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Items: 1 to 20 of 24

1.

Short template switch events explain mutation clusters in the human genome.

Löytynoja A, Goldman N.

Genome Res. 2017 Jun;27(6):1039-1049. doi: 10.1101/gr.214973.116. Epub 2017 Apr 6.

2.

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.

Veidenberg A, Medlar A, Löytynoja A.

Mol Biol Evol. 2016 Apr;33(4):1126-30. doi: 10.1093/molbev/msv333. Epub 2015 Dec 3.

PMID:
26635364
3.

A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array.

Kiiski K, Lehtokari VL, Löytynoja A, Ahlstén L, Laitila J, Wallgren-Pettersson C, Pelin K.

Eur J Hum Genet. 2016 Apr;24(4):574-80. doi: 10.1038/ejhg.2015.166. Epub 2015 Jul 22.

4.

Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus).

Aivelo T, Medlar A, Löytynoja A, Laakkonen J, Jernvall J.

Parasitology. 2015 Jul;142(8):1095-107. doi: 10.1017/S0031182015000438. Epub 2015 Apr 20.

PMID:
25892063
5.

Séance: reference-based phylogenetic analysis for 18S rRNA studies.

Medlar A, Aivelo T, Löytynoja A.

BMC Evol Biol. 2014 Nov 30;14:235. doi: 10.1186/s12862-014-0235-7.

6.

Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts.

Buchmann JP, Löytynoja A, Wicker T, Schulman AH.

Mob DNA. 2014 Sep 1;5:24. doi: 10.1186/1759-8753-5-24. eCollection 2014.

7.

Cleavage of the Drosophila screw prodomain is critical for a dynamic BMP morphogen gradient in embryogenesis.

Künnapuu J, Tauscher PM, Tiusanen N, Nguyen M, Löytynoja A, Arora K, Shimmi O.

Dev Biol. 2014 May 15;389(2):149-59. doi: 10.1016/j.ydbio.2014.02.007. Epub 2014 Feb 19.

8.

Phylogeny-aware alignment with PRANK.

Löytynoja A.

Methods Mol Biol. 2014;1079:155-70. doi: 10.1007/978-1-62703-646-7_10.

PMID:
24170401
9.

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.

Löytynoja A, Vilella AJ, Goldman N.

Bioinformatics. 2012 Jul 1;28(13):1684-91. doi: 10.1093/bioinformatics/bts198. Epub 2012 Apr 23.

10.

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

Löytynoja A.

Methods Mol Biol. 2012;855:203-35. doi: 10.1007/978-1-61779-582-4_7. Review.

PMID:
22407710
11.

Genome content of uncultivated marine Roseobacters in the surface ocean.

Luo H, Löytynoja A, Moran MA.

Environ Microbiol. 2012 Jan;14(1):41-51. doi: 10.1111/j.1462-2920.2011.02528.x. Epub 2011 Aug 19.

PMID:
21854517
12.

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.

Löytynoja A, Goldman N.

BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.

13.

Evolution. Uniting alignments and trees.

Löytynoja A, Goldman N.

Science. 2009 Jun 19;324(5934):1528-9. doi: 10.1126/science.1175949. No abstract available.

PMID:
19541988
14.

A model of evolution and structure for multiple sequence alignment.

Löytynoja A, Goldman N.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3913-9. doi: 10.1098/rstb.2008.0170.

15.

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.

Löytynoja A, Goldman N.

Science. 2008 Jun 20;320(5883):1632-5. doi: 10.1126/science.1158395.

16.

Determination and validation of principal gene products.

Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A.

Bioinformatics. 2008 Jan 1;24(1):11-7. Epub 2007 Nov 15.

17.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, 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, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

18.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

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, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.

Genome Res. 2007 Jun;17(6):760-74.

19.

MATLIGN: a motif clustering, comparison and matching tool.

Kankainen M, Löytynoja A.

BMC Bioinformatics. 2007 Jun 8;8:189.

20.

An algorithm for progressive multiple alignment of sequences with insertions.

Löytynoja A, Goldman N.

Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10557-62. Epub 2005 Jul 6.

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