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Items: 1 to 20 of 32

1.

GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm.

Ali RH, Muhammad SA, Arvestad L.

BMC Evol Biol. 2016 Jun 4;16(1):120. doi: 10.1186/s12862-016-0684-2.

2.

Assembly scaffolding with PE-contaminated mate-pair libraries.

Sahlin K, Chikhi R, Arvestad L.

Bioinformatics. 2016 Mar 2. pii: btw064. [Epub ahead of print]

3.

Gene-pseudogene evolution: a probabilistic approach.

Mahmudi O, Sennblad B, Arvestad L, Nowick K, Lagergren J.

BMC Genomics. 2015;16 Suppl 10:S12. doi: 10.1186/1471-2164-16-S10-S12. Epub 2015 Oct 2.

4.

BESST--efficient scaffolding of large fragmented assemblies.

Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L.

BMC Bioinformatics. 2014 Aug 15;15:281. doi: 10.1186/1471-2105-15-281.

5.

Forensic informativity of ~3000 bp of coding sequence of domestic dog mtDNA.

Angleby H, Oskarsson M, Pang J, Zhang YP, Leitner T, Braham C, Arvestad L, Lundeberg J, Webb KM, Savolainen P.

J Forensic Sci. 2014 Jul;59(4):898-908. doi: 10.1111/1556-4029.12504. Epub 2014 May 11.

PMID:
24814664
6.

Quantitative synteny scoring improves homology inference and partitioning of gene families.

Ali RH, Muhammad S, Khan M, Arvestad L.

BMC Bioinformatics. 2013;14 Suppl 15:S12. doi: 10.1186/1471-2105-14-S15-S12. Epub 2013 Oct 15.

7.

A Bayesian method for analyzing lateral gene transfer.

Sjöstrand J, Tofigh A, Daubin V, Arvestad L, Sennblad B, Lagergren J.

Syst Biol. 2014 May;63(3):409-20. doi: 10.1093/sysbio/syu007. Epub 2014 Feb 20.

PMID:
24562812
8.

Fastphylo: fast tools for phylogenetics.

Khan MA, Elias I, Sjölund E, Nylander K, Guimera RV, Schobesberger R, Schmitzberger P, Lagergren J, Arvestad L.

BMC Bioinformatics. 2013 Nov 20;14:334. doi: 10.1186/1471-2105-14-334.

9.

Excap: maximization of haplotypic diversity of linked markers.

Kahles A, Sarqume F, Savolainen P, Arvestad L.

PLoS One. 2013 Nov 7;8(11):e79012. doi: 10.1371/journal.pone.0079012. eCollection 2013.

10.

GAM-NGS: genomic assemblies merger for next generation sequencing.

Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.

BMC Bioinformatics. 2013;14 Suppl 7:S6. doi: 10.1186/1471-2105-14-S7-S6. Epub 2013 Apr 22.

11.

GenPhyloData: realistic simulation of gene family evolution.

Sjöstrand J, Arvestad L, Lagergren J, Sennblad B.

BMC Bioinformatics. 2013 Jun 27;14:209. doi: 10.1186/1471-2105-14-209.

12.

The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S.

Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.

PMID:
23698360
13.

DLRS: gene tree evolution in light of a species tree.

Sjöstrand J, Sennblad B, Arvestad L, Lagergren J.

Bioinformatics. 2012 Nov 15;28(22):2994-5. doi: 10.1093/bioinformatics/bts548. Epub 2012 Sep 14.

14.

Improved gap size estimation for scaffolding algorithms.

Sahlin K, Street N, Lundeberg J, Arvestad L.

Bioinformatics. 2012 Sep 1;28(17):2215-22.

15.

Evolution and human tissue expression of the Cres/Testatin subgroup genes, a reproductive tissue specific subgroup of the type 2 cystatins.

Frygelius J, Arvestad L, Wedell A, Töhönen V.

Evol Dev. 2010 May-Jun;12(3):329-42. doi: 10.1111/j.1525-142X.2010.00418.x.

PMID:
20565543
16.

Classification of DNA sequences using Bloom filters.

Stranneheim H, Käller M, Allander T, Andersson B, Arvestad L, Lundeberg J.

Bioinformatics. 2010 Jul 1;26(13):1595-600. doi: 10.1093/bioinformatics/btq230. Epub 2010 May 13.

17.

Identification of the cellulose synthase genes from the Oomycete Saprolegnia monoica and effect of cellulose synthesis inhibitors on gene expression and enzyme activity.

Fugelstad J, Bouzenzana J, Djerbi S, Guerriero G, Ezcurra I, Teeri TT, Arvestad L, Bulone V.

Fungal Genet Biol. 2009 Oct;46(10):759-67. doi: 10.1016/j.fgb.2009.07.001. Epub 2009 Jul 7.

PMID:
19589393
18.

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis.

Akerborg O, Sennblad B, Arvestad L, Lagergren J.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5714-9. doi: 10.1073/pnas.0806251106. Epub 2009 Mar 19.

19.

MAP20, a microtubule-associated protein in the secondary cell walls of hybrid aspen, is a target of the cellulose synthesis inhibitor 2,6-dichlorobenzonitrile.

Rajangam AS, Kumar M, Aspeborg H, Guerriero G, Arvestad L, Pansri P, Brown CJ, Hober S, Blomqvist K, Divne C, Ezcurra I, Mellerowicz E, Sundberg B, Bulone V, Teeri TT.

Plant Physiol. 2008 Nov;148(3):1283-94. doi: 10.1104/pp.108.121913. Epub 2008 Sep 19.

20.

Evolution of a domain conserved in microtubule-associated proteins of eukaryotes.

Rajangam AS, Yang H, Teeri TT, Arvestad L.

Adv Appl Bioinform Chem. 2008;1:51-69. Epub 2008 Sep 23.

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