)
Wang et al. 2024. Improved assembly of the Pungitius pungitius reference genome. G3 (Bethesda) 14(8) (DOI)
Feng, Merilä, Löytynoja 2024. Secondary contact, introgressive hybridization, and genome stabilization in sticklebacks. Mol. Biol. Evol. 41(2) (DOI)
Kivikoski et al. 2023. Repeatability of crossover rate in wild sticklebacks. Biol. J. Linn. Soc. Lond. 140(1):74–84 (DOI)
Feng, Merilä, Löytynoja 2022. Complex population history affects admixture analyses in nine-spined sticklebacks. Mol. Ecol. 31(20):5386–5401 (DOI)
Kivikoski et al. 2021. Automated improvement of stickleback reference genome assemblies with Lep-Anchor software. Mol. Ecol. Resour. 21(6):2166–2176 (DOI)
Kemppainen et al. 2021. Genetic population structure constrains local adaptation in sticklebacks. Mol. Ecol. 30(9):1946–1961 (DOI)
Li et al. 2019. Effects of marker type and filtering criteria on QST-FST comparisons. R Soc Open Sci 6(11):190666 (DOI)
Varadharajan et al. 2019. A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biol. Evol. 11(11):3291–3308 (DOI)
Software and analysis methods
Veidenberg, Löytynoja 2021. Evolutionary Sequence Analysis and Visualization with Wasabi. In Multiple Sequence Alignment: Methods and Protocols (Methods in Molecular Biology, vol. 2231), pp. 225–240. Springer (DOI)
Löytynoja 2021. Phylogeny-Aware Alignment with PRANK and PAGAN. In Multiple Sequence Alignment: Methods and Protocols (Methods in Molecular Biology, vol. 2231), pp. 17–37. Springer (DOI)
Veidenberg, Medlar, Löytynoja 2016. Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization. Mol. Biol. Evol. 33(4):1126–1130 (DOI)
Tan et al. 2015. Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proc. Natl. Acad. Sci. U. S. A. 112(2):E99–100 (DOI)
Medlar, Aivelo, Löytynoja 2014. Séance: reference-based phylogenetic analysis for 18S rRNA studies. BMC Evol. Biol. 14(1):235 (DOI)
Löytynoja 2014. Phylogeny-aware alignment with PRANK. In Multiple Sequence Alignment Methods (Methods in Molecular Biology, vol. 1079), pp. 155–170. Springer (DOI)
Löytynoja 2012. Alignment methods: strategies, challenges, benchmarking, and comparative overview. In Evolutionary Genomics: Statistical and Computational Methods, volume 1 (Methods in Molecular Biology, vol. 855), pp. 203–235. Springer (DOI)
Löytynoja, Vilella, Goldman 2012. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28(13):1684–1691 (DOI)
Löytynoja, Goldman 2010. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11:579 (DOI)
Löytynoja, Goldman 2009. Evolution. Uniting alignments and trees. Science 324(5934):1528–1529 (DOI)
Löytynoja, Goldman 2008. A model of evolution and structure for multiple sequence alignment. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363(1512):3913–3919 (DOI)
Löytynoja, Goldman 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320(5883):1632–1635 (DOI)
Kankainen, Löytynoja 2007. MATLIGN: a motif clustering, comparison and matching tool. BMC Bioinformatics 8:189 (DOI)
Löytynoja, Goldman 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl. Acad. Sci. U. S. A. 102(30):10557–10562 (DOI)
Löytynoja, Milinkovitch 2003. A hidden Markov model for progressive multiple alignment. Bioinformatics 19(12):1505–1513 (DOI)
Löytynoja, Milinkovitch 2001. SOAP, cleaning multiple alignments from unstable blocks. Bioinformatics 17(6):573–574 (DOI)
Genomics and applied bioinformatic analyses
Wang et al. 2020. An inducible genome editing system for plants. Nat Plants 6(7):766–772 (DOI)
Aivelo et al. 2018. Metabarcoding Gastrointestinal Nematodes in Sympatric Endemic and Nonendemic Species in Ranomafana National Park, Madagascar. Int. J. Primatol. 39(1):49–64 (DOI)
Aivelo et al. 2015. Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus). Parasitology 142(8):1095–1107 (DOI)
Buchmann, Löytynoja, Wicker 2014. Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts. Mob. DNA 5:24 (DOI)
Luo, Löytynoja, Moran 2012. Genome content of uncultivated marine Roseobacters in the surface ocean. Environ. Microbiol. 14(1):41–51 (DOI)
Consortium et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799–816 (DOI)
Margulies et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17(6):760–774 (DOI)
All peer-reviewed publications
Chen et al. 2025. Dynamics of deleterious mutations and purifying selection in small population isolates. Mol. Biol. Evol. 42(7):msaf110 (DOI)
Löytynoja et al. 2025. Deep origins, distinct adaptations, and species-level status indicated for a glacial relict seal. Proc. Natl. Acad. Sci. U. S. A. 122(25):e2503368122 (DOI)
Feng, Löytynoja, Merilä 2025. Estimating recent and historical effective population size of marine and freshwater sticklebacks. Mol. Ecol.:e17825 (DOI)
Tange Olsen et al. 2025. Complex origins and history of the relict Fennoscandian ringed seals. Ecol. Evol. 15(3):e71067 (DOI)
Yi et al. 2024. Sex chromosome turnover in hybridizing stickleback lineages. Evol. Lett. 8(5):658–668 (DOI)
Wang et al. 2024. Improved assembly of the Pungitius pungitius reference genome. G3 (Bethesda) 14(8) (DOI)
Feng, Merilä, Löytynoja 2024. Secondary contact, introgressive hybridization, and genome stabilization in sticklebacks. Mol. Biol. Evol. 41(2) (DOI)
Olkkonen, Löytynoja 2023. Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data. STAR Protoc. 4(4):102567 (DOI)
Mönttinen, Frilander, Löytynoja 2023. Generation of de novo miRNAs from template switching during DNA replication. Proc. Natl. Acad. Sci. U. S. A. 120(49):e2310752120 (DOI)
Rosing-Asvid et al. 2023. An evolutionarily distinct ringed seal in the Ilulissat Icefjord. Mol. Ecol. 32(22):5932–5943 (DOI)
Kivikoski et al. 2023. Repeatability of crossover rate in wild sticklebacks. Biol. J. Linn. Soc. Lond. 140(1):74–84 (DOI)
Löytynoja et al. 2023. Fragmented habitat compensates for the adverse effects of genetic bottleneck. Curr. Biol. 33(6):1009–1018.e7 (DOI)
Feng, Merilä, Löytynoja 2022. Complex population history affects admixture analyses in nine-spined sticklebacks. Mol. Ecol. 31(20):5386–5401 (DOI)
Löytynoja 2022. Thousands of human mutation clusters are explained by short-range template switching. Genome Res. 32(8):1437–1447 (DOI)
Mönttinen, Löytynoja 2022. Template switching in DNA replication can create and maintain RNA hairpins. Proc. Natl. Acad. Sci. U. S. A. 119(4):e2107005119 (DOI)
Kivikoski et al. 2021. Automated improvement of stickleback reference genome assemblies with Lep-Anchor software. Mol. Ecol. Resour. 21(6):2166–2176 (DOI)
Kemppainen et al. 2021. Genetic population structure constrains local adaptation in sticklebacks. Mol. Ecol. 30(9):1946–1961 (DOI)
Wang et al. 2020. An inducible genome editing system for plants. Nat Plants 6(7):766–772 (DOI)
Li et al. 2019. Effects of marker type and filtering criteria on QST-FST comparisons. R Soc Open Sci 6(11):190666 (DOI)
Varadharajan et al. 2019. A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biol. Evol. 11(11):3291–3308 (DOI)
Vaattovaara et al. 2019. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Commun. Biol. 2(1):56 (DOI)
Savriama et al. 2018. Bracketing phenogenotypic limits of mammalian hybridization. Royal Soc. Open Sci. 5(11):180903 (DOI)
Aivelo et al. 2018. Metabarcoding Gastrointestinal Nematodes in Sympatric Endemic and Nonendemic Species in Ranomafana National Park, Madagascar. Int. J. Primatol. 39(1):49–64 (DOI)
Löytynoja, Goldman 2017. Short template switch events explain mutation clusters in the human genome. Genome Res. 27(6):1039–1049 (DOI)
Veidenberg, Medlar, Löytynoja 2016. Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization. Mol. Biol. Evol. 33(4):1126–1130 (DOI)
Kiiski et al. 2016. A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array. Eur. J. Hum. Genet. 24(4):574–580 (DOI)
Aivelo et al. 2015. Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus). Parasitology 142(8):1095–1107 (DOI)
Tan et al. 2015. Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proc. Natl. Acad. Sci. U. S. A. 112(2):E99–100 (DOI)
Medlar, Aivelo, Löytynoja 2014. Séance: reference-based phylogenetic analysis for 18S rRNA studies. BMC Evol. Biol. 14(1):235 (DOI)
Buchmann, Löytynoja, Wicker 2014. Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts. Mob. DNA 5:24 (DOI)
Künnapuu et al. 2014. Cleavage of the Drosophila screw prodomain is critical for a dynamic BMP morphogen gradient in embryogenesis. Dev. Biol. 389(2):149–159 (DOI)
Luo, Löytynoja, Moran 2012. Genome content of uncultivated marine Roseobacters in the surface ocean. Environ. Microbiol. 14(1):41–51 (DOI)
Löytynoja, Vilella, Goldman 2012. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28(13):1684–1691 (DOI)
Löytynoja, Goldman 2010. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11:579 (DOI)
Tress et al. 2008. Determination and validation of principal gene products. Bioinformatics 24(1):11–17 (DOI)
Löytynoja, Goldman 2008. A model of evolution and structure for multiple sequence alignment. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363(1512):3913–3919 (DOI)
Löytynoja, Goldman 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320(5883):1632–1635 (DOI)
Consortium et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799–816 (DOI)
Margulies et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17(6):760–774 (DOI)
Kankainen, Löytynoja 2007. MATLIGN: a motif clustering, comparison and matching tool. BMC Bioinformatics 8:189 (DOI)
Löytynoja, Goldman 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl. Acad. Sci. U. S. A. 102(30):10557–10562 (DOI)
Löytynoja, Milinkovitch 2003. A hidden Markov model for progressive multiple alignment. Bioinformatics 19(12):1505–1513 (DOI)
Löytynoja, Milinkovitch 2001. Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: the Plantae/Fungi/Metazoa trichotomy revisited. Proc. Natl. Acad. Sci. U. S. A. 98(18):10202–10207 (DOI)
Löytynoja, Milinkovitch 2001. SOAP, cleaning multiple alignments from unstable blocks. Bioinformatics 17(6):573–574 (DOI)
Nilsson et al. 2001. Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area. Mol. Ecol. 10(1):89–102 (DOI)
Book chapters and perpectives
Veidenberg, Löytynoja 2021. Evolutionary Sequence Analysis and Visualization with Wasabi. In Multiple Sequence Alignment: Methods and Protocols (Methods in Molecular Biology, vol. 2231), pp. 225–240. Springer (DOI)
Löytynoja 2021. Phylogeny-Aware Alignment with PRANK and PAGAN. In Multiple Sequence Alignment: Methods and Protocols (Methods in Molecular Biology, vol. 2231), pp. 17–37. Springer (DOI)
Löytynoja 2014. Phylogeny-aware alignment with PRANK. In Multiple Sequence Alignment Methods (Methods in Molecular Biology, vol. 1079), pp. 155–170. Springer (DOI)
Löytynoja 2012. Alignment methods: strategies, challenges, benchmarking, and comparative overview. In Evolutionary Genomics: Statistical and Computational Methods, volume 1 (Methods in Molecular Biology, vol. 855), pp. 203–235. Springer (DOI)
Löytynoja, Goldman 2009. Evolution. Uniting alignments and trees. Science 324(5934):1528–1529 (DOI)