Koetschan et al. (2010) NAR 38:D275-9
Selig et al. (2008) NAR 36:D377-380.
Schultz et al. (2006) NAR 34:W704-7.
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ITS2 3D structure
(Keller et al. 2010)


Chlorophyta hypertree

(Buchheim et al. 2011)
Fig1, Fig2, Fig3, Fig4

Cited by

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    Barcoding a quantified food web: crypsis, concepts, ecology and hypotheses.
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    Efficiency of DNA barcodes for species delimitation: A case in Pterygiella Oliv. (Orobanchaceae)
    Journal of Systematics and Evolution 49(3):189-202
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    Identifying and searching for conserved RNA localisation signals.
    Methods in Molecular Biology 714:447-66
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    Delimitation of an almost forgotten species Spongipellis litschaueri (Polyporales, Basidiomycota) and its taxonomic position within the genus
    Mycological Progress
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    Phylogenetic relationships within Chamaecrista sect. Xerocalyx (Leguminosae, Caesalpinioideae) inferred from the cpDNA trnE-trnT intergenic spacer and nrDNA ITS sequences
    Genetics and Molecular Biology 34(2):244:251
  • Assunção P., Jaén-Molina R., Caujapé-Castells J., de la Jara A., Carmona L., Freijanes K., Mendoza H. (2011):
    Phylogenetic position of Dunaliella acidophila (Chlorophyceae) based on ITS and rbcL sequences
    Journal of Applied Phycology
  • Wełnicz W., Grohme M.A., Kaczmarek Ł., Schill R.O., Frohme M. (2011)
    ITS-2 and 18S rRNA data from Macrobiotus polonicus and Milnesium tardigradum (Eutardigrada, Tardigrada)
    Journal of Zoological Systematics and Evolutionary Research 49(1):34-49
  • Hřibová E., Cižková J., Christelová P., Taudien S., de Langhe E., Doležel J. (2011)
    The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny
    Plos One 6(3):e17863
  • Ghatani S., Shylla J.A., Tandon V., Chatterjee A., Roy B. (2011)
    Molecular characterization of pouched amphistome parasites (Trematoda: Gastrothylacidae) using ribosomal ITS2 sequence and secondary structures
    Journal of Helminthology [E-pub ahead of print]
  • Xie Q., Lin J., Qin Y., Zhou J., Bu W. (2011)
    Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.
    Protein Cell 2(2):161-70
  • Wan X., Li J., Kim M.J., Kang T.H., Jin B.R., Kim I. (2011)
    Population genetic structure of the migratory rice leaf roller, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), inferred from the mitochondrial A+T-rich region and nuclear ITS2 sequences.
    Genetics and Molecular Research 10(1):273-94
  • Pang X.-H., Song J.-Y., Sun C. (2011)
    Authentication of Lysimachia christinae and its adulterants by analysis of ITS2 sequences
    Global Traditional Chinese Medicine 007
  • Ciarmiello L.F., Piccirillo P., Pontecorvo G., De Luca A., Kafantaris I., Woodrow P. (2011)
    A PCR based SNPs marker for specific characterization of English walnut (Juglans regia L.) cultivars.
    Molecular Biology Reports 38(2):1237-49
  • Tandon V., Biswal D.K., Prasad P.K., Malsawmtluangi C. (2011):
    Reconstructing the phylogenetic relationships of the Cyclophyllidean Cestodes: a case study using ITS2 rDNA and sequence-structure alignment.
    pp. 309-321 Part IV Bioinformatics In: Fred A., Filipe J., Gamboa H. (Eds.) (2011): Biomedical Engineering Systems and Technologies
    (Third International Joint Conference, BIOSTEC 2010 Valencia, Spain, January 2010, Revised Selected Papers),
    Communications in Computer and Information Science 127, Springer-Verlag Berlin Heidelberg 2011.
  • Alama-Bermejo G., Montero F.E., Raga J.A., Holzer A.S. (2011):
    Skoulekia meningialis n. gen., n. sp. (Digenea: Aporocotylidae Odhner, 1912) a parasite surrounding the brain of the Mediterranean common two-banded seabream Diplodus vulgaris (Geoffroy Saint-Hilaire, 1817) (Teleostei: Sparidae): description, molecular phylogeny, habitat and pathology.
    Parasitology International 11(1):37
  • Huang D., Licuanan W.Y., Baird A.H., Fukami H. (2011):
    Cleaning up the 'Bigmessidae': Molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae.
    BMC Evolutionary Biology 11(1):37
  • Benali S., Mohamed B., Eddine H.J., Neema C. (2011):
    Advances of Molecular Markers Application in Plant Pathology Research
    European Journal of Scientific Research 50(1):110-123
  • Vesgueiro F.T., Demari-Silva B., Malafronte Rdos S., Sallum M.A.M., Marrelli M.T. (2011):
    Intragenomic variation in the second internal transcribed spacer of the ribosomal DNA of species of the genera Culex and Lutzia (Diptera: Culicidae)
    Memórias do Instituto Oswaldo Cruz 106(1):1-8
  • Harrower E. (2011):
    Using Barcode Similarity Groups to Organize Cortinarius Sequences
    Master thesis, University of Toronto
    http://hdl.handle.net/1807/25613
  • Hibbett D.S., Ohman A., Glotzer D., Nuhn M., Kirk P., Nilsson R.H. (2011):
    Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences
    Fungal Biology Reviews 25:38-47
  • de Sousa Queiroz C., de Carvalho Batista F.R., de Oliveira L.O. (2011):
    Evolution of the 5.8S nrDNA gene and internal transcribed spacers in Carapichea ipecacuanha (Rubiaceae) within a phylogeographic context
    Molecular Phylogenetics and Evolution [Epub ahead of print]
  • Buchheim M.A., Keller A., Koetschan C., Förster F., Merget B., Wolf M. (2011):
    Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: Towards an automated reconstruction of the green algal tree of life
    Plos One 6(2):e16931
  • Junker R.R., Daehler C.C., Dötterl S., Keller A., Blüthgen N. (2011):
    Ant-flower networks 1 in Hawai'i: nectar-thieving ants prefer undefended native over introduced plants with floral defenses
    Ecological Monographs (in press)
  • Downie A.J., Bray R.A., Jones B.E., Cribb T.H. (2011):
    Taxonomy, host-specificity and biogeography of Symmetrovesicula Yamaguti, 1938 (Digenea: Fellodistomidae) from chaetodontids (Teleostei: Perciformes) in the tropical Indo-west Pacific region.
    Systematic Parasitology 78(1):1-18
  • Stat M., Bird C.E., Pochon X., Chasqui L., Chauka L.J., Concepcion G.T., Logan D., Takabayashi M., Toonen R.J., Gates R.D. (2011):
    Variation in Symbiodinium ITS2 Sequence Assemblages among Coral Colonies.
    Plos One 6(1):e15854
  • Pang X., Song J., Zhu Y., Xu H., Huang L., Chen S. (2011):
    Applying plant DNA barcodes for Rosaceae species identification
    Cladistics 26:1-6
  • Krienitz L., Bock C., Nozaki H., Wolf M. (2011):
    SSU rRNA gene phylogeny of morphospecies affiliated to the bioassay alga "Selenastrum capricornutum" recovered the polyphyletic origin of crescent-shaped Chlorophyta
    Journal of Phycology (in press)
  • Agüero-Chapin G., de la Riva G.A., Molina-Ruiz R., Sánchez-Rodríguez A., Pérez-Machado G., Vasconcelos V., Antunes A. (2011):
    Non-linear models based on simple topological indices to identify RNase III protein members
    Journal of Theoretical Biology [Epub ahead of print]
  • Förster F., Beisser D., Frohme M., Schill R.O., Dandekar T. (2011)
    Bioinformatics identifies tardigrade molecular adaptations including the DNA-j family and first steps towards dynamical modelling
    Journal of Zoological Systematics and Evolutionary Research 25:38-47
  • Gryganskyi A.P. Lee S.C., Litvintseva A.P., Smith M.E., Bonito G. Porter T.M., Anishchenko I.M., Heitman J. Vilgalys R. (2010):
    Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex.
    Plos One 5(12):e15273
  • Pang X.H., Song J.Y., Zhu Y.J., Xie C.X., Chen S.L. (2010):
    Using DNA Barcoding to Identify Species within Euphorbiaceae
    Planta Medica 76(15):1784-6
  • Merget B., Wolf M. (2010):
    A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data
    BMC Research Notes 3:320
  • Milyutina I.A., Goryunov D.V., Ignatov M.S., Ignatova E.A., Troitskii A.V. (2010)
    FILOGENIYa MKhOV RODA Schistidium (BRYOPHYTA, GRIMMIACEAE) PO NUKLEOTIDNYM POSLEDOVATEL'NOSTYaM I VTORIChNOI STRUKTURE VNUTRENNIKh TRANSKRIBIRUEMYKh SPEISEROV YaDERNOI rDNK
    Molekulyarnaya Biologiya 44(6):994-1009
  • Förster F., Wolf M. (2010):
    ITS2-Update - Die ITS2 Datenbank als Werkzeug
    GfBS news 24:26-27
  • Gao T., Yao H., Song J., Zhu Y., Liu C., Chen S. (2010):
    Evaluating the feasibility of using candidate DNA barcodes in discriminating species of the large Asteraceae family.
    BMC Evolutionary Biology 10:324
  • Miller T.L., Adlard R.D., Rodney A.B., Justine J.-L., Cribb T.H. (2010):
    Cryptic species of Euryakaina n. g. (Digenea: Cryptogonimidae) from sympatric lutjanids in the Indo-West Pacific
    Systematic Parasitology 77(3):185-204
  • Yao H., Song J., Liu C., Luo K., Han J., Li Y., Pang X., Xu H., Zhu Y., Xiao P., Chen S. (2010):
    Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
    Plos One 5(10):e13102
  • Marek M., Zouhar M., Douda O., Mazakova J., Rysanek P. (2010):
    Bioinformatics-assisted characterization of the ITS1-58.S-ITS2 segments of nuclear rRNA gene clusters, and its exploitation in molecular diagnostics of European crop-parasitic nematodes of the genus Ditylenchus
    Plant Pathology 59(5):931-943
  • Fechner L.C., Vincent-Hubert F., Gaubert P., Bouchez T., Gourlay-Francé C., Tusseau-Vuillemin M.-H. (2010):
    Combined eukaryotic and bacterial community fingerprinting of natural freshwater biofilms using automated ribosomal intergenic spacer analysis
    FEMS Microbiology Ecology 74(3):542-553
  • McFadden C.S., Sánchez J.A., France S.C. (2010):
    Molecular Phylogenetic Insights into the Evolution of Octocorallia: A Review
    Integrative and Comparative Biology 50(3):389-410
  • Rix M.G., Harvey M.S., Roberts J.D. (2010):
    A revision of the textricellin spider genus Raveniella (Araneae : Araneoidea : Micropholcommatidae): exploring patterns of phylogeny and biogeography in an Australian biodiversity hotspot
    Invertebrate Systematics 24(3):209-237
  • Mathews D.H., Moss W.N., Turner D.H. (2010):
    Folding and Finding RNA Secondary Structure
    Cold Spring Harbor Perspectives in Biology
  • Budziszewska J., Piątkowska, J., Wrzosek M. (2010):
    Taxonomic position of Mucor hiemalis f. luteus
    Mycotaxon 111(1):75-85
  • Taneda A. (2010):
    Multi-objective pairwise RNA sequence alignment
    Bioinformatics 26(19):2383-90
  • Milyutina I.A., Goryunov D.V., Ignatov M.S., Ignatova E.A., Troitsky A.V. (2010):
    The Phylogeny of Schistidium (Bryophyta, Grimmiaceae) Based on the Primary and Secondary Structure of Nuclear rDNA Internal Transcribed Spacers
    Molecular Biology 44(6):883-897
  • Luo K., Chen S.L., Chen K.L., Song J., Yao H., Ma X., Zhu Y., Pang X., Yu H., Li X., Liu Z. (2010):
    Assessment of candidate plant DNA barcodes using the Rutaceae family
    Science China-Life Sciences 53(6):701-708
  • Gebiola M., Bernardo U., Burks R.A. (2010):
    A reevaluation of the generic limits of Pnigalio Schrank (Hymenoptera: Eulophidae) based on molecular and morphological evidence
    Zootaxa 2484:35-44
  • Miettinen O., Larsson K.-H. (2010):
    Sidera, a new genus in Hymenochaetales with poroid and hydnoid species
    Mycological Progress
  • Aguilar C., Reimer J.D. (2010):
    Molecular phylogenetic hypotheses of Zoanthus species (Anthozoa:Hexacorallia) using RNA secondary structure of the internal transcribed spacer 2 (ITS2)
    Marine Biodiversity 40(3):195-204
  • Moschandreou K.K., Papaefthimiou D., Katikou P., Kalopesa E., Panou A., Nikolaidis G. (2010):
    Morphology, phylogeny and toxin analysis of Pseudo-nitzschia pseudodelicatissima (Bacillariophyceae) isolated from the Thermaikos Gulf, Greece
    Phycologia 49(3):260-273
  • Barnett L.J., Miller T.L., Cribb T.H. (2010):
    Two new Stephanostomum-like cercariae (Digenea: Acanthocolpidae) from Nassarius dorsatus and N. olivaceus (Gastropoda: Nassariidae) in Central Queensland, Australia
    Zootaxa 2445:35-52
  • Gao T., Yao H., Song J., Liu C., Zhu Y., Ma X., Pang X., Xu h., Chen S. (2010):
    Identification of Medicinal Plants in the Family Fabaceae using a Potential DNA Barcode ITS2.
    Journal of Ethnopharmacology 130(1):116-21
  • Agnarsson I. (2010):
    The utility of ITS2 in spider phylogenetics: notes on prior work and an example from Anelosimus
    Journal of Arachnology 38(2):377-382
  • Salvi D., Bellavia G., Cervelli M., Mariottini P. (2010):
    The analysis of rRNA Sequence-Structure in phylogenetics: an application to the family Pectinidae (Mollusca: Bivalvia)
    Molecular Phylogenetics and Evolution 56(3):1059-67
  • Lesser M.P., Slattery M., Stat M., Ojimi M., Gates R.D., Grottoli A. (2010):
    Photoacclimatization by the coral Montastraea cavernosa in the mesophotic zone: light, food, and genetics
    Ecology 91(4) 990-1003
  • Pochon X., Gates R.D. (2010):
    A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawai’i
    Molecular Phylogenetics and Evolution 56(1):492-7
  • Schill R.O., Förster F., Dandekar T., Wolf M. (2010):
    Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada)
    Organisms Diversity and Evolution 10(4):287-296
  • Keller A., Wolf M., Dandekar T. (2010):
    Ribosomal RNA phylogenetics: the third dimension
    Biologia 65(3):388-391
  • Sun P., Clamp J.C., Xu D. (2010):
    Analysis of the secondary structure of ITS transcripts in Peritrich ciliates (Ciliophora, Oligohymenophorea): Implications for structural evolution and phylogenetic reconstruction
    Molecular Phylogenetics and Evolution 56(1):242-51
  • Xiao L.Q., Möller M., Zhu H. (2010):
    High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: Incomplete concerted evolution and the origin of pseudogenes
    Molecular Phylogenetics and Evolution 55(1):168-177
  • Ruhl M.W., Wolf M., Jenkins T.M. (2010):
    Compensatory base changes illuminate morphologically difficult taxonomy.
    Molecular Phylogenetics and Evolution 54(2):664-9
  • Leaw C.P., Lim P.T., Cheng K.W., Ng B.K., Usup G. (2010):
    Morphology and molecular characterization of a new species of Thecate Benthic Dinoflagellate, Coolia Malayensis Sp. Nov. (Dinophyceae)
    Journal of Phycology 46(1):162-171
  • Hegewald E., Wolf M., Keller A., Friedl T., Krienitz L. (2010):
    ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus
    Phycologia 49(4):325-335
  • Keller A., Förster F., Müller T., Dandekar T., Schultz J., Wolf M. (2010):
    Including RNA Secondary Structures improves Accuracy and Robustness in Reconstruction of Phylogenetic Trees
    Biology Direct 5(1):4
  • Hamilton K.M., Morritt D., Shaw P.W. (2010):
    Genetic diversity of the crustacean parasite Hematodinium (Alveolata, Syndinea)
    European Journal of Protistology 46(1):17-28
  • Kania P.W., Taraschewski H., Han Y.-S., Cone D.K., Buchmann K. (2010):
    Divergence between Asian, European and Canadian populations of the monogenean Pseudodactylogyrus bini indicated by ribosomal DNA patterns
    Journal of Helminthology
  • Chen S., Yao H., Han J., Liu C., Song J., Shi L., Zhu Y., Ma X., Gao T., Pang X., Luo K., Li Y., Li X., Jia X., Lin Y., Leon C. (2010):
    Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.
    PLoS One 5(1):e8613
  • Friedrich T., Koetschan C., Müller T. (2010):
    Optimisation of HMM Topologies enhances DNA and Protein Sequence Modelling
    Statistical Applications in Genetics and Molecular Biology 9(1):6
  • Koetschan C., Förster F., Keller A., Schleicher T., Ruderisch B., Schwarz R., Müller T., Wolf M., Schultz J. (2010):
    The ITS2 Database III - sequences and structures for phylogeny
    Nucleic Acids Research 38:D275-9
  • Sorhannus U., Ortiz J.D., Wolf M., Fox M.G. (2010):
    Microevolution and speciation in Thalassiosira weissflogii
    Protist 161(2):237-249
  • Poczai P., Hyvönen J. (2010):
    Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects
    Molecular Biology Reports 37(4):1897-912
  • Zhu Y.-J., Chen S.-L., Yao H., Tan R., Song J.-Y., Luo K., Lu J. (2010):
    DNA barcoding the medicinal plants of the genus Paris
    Acta Pharmaceutica Sinica 45(3):376-382
  • Wiemers M., Keller A., Wolf M. (2009):
    ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus)
    BMC Evolutionary Biology 9(1):300
  • Ullrich B., Reinhold K., Niehuis Ol, Misof B. (2009):
    Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini)
    Journal of Zoological Systematics and Evolutionary Research 48(3):219-228
  • Prasad P.K., Tandon V., Biswal D.K., Goswami L.M., Chatterjee A. (2009):
    Phylogenetic reconstruction using secondary structures and sequence motifs of ITS2 rDNA of Paragonimus westermani (Kerbert, 1878) Braun, 1899 (Digenea: Paragonimidae) and related species
    BMC Genomics 10(3):25
  • Damare V. (2009)
    Ecological Studies and Molecular Characterization of Thraustochytrids and Aplanochytrids from Oceanic Water Column
    Ph.D. thesis, Goa University- National Institute of Oceanography, Goa, India; 271pp.
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    Studies on Anopheles (Kerteszia) homunculus Komp (Diptera: Culicidae)
    Zootaxa 2299:1-18
  • Skaloud P., Peksa O. (2009)
    Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta)
    Molecular Phylogenetics and Evolution 54(1):36-46
  • Calonje M., Martín-Bravo S., Dobes C., Gong W., Jordon-Tharden I., Kiefer C., Kiefer M., Paule J., Schmickl R., Koch M.A. (2009):
    Non-coding nuclear DNA markers in phylogenetic reconstruction
    Plant Systematics and Evolution 282:257-280
  • Wolf M., Schultz J. (2009):
    ITS better than its reputation
    Science (E-Letter, 10 December 2009)
    http://www.sciencemag.org/content/325/5941/682.full/reply#sci_el_12692
  • Mullineux T., Hausner G. (2009):
    Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium.
    Fungal Genetics and Biology 46(11):855-67
  • Miller T.L., Cribb T.H. (2009):
    Gynichthys diakidnus n. g., n. sp (Digenea: Cryptogonimidae) from the grunt Plectorhinchus gibbosus (Lac,pSde, 1802) (Perciformes: Haemulidae) off the Great Barrier Reef, Australia
    Systematic Parasitology 74(2):103-112
  • Chan Y.L., Pochon X., Fisher M.A., Wagner D., Concepcion G.T., Kahng S.E., Toonen R.J., Gates R.D. (2009):
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    BMC Ecology 9(1):21
  • Oh H.K., Yoon H.J., Kim M.J., Jeong H.U., Kim S.R., Hwang J.S., Bae C.H., Dim I. (2009):
    ITS2 Ribosomal DNA Sequence Variation of the Bumblebee, Bombus ardens (Hymenoptera: Apidae)
    Genes & Genomics 31(4):293-303
  • Hu Z., Guiry M.D., Duan D. (2009):
    Using the ribosomal internal transcribed spacer (ITS) as a complement marker for species identification of red macroalgae
    Hydrobiologia 635:279-287
  • Moniz M.B.J., Kaczmarska I. (2009):
    Barcoding of Diatoms: Nuclear Encoded ITS Revisited
    Protist 161(1):7-34
  • Dorado D., Sánchez J.A. (2009):
    Internal Transcribed Spacer 2 (ITS2) Variation in the Gorgonian Coral Pseudopterogorgia bipinnata in Belize and Panama
    Smithsonian Contributions to the Marine Sciences 38:173-179
  • Stat M., Pochon X., Cowie R.O.M., Gates R.D. (2009):
    Specificity in communities of Symbiodinium in corals from Johnston Atoll
    Marine Ecology Progress Series 386:83-96
  • Nam H.H., Corneli P.S., Watkins M., Olivera B., Bandyopadhyay P. (2010):
    Multiple genes elucidate the evolution of venomous snail-hunting Conus species
    Molecular Phylogenetics and Evolution 53(3):645-52
  • Leliaert F., Verbruggen H., Wysor B., De Clerck O. (2009):
    DNA taxonomy in morphologically plastic taxa: Algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales)
    Molecular Phylogenetics and Evolution 53(1):122-33
  • Hoshina R., Imamura N. (2009):
    Origins of Algal Symbionts of Paramecium bursaria
    Microbiology Monographs 12:1-29, in: M. Fujishima (ed.), Endosymbionts in Paramecium, Springer-Verlag Berlin Heidelberg
  • Lehtonen M.J. (2009):
    Rhizoctonia solani as a potato pathogen - variation of isolates in Finland and host response
    Department of Applied Biology, Faculty of Agriculture and Forestry, Viikki Graduate School in Molecular Biosciences, University of Helsinki, Finland
  • Ahvenniemi P., Wolf M., Lehtonen M.J., Wilson P., German-Kinnari M., Valkonen J.P.T. (2009):
    Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani
    Journal of Molecular Evolution 69(2):150-63
  • Nilsson R.H., Ryberg M., Abarenkov K., Sjökvist E., Kristiansson E. (2009):
    The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.
    FEMS Microbiology Letters 296(1): 97-101
  • Jenkins T.M., Braman S.K., Chen Z.B., Eaton T.D., Pettis G.V., Boyd D.W. (2009):
    Insights Into Flea Beetle (Coleoptera: Chrysomelidae: Galerucinae) Host Specificity From Concordant Mitochondrial and Nuclear DNA Phylogenies
    Annals of the Entomological Society of America 102(3): 386-395
  • Trizzino M., Audisio P., Antonini G., De Biase A., Mancini E. (2009):
    Comparative analysis of sequences and secondary structures of the rRNA internal transcribed spacer 2 (ITS2) in pollen beetles of the subfamily Meligethinae (Coleoptera, Nitidulidae): potential use of slippage-derived sequences in molecular systematics.
    Molecular Phylogenetics and Evolution 51(2): 215-26
  • Moniz M.B.J., Kaczmarska I. (2009):
    Barcoding diatoms: Is there a good marker?
    Molecular Ecology Resources 9: 65-74
  • Prasad P., Tandon V., Biswald D., Goswami L., Chatterjee A. (2009):
    Use of sequence motifs as barcodes and secondary structures of Internal Transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae).
    Bioinformation 3 (7): 314-20
  • Moussalli A., Herbert D.G., Stuart-Fox D. (2009):
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    Molecular Phylogenetics and Evolution 52(1): 167-82
  • Schultz, J., Wolf, M. (2009):
    ITS2 Sequence-Structure Analysis in Phylogenetics: A How-to Manual for Molecular Systematics
    Molecular Phylogenetics and Evolution 52(2): 520-3.
  • Keller, A., Schleicher, T., Schultz, J., Müller, T., Dandekar, T. and Wolf, M. (2009):
    5.8S-28S rRNA interaction and HMM-based ITS2 annotation
    Gene 430:50-57.
  • Harrington M.G., Biffin E., Gadek P.A. (2009):
    Comparative study of the evolution of nuclear ribosomal spacers incorporating secondary structure analyzes within Dodonaeoideae, Hippocastanoideae and Xanthoceroideae (Sapindaceae)
    Molecular Phylogenetics and Evolution 50 (2): 364-375
  • Coleman, A.W. (2009):
    Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide
    Molecular Phylogenetics and Evolution 50 (1): 197-203
  • Engelmann, J.C., Rahmann, S., Wolf, M., Schultz, J., Fritzilas, E., Kneitz, S., Dandekar, T. and Müller, T. (2009):
    Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species
    Molecular Ecology Resources 9:83-93
  • Harrington M. (2008):
    Phylogeny and evolutionary history of Sapindaceae and Dodonaea
    PhD thesis, James Cook University
    http://eprints.jcu.edu.au/7893/
  • Itskovich V., Gontcharov A., Masuda Y., Nohno T., Belikov S., Elfremova S., Meixner M., Janussen D. (2008):
    Ribosomal ITS sequences allow resolution of freshwater sponge phylogeny with alignments guided by secondary structure prediction.
    Journal of Molecular Evolution 67(6):608-20
  • Surek B. (2008):
    Meeting Report: Algal Culture Collections 2008. An International Meeting at the Culture Collection of Algae and Protozoa (CCAP), Dunstaffnage Marine Laboratory, Dunbeg, Oban, United Kingdom; June 8-11, 2008.
    Protist 159(4):509:17
  • Philipp N Seibel, Tobias Müller, Thomas Dandekar, Matthias Wolf (2008):
    Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
    BMC Res Notes 1:91
  • Song Z.K., Wang X.Z., Liang G.Q. (2008):
    Molecular evolution and phylogenetic utility of the internal transcribed spacer 2 (ITS2) in Calyptratae (Diptera: Brachycera).
    Journal of Molecular Evolution 67(5):448-64
  • Pröschold T., Seibel P.N., Wolf M., Coleman A.W. (2008):
    ITS-2 as universal barcode for protists
    Algal Culture Collections 2008 An International Meeting at the Culture Collection of Algae and Protozoa (CCAP), Dunstaffnage Marine Laboratory, Dunbeg, Oban, United Kingdom; June 8-11 (abstract).
  • Prasad P.K., Tandon V., Biswal D.K., et al. (2008):
    Molecular identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae) based on the ribosomal internal transcribed spacer regions. (2008)
    Parasitology Research 103(6):1247-55
  • Sánches J.A., Dorado D. (2008):
    Intragenomic ITS2 variation in Caribbean seafans
    Proceedings of the 11th International Coral Reef Symposium, Ft. Lauderdale, Florida, 7-11 July 2008, Session number 26
  • Holzer A.S., Montero F.E., Repulles A., et al. (2008):
    Cardicola aurata sp n. (Digenea: Sanguinicolidae) from Mediterranean Sparus aurata L. (Teleostei: Sparidae) and its unexpected phylogenetic r elationship with Paradeontacylix McIntosh, 1934
    Parasitology International 57(4):472-82
  • Taneda A. (2008):
    An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast
    BMC Bioinformatics 9:521
  • Morrison, D.A. (2008):
    A framework for phylogenetic sequence alignment.
    Plant Systematics and Evolution 282(3-4):127-149
  • Kocat K.M., Santos S.R. (2008):
    Secondary structural modeling of the second internal transcribed spacer (ITS2) from Pfiesteria-like dinoflagellates (Dinophyceae)
    Harmful Algae 8(3):441-446
  • Wolf, M., Ruderisch, B., Dandekar, T., Schultz, J. and Müller, T. (2008):
    ProfDistS: (Profile-) Distance based phylogeny on sequence - structure alignments.
    Bioinformatics 24:2401-2
  • Ma, H., Overstreet, R.M. and Subbotin, S.A. (2008):
    ITS2 secondary structure and phylogeny of cyst-forming nematodes of the genus Heterodera (Tylenchida: Heteroderidae).
    Organisms Diversity and Evolution 8(3):182-193
  • Miao, M., Warren, A., Song, W., Wang, S., Shang, H. and Chen, Z. (2008):
    Analysis of the Internal Transcribed Spacer 2 (ITS2) Region of Scuticociliates and Related Taxa (Ciliophora, Oligohymenophorea) to Infer their Evolution and Phylogeny.
    Protist 159(4):519-33
  • Tippery, N.P. and Les, D.H. (2008):
    Phylogenetic Analysis of the Internal Transcribed Spacer (ITS) Region in Menyanthaceae Using Predicted Secondary Structure.
    Molecular Phylogenetics and Evolution, 49(2):526-37
  • Keller, A., Schleicher, T., Forster, F., Ruderisch, B., Dandekar, T., Muller, T. and Wolf, M. (2008):
    ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales).
    BMC Evolutionary Biology 8(1):218
  • Brannstrom, S., Morrison, D. A., Mattsson, J. G. and Chirico, J. (2008):
    Genetic differences in internal transcribed spacer 1 between Dermanyssus gallinae from wild birds and domestic chickens
    Medical and Veterinary Entomology 22(2):152-155
  • Cook, L.G., Morris, D.C., Edwards, R.D. and Crisp, M.D. (2008):
    Reticulate evolution in the natural range of the invasive wetland tree species Melaleuca quinquenervia
    Molecular Phylogenetics and Evolution 47(2):506-522
  • Wilm, A., Linnenbrink, K. and Steger, G. (2008):
    ConStruct: Improved construction of RNA consensus structures.
    BMC Bioinformatics 9:219
  • Kruger, D. and Gargas, A. (2008):
    Secondary structure of ITS2 rRNA provides taxonomic characters for systematic studies - a case in Lycoperdaceae (Basidiomycota)
    Mycological Research 112:316-330
  • Gruber, A.R., Bernhart, S.H., Hofacker, I.L. and Washietl S. (2008):
    Strategies for measuring evolutionary conservation of RNA secondary structures
    BMC Bioinformatics 9:122
  • Škaloud P. (2008):
    Polyphasic approaches in the taxonomy of green aerophytic algae
    Ph.D. thesis, Charles University in Prague, Faculty of Science, Department of Botany
  • Selig, C., Wolf, M., Müller, T., Dandekar, T. and Schultz, J. (2008):
    The ITS2 Database II: homology modelling RNA structure for molecular systematics
    Nucleic Acids Research 36:D377-380
  • Cristancho Ardila M.A., Escobar O.C., Ocampo J.D. (2007):
    Evolución de razas de H. vastatrix en Colombia.
    Cenicafé 58(4): 340-359
  • Landis, Frank C. and Gargas, A. (2007):
    Using ITS2 secondary structure to create species-specific oligonucleotide probes for fungi
    Mycologia 99(5):681-692
  • De la Rúa, P., de J. May-Itzá, W., Serrano, J. and Quezada-Euán, J.J.G. (2007):
    Sequence and RFLP analysis of the ITS2 ribosomal DNA in two Neotropical social bees, Melipona beecheii and Melipona yucatanica (Apidae, Meliponini)
    Insectes Sociaux 54(4):418-423
  • Korabecna M. (2007):
    The Variability in the Fungal Ribosomal DNA (ITS1,ITS2, and 5.8 S rRNA Gene): Its Biological Meaning and Application in Medical Mycology
    Communicating Current Research and Educational Topics and Trends in Applied Microbiology (A. Méndez-Vilas (Ed.))
  • Wolf, M., Selig, C., Müller, T., Philippi, N. and Dandekar, T. (2007):
    Placozoa: at least two
    Biologia 62(6):641-645
  • Nieto Feliner, G. and Rosselló, J.A. (2007):
    Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants.
    Molecular Phylogenetics and Evolution 44(2):911-919
  • Subbotin, S.A., Sturhan, D., Vovlas, N., Castillo, P., Tambe, J.T., Moens, M. and Baldwin, J.G. (2007):
    Application of the secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934.
    Molecular Phylogenetics and Evolution 43(3):881-890
  • Müller, T., Philippi, N., Dandekar, T., Schultz, J. and Wolf, M. (2007):
    Distinguishing species
    RNA 13(9):1469-1472
  • Bauer, M., Klau, G.W. and Reinert, K. (2007):
    Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
    BMC Bioinformatics 8(1):271
  • Hoef-Emden, K. (2007):
    Revision of the Genus Cryptomonas (Cryptophyceae) II: Incongruences between the Classical Morphospecies Concept and Molecular Phylogeny in Smaller Pyrenoid-less Cells
    Phycologia 46:402-428
  • Grajales-V, A., Aguilar, C. and Sanchez, J.A. (2007):
    Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals
    BMC Evolutionary Biology 7(1):90
  • Hamilton, R.S. and Davis I. (2007):
    RNA localization signals: deciphering the message with bioinformatics
    Seminars in Cell and Developmental Biology 18(2):178-85
  • Amato, A., Kooistra, W.H.C.F., Ghiron, J.H.L., Mann, D.G., Pröschold, T. and Montresor, M. (2007):
    Reproductive Isolation among Sympatric Cryptic Species in Marine Diatoms
    Protist 158(2):193-207
  • Thines, M. (2007):
    Characterisation and phylogeny of repeated elements giving rise to exceptional length of ITS2 in several downy mildew genera (Peronosporaceae)
    Fungal Genetics and Biology 44(3):199-207
  • Coleman, A. (2007):
    Pan-eukaryote ITS2 homologies revealed by RNA secondary structure
    Nucleic Acids Research 35(10):3322-9
  • Guelfi A. (2006):
    Bioinformática Estrutural Aplicada à Evolução des Glutationas Transferases
    University of São Paulo, 2006
  • Biffin, E., Harrington, M.G., Crisp, M.D., Craven, L.A. and Gadek, P.A. (2007):
    Structural partitioning, paired-sites models and evolution of the ITS transcript in Syzygium and Myrtaceae
    Molecular Phylogenetics and Evolution 43(1):124-139
  • Aguilar, C. and Sànchez, A. (2006):
    Phylogenetic hypotheses of gorgoniid octocorals according to ITS2 and their predicted RNA secondary structures
    Molecular Phylogenetics and Evolution 43(3):774-786
  • Seibel, P., Müller, T., Dandekar, T., Schultz, J. and Wolf, M. (2006):
    4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing
    BMC Bioinformatics 7:498, Spanish version 7:498
  • Degtjareva, G.V., Casper, S.J., Hellwig, F.H., Schmidt, A.R., Steiger, J. and Sokoloff, D.D. (2006):
    Morphology and nrITS phylogeny of the genus Pinguicula L. (Lentibulariaceae), with special attention to embryo evolution.
    Plant Biology 8(6):778-90
  • Seibel, P.N., Krüger J., Hartmeier S., Schwarzer K., Löwenthal K., Mersch H., Dandekar T. and Giegerich R. (2006):
    XML schemas for common bioinformatic data types and their application in workflow systems
    BMC Bioinformatics 7(1):490
  • Morrison, D.A. (2006):
    Multiple sequence alignment for phylogenetic purposes.
    Australian Systematic Botany 19: 479-539.
  • Lam K.K.Y., Loo A.H.B., Todd P.A., Chew, F.T. and Chou, L.M. (2006):
    Existence of intra-colonial paralogues of the ribosomal internal transcribed spacer (ITS) impedes studies of intra-colonial genetic variation in the scleractinian coral Diploastrea heliopora (Lamark 1816)
    The Raffles Bulletin of Zoology 54(2):485-489
  • Krüger, D., Petersen, R.H. and Hughes, K.W. (2006):
    Molecular phylogenies and mating study data in Polyporus with special emphasis on group Melanopus (Basidiomycota)
    Mycological Progress 5(4):185-206
  • Schultz, J., Müller, T., Achtziger, M., Seibel, P.N., Dandekar, T., Wolf, M. (2006):
    The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses.
    Nucleic Acids Research 34:W704-707.
  • Wilm, A. (2006):
    RNA-Alignments und RNA-Struktur in silico
    doctoral thesis, Heinrich-Heine-Universität Düsseldorf, available through open publication server
  • Wolf, M., Achtziger, M., Schultz, J., Dandekar, T., Müller, T. (2005):
    Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures.
    RNA 11:1616-1623.
  • Schultz, J., Maisel, S., Gerlach, D., Müller, T., Wolf, M. (2005):
    A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota.
    RNA 11:361-364.

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