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Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.

Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Forn I, Forster D, Guillou L, Jaillon O, Kooistra WH, Logares R, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simon N, Stoeck T, Vaulot D, Zingone A, de Vargas C.

Environ Microbiol. 2015 Oct;17(10):4035-49. doi: 10.1111/1462-2920.12955. Epub 2015 Aug 4.


BIR Pipeline for Preparation of Phylogenomic Data.

Kumar S, Krabberød AK, Neumann RS, Michalickova K, Zhao S, Zhang X, Shalchian-Tabrizi K.

Evol Bioinform Online. 2015 Apr 27;11:79-83. doi: 10.4137/EBO.S10189. eCollection 2015. Review.


BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data.

Neumann RS, Kumar S, Haverkamp TH, Shalchian-Tabrizi K.

BMC Bioinformatics. 2014 May 5;15:128. doi: 10.1186/1471-2105-15-128.


Patterns of rare and abundant marine microbial eukaryotes.

Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WH, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards TA, de Vargas C, Massana R.

Curr Biol. 2014 Apr 14;24(8):813-21. doi: 10.1016/j.cub.2014.02.050. Epub 2014 Apr 3.


Sulcozoa revealed as a paraphyletic group in mitochondrial phylogenomics.

Zhao S, Shalchian-Tabrizi K, Klaveness D.

Mol Phylogenet Evol. 2013 Dec;69(3):462-8. doi: 10.1016/j.ympev.2013.08.005. Epub 2013 Aug 22.


The catalytic domain CysPc of the DEK1 calpain is functionally conserved in land plants.

Liang Z, Demko V, Wilson RC, Johnson KA, Ahmad R, Perroud PF, Quatrano R, Zhao S, Shalchian-Tabrizi K, Otegui MS, Olsen OA, Johansen W.

Plant J. 2013 Sep;75(5):742-54. doi: 10.1111/tpj.12235. Epub 2013 Jun 13.


BLAST output visualization in the new sequencing era.

Neumann RS, Kumar S, Shalchian-Tabrizi K.

Brief Bioinform. 2014 Jul;15(4):484-503.


Massive expansion of the calpain gene family in unicellular eukaryotes.

Zhao S, Liang Z, Demko V, Wilson R, Johansen W, Olsen OA, Shalchian-Tabrizi K.

BMC Evol Biol. 2012 Sep 29;12:193. doi: 10.1186/1471-2148-12-193.


Genome fragmentation is not confined to the peridinin plastid in dinoflagellates.

Espelund M, Minge MA, Gabrielsen TM, Nederbragt AJ, Shalchian-Tabrizi K, Otis C, Turmel M, Lemieux C, Jakobsen KS.

PLoS One. 2012;7(6):e38809. doi: 10.1371/journal.pone.0038809. Epub 2012 Jun 18.


Radiolaria associated with large diversity of marine alveolates.

Bråte J, Krabberød AK, Dolven JK, Ose RF, Kristensen T, Bjørklund KR, Shalchian-Tabrizi K.

Protist. 2012 Sep;163(5):767-77. doi: 10.1016/j.protis.2012.04.004. Epub 2012 May 31.


Genomic survey of premetazoans shows deep conservation of cytoplasmic tyrosine kinases and multiple radiations of receptor tyrosine kinases.

Suga H, Dacre M, de Mendoza A, Shalchian-Tabrizi K, Manning G, Ruiz-Trillo I.

Sci Signal. 2012 May 1;5(222):ra35. doi: 10.1126/scisignal.2002733.


Collodictyon--an ancient lineage in the tree of eukaryotes.

Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K.

Mol Biol Evol. 2012 Jun;29(6):1557-68. doi: 10.1093/molbev/mss001. Epub 2012 Jan 6.


Radiolaria divided into Polycystina and Spasmaria in combined 18S and 28S rDNA phylogeny.

Krabberød AK, Bråte J, Dolven JK, Ose RF, Klaveness D, Kristensen T, Bjørklund KR, Shalchian-Tabrizi K.

PLoS One. 2011;6(8):e23526. doi: 10.1371/journal.pone.0023526. Epub 2011 Aug 10.


Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains.

Torruella G, Derelle R, Paps J, Lang BF, Roger AJ, Shalchian-Tabrizi K, Ruiz-Trillo I.

Mol Biol Evol. 2012 Feb;29(2):531-44. doi: 10.1093/molbev/msr185. Epub 2011 Jul 18.


CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation.

Kumar S, Carlsen T, Mevik BH, Enger P, Blaalid R, Shalchian-Tabrizi K, Kauserud H.

BMC Bioinformatics. 2011 May 20;12:182. doi: 10.1186/1471-2105-12-182.


Genome evolution of a tertiary dinoflagellate plastid.

Gabrielsen TM, Minge MA, Espelund M, Tooming-Klunderud A, Patil V, Nederbragt AJ, Otis C, Turmel M, Shalchian-Tabrizi K, Lemieux C, Jakobsen KS.

PLoS One. 2011 Apr 26;6(4):e19132. doi: 10.1371/journal.pone.0019132.


Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences.

Shalchian-Tabrizi K, Reier-Røberg K, Ree DK, Klaveness D, Bråte J.

J Eukaryot Microbiol. 2011 Jul-Aug;58(4):315-8. doi: 10.1111/j.1550-7408.2011.00547.x. Epub 2011 Apr 21.


A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum.

Minge MA, Shalchian-Tabrizi K, Tørresen OK, Takishita K, Probert I, Inagaki Y, Klaveness D, Jakobsen KS.

BMC Evol Biol. 2010 Jun 21;10:191. doi: 10.1186/1471-2148-10-191.


Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations.

Bråte J, Klaveness D, Rygh T, Jakobsen KS, Shalchian-Tabrizi K.

BMC Microbiol. 2010 Jun 9;10:168. doi: 10.1186/1471-2180-10-168.


Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA.

Bråte J, Logares R, Berney C, Ree DK, Klaveness D, Jakobsen KS, Shalchian-Tabrizi K.

ISME J. 2010 Sep;4(9):1144-53. doi: 10.1038/ismej.2010.39. Epub 2010 Apr 15.

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