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Ari Löytynoja, Ph.D. - Publications

Affiliations: 
University of Helsinki, Helsingfors, Finland 
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Olkkonen E, Löytynoja A. Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data. Star Protocols. 4: 102567. PMID 37740912 DOI: 10.1016/j.xpro.2023.102567  0.314
2022 Löytynoja A. Thousands of human mutation clusters are explained by short-range template switching. Genome Research. PMID 35760560 DOI: 10.1101/gr.276478.121  0.311
2021 Kivikoski M, Rastas P, Löytynoja A, Merilä J. Automated improvement of stickleback reference genome assemblies with Lep-Anchor software. Molecular Ecology Resources. PMID 33955177 DOI: 10.1111/1755-0998.13404  0.329
2021 Veidenberg A, Löytynoja A. Evolutionary Sequence Analysis and Visualization with Wasabi. Methods in Molecular Biology (Clifton, N.J.). 2231: 225-240. PMID 33289896 DOI: 10.1007/978-1-0716-1036-7_14  0.764
2021 Löytynoja A. Phylogeny-Aware Alignment with PRANK and PAGAN. Methods in Molecular Biology (Clifton, N.J.). 2231: 17-37. PMID 33289884 DOI: 10.1007/978-1-0716-1036-7_2  0.389
2020 Wang X, Ye L, Lyu M, Ursache R, Löytynoja A, Mähönen AP. An inducible genome editing system for plants. Nature Plants. PMID 32601420 DOI: 10.1038/S41477-020-0695-2  0.374
2019 Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J. A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome. Genome Biology and Evolution. PMID 31687752 DOI: 10.1093/Gbe/Evz240  0.484
2019 Vaattovaara A, Brandt B, Rajaraman S, Safronov O, Veidenberg A, Luklová M, Kangasjärvi J, Löytynoja A, Hothorn M, Salojärvi J, Wrzaczek M. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Communications Biology. 2: 56. PMID 30775457 DOI: 10.1038/s42003-019-0306-9  0.759
2018 Aivelo T, Medlar A, Löytynoja A, Laakkonen J, Jernvall J. Metabarcoding Gastrointestinal Nematodes in Sympatric Endemic and Nonendemic Species in Ranomafana National Park, Madagascar International Journal of Primatology. 39: 49-64. DOI: 10.1007/s10764-017-0010-x  0.66
2017 Löytynoja A, Goldman N. Short template switch events explain mutation clusters in the human genome. Genome Research. PMID 28385709 DOI: 10.1101/Gr.214973.116  0.589
2015 Veidenberg A, Medlar A, Löytynoja A. Wasabi: an integrated platform for evolutionary sequence analysis and data visualisation. Molecular Biology and Evolution. PMID 26635364 DOI: 10.1093/Molbev/Msv333  0.753
2015 Kiiski K, Lehtokari VL, Löytynoja A, Ahlstén L, Laitila J, Wallgren-Pettersson C, Pelin K. A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array. European Journal of Human Genetics : Ejhg. PMID 26197980 DOI: 10.1038/Ejhg.2015.166  0.354
2015 Aivelo T, Medlar A, Löytynoja A, Laakkonen J, Jernvall J. Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus). Parasitology. 142: 1095-107. PMID 25892063 DOI: 10.1017/S0031182015000438  0.691
2015 Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C. Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proceedings of the National Academy of Sciences of the United States of America. 112: E99-100. PMID 25564672 DOI: 10.1073/Pnas.1417526112  0.702
2015 Aivelo T, Medlar A, Löytynoja A, Laakkonen J, Jernvall J. Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus) Parasitology. 142: 1095-1107. DOI: 10.1017/S0031182015000438  0.646
2014 Medlar A, Aivelo T, Löytynoja A. Séance: reference-based phylogenetic analysis for 18S rRNA studies. Bmc Evolutionary Biology. 14: 235. PMID 25433763 DOI: 10.1186/S12862-014-0235-7  0.762
2014 Buchmann JP, Löytynoja A, Wicker T, Schulman AH. Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts. Mobile Dna. 5: 24. PMID 25206928 DOI: 10.1186/1759-8753-5-24  0.392
2014 Löytynoja A. Phylogeny-aware alignment with PRANK Methods in Molecular Biology. 1079: 155-170. PMID 24170401 DOI: 10.1007/978-1-62703-646-7_10  0.48
2012 Löytynoja A, Vilella AJ, Goldman N. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics (Oxford, England). 28: 1684-91. PMID 22531217 DOI: 10.1093/Bioinformatics/Bts198  0.669
2012 Löytynoja A. Alignment methods: Strategies, challenges, benchmarking, and comparative overview Methods in Molecular Biology. 855: 203-235. PMID 22407710 DOI: 10.1007/978-1-61779-582-4_7  0.447
2012 Luo H, Löytynoja A, Moran MA. Genome content of uncultivated marine Roseobacters in the surface ocean Environmental Microbiology. 14: 41-51. PMID 21854517 DOI: 10.1111/J.1462-2920.2011.02528.X  0.453
2010 Löytynoja A, Goldman N. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. Bmc Bioinformatics. 11: 579. PMID 21110866 DOI: 10.1186/1471-2105-11-579  0.661
2009 Löytynoja A, Goldman N. Evolution. Uniting alignments and trees. Science (New York, N.Y.). 324: 1528-9. PMID 19541988 DOI: 10.1126/Science.1175949  0.633
2008 Löytynoja A, Goldman N. A model of evolution and structure for multiple sequence alignment. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3913-9. PMID 18852103 DOI: 10.1098/Rstb.2008.0170  0.64
2008 Löytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science (New York, N.Y.). 320: 1632-5. PMID 18566285 DOI: 10.1126/Science.1158395  0.65
2008 Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics (Oxford, England). 24: 11-7. PMID 18006548 DOI: 10.1093/Bioinformatics/Btm547  0.722
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.74
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  0.757
2007 Kankainen M, Löytynoja A. MATLIGN: A motif clustering, comparison and matching tool Bmc Bioinformatics. 8. PMID 17559640 DOI: 10.1186/1471-2105-8-189  0.443
2005 Löytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences of the United States of America. 102: 10557-62. PMID 16000407 DOI: 10.1073/Pnas.0409137102  0.565
2003 Löytynoja A, Milinkovitch MC. A hidden Markov model for progressive multiple alignment Bioinformatics. 19: 1505-1513. PMID 12912831 DOI: 10.1093/bioinformatics/btg193  0.335
2001 Nilsson J, Gross R, Asplund T, Dove O, Jansson H, Kelloniemi J, Kohlmann K, Löytynoja A, Nielsen EE, Paaver T, Primmer CR, Titov S, Vasemägi A, Veselov A, Öst T, et al. Matrilinear phylogeography of atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the baltic sea area Molecular Ecology. 10: 89-102. PMID 11251790 DOI: 10.1046/J.1365-294X.2001.01168.X  0.307
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