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Items: 27

1.

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

Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J.

Genome Biol Evol. 2019 Nov 1;11(11):3291-3308. doi: 10.1093/gbe/evz240.

PMID:
31687752
2.

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

Hill J, Rastas P, Hornett EA, Neethiraj R, Clark N, Morehouse N, de la Paz Celorio-Mancera M, Cols JC, Dircksen H, Meslin C, Keehnen N, Pruisscher P, Sikkink K, Vives M, Vogel H, Wiklund C, Woronik A, Boggs CL, Nylin S, Wheat CW.

Sci Adv. 2019 Jun 12;5(6):eaau3648. doi: 10.1126/sciadv.aau3648. eCollection 2019 Jun.

3.

Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

Salojärvi J, Smolander OP, Nieminen K, Rajaraman S, Safronov O, Safdari P, Lamminmäki A, Immanen J, Lan T, Tanskanen J, Rastas P, Amiryousefi A, Jayaprakash B, Kammonen JI, Hagqvist R, Eswaran G, Ahonen VH, Serra JA, Asiegbu FO, de Dios Barajas-Lopez J, Blande D, Blokhina O, Blomster T, Broholm S, Brosché M, Cui F, Dardick C, Ehonen SE, Elomaa P, Escamez S, Fagerstedt KV, Fujii H, Gauthier A, Gollan PJ, Halimaa P, Heino PI, Himanen K, Hollender C, Kangasjärvi S, Kauppinen L, Kelleher CT, Kontunen-Soppela S, Koskinen JP, Kovalchuk A, Kärenlampi SO, Kärkönen AK, Lim KJ, Leppälä J, Macpherson L, Mikola J, Mouhu K, Mähönen AP, Niinemets Ü, Oksanen E, Overmyer K, Palva ET, Pazouki L, Pennanen V, Puhakainen T, Poczai P, Possen BJHM, Punkkinen M, Rahikainen MM, Rousi M, Ruonala R, van der Schoot C, Shapiguzov A, Sierla M, Sipilä TP, Sutela S, Teeri TH, Tervahauta AI, Vaattovaara A, Vahala J, Vetchinnikova L, Welling A, Wrzaczek M, Xu E, Paulin LG, Schulman AH, Lascoux M, Albert VA, Auvinen P, Helariutta Y, Kangasjärvi J.

Nat Genet. 2019 Jul;51(7):1187-1189. doi: 10.1038/s41588-019-0442-7. No abstract available.

PMID:
31197270
4.

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

Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR.

Genetics. 2019 Jul;212(3):815-835. doi: 10.1534/genetics.119.302045. Epub 2019 May 21.

5.

Kermit: linkage map guided long read assembly.

Walve R, Rastas P, Salmela L.

Algorithms Mol Biol. 2019 Mar 20;14:8. doi: 10.1186/s13015-019-0143-x. eCollection 2019.

6.

Genetic dissection of assortative mating behavior.

Merrill RM, Rastas P, Martin SH, Melo MC, Barker S, Davey J, McMillan WO, Jiggins CD.

PLoS Biol. 2019 Feb 7;17(2):e2005902. doi: 10.1371/journal.pbio.2005902. eCollection 2019 Feb.

7.

The genetic architecture of adaptation: convergence and pleiotropy in Heliconius wing pattern evolution.

Morris J, Navarro N, Rastas P, Rawlins LD, Sammy J, Mallet J, Dasmahapatra KK.

Heredity (Edinb). 2019 Aug;123(2):138-152. doi: 10.1038/s41437-018-0180-0. Epub 2019 Jan 22.

8.

Bracketing phenogenotypic limits of mammalian hybridization.

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.

R Soc Open Sci. 2018 Nov 28;5(11):180903. doi: 10.1098/rsos.180903. eCollection 2018 Nov.

9.

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

Van Belleghem SM, Vangestel C, De Wolf K, De Corte Z, Möst M, Rastas P, De Meester L, Hendrickx F.

PLoS Genet. 2018 Nov 13;14(11):e1007796. doi: 10.1371/journal.pgen.1007796. eCollection 2018 Nov.

10.

A High-Resolution Genetic Map for the Laboratory Rat.

Littrell J, Tsaih SW, Baud A, Rastas P, Solberg-Woods L, Flister MJ.

G3 (Bethesda). 2018 Jul 2;8(7):2241-2248. doi: 10.1534/g3.118.200187.

11.

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

Nguyen NH, Rastas PMA, Premachandra HKA, Knibb W.

Front Genet. 2018 Apr 17;9:127. doi: 10.3389/fgene.2018.00127. eCollection 2018.

12.

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

Li Z, Kemppainen P, Rastas P, Merilä J.

Mol Ecol Resour. 2018 Jul;18(4):809-824. doi: 10.1111/1755-0998.12893. Epub 2018 May 7.

PMID:
29673105
13.

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

Gutierrez AP, Bean TP, Hooper C, Stenton CA, Sanders MB, Paley RK, Rastas P, Bryrom M, Matika O, Houston RD.

G3 (Bethesda). 2018 Mar 28;8(4):1273-1280. doi: 10.1534/g3.118.200113.

14.

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

Rastas P.

Bioinformatics. 2017 Dec 1;33(23):3726-3732. doi: 10.1093/bioinformatics/btx494.

PMID:
29036272
15.

No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions.

Davey JW, Barker SL, Rastas PM, Pinharanda A, Martin SH, Durbin R, McMillan WO, Merrill RM, Jiggins CD.

Evol Lett. 2017 Jun 14;1(3):138-154. doi: 10.1002/evl3.12. eCollection 2017 Aug.

16.

Complex modular architecture around a simple toolkit of wing pattern genes.

Van Belleghem SM, Rastas P, Papanicolaou A, Martin SH, Arias CF, Supple MA, Hanly JJ, Mallet J, Lewis JJ, Hines HM, Ruiz M, Salazar C, Linares M, Moreira GRP, Jiggins CD, Counterman BA, McMillan WO, Papa R.

Nat Ecol Evol. 2017;1(3):52. doi: 10.1038/s41559-016-0052. Epub 2017 Jan 30.

17.

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

Salojärvi J, Smolander OP, Nieminen K, Rajaraman S, Safronov O, Safdari P, Lamminmäki A, Immanen J, Lan T, Tanskanen J, Rastas P, Amiryousefi A, Jayaprakash B, Kammonen JI, Hagqvist R, Eswaran G, Ahonen VH, Serra JA, Asiegbu FO, de Dios Barajas-Lopez J, Blande D, Blokhina O, Blomster T, Broholm S, Brosché M, Cui F, Dardick C, Ehonen SE, Elomaa P, Escamez S, Fagerstedt KV, Fujii H, Gauthier A, Gollan PJ, Halimaa P, Heino PI, Himanen K, Hollender C, Kangasjärvi S, Kauppinen L, Kelleher CT, Kontunen-Soppela S, Koskinen JP, Kovalchuk A, Kärenlampi SO, Kärkönen AK, Lim KJ, Leppälä J, Macpherson L, Mikola J, Mouhu K, Mähönen AP, Niinemets Ü, Oksanen E, Overmyer K, Palva ET, Pazouki L, Pennanen V, Puhakainen T, Poczai P, Possen BJHM, Punkkinen M, Rahikainen MM, Rousi M, Ruonala R, van der Schoot C, Shapiguzov A, Sierla M, Sipilä TP, Sutela S, Teeri TH, Tervahauta AI, Vaattovaara A, Vahala J, Vetchinnikova L, Welling A, Wrzaczek M, Xu E, Paulin LG, Schulman AH, Lascoux M, Albert VA, Auvinen P, Helariutta Y, Kangasjärvi J.

Nat Genet. 2017 Jun;49(6):904-912. doi: 10.1038/ng.3862. Epub 2017 May 8. Erratum in: Nat Genet. 2019 Jul;51(7):1187-1189.

PMID:
28481341
18.

Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example.

Rastas P, Calboli FC, Guo B, Shikano T, Merilä J.

Genome Biol Evol. 2015 Dec 14;8(1):78-93. doi: 10.1093/gbe/evv250.

19.

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

Kvist J, Mattila AL, 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 MJ, Hanski I.

Mol Ecol. 2015 Oct;24(19):4886-900. doi: 10.1111/mec.13359.

PMID:
26331775
20.

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.

DNA Res. 2015 Apr;22(2):161-70. doi: 10.1093/dnares/dsv001. Epub 2015 Mar 11.

21.

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, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander OP, Vogel H, McCoy RC, Qian K, Chong WS, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse-Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I.

Nat Commun. 2014 Sep 5;5:4737. doi: 10.1038/ncomms5737.

22.

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

Rastas P, Paulin L, Hanski I, Lehtonen R, Auvinen P.

Bioinformatics. 2013 Dec 15;29(24):3128-34. doi: 10.1093/bioinformatics/btt563. Epub 2013 Sep 26.

23.

DNA-binding specificities of human transcription factors.

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J.

Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009.

24.

High genetic load in an old isolated butterfly population.

Mattila AL, Duplouy A, Kirjokangas M, Lehtonen R, Rastas P, Hanski I.

Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):E2496-505. doi: 10.1073/pnas.1205789109. Epub 2012 Aug 20.

25.

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

Karinen S, Saarinen S, Lehtonen R, Rastas P, Vahteristo P, Aaltonen LA, Hautaniemi S.

Genome Med. 2012 Mar 19;4(3):21.

26.

Finding significant matches of position weight matrices in linear time.

Pizzi C, Rastas P, Ukkonen E.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):69-79. doi: 10.1109/TCBB.2009.35.

PMID:
21071798
27.

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

Korhonen J, Martinmäki P, Pizzi C, Rastas P, Ukkonen E.

Bioinformatics. 2009 Dec 1;25(23):3181-2. doi: 10.1093/bioinformatics/btp554. Epub 2009 Sep 22.

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