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Items: 1 to 50 of 59

1.

Unicellular Origin of the Animal MicroRNA Machinery.

Bråte J, Neumann RS, Fromm B, Haraldsen AAB, Tarver JE, Suga H, Donoghue PCJ, Peterson KJ, Ruiz-Trillo I, Grini PE, Shalchian-Tabrizi K.

Curr Biol. 2018 Oct 22;28(20):3288-3295.e5. doi: 10.1016/j.cub.2018.08.018. Epub 2018 Oct 11.

2.

Correction to: Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution.

Orr RJS, Zhao S, Klaveness D, Yabuki A, Ikeda K, Watanabe MM, Shalchian-Tabrizi K.

BMC Evol Biol. 2018 Aug 3;18(1):118. doi: 10.1186/s12862-018-1233-y.

3.

Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution.

Orr RJS, Zhao S, Klaveness D, Yabuki A, Ikeda K, Watanabe MM, Shalchian-Tabrizi K.

BMC Evol Biol. 2018 Jul 18;18(1):115. doi: 10.1186/s12862-018-1224-z. Erratum in: BMC Evol Biol. 2018 Aug 3;18(1):118.

4.

Erratum for Orr et al., "Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples".

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Oct 12;5(41). pii: e01175-17. doi: 10.1128/genomeA.01175-17. No abstract available.

5.

Erratum for Orr et al., "Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples".

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Oct 12;5(41). pii: e01152-17. doi: 10.1128/genomeA.01152-17. No abstract available.

6.

Erratum for Orr et al., "Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples".

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Oct 5;5(40). pii: e01176-17. doi: 10.1128/genomeA.01176-17. No abstract available.

7.

Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples.

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Aug 24;5(34). pii: e00894-17. doi: 10.1128/genomeA.00894-17. Erratum in: Genome Announc. 2017 Oct 12;5(41):.

8.

Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples.

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Aug 24;5(34). pii: e00884-17. doi: 10.1128/genomeA.00884-17. Erratum in: Genome Announc. 2017 Oct 5;5(40):.

9.

Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples.

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Aug 17;5(33). pii: e00787-17. doi: 10.1128/genomeA.00787-17. Erratum in: Genome Announc. 2017 Oct 12;5(41):.

10.

X-Cells Are Globally Distributed, Genetically Divergent Fish Parasites Related to Perkinsids and Dinoflagellates.

Freeman MA, Fuss J, Kristmundsson Á, Bjorbækmo MFM, Mangot JF, Del Campo J, Keeling PJ, Shalchian-Tabrizi K, Bass D.

Curr Biol. 2017 Jun 5;27(11):1645-1651.e3. doi: 10.1016/j.cub.2017.04.045. Epub 2017 May 18.

11.

Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria.

Krabberød AK, Orr RJS, Bråte J, Kristensen T, Bjørklund KR, Shalchian-Tabrizi K.

Mol Biol Evol. 2017 Jul 1;34(7):1557-1573. doi: 10.1093/molbev/msx075.

12.

Benthic protists: the under-charted majority.

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

FEMS Microbiol Ecol. 2016 Aug;92(8). pii: fiw120. doi: 10.1093/femsec/fiw120. Epub 2016 Jun 5.

PMID:
27267932
13.

Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum.

Bråte J, Adamski M, Neumann RS, Shalchian-Tabrizi K, Adamska M.

Proc Biol Sci. 2015 Dec 22;282(1821):20151746. doi: 10.1098/rspb.2015.1746.

14.

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.

PMID:
26119494
15.

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.

16.

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.

17.

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.

18.

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.

PMID:
23973893
19.

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.

20.

BLAST output visualization in the new sequencing era.

Neumann RS, Kumar S, Shalchian-Tabrizi K.

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

PMID:
23603091
21.

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.

22.

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.

23.

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.

PMID:
22658831
24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

PMID:
21518078
31.

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.

32.

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.

33.

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.

PMID:
20393574
34.

AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.

Kumar S, Skjaeveland A, Orr RJ, Enger P, Ruden T, Mevik BH, Burki F, Botnen A, Shalchian-Tabrizi K.

BMC Bioinformatics. 2009 Oct 28;10:357. doi: 10.1186/1471-2105-10-357.

35.

Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11).

Logares R, Bråte J, Heinrich F, Shalchian-Tabrizi K, Bertilsson S.

Mol Biol Evol. 2010 Feb;27(2):347-57. doi: 10.1093/molbev/msp239. Epub 2009 Oct 6.

PMID:
19808864
36.

Infrequent marine-freshwater transitions in the microbial world.

Logares R, Bråte J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K.

Trends Microbiol. 2009 Sep;17(9):414-22. doi: 10.1016/j.tim.2009.05.010. Epub 2009 Aug 31. Review.

PMID:
19726194
37.

Revisiting the phylogenetic position of Synchroma grande.

Patil V, Bråte J, Shalchian-Tabrizi K, Jakobsen KS.

J Eukaryot Microbiol. 2009 Jul-Aug;56(4):394-6. doi: 10.1111/j.1550-7408.2009.00389.x.

PMID:
19602087
38.

Seven gene phylogeny of heterokonts.

Riisberg I, Orr RJ, Kluge R, Shalchian-Tabrizi K, Bowers HA, Patil V, Edvardsen B, Jakobsen KS.

Protist. 2009 May;160(2):191-204. doi: 10.1016/j.protis.2008.11.004. Epub 2009 Feb 12.

PMID:
19213601
39.

Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates.

Burki F, Inagaki Y, Bråte J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen KS, Pawlowski J, Shalchian-Tabrizi K.

Genome Biol Evol. 2009 Jul 27;1:231-8. doi: 10.1093/gbe/evp022.

40.

Evolutionary position of breviate amoebae and the primary eukaryote divergence.

Minge MA, Silberman JD, Orr RJ, Cavalier-Smith T, Shalchian-Tabrizi K, Burki F, Skjaeveland A, Jakobsen KS.

Proc Biol Sci. 2009 Feb 22;276(1657):597-604. doi: 10.1098/rspb.2008.1358.

41.

Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny.

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

Environ Microbiol. 2008 Oct;10(10):2635-44. doi: 10.1111/j.1462-2920.2008.01685.x. Epub 2008 Jul 16.

PMID:
18643928
42.

Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes.

Burki F, Shalchian-Tabrizi K, Pawlowski J.

Biol Lett. 2008 Aug 23;4(4):366-9. doi: 10.1098/rsbl.2008.0224.

43.

Multigene phylogeny of choanozoa and the origin of animals.

Shalchian-Tabrizi K, Minge MA, Espelund M, Orr R, Ruden T, Jakobsen KS, Cavalier-Smith T.

PLoS One. 2008 May 7;3(5):e2098. doi: 10.1371/journal.pone.0002098.

44.
45.

Extensive dinoflagellate phylogenies indicate infrequent marine-freshwater transitions.

Logares R, Shalchian-Tabrizi K, Boltovskoy A, Rengefors K.

Mol Phylogenet Evol. 2007 Dec;45(3):887-903. Epub 2007 Aug 26.

PMID:
17928239
46.

Phylogenomics reshuffles the eukaryotic supergroups.

Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, Jakobsen KS, Pawlowski J.

PLoS One. 2007 Aug 29;2(8):e790.

47.

Accelerated nrDNA evolution and profound AT bias in the medicinal fungus Cordyceps sinensis.

Stensrud Ø, Schumacher T, Shalchian-Tabrizi K, Svegården IB, Kauserud H.

Mycol Res. 2007 Apr;111(Pt 4):409-15. Epub 2007 Feb 4.

PMID:
17509850
48.

Structural analysis of a non-ribosomal halogenated cyclic peptide and its putative operon from Microcystis: implications for evolution of cyanopeptolins.

Tooming-Klunderud A, Rohrlack T, Shalchian-Tabrizi K, Kristensen T, Jakobsen KS.

Microbiology. 2007 May;153(Pt 5):1382-93. Erratum in: Microbiology. 2009 Jun;155(Pt 6):2106-8.

PMID:
17464052
49.

Phenotypically different microalgal morphospecies with identical ribosomal DNA: a case of rapid adaptive evolution?

Logares R, Rengefors K, Kremp A, Shalchian-Tabrizi K, Boltovskoy A, Tengs T, Shurtleff A, Klaveness D.

Microb Ecol. 2007 May;53(4):549-61. Epub 2007 Apr 5.

PMID:
17410396
50.

Analysis of environmental 18S ribosomal RNA sequences reveals unknown diversity of the cosmopolitan phylum Telonemia.

Shalchian-Tabrizi K, Kauserud H, Massana R, Klaveness D, Jakobsen KS.

Protist. 2007 Apr;158(2):173-80. Epub 2006 Dec 29.

PMID:
17196879

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