Ari Löytynoja, Ph.D. - Publications

University of Helsinki, Helsingfors, Finland 

25 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
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  0.88
2018 Savriama Y, Valtonen M, Kammonen JI, Rastas P, Smolander OP, Lyyski A, Häkkinen TJ, Corfe IJ, Gerber S, Salazar-Ciudad I, Paulin L, Holm L, Löytynoja A, Auvinen P, Jernvall J. Bracketing phenogenotypic limits of mammalian hybridization. Royal Society Open Science. 5: 180903. PMID 30564397 DOI: 10.1098/rsos.180903  0.48
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  1
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  0.88
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  0.88
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  1
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  1
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  0.88
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  1
2014 Künnapuu J, Tauscher PM, Tiusanen N, Nguyen M, Löytynoja A, Arora K, Shimmi O. Cleavage of the Drosophila screw prodomain is critical for a dynamic BMP morphogen gradient in embryogenesis. Developmental Biology. 389: 149-59. PMID 24560644 DOI: 10.1016/j.ydbio.2014.02.007  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2003 Löytynoja A, Milinkovitch MC. A hidden Markov model for progressive multiple alignment Bioinformatics. 19: 1505-1513. PMID 12912831 DOI: 10.1093/bioinformatics/btg193  1
2001 Löytynoja A, Milinkovitch MC. Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: The plantae/fungi/metazoa trichotomy revisited Proceedings of the National Academy of Sciences of the United States of America. 98: 10202-10207. PMID 11517311 DOI: 10.1073/pnas.181187698  1
2001 Löytynoja A, Milinkovitch MC. SOAP, cleaning multiple alignments from unstable blocks Bioinformatics. 17: 573-574. PMID 11395440  1
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