Kamran Shalchian-Tabrizi

• Gulbrandsen, Øyvind Sætren; Andresen, Ina Jungersen; Krabberød, Anders Kristian; Bråte, Jon & Shalchian-Tabrizi, Kamran (2021). Phylogenomic analysis restructures the Ulvophyceae. Journal of Phycology.  ISSN 0022-3646. . doi: 10.1111/jpy.13168
• Bråte, Jon; Neumann, Ralf Stefan; Fromm, Bastian; Haraldsen, Arthur Alexander Blørstad; Tarver, James E.; Suga, Hiroshi; Donoghue, Philip C.J.; Peterson, Kevin J.; Ruiz-Trillo, Iñaki; Grini, Paul Eivind & Shalchian-Tabrizi, Kamran (2018). Unicellular origin of the animal microRNA machinery. Current Biology.  ISSN 0960-9822.  28(20), s 3288- 3295.e5 . doi: 10.1016/j.cub.2018.08.018 Fulltekst i vitenarkiv.
• Orr, Russell; Zhao, Sen; Klaveness, Dag; Yabuki, Akinori; Ikeda, Keiji; Makoto, Watanabe M. & Shalchian-Tabrizi, Kamran (2018). Enigmatic diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution. BMC Evolutionary Biology.  ISSN 1471-2148.  18(115), s 1- 13 . doi: 10.1186/s12862-018-1224-z Fulltekst i vitenarkiv.
• Freeman, Mark A.; Fuss, Janina; Kristmundsson, Árni; Bjorbækmo, Marit Fredrikke Markussen; Mangot, Jean-Francois; del Campo, Javier; Keeling, Patrick J; Shalchian-Tabrizi, Kamran & Bass, David (2017). X-Cells Are Globally Distributed, Genetically Divergent Fish Parasites Related to Perkinsids and Dinoflagellates. Current Biology.  ISSN 0960-9822.  27(11), s 1645- 1651 . doi: 10.1016/j.cub.2017.04.045
• Krabberød, Anders Kristian; Bjorbækmo, Marit Markussen; Shalchian-Tabrizi, Kamran & Logares, Ramiro (2017). Exploring the oceanic microeukaryotic interactome with metaomics approaches. Aquatic Microbial Ecology.  ISSN 0948-3055.  79(1), s 1- 12 . doi: 10.3354/ame01811
• Krabberød, Anders Kristian; Orr, Russell; Bråte, Jon; Kristensen, Tom; Bjørklund, Kjell Rasmus & Shalchian-Tabrizi, Kamran (2017). Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria. Molecular Biology and Evolution (MBE).  ISSN 0737-4038. . doi: /10.1093/molbev/msx075 Vis sammendrag

  The innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport and cytokinesis, and is responsible for the diversity of eukaryotic morphologies. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton we provide the first single cell transcriptomes from uncultured, free-living unicellular eukaryotes: the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida). A phylogenomic approach using 255 genes finds Radiolaria and Foraminifera as separate monophyletic groups (together as Retaria), while Cercozoa is shown to be paraphyletic. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these to the revised phylogeny of Rhizaria reveal lineage-specific gene duplications and neofunctionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution in uncultured protist species.

• Orr, Russell; Rombauts, Stephane; Van de Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Draft genome sequences of two unclassified bacteria, Hydrogenophaga sp. strains IBVHS1 and IBVHS2, isolated from environmental samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(34) . doi: 10.1128/genomeA.00884-17
• Orr, Russell; Shalchian-Tabrizi, Kamran; Van de Peer, Yves & Rombauts, S (2017). Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(34) . doi: 10.1128/genomeA.00894-17
• Orr, Russell; Shalchian-Tabrizi, Kamran; Van de Peer, Yves & Rombauts, S (2017). Draft genome Sequences of two Unclassified Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287. . doi: 10.1128/genomeA.00787-17
• Forster, Dominik; Dunthorn, Micah; Mahé, Frédéric; Dolan, John R.; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Edvardsen, Bente; Egge, Elianne Dunthorn; Eikrem, Wenche; Gobet, Angélique; Kooistra, Wiebe H.C.F.; Logares, Ramiro; Massana, Ramon; Montresor, Marina; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C.; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Richards, Thomas A.; Santini, Sébastien; Sarno, Diana; Siano, Raffaele; Vaulot, Daniel; Wincker, Patrick; Zingone, Adriana; De Vargas, Colomban & Stoeck, Thorsten (2016). Benthic protists: The under-charted majority. FEMS Microbiology Ecology.  ISSN 0168-6496.  92(8), s 1- 11 . doi: 10.1093/femsec/fiw120
• Bråte, Jon; Adamski, Marcin; Neumann, Ralf Stefan; Shalchian-Tabrizi, Kamran & Adamska, Maja (2015). Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum. Proceedings of the Royal Society of London. Biological Sciences.  ISSN 0962-8452.  282(1821), s 1- 9 . doi: 10.1098/rspb.2015.1746 Fulltekst i vitenarkiv. Vis sammendrag

  Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation was important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analysed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge Sycon ciliatum and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signalling molecules. This study provides insights into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was likely present in the last common ancestor of animals.

• Kumar, Surendra; Krabberød, Anders Kristian; Neumann, Ralf Stefan; Michalickova, Katerina; Zhao, Sen; Zhang, Xiaoli & Shalchian-Tabrizi, Kamran (2015). BIR pipeline for preparation of phylogenomic data. Evolutionary Bioinformatics.  ISSN 1176-9343.  11, s 79- 83 . doi: 10.4137/EBO.S10189
• Massana, Ramon; Gobet, Angelique; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Chambouvet, Aurélie; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R.; Dunthorn, Micah; Edvardsen, Bente; Forn, Irene; Forster, Dominik; Guillou, Laure; Jaillon, Olivier; Kooistra, Wiebe H. C. F.; Logares, Ramiro; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C.; Probert, Ian; Romac, Sarah; Richards, Thomas; Santini, Sebastien; Shalchian-Tabrizi, Kamran; Siano, Raffaele; Simon, Nathalie; Stoeck, Thorsten; Vaulot, Daniel; Zingone, Adriana & de Vargas, Colomban (2015). Marine protist diversity in European coastal watersand sediments as revealed by high-throughputsequencing. Environmental Microbiology.  ISSN 1462-2912.  17(10), s 4035- 4049 . doi: 10.1111/1462-2920.12955
• Logares, Ramiro; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R.; Dunthorn, Micah; Edvardsen, Bente; Gobet, Angelique; Kooistra, Wiebe H.C.F.; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C.; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Stoeck, Thorsten; Santini, Sebastien; Siano, Raffaele; Wincker, Patrick; Zingone, Adriana; Richards, Thomas A.; de Vargas, Colomban & Massana, Ramon (2014). Patterns of Rare and Abundant Marine Microbial Eukaryotes. Current Biology.  ISSN 0960-9822.  24(8), s 813- 821 . doi: 10.1016/j.cub.2014.02.050
• Neumann, Ralf Stefan; Kumar, Surendra; Haverkamp, Thomas Hendricus Augustus & Shalchian-Tabrizi, Kamran (2014). BLASTGrabber: A bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data. BMC Bioinformatics.  ISSN 1471-2105.  15(128) . doi: 10.1186/1471-2105-15-128 Fulltekst i vitenarkiv.
• Neumann, Ralf Stefan; Kumar, Surendra & Shalchian-Tabrizi, Kamran (2014). BLAST output visualization in the new sequencing era. Briefings in Bioinformatics.  ISSN 1467-5463.  15(4), s 484- 503 . doi: 10.1093/bib/bbt009
• Liang, Zhe; Demko, Viktor; Wilson, Robert Charles; Johnson, Kenneth; Ahmad, Rafi; Perroud, Pierre-Francois; Quatrano, Ralph; Zhao, Sen; Shalchian-Tabrizi, Kamran; Otegui, Marisa; Olsen, Odd-Arne & Johansen, Wenche (2013). The catalytic domain CysPc of the DEK1 calpain is functionally conserved in land plants. The Plant Journal.  ISSN 0960-7412.  75(5), s 742- 754 . doi: 10.1111/tpj.12235
• Zhao, Sen; Shalchian-Tabrizi, Kamran & Klaveness, Dag (2013). Sulcozoa revealed as a paraphyletic group in mitochondrial phylogenomics. Molecular Phylogenetics and Evolution.  ISSN 1055-7903.  69(3), s 462- 468 . doi: 10.1016/j.ympev.2013.08.005 Vis sammendrag

  Recently, phylogenomic analyses have been used to assign the vast majority of eukaryotes into only a handful of supergroups. However, a few enigmatic lineages still do not fit into this simple picture. Such lineages may have originated early in the history of eukaryotes and are therefore of key importance in deduction of cellular evolution. In this study, we focus on two deeply diverging lineages, Diphyllatea and Thecamonadea. They are classified in the same phylum, Sulcozoa, but previous multigene phylogenetic analyses have included only one of these two lineages. It is therefore unclear whether they constitute one group or two distinct lineages. The study of rare genomic changes reveals that both have the fused dihydrofolate reductase (DHFR) and thymidylate synthase (TS) genes (i.e. DHFR–TS), which are separated in all other unikonts that have been investigated, indicating a possible close relationship. Their phylogenetic positions have implications for the classification of Sulcozoa and the early eukaryote evolution. Here we present a phylogenomic analysis of these species that include Illumina and 454 transcriptome data from two Collodictyon strains. A total of 42 mitochondrial proteins, which correspond to orthologs published from Thecamonas trahens (Thecamonadea), were used to reconstruct their phylogenies. In the resulting trees, Collodictyon appears as sister to Amoebozoa, whereas Thecamonas branches as the closest relative of Opisthokonta (i.e. the animal, fungi and unicellular Choanozoa). In contrast, the position of another early diverging eukaryote, Malawimonas, is unresolved. The separation of Collodictyon and Thecamonas in our studies suggests that the recently proposed Sulcozoa group is most likely paraphyletic. Furthermore, the data support the hypothesis that the two supergroups Opisthokonta and Amoebozoa, which comprise a great diversity of eukaryotes, have originated from a sulcozoan ancestor.

• Bråte, Jon; Krabberød, Anders Kristian; Dolven, Jane Karine Lønne; Ose, Randi Frida; Kristensen, Tom; Bjørklund, Kjell Rasmus & Shalchian-Tabrizi, Kamran (2012). Radiolaria Associated with Large Diversity of Marine Alveolates. Protist.  ISSN 1434-4610.  163(5), s 767- 777 . doi: 10.1016/j.protis.2012.04.004 Vis sammendrag

  We have isolated cells of unculturable radiolarians from marine coastal waters. Individual cells were subjected to single cell whole genome amplification (SCWGA) and gene-targeted PCR. Using this approach we recover a surprisingly large diversity of sequences related to the enigmatic marine alveolate groups 1 and 2 (MALV I and MALV II) that most likely represent intracellular symbionts or parasites of the radiolarian cells. 18S rDNA phylogeny of the MALV sequences reveals 4 distinct clades of radiolarian associates here named Radiolarian Associated Sequences (RAS) 1-4. One clade of both phaeodarian and radiolarian associates and one clade of only phaeodarian associates are also identified. The MALV sequences cluster according to host type, i.e. sequences from associates identified in radiolarians, fish, copepods, ciliates or dinoflagellates are not intermixed but separated into distinct clades. This implies several independent colonizations of host lineages and links a large diversity of MALV to radiolarian-associated species. This demonstrates that radiolarians may be an important reservoir for MALV, making them a key group for understanding the impact of intracellular symbionts on the marine ecosystem. This study shows that applying SCWGA on unculturable cells is a promising approach to study the vast diversity and interactions of intracellular eukaryote organisms.

• Espelund, Mari; Minge, Marianne Aastebøl; Gabrielsen, Tove M; Nederbragt, Alexander Johan; Shalchian-Tabrizi, Kamran; Otis, Christian; Turmel, Monique; Lemieux, Claude & Jakobsen, Kjetill Sigurd (2012). Genome Fragmentation Is Not Confined to the Peridinin Plastid in Dinoflagellates. PLOS ONE.  ISSN 1932-6203.  7(6) . doi: 10.1371/journal.pone.0038809 Fulltekst i vitenarkiv.
• Suga, Hiroshi; Dacre, Michael; de Mendoza, Alex; Shalchian-Tabrizi, Kamran; Manning, G & Ruiz-Trillo, Iñaki (2012). Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine Kinases. Science Signaling.  ISSN 1945-0877.  5(222) . doi: 10.1126/scisignal.2002733
• Torruella, Guifré; Derelle, Romain; Paps, Jordi; Lang, B. Franz; Roger, Andrew J.; Shalchian-Tabrizi, Kamran & Ruiz-Trillo, Iñaki (2012). Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Molecular Biology and Evolution (MBE).  ISSN 0737-4038.  29(2), s 531- 544 . doi: 10.1093/molbev/msr185
• Zhao, Sen; Burki, Fabien; Bråte, Jon; Keeling, Patrick J; Klaveness, Dag & Shalchian-Tabrizi, Kamran (2012). Collodictyon - An Ancient Lineage in the Tree of Eukaryotes. Molecular Biology and Evolution (MBE).  ISSN 0737-4038.  29(6), s 1557- 1568 . doi: 10.1093/molbev/mss001
• Zhao, Sen; Liang, Zhe; Demko, Viktor; Wilson, Robert; Johansen, Wenche; Olsen, Odd-Arne & Shalchian-Tabrizi, Kamran (2012). Massive expansion of the calpain gene family in unicellular eukaryotes. BMC Evolutionary Biology.  ISSN 1471-2148.  12(193) . doi: 10.1186/1471-2148-12-193
• Gabrielsen, Tove M; Minge, Marianne Aastebøl; Espelund, Mari; Tooming-Klunderud, Ave; Patil, Viswanath; Nederbragt, Alexander Johan; Otis, Christian; Turmel, Monique; Shalchian-Tabrizi, Kamran; Lemieux, Claude & Jakobsen, Kjetill Sigurd (2011). Genome Evolution of a Tertiary Dinoflagellate Plastid. PLOS ONE.  ISSN 1932-6203.  6(4), s e19132 . doi: 10.1371/journal.pone.0019132
• Klaveness, Dag; Bråte, Jon; Patil, Viswanath; Shalchian-Tabrizi, Kamran; Kluge, Ragnhild; Gislerød, Hans Ragnar & Jakobsen, Kjetill Sigurd (2011). The 18S and 28S rDNA indentity and phylogeny of the common lotic chrysophyte Hydrurus foetidus. European journal of phycology.  ISSN 0967-0262.  46(3), s 282- 291 . doi: 10.1080/09670262.2011.598950
• Krabberød, Anders Kristian; Bråte, Jon; Dolven, Jane Karine Lønne; Ose, Randi Frida; Klaveness, Dag; Kristensen, Tom; Bjørklund, Kjell Rasmus & Shalchian-Tabrizi, Kamran (2011). Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny. PLOS ONE.  ISSN 1932-6203.  6(8) . doi: 10.1371/journal.pone.0023526 Vis sammendrag

  Radiolarians are marine planktonic protists that belong to the eukaryote supergroup Rhizaria together with Foraminifera and Cercozoa. Radiolaria has traditionally been divided into four main groups based on morphological characters; i.e. Polycystina, Acantharia, Nassellaria and Phaeodaria. But recent 18S rDNA phylogenies have shown that Phaeodaria belongs within Cerocozoa, and that the previously heliozoan group Taxopodida should be included in Radiolaria. 18S rDNA phylogenies have not yet resolved the sister relationship between the main Radiolaria groups, but nevertheless suggests that Spumellaria, and thereby also Polycystina, are polyphyletic. Very few sequences other than 18S rDNA have so far been generated from radiolarian cells, mostly due to the fact that Radiolaria has been impossible to cultivate and single cell PCR has been hampered by low success rate. Here we have therefore investigated the mutual evolutionary relationship of the main radiolarian groups by using the novel approach of combining single cell whole genome amplification with targeted PCR amplification of the 18S and 28S rDNA genes. Combined 18S and 28S phylogeny of sequences obtained from single cells shows that Radiolaria is divided into two main lineages: Polycystina (Spumellaria+Nassellaria) and Spasmaria (Acantharia+Taxopodida). Further we show with high support that Foraminifera groups within Radiolaria supporting the Retaria hypothesis.

• Kumar, Surendra; Carlsen, Tor; Mevik, Bjørn-Helge; Enger, Pål; Blaalid, Rakel; Shalchian-Tabrizi, Kamran & Kauserud, Håvard (2011). CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinformatics.  ISSN 1471-2105.  12 . doi: 10.1186/1471-2105-12-182 Fulltekst i vitenarkiv. Vis sammendrag

  Background:The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce CLOTU, an online and open access pipeline for processing 454 amplicon reads. CLOTU has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets. Results:In CLOTU, the user can filter out low quality sequences, trim tags, primers, adaptors, perform clustering of sequence reads, and run BLAST against NCBInr or a customized database in a high performance computing environment. The resulting data may be browsed in a user-friendly manner and easily forwarded to downstream analyses. Although CLOTU is specifically designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be processed. A fungal ITS sequence dataset generated by 454 sequencing of environmental samples is used to demonstrate the utility of CLOTU. Conclusions:CLOTU is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. CLOTU is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal web-based bioinformatics service (http://www.bioportal.uio.no).

• Shalchian-Tabrizi, Kamran; Røberg, Kjetil; Ree, Dan Kristofer; Klaveness, Dag & Bråte, Jon (2011). Marine-Freshwater Colonizations of Haptophytes Inferred from Phylogeny of Environmental 18S rDNA Sequences. Journal of Eukaryotic Microbiology.  ISSN 1066-5234.  58(4), s 315- 318 . doi: 10.1111/j.1550-7408.2011.00547.x
• Bråte, Jon; Klaveness, Dag; Rygh, T; Jakobsen, Kjetill Sigurd & Shalchian-Tabrizi, Kamran (2010). Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations. BMC Microbiology.  ISSN 1471-2180.  10(168) . doi: 10.1186/1471-2180-10-168
• Bråte, Jon; Logares, Ramiro; Berney, Cedric; Ree, Dan Kristofer; Klaveness, Dag; Jakobsen, Kjetill Sigurd & Shalchian-Tabrizi, Kamran (2010). Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. The ISME Journal.  ISSN 1751-7362.  4(9), s 1144- 1153 . doi: 10.1038/ismej.2010.39
• Logares, Ramiro; Bråte, Jon; Heinrich, F; Shalchian-Tabrizi, Kamran & Bertilsson, Stefan (2010). Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11). Molecular Biology and Evolution (MBE).  ISSN 0737-4038.  27(2), s 347- 357 . doi: 10.1093/molbev/msp239
• Minge, Marianne Aastebøl; Shalchian-Tabrizi, Kamran; Tørresen, Ole Kristian; Takishita, Kiyotaka; Probert, Ian; Inagaki, Yuji; Klaveness, Dag & Jakobsen, Kjetill Sigurd (2010). A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum. BMC Evolutionary Biology.  ISSN 1471-2148.  10 . doi: 10.1186/1471-2148-10-191 Fulltekst i vitenarkiv.
• Riisberg, Ingvild; Orr, Russell; Kluge, Ragnhild; Shalchian-Tabrizi, Kamran; Bowers, HA; Vishwanath, Patil; Edvardsen, Bente & Jakobsen, Kjetill Sigurd (2009). Seven Gene Phylogeny of Heterokonts. Protist.  ISSN 1434-4610.  160(2), s 191- 204 . doi: 10.1016/j.protis.2008.11.004
• Vishwanath, Patil; Bråte, Jon; Shalchian-Tabrizi, Kamran & Jakobsen, Kjetill Sigurd (2009). Revisiting the Phylogenetic Position of Synchroma grande. Journal of Eukaryotic Microbiology.  ISSN 1066-5234.  56(4), s 394- 396
• Burki, Fabien; Inagaki, Yuji; Bråte, Jon; Archibald, John M; Keeling, Patrick J; Cavalier-Smith, Thomas; Sakaguchi, Miako; Hashimoto, Tetsuo; Horak, Ales; Kumar, Surendra; Klaveness, Dag; Jakobsen, Kjetill Sigurd; Pawlowski, Jan & Shalchian-Tabrizi, Kamran (2009). Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates. Genome Biology and Evolution (GBE).  ISSN 1759-6653.  1(1), s 231- 238 . doi: 10.1093/gbe/evp022
• Kumar, Surendra; Skjæveland, Åsmund; Orr, Russell; Enger, Pål; Ruden, Torgeir Andersen; Mevik, Bjørn-Helge; Burki, Fabien; Botnen, Andreas Valeur & Shalchian-Tabrizi, Kamran (2009). AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics.  ISSN 1471-2105.  10 . doi: 10.1186/1471-2105-10-357 Fulltekst i vitenarkiv. Vis sammendrag

  Background: Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites. Results: Here we present a batch-oriented web-based program package, named AIR that allows 1) transformation of several single genes to one multigene alignment, 2) identification of evolutionary rates in multigene alignments and 3) removal of fast evolving sites. These three processes can be done with the programs AIR-Appender, AIR-Identifier, and AIR-Remover (AIR), which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal (www.bioportal.uio.no), University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses. Conclusions: The AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.

• Logares, Ramiro; Bråte, Jon; Bertilsson, Stefan; Clasen, Jessica L; Shalchian-Tabrizi, Kamran & Rengefors, Karin (2009). Infrequent marine-freshwater transitions in the microbial world. Trends in Microbiology.  ISSN 0966-842X.  17(9), s 414- 422 . doi: 10.1016/j.tim.2009.05.010
• Logares, Ramiro; Bråte, Jon; Friederike, Heinrich; Shalchian-Tabrizi, Kamran & Bertilsson, Stefan (2009). Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Molecular Biology and Evolution (MBE).  ISSN 0737-4038. . doi: 10.1093/molbev/msp239
• Minge, Marianne Aastebøl; Silberman, Jeffrey; Orr, Russell; Cavalier-Smith, Thomas; Shalchian-Tabrizi, Kamran; Burki, Fabien; Skjæveland, Åsmund & Jakobsen, Kjetill Sigurd (2009). Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proceedings of the Royal Society of London. Biological Sciences.  ISSN 0962-8452.  276(1657), s 597- 604 . doi: 10.1098/rspb.2008.1358
• Burki, F; Shalchian-Tabrizi, Kamran & Pawlowski, J (2008). Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biology Letters.  ISSN 1744-9561.  4, s 366- 369 . doi: 10.1098/rsbl.2008.0224
• Shalchian-Tabrizi, Kamran; Bråte, Jon; Logares, R; Klaveness, Dag; Berney, Cedrik & Jakobsen, Kjetill Sigurd (2008). Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environmental Microbiology.  ISSN 1462-2912.  10(10), s 2635- 2644 . doi: 10.1111/j.1462-2920.2008.01685.x
• Shalchian-Tabrizi, Kamran; Minge, Marianne Aastebøl; Espelund, Mari; Orr, Russell; Ruden, Torgeir Andersen; Jakobsen, Kjetill Sigurd & Cavalier-Smith, Thomas (2008). Multigene Phylogeny of Choanozoa and the Origin of Animals. PLOS ONE.  ISSN 1932-6203.  3(5)
• Edvardsen, B; Eikrem, W; Shalchian-Tabrizi, K; Riisberg, I; Johnsen, Geir; Naustvoll, L & Throndsen, J (2007). Verrucophora farcimen gen. et sp nov (Dictyochophyceae, Heterokonta) - A bloom-forming ichthyotoxic flagellate from the Skagerrak, Norway. Journal of Phycology.  ISSN 0022-3646.  43, s 1054- 1070 . doi: 10.1111/j.1529-8817.2007.00390.x
• Burki, Fabien; Shalchian-Tabrizi, Kamran; Minge, Marianne Aastebøl; Skjæveland, Åsmund; Nikolajev, Sergey I; Jakobsen, Kjetill Sigurd & Jan, Pawlowski (2007). Phylogenomics Reshuffles the Eukaryotic Supergroups. PLOS ONE.  ISSN 1932-6203.  2(8) . doi: 10.1371/journal.pone.0000790
• Kauserud, Håvard; Shalchian-Tabrizi, Kamran & DeCock, Cony (2007). Multi-locus sequencing reveals multiple geographically structured lineages of Coniophora arida and C. olivacea (Boletales) in North America. Mycologia.  ISSN 0027-5514.  99, s 705- 713
• Logares, Ramiro; Rengefors, Karin; Kremp, Anke; Shalchian-Tabrizi, Kamran; Boltovskoy, Andrés; Tengs, Torstein; Shurtleff, Aaron & Klaveness, Dag (2007). Phenotypically different microalgal morphospecies with identical ribosomal DNA: A case of rapid adaptive evolution?. Microbial Ecology.  ISSN 0095-3628.  53, s 549- 561 . doi: 10.1007/s00248-006-9088-y
• Logares, Ramiro; Shalchian-Tabrizi, Kamran; Boltovskoy, Andrés & Rengefors, Karin (2007). Extensive dinoflagellate phylogenies indicate infrequent and usually not recent marine-freshwater transitions. Molecular Phylogenetics and Evolution.  ISSN 1055-7903.  45, s 887- 903 . doi: 10.1016/j.ympev.2007.08.005
• Shalchian-Tabrizi, Kamran; Kauserud, Håvard; Massana, R; Klaveness, Dag & Jakobsen, Kjetill Sigurd (2007). Analysis of environmental 18S ribosomal RNA sequences reveals unknown diversity of the cosmopolitan phylum Telonemia. Protist.  ISSN 1434-4610.  158, s 173- 180 . doi: 10.1016/j.protis.2006.10.003
• Stensrud, Øyvind; Schumacher, Trond; Shalchian-Tabrizi, Kamran; Svegården, Ingeborg Bjorvand & Kauserud, Håvard (2007). Accelerated nrDNA evolution and profound AT bias in the medicinal fungus Cordyceps sinensis. Mycological Research.  ISSN 0953-7562.  111(4), s 409- 415 . doi: 10.1016/j.mycres.2007.01.015 Vis sammendrag

  Cordyceps sinensis is a reputed medicinal fungus growing parasitically on buried larvae of ghost moths in Asian high-altitude grassland ecosystems. We have analysed the intraspecific ITS nrDNA (ITS1, 5.8S gene, ITS2) variation among 71 sequences of C. sinensis available in EMBL/Genbank. The ITS sequences, submitted to Bayesian ML analyses, were distributed into five groups, referred to as A-E. Nine of the sequences (groups D and E) grouped with distantly related hypocrealean/clavicipitalean taxa and are interpreted as sequences erroneously accessioned under wrong taxon names. The remaining 62 sequences constituted three highly supported clades (groups A-C), that may represent cryptic (phylogenetic) species currently ascribed to C. sinensis. A remarkably high sequence divergence occurred in the 5.8S gene between the three groups. Sequences of groups B and C showed accelerated substitution rates and high AT nucleotide bias. We hypothesize that the accelerated evolution and AT bias have been caused by a shift in life historical attributes or ecology. We also suggest that the recorded differences in medicinal effects among C. sinensis populations may be attributed to the existence of genetically differentiated chemotypes in this morphotaxon.

• Tooming-Klunderud, Ave; Rohrlack, Thomas; Shalchian-Tabrizi, Kamran; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2007). Structural analysis of a non-ribosomal halogenated cyclic peptide and its putative operon from Microcystis: implications for evolution of cyanopeptolins. Microbiology.  ISSN 1350-0872.  153(5), s 1382- 1393 . doi: 10.1099/mic.0.2006/001123-0
• Kauserud, Håvard; Stensrud, Øyvind; DeCock, Cony; Shalchian-Tabrizi, Kamran & Schumacher, Trond (2006). Multiple gene genealogies and AFLPs suggest cryptic speciation and long-distance dispersal in the basidiomycete Serpula himantioides (Boletales). Molecular Ecology.  ISSN 0962-1083.  15(2), s 421- 431 . doi: 10.1111/j.1365-294X.2005.02768 Vis sammendrag

  Serpula himantioides (Boletales, Basidiomycota) produces thin resupinate basidiocarps on dead coniferous wood worldwide and causes damage in buildings as well. In this study, we present evidence for the existence of at least three phylogenetically defined cryptic species (referred to as Sib I–III) within the morphospecies S. himantioides, a conclusion based on analyses of sequence data from four DNA regions and amplified fragment length polymorphisms (AFLPS). A low degree of shared sequence polymorphisms was observed among the three lineages indicating a long-lasting separation. The AFLPs revealed two additional subgroups within Sib III. Results from mating studies were consistent with the molecular data. In Sib III, no correspondence between genetic and geographical distance was observed among isolates worldwide, presumably reflecting recent dispersal events. Our results indicate that at least two of the lineages (Sib II and Sib III) have wide sympatric distributions. A population genetic analysis of Sib III isolates, scoring sequence polymorphisms as codominant SNP markers, indicates that panmictic conditions exist in the Sib III group. This study supports the view that cryptic speciation is a common phenomenon in basidiomycete fungi and that phylogenetic species recognition can be a powerful inference to detect cryptic species. Furthermore, this study shows that AFLP data are a valuable supplement to DNA sequence data in that they may detect a finer level of genetic variation.

• Shalchian-Tabrizi, Kamran; Eikrem, Wenche; Klaveness, Dag; Vaulot, Daniel; Minge, Marianne Aastebøl; LeGall, F; Romari, K; Throndsen, Jahn; Botnen, Andreas; Massana, R; Thomsen, Helge A. & Jakobsen, Kjetill Sigurd (2006). Telonemia, a new protist phylum with affinity to chromist lineages. Proceedings of the Royal Society of London. Biological Sciences.  ISSN 0962-8452.  273, s 1833- 1842 . doi: 10.1098/rspb.2006.3515
• Shalchian-Tabrizi, Kamran; Minge, Marianne Aastebøl; Cavalier-Smith, Thomas; Nedreklepp, Joachim; Klaveness, Dag & Jakobsen, Kjetill Sigurd (2006). Combined Heat Shock Protein 90 and Ribosomal RNA Sequence Phylogeny Supports Multiple Replacements of Dinoflagellate Plastids. Journal of Eukaryotic Microbiology.  ISSN 1066-5234.  53(3), s 217- 224
• Shalchian-Tabrizi, Kamran; Skånseng, Marianne; Ronqvist, Fredrik; Klaveness, Dag; Bachvaroff, Tsvetan R; Delwiche, Charles F.; Botnen, Andreas Valeur; Tengs, T & Jakobsen, Kjetill Sigurd (2006). Heterotachy Processes in Rhodophyte-Derived Secondhand Plastid Genes: Implications for Addressing the Origin and Evolution of Dinoflagellate Plastids. Molecular Biology and Evolution (MBE).  ISSN 0737-4038.  23, s 1504- 1515 . doi: 10.1093/molbev/msl011

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• Spilde, Ingrid; Bråte, Jon & Shalchian-Tabrizi, Kamran (2019, 04. februar). Knøttlite mysterium: Hva er egentlig forskjellen på deg og en encellet skapning?. [Fagblad].  Forskning.no.
• Orr, Russell; Rombauts, S; Van De Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Erratum to "Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples" [Genome Announc., 2017, 5 (34):e00894-17.] Doi: 10.1128/genomeA.00894-17.. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(41) . doi: 10.1128/genomeA.01175-17
• Orr, Russell; Rombauts, Stephane; Van de Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Draft genome sequences of two unclassified Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, isolated from environmental samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(33), s 1- 3 . doi: 10.1128/genomeA.00787-17
• Orr, Russell; Rombauts, Stephane; Van de Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Draft genome sequences of two unclassified bacteria, Sphingomonas sp. strains IBVSS1 and IBVSS2, isolated from environmental samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5:e00894-17(34), s 1- 3 . doi: 10.1128/genomeA.00894-17
• Orr, Russell; Rombauts, Stephane; Van de Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Erratum: "Draft genome sequences of two unclassified Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, isolated from environmental samples" [Genome Announc, 5, 33, (2017), (e00787-17)] DOI:10.1128/genomeA.00787-17. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(41:e01152-17), s 1- 1 . doi: 10.1128/genomeA.01152-17
• Evenstad, Andreas; Lieblein Røsæg, Line; Andresen, Ina Jungersen; Shalchian-Tabrizi, Kamran & Bråte, Jon (2016). Evolution of non-coding RNAs in ctenophores.
• Haraldsen, Arthur Alexander Blørstad; Bråte, Jon; Neumann, Ralf Stefan; Fromm, Bastian; Grini, Paul Eivind & Shalchian-Tabrizi, Kamran (2016). Pre-metazoan origin of animal microRNAs.
• Lieblein Røsæg, Line; Evenstad, Andreas; Andresen, Ina Jungersen; Bråte, Jon & Shalchian-Tabrizi, Kamran (2016). Postembryonic development of Mnemiopsis leidyi inferred from gene expression data.
• Orr, Russell; Zhao, Sen; Yabuki, Akinori & Shalchian-Tabrizi, Kamran (2016). PacBio sequencing reveals the diversity and ecology of a deeply diverging eukaryote lineage.
• Bjorbækmo, Marit Markussen; Neumann, Ralf Stefan; Haraldsen, Arthur Alexander Blørstad & Shalchian-Tabrizi, Kamran (2015). Expanding our knowledge about parasites using PATHOS-DB (The PArasiTe–HOSt-DataBase).
• Bjorbækmo, Marit Markussen; Neumann, Ralf Stefan; Haraldsen, Arthur Alexander Blørstad & Shalchian-Tabrizi, Kamran (2015). HIDDEN PROTIST PARASITES: HOW CAN THEY BE DETECTED?.
• Fuss, Janina; Grønneberg, Estelle; Gylt, Torbjørn; Bjorbækmo, Marit Markussen; Mangot, Jean-Francois; Shalchian-Tabrizi, Kamran & Klaveness, Dag (2015). Pee, poo and parasitic protists - what is living inside the fish we eat?.
• Fuss, Janina; Mangot, Jean-Francois; Bjorbækmo, Marit Markussen; Freeman, Mark A.; Bass, David; Shalchian-Tabrizi, Kamran & Klaveness, Dag (2015). THE ENIGMATIC BASAL ALVEOLATE PARASITE X-CELL: CAN MULTIPLE GENOMIC APPROACHES REVEAL MORE?.
• Haraldsen, Arthur Alexander Blørstad; Bjorbækmo, Marit Markussen; Mangot, Jean-Francois; Fuss, Janina; Shalchian-Tabrizi, Kamran; Hansen, Haakon & Klaveness, Dag (2015). Protist diversity in a marine and lacustrine system: Patterns across a salinity gradient. Vis sammendrag

  During the last decade, the improvement of high-throughput sequencing (HTS) techniques has substantially increased our insight into microbial ecology, by capturing a much more detailed picture of their diversity. Due to the increasing amount of data obtained by HTS methods, specific questions on the biogeography and factors explaining the distribution of these microorganisms can now be fully examined. Here, the composition and structure of a metabolically active benthic protistan community was investigated along a salinity gradient of closely associated marine and freshwater systems. Amplicons of rDNA and rRNA, were sequenced using the Illumina MiSeq technology. This approach seemed to successfully capture the majority of the protist community in these habitats. The marine environments displayed a higher species richness compared to the lacustrine systems investigated, and a considerable difference in protist composition was observed between marine and freshwater systems. Nevertheless, some protists were found in both saline and freshwater environments, indicating the ability to survive rather diverse environmental conditions. It is noteworthy that some of the OTUs from both habitats form putative new clades in the enigmatic X-cell group.

• Enevoldsen, Emily; Liow, Lee Hsiang; Voje, Kjetil L.; Orr, Russell; Shalchian-Tabrizi, Kamran & Krabberød, Anders Kristian (2014). Macroevolution through molecular and morphological lenses: a history of microporellids.
• Demko, Viktor; Johansen, Wenche; Perroud, Pierre-francois; Liang, Zhe; Shalchian-Tabrizi, Kamran; Zhao, Sen; Olsen, Odd-Arne; Quatrano, Ralph S. & Wilson, Robert Charles (2013). The evolutionary history of eukaryotic calpains displays multiple variants of regulatory mechanisms for CysPc activity.
• Demko, Viktor; Ako, Ako Eugene; Perroud, Pierre-Francois; Liang, Zhe; Johansen, Wenche; Wilson, Robert; Shalchian-Tabrizi, Kamran; Thiede, Bernd; Quatrano, Ralph & Olsen, Odd-Arne (2012). Searching for cellular targets of the plant calpain DEK1.
• Liang, Zhe; Demko, Viktor; Zhao, Sen; Wilson, Robert; Shalchian-Tabrizi, Kamran; Johansen, Wenche & Olsen, Odd-Arne (2012). The DEK1 protein evolved from an ancient form of membrane bound calpain and is highly conserved in land plants.
• Liang, Zhe; Olsen, Odd-Arne; Shalchian-Tabrizi, Kamran; Wilson, Robert & Johansen, Wenche (2012). The DEK1 protein evolved from an ancient form of membrane bound calpain and is highly conserved in land plants.
• Tidemann, Grethe; Shalchian-Tabrizi, Kamran; Vrålstad, Trude & Carlsen, Tor (2012, 20. mars). Hvordan skape et toppforskningsmiljø på under fem år.  Uniforum.
• Demko, Viktor; Perroud, Pierre-Francois; Johansen, Wenche; Wilson, Robert Charles; Liang, Zhe; Shalchian-Tabrizi, Kamran & Olsen, Odd-Arne (2011). The DEK1 and CRINKLY4 proteins play a fundamental role in the development of land plants - from Arabidopsis back to the moss Physcomitrella patens.
• Johansen, Wenche; Liang, Zhe; Demko, Viktor; Zhao, Sen; Wilson, Robert Charles; Shalchian-Tabrizi, Kamran & Olsen, Odd-Arne (2011). Dek1 calpain evolution.
• Liang, Zhe; Demko, Viktor; Zhao, Sen; Wilson, Robert Charles; Shalchian-Tabrizi, Kamran; Olsen, Odd-Arne & Johansen, Wenche (2011). The calpain module of the DEK1 protein from the moss Physcomitrella functionally complements the Arabidopsis dek1-3 mutant.
• Perroud, Pierre-Francois; Wilson, Robert Charles; Demko, Viktor; Liang, Zhe; Johansen, Wenche; Shalchian-Tabrizi, Kamran; Cove, D.J.; Olsen, Odd-Arne & Quatrano, R.S. (2011). Multiple roles for DEK1 in Physcomitrella patens.
• Bråte, Jon; Krabberød, Anders Kristian; Dolven, Jane Karine Lønne; Ose, Randi Frida; Kristensen, Tom; Bjørklund, Kjell Rasmus & Shalchian-Tabrizi, Kamran (2010). Diversity of unculturable Radiolaria and their symbionts revealed by 18S rDNA phylogeny.
• Dittami, Simon; Riisberg, Ingvild; John, Uwe; Orr, Russell; Shalchian-Tabrizi, Kamran; Jakobsen, Kjetill Sigurd & Edvardsen, Bente (2010). Analysis of expressed sequence tags from the ichtyotoxic dictyochophyte Pseudochattonella farcimen. Vis sammendrag

  Pseudochattonella farcimen (Eikrem, Edvardsen, et Throndsen) is an ichthyotoxic alga within the Dictyochophyceae (Heterokonta), which has been shown to form blooms in Scandinavian waters every year since 1998. To improve our understanding of the biology of this alga and to facilitate future genomic studies, we report the sequencing and analysis of >10,000 expressed sequence tags (ESTs) corresponding to 8149 unique sequences from this species. A direct comparison with EST libraries from other heterokonts revealed several functional categories to be significantly overrepresented among the P. facimen ESTs, such as genes involved in cell communication, transporters, or genes targeted to cell organelles. Interestingly, P. farcimen ESTs also code for a high proportion (1.4%) of proteins related to fatty acid metabolism, including eight fatty acid desaturases and two phospholipase A2 genes. Three of the desaturases belong to a family of delta-4 desaturases, known so far only from haptophytes, where they catalyze the conversion of n3-docosapentaenoic (n3-DPA) acid to docosahexaenoic acid (DHA). These findings may partially explain the unusual fatty acid profiles observed in P. farcimen and are discussed both from an evolutionary point of view and in relation the ichthyotoxic effects of this alga.

• Olsen, Odd-Arne; Johansen, Wenche; Emilsen, Sidsel; Belova, Tatiana; Liang, Zhe; Smalås, Arne; Johnson, Ken; Helland, Ronny; Schrøder Leiros, Hanna-Kirsti; Jakobsen, Kjetill S.; Shalchian-Tabrizi, Kamran; Quatrano, Ralph; Cove, David; Perroud, Pierre-Francois; Dutcher, Susan; Wilson, Robert & Wilson, Robert (2010). Structural & functional significance of the DEK1 phytocalpain during land plant evolution from green algae.
• Wilson, Robert; Perroud, Pierre-Francois; Johansen, Wenche; Liang, Zhe; Belova, Tatiana; Lorentzen, Marit; Jakobsen, Kjetill S.; Johnson, Ken; Brown, Roy; Lemmon, Betty; Cove, David; Shalchian-Tabrizi, Kamran; Quatrano, Ralph & Olsen, Odd-Arne (2010). Was the transmembrane-anchored DEK1 calpain key to the development of differentiated multicellular land plants?.
• Dolven, Jane Karine Lønne; Bjørklund, Kjell Rasmus; Bråte, Jon; Krabberød, Anders Kristian; Klaveness, Dag & Shalchian-Tabrizi, Kamran (2009). Polycystina. Polycystine radiolarians. [www ].
• Shalchian-Tabrizi, Kamran (2009). Bioportal Bioinformatics Service.
• Patil, Vishwanath; Bråte, Jon; Klaveness, Dag; Kluge, Ragnhild; Shalchian-Tabrizi, Kamran; Gislerød, Hans Ragnar & Jakobsen, Kjetill Sigurd (2008). Molecular phylogeny of Hydrurus, a fresh water chrysophyte rich in lipids.
• Minge, Marianne Aastebøl; Shalchian-Tabrizi, Kamran & Jakobsen, Kjetill Sigurd (2008). Chimeric proteomes: The plastid evolution of the green dinoflagellate Lepidodinium chlorophorum.
• Minge, Marianne Aastebøl; Silberman, Jeffrey; Orr, Russell; Cavalier-Smith, Thomas; Shalchian-Tabrizi, Kamran; Burki, Fabien; Skjæveland, Åsmund & Jakobsen, Kjetill Sigurd (2008). Breviata anathema - an unusual Amoebozoa.
• Shalchian-Tabrizi, Kamran (2008). Cross-colonisation of marine and freshwater in Telonemia, cryptomonads and Perkinsea.
• Shalchian-Tabrizi, Kamran (2008, 09. juni). Dyrenes opprinnelse. [Internett].  Forskning.no.
• Shalchian-Tabrizi, Kamran (2008, 27. juni). EVOLUTION: Building the Tree of Life, Genome by Genome.  Science Magazine.
• Shalchian-Tabrizi, Kamran (2008, 12. desember). Ein portal å rekna med.  Uniforum, UiO.
• Shalchian-Tabrizi, Kamran (2008). Phylogenomic analyses of the Tree Of Life, with focus on Telonemia.
• Shalchian-Tabrizi, Kamran (2008). Telonemia - origin and diversity.
• Shalchian-Tabrizi, Kamran; Minge, Marianne Aastebøl; Espelund, Mari; Orr, Russell; Ruden, Torgeir A.; Jakobsen, Kjetill Sigurd & Cavalier-Smith, Thomas (2008). The Choanozoan Ministeria vibrans: Multigene Phylogeny and the Origin of Animals. Vis sammendrag

  Ministeria vibrans is a unicellular protozoan belonging to the phylum Choanozoa, the evolutionary closest related group to the animals. Ministeria is a minute bacteria-eating cell possessing slender radiating tentacles, that has recently been shown to be the most close relative to Capsaspora, another protozoan with thread-like (filose) tentacles. Forming the novel clade Filasterea, Ministeria/Capsaspora was shown to be sister to animals and choanoflagellates. Presumably, their last common ancestor evolved filose tentacles well before they were aggregated as a periciliary collar in the choanoflagellates. Several successive evolutionary innovations occurred among the unicellular closest relatives of the animals prior to the origin of multicellularity. We have analysed an EST library from this early branching choanozoan organism and have found many domains of key significance for animal cell biology. New domain combinations as well as domain duplications must have taken place along the path to multicellularity.

• Shalchian-Tabrizi, Kamran (2007, 22. januar). Brukarforum for bioinformatikk på Blindern.  IT-avisa, UiO.
• Shalchian-Tabrizi, Kamran (2007, 06. desember). Livets tre har mistet en gren.  Apollon.
• Stensrud, Øyvind; Schumacher, Trond; Shalchian-Tabrizi, Kamran; Svegården, Ingeborg Bjorvand & Kauserud, Håvard (2006). Accelerated evolution and profound AT bias among lineages of the medicinal fungus Cordyceps sinensis. Vis sammendrag

  Cordyceps sinensis (Berk.) Sacc. grows parasitically on buried larvae of ghost moths (Thitarodes/Hepialus spp.) in Asian high-altitude grasslands and is known as a highly reputed medicinal fungus. In this study, the intraspecific variation in C. sinensis was analyzed employing 71 nrDNA ITS sequences accessioned in GenBank. Bayesian maximum likelihood analyses distributed the C. sinensis ITS sequences into five groups, referred to as A-E. Two groups (D-E), including a total of nine C. sinensis sequences as well as other Hypocreales/Clavicipitales taxa, were interpreted as erroneously accessioned sequences. The remaining sequences (62) constituted three highly supported clades (groups A, B and C), that may represent cryptic (phylogenetic) species currently ascribed to C. sinensis. Two sequences, accessioned as C. multiaxialis and C. nepalensis, also merged with the C. sinensis sequences of clades A-C. Sequences of groups B and C showed accelerated substitution rates and high AT nucleotide bias throughout the entire ITS region. A remarkably high sequence variation occurred in the 5.8S gene, which far exceeds what is normally observed in fungi. Compelling evidence from other studies exists for that reduced recombination frequencies can lead to AT bias due to lack of GC biased gene conversion, a process coupled to the meiosis. We hypothesize that a transition in life history attributes or ecology has happened among the putative cryptic species of C. sinensis, leading to accelerated evolution and AT bias. We also suggest that observed differences in medicinal effects among C. sinensis populations may be attributed to the existence of cryptic species in this morphotaxon.

• Shalchian-Tabrizi, Kamran (2006, 05. juli). Norske forskere finner ny livsform. [Internett].  Forsknin.no.
• Edvardsen, Bente; Eikrem, Wenche; Shalchian-Tabrizi, Kamran; Riisberg, Ingvild; Johnsen, Geir; Naustvoll, Lars & Throndsen, Jahn (2005). Phylogeny of a new ichthyotoxic dictyochophyte forming blooms in the North Sea.

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