Published

 

Past works representing the group’s current interests

  • Löytynoja & Goldman. 2017. Short template switch events explain mutation clusters in the human genome. Genome Res adv online. (link)
  • Veidenberg, Medlar, and Löytynoja. 2016. Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization. Mol Biol Evol 33, 1126-1130. (link)
  • Aivelo, Medlar, Löytynoja, Laakkonen, and Jernvall. 2015. Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus). Parasitology 142, 1095–1107. (link)
  • Tan, Gil, Löytynoja, Goldman, and Dessimoz. 2015. Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proc Nat Acad Sciences USA. 112, E99–100. (link)
  • Medlar, Aivelo, and Löytynoja. 2014. Séance: reference-based phylogenetic analysis for 18S rRNA studies. BMC Evol Biol 14, 235. (link)
  • Buchmann, Löytynoja, Wicker and Schulman. 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. (link)
  • Löytynoja. 2014. Phylogeny-aware alignment with PRANK. Methods Mol Biol 1079:155–170. (link)
  • Löytynoja, Vilella and Goldman. 2012. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics, 28:1684-1691.(link)
  • Löytynoja. 2012. Alignment methods: strategies, challenges, benchmarking, and comparative overview. Methods Mol Biol, 855:203-235.(link)
  • Luo, Löytynoja & Moran. 2012. Genome content of uncultivated marine Roseobacters in the surface ocean. Envir Microbiol 14:41-51.(link)
  • Löytynoja & Goldman. 2010. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics, 11:579.(link)
  • Löytynoja & Goldman. 2009. Uniting Alignments and Trees. Science, 324:1528–1529.(link)
  • Löytynoja & Goldman. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320:1632–1635.(link)
  • Löytynoja & Goldman. 2008. A model of evolution and structure for multiple sequence alignment. Phil Trans Royal Soc B, 363:3913–3919.(link)
  • ENCODE Project Consortium. 2007. Identi?cation and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447:799–816.(link)
  • Margulies et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research, 17:760–774.(link)
  • Kankainen & Löytynoja. 2007. MATLIGN: a motif clustering, comparison and matching tool. BMC Bioinformatics, 8:189.(link)
  • Löytynoja & Goldman. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proc Nat Acad Sciences USA, 102:10557–10562.(link)
  • Löytynoja & Milinkovitch. 2003. A hidden Markov model for progressive multiple alignment. Bioinformatics, 19:1505–1513.(link)