20052020

Research output per year

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Publications

2020

A major locus controls a biologically active pheromone component in Heliconius melpomene

Byers, K. J. R. P., Darragh, K., Musgrove, J., Abondano Almeida, D., Fernanda Garza, S., Warren, I. A., Rastas, P. M., Kucka, M., Chan, Y. F., Merrill, R. M., Schulz, S., Owen McMillan, W. & Jiggins, C. D., Feb 2020, In : Evolution. 74, 2, p. 349-364 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

ELIMAKI Locus Is Required for Vertical Proprioceptive Response in Birch Trees

Alonso Serra, J. A., Shi, X., Peaucelle, A., Rastas, P., Bourdon, M., Immanen, J., Takahashi, J., Koivula, H., Eswaran, G., Muranen, S. J., Help-Rinta-Rahko, H., Smolander, O-P., Su, C., Safronov, O., Gerber, L., Salojärvi, J., Hagqvist, R., Mähönen, A. P., Helariutta, Y. & Nieminen, K., 24 Feb 2020, In : Current Biology. 30, 4, p. 589-599 16 p.

Research output: Contribution to journalArticleScientificpeer-review

2019

A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome

Varadharajan, S., Rastas, P., Löytynoja, A., Matschiner, M., Calboli, F. C. F., Guo, B., Nederbragt, A. J., Jakobsen, K. S. & Merilä, J., Nov 2019, In : Genome Biology and Evolution. 11, 11, p. 3291-3308 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua

Veltsos, P., Ridout, K. E., Toups, M. A., Gonzalez-Martinez, S. C., Muyle, A., Emery, O., Rastas, P., Hudzieczek, V., Hobza, R., Vyskot, B., Marais, G. A. B., Filatov, D. A. & Pannell, J. R., Jul 2019, In : Genetics. 212, 3, p. 815-835 21 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Kermit: Linkage map guided long read assembly

Walve, R., Rastas, P. & Salmela, L., 20 Mar 2019, In : Algorithms for Molecular Biology. 14, 1, 10 p., 8.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution

Hill, J., Rastas, P., Hornett, E. A., Neethiraj, R., Clark, N., Morehouse, N., Celorio-Mancera, M. D. L. P., Carnicer, J., Dircksen, H., Meslin, C., Keehnen, N., Pruisscher, P., Sikkink, K., Vives, M., Vogel, H., Wiklund, C., Woronik, A., Boggs, C. L., Nylin, S. & Wheat, C. W., Jun 2019, In : Science Advances. 5, 6, 12 p., 3648.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2018

A Genome-Wide Association Study for Host Resistance to Ostreid Herpesvirus in Pacific Oysters (Crassostrea gigas)

Gutierrez, A. P., Bean, T. P., Hooper, C., Stenton, C. A., Sanders, M. B., Paley, R. K., Rastas, P., Bryrom, M., Matika, O. & Houston, R. D., Apr 2018, In : G3 - Genes genomes genetics. 8, 4, p. 1273-1280 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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A High-Resolution Genetic Map for the Laboratory Rat

Littrell, J., Tsaih, S-W., Baud, A., Rastas, P., Solberg-Woods, L. & Flister, M. J., Jul 2018, In : G3 - Genes genomes genetics. 8, 7, p. 2241-2248 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Bracketing phenogenotypic limits of mammalian hybridization

Savriama, Y., Valtonen, M., Kammonen, J. I., Rastas, P., Smolander, O-P., Lyyski, A., Häkkinen, T. J., Corfe, I. J., Gerber, S., Salazar-Ciudad, I., Paulin, L., Holm, L., Löytynoja, A., Auvinen, P. & Jernvall, J., 28 Nov 2018, In : Royal Society Open Science. 5, 11, 12 p., 180903.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution

Van Belleghem, S. M., Vangestel, C., De Wolf, K., De Corte, Z., Most, M., Rastas, P., De Meester, L. & Hendrickx, F., Nov 2018, In : PLoS Genetics. 14, 11, 26 p., 1007796.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi

Nguyen, N. H., Rastas, P. M. A., Premachandra, H. K. A. & Knibb, W., 17 Apr 2018, In : Frontiers in Genetics. 9, 11 p., 127.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly

Fountain, T., Husby, A., Nonaka, E., DiLeo, M., Korhonen, J. H., Rastas, P., Schulz, T. M., Saastamoinen, M. A. K. & Hanski, I. A., Mar 2018, In : Evolutionary Applications. 11, 3, p. 287-297 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Kermit: Guided Long Read Assembly using Coloured Overlap Graphs

Walve, R. M., Rastas, P. M. A. & Salmela, L. M., 2018, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Parida, L. & Ukkonen, E. (eds.). Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, p. 11:1-11:11 11 p. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 113).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
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Linkage disequilibrium clustering-based approach for association mapping with tightly linked genomewide data

Li, Z., Kemppainen, P., Rastas, P. & Merilä, J., Jul 2018, In : Molecular Ecology Resources. 18, 4, p. 809-824 16 p.

Research output: Contribution to journalArticleScientificpeer-review

2017

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi, J., Smolander, O-P., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., Lamminmäki, A., Immanen, J., Lan, T., Tanskanen, J., Rastas, P., Amiryousefi, A., Jayaprakash, B., Kammonen, J. I., Hagqvist, R., Eswaran, G., Ahonen, V. H., Serra, J. A., Asiegbu, F. O., Barajas-Lopez, J. D. D. & 65 others, Blande, D., Blokhina, O., Blomster, T., Broholm, S., Brosche, M., Cui, F., Dardick, C., Ehonen, S. E., Elomaa, P., Escamez, S., Fagerstedt, K. V., Fujii, H., Gauthier, A., Gollan, P. J., Halimaa, P., Heino, P. I., Himanen, K., Hollender, C., Kangasjarvi, S., Kauppinen, L., Kelleher, C. T., Kontunen-Soppela, S., Koskinen, J. P., Kovalchuk, A., Karenlampi, S. O., Kärkönen, A. K., Lim, K-J., Leppälä, J., Macpherson, L., Mikola, J., Mouhu, K., Mähönen, A. P., Niinemets, U., Oksanen, E., Overmyer, K., Palva, E. T., Pazouki, L., Pennanen, V., Puhakainen, T., Poczai, P., Possen, B. J. H. M., Punkkinen, M., Rahikainen, M. M., Rousi, M., Ruonala, R., van der Schoot, C., Shapiguzov, A., Sierla, M., Sipilä, T. P., Sutela, S., Teeri, T. H., Tervahauta, A. I., Vaattovaara, A., Vahala, J., Vetchinnikova, L., Welling, A., Wrzaczek, M., Xu, E., Paulin, L. G., Schulman, A. H., Lascoux, M., Albert, V. A., Auvinen, P., Helariutta, Y. & Kangasjarvi, J., 8 May 2017, In : Nature Genetics. 49, 6, p. 904-912 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data

Rastas, P., 1 Dec 2017, In : Bioinformatics. 33, 23, p. 3726-3732 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2016

Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F-2 Recombinant Crosses as an Example

Rastas, P., Calboli, F. C. F., Guo, B., Shikano, T. & Merilä, J., Jan 2016, In : Genome Biology and Evolution. 8, 1, p. 78-93 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2015

Flight-induced changes in gene expression in the Glanville fritillary butterfly

Kvist, J., Mattila, A. L. K., Somervuo, P., Ahola, V., Koskinen, P., Paulin, L., Salmela, L., Fountain, T., Rastas, P., Ruokolainen, A., Taipale, M., Holm, L., Auvinen, P., Lehtonen, R., Frilander, M. J. & Hanski, I., Oct 2015, In : Molecular Ecology. 24, 19, p. 4886-4900 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

Shao, C., Niu, Y., Rastas, P., Liu, Y., Xie, Z., Li, H., Wang, L., Jiang, Y., Tai, S., Tian, Y., Sakamoto, T. & Chen, S., Apr 2015, In : DNA Research. 22, 2, p. 161-170 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2014

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Valimaki, N., Paulin, L., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E. A., Ferguson, L. C., Luo, S., Cao, Z., de Jong, M. A., Duplouy, A., Smolander, O-P., Vogel, H., McCoy, R. C. & 27 others, Qian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J. K., Joshi, A., Salojarvi, J., Wheat, C. W., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkanen, E., Ylinen, J., Waterhouse, R. M., Turunen, M., Vaharautio, A., Ojanen, S. P., Schulman, A. H., Taipale, M., Lawson, D., Ukkonen, E., Makinen, V., Goldsmith, M. R., Holm, L., Auvinen, P., Frilander, M. J. & Hanski, I., Sep 2014, In : Nature Communications. 5, 9 p., 4737.

Research output: Contribution to journalArticleScientificpeer-review

2013

DNA-Binding Specificities of Human Transcription Factors

Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K. R., Rastas, P., Morgunova, E., Enge, M., Taipale, M. J. O., Wei, G., Palin, K., Vaquerizas, J. M., Vincentelli, R., Luscombe, N. M., Hughes, T. R., Lemaire, P., Ukkonen, E., Kivioja, T. & Taipale, J., 17 Jan 2013, In : Cell. 152, 1-2, p. 327-339 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Lep-MAP: fast and accurate linkage map construction for large SNP datasets

Rastas, P., Paulin, L., Hanski, I., Lehtonen, R. J. & Auvinen, P., 2013, In : Bioinformatics. 29, 24, p. 3128-3134 7 p.

Research output: Contribution to journalArticleScientificpeer-review

2012

High genetic load in an old isolated butterfly population

Mattila, A., Duplouy, A., Kirjokangas, M., Lehtonen, R. J., Rastas, P. & Hanski, I., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 37, p. E2496-2505 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Rule-based induction method for haplotype comparison and identification of candidate disease loci

Karinen, S. H., Saarinen, S., Lehtonen, R. J., Rastas, P., Vahteristo, P. M., Aaltonen, L. A. & Hautaniemi, S., 2012, In : Genome medicine. 4, 3, p. 21

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2011

Finding significant matches of position weight matrices in linear time

Pizzi, C., Rastas, P. & Ukkonen, E., 2011, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, 1, p. 69-79 11 p.

Research output: Contribution to journalArticleScientificpeer-review

2009

A general framework for local pairwise alignment statistics with gaps

Rastas, P., 2009, Algorithms in bioinformatics: Steven L. Salzberg, Tandy Warnow (eds.). Berlin: Springer, p. 233-245 13 p. (Lecture Notes in Bioinformatics).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Computational techniques for haplotype inference and for local alignment significance

Rastas, P., 2009, Helsinki: University of Helsinki. 64 p.

Research output: ThesisDoctoral ThesisMonograph

MOODS: fast search for position weight matrix matches in DNA sequences

Korhonen, J. H., Martinmäki, P., Pizzi, C., Rastas, P. & Ukkonen, E., 15 Sep 2009, In : Bioinformatics. 25, 23, p. 3181-3182 2 p.

Research output: Contribution to journalArticleScientificpeer-review

MOODS

Korhonen, J. H., Petri, M., Rastas, P. M. A., Pizzi, C. & Ukkonen, E., 2009

Research output: Non-textual formSoftwareScientific

2008

Fast Bayesian haplotype inference via Context Tree Weighting

Rastas, P., Kollin, J. & Koivisto, M., 2008, Proceedings of the 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. p. 259-270 12 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Phasing genotypes using a hidden Markov model

Rastas, P., Koivisto, M., Mannila, H. & Ukkonen, E., 2008, Bioinformatics algorithms. Hoboken, N.J: Wiley-Interscience, p. 355-372 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

2007

Fast search algorithms for position specific scoring matrices

Pizzi, C., Rastas, P. & Ukkonen, E., 2007, Bioinformatics Research and Development. Springer-Verlag, p. 239-250 12 p. (Lecture Notes in Computer Science; vol. 4414).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Haplotype inference via hierarchical genotype parsing

Rastas, P. & Ukkonen, E., 2007, Algorithms in Bioinformatics (WABI 2007). Springer-Verlag, p. 85-97 13 p. (Lecture Notes in Computer Science; vol. 4645).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2005

A hidden Markov technique for haplotype reconstruction

Rastas, P., Koivisto, M., Mannila, H. & Ukkonen, E., 2005, Algorithms in Bioinformatics (WABI-2005). Springer-Verlag, p. 140-151 12 p. (Lecture Notes in Computer Science; vol. 3692).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review