| Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ... nature 447 (7146), 799-816, 2007 | 6103 | 2007 |
| An algorithm for progressive multiple alignment of sequences with insertions A Löytynoja, N Goldman Proceedings of the National Academy of Sciences 102 (30), 10557-10562, 2005 | 1050 | 2005 |
| Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis A Löytynoja, N Goldman Science 320 (5883), 1632-1635, 2008 | 896 | 2008 |
| Phylogeny-aware alignment with PRANK A Löytynoja Multiple Sequence Alignment Methods, 155-170, 2014 | 694 | 2014 |
| webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser A Löytynoja, N Goldman BMC bioinformatics 11, 1-7, 2010 | 485 | 2010 |
| Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome EH Margulies, GM Cooper, G Asimenos, DJ Thomas, CN Dewey, A Siepel, ... Genome research 17 (6), 760-774, 2007 | 252 | 2007 |
| Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area J Nilsson, R Gross, T Asplund, O Dove, H Jansson, J Kelloniemi, ... Molecular Ecology 10 (1), 89-102, 2001 | 225 | 2001 |
| A hidden Markov model for progressive multiple alignment A Löytynoja, MC Milinkovitch Bioinformatics 19 (12), 1505-1513, 2003 | 193 | 2003 |
| SOAP, cleaning multiple alignments from unstable blocks A Löytynoja, MC Milinkovitch Bioinformatics 17 (6), 573-574, 2001 | 167 | 2001 |
| Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm A Löytynoja, AJ Vilella, N Goldman Bioinformatics 28 (13), 1684-1691, 2012 | 157 | 2012 |
| An inducible genome editing system for plants X Wang, L Ye, M Lyu, R Ursache, A Löytynoja, AP Mähönen Nature plants 6 (7), 766-772, 2020 | 95 | 2020 |
| Mechanistic insights into the evolution of DUF26-containing proteins in land plants A Vaattovaara, B Brandt, S Rajaraman, O Safronov, A Veidenberg, ... Communications biology 2 (1), 56, 2019 | 95 | 2019 |
| A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome S Varadharajan, P Rastas, A Löytynoja, M Matschiner, FCF Calboli, ... Genome biology and evolution 11 (11), 3291-3308, 2019 | 73 | 2019 |
| Wasabi: an integrated platform for evolutionary sequence analysis and data visualization A Veidenberg, A Medlar, A Löytynoja Molecular biology and evolution 33 (4), 1126-1130, 2016 | 64 | 2016 |
| A model of evolution and structure for multiple sequence alignment A Löytynoja, N Goldman Philosophical Transactions of the Royal Society B: Biological Sciences 363 …, 2008 | 61 | 2008 |
| Genome content of uncultivated marine Roseobacters in the surface ocean H Luo, A Löytynoja, MA Moran Environmental microbiology 14 (1), 41-51, 2012 | 53 | 2012 |
| Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: The Plantae/Fungi/Metazoa trichotomy revisited A Löytynoja, MC Milinkovitch Proceedings of the National Academy of Sciences 98 (18), 10202-10207, 2001 | 43 | 2001 |
| A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array K Kiiski, VL Lehtokari, A Löytynoja, L Ahlstén, J Laitila, ... European Journal of Human Genetics 24 (4), 574-580, 2016 | 37 | 2016 |
| Uniting alignments and trees A Löytynoja, N Goldman Science 324 (5934), 1528-1529, 2009 | 35 | 2009 |
| MATLIGN: a motif clustering, comparison and matching tool M Kankainen, A Löytynoja BMC bioinformatics 8, 1-7, 2007 | 35 | 2007 |
