Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species

Engelmann JA, Rahmann S, Wolf M, Schultz J, Fritzilas E, Kneitz S, Dandekar T, Müller T (2009)
Molecular Ecology Resources 9(1): 83-93.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Engelmann, Julia A.; Rahmann, Sven; Wolf, Matthias; Schultz, Jörg; Fritzilas, Epameinondas; Kneitz, Susanne; Dandekar, Thomas; Müller, Tobias
Erscheinungsjahr
2009
Zeitschriftentitel
Molecular Ecology Resources
Band
9
Ausgabe
1
Seite(n)
83-93
ISSN
1755-098X
eISSN
1755-0998
Page URI
https://pub.uni-bielefeld.de/record/2427118

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Engelmann JA, Rahmann S, Wolf M, et al. Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources. 2009;9(1):83-93.
Engelmann, J. A., Rahmann, S., Wolf, M., Schultz, J., Fritzilas, E., Kneitz, S., Dandekar, T., et al. (2009). Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources, 9(1), 83-93. https://doi.org/10.1111/j.1755-0998.2008.02199.x
Engelmann, Julia A., Rahmann, Sven, Wolf, Matthias, Schultz, Jörg, Fritzilas, Epameinondas, Kneitz, Susanne, Dandekar, Thomas, and Müller, Tobias. 2009. “Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species”. Molecular Ecology Resources 9 (1): 83-93.
Engelmann, J. A., Rahmann, S., Wolf, M., Schultz, J., Fritzilas, E., Kneitz, S., Dandekar, T., and Müller, T. (2009). Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources 9, 83-93.
Engelmann, J.A., et al., 2009. Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources, 9(1), p 83-93.
J.A. Engelmann, et al., “Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species”, Molecular Ecology Resources, vol. 9, 2009, pp. 83-93.
Engelmann, J.A., Rahmann, S., Wolf, M., Schultz, J., Fritzilas, E., Kneitz, S., Dandekar, T., Müller, T.: Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources. 9, 83-93 (2009).
Engelmann, Julia A., Rahmann, Sven, Wolf, Matthias, Schultz, Jörg, Fritzilas, Epameinondas, Kneitz, Susanne, Dandekar, Thomas, and Müller, Tobias. “Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species”. Molecular Ecology Resources 9.1 (2009): 83-93.

38 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A Network Pharmacology Approach to Uncover the Multiple Mechanisms of Hedyotis diffusa Willd. on Colorectal Cancer.
Liu X, Wu J, Zhang D, Wang K, Duan X, Zhang X., Evid Based Complement Alternat Med 2018(), 2018
PMID: 29619072
Guano exposed: Impact of aerobic conditions on bat fecal microbiota.
Fofanov VY, Furstenau TN, Sanchez D, Hepp CM, Cocking J, Sobek C, Pagel N, Walker F, Chambers CL., Ecol Evol 8(11), 2018
PMID: 29938074
Escaping introns in COI through cDNA barcoding of mushrooms: Pleurotus as a test case.
Avin FA, Subha B, Tan YS, Braukmann TWA, Vikineswary S, Hebert PDN., Ecol Evol 7(17), 2017
PMID: 28904776
The complete mitochondrial genome of Engyodontium album and comparative analyses with Ascomycota mitogenomes.
Yuan XL, Mao XX, Liu XM, Cheng S, Zhang P, Zhang ZF., Genet Mol Biol 40(4), 2017
PMID: 29064513
Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas.
Porter TM, Shokralla S, Baird D, Golding GB, Hajibabaei M., PLoS One 11(1), 2016
PMID: 26731732
Highlights of DNA Barcoding in identification of salient microorganisms like fungi.
Dulla EL, Kathera C, Gurijala HK, Mallakuntla TR, Srinivasan P, Prasad V, Mopati RD, Jasti PK., J Mycol Med 26(4), 2016
PMID: 27402509
How many DNA markers are needed to reveal cryptic fungal species?
Balasundaram SV, Engh IB, Skrede I, Kauserud H., Fungal Biol 119(10), 2015
PMID: 26399188
Molecular divergence and species delimitation of the cultivated oyster mushrooms: integration of IGS1 and ITS.
Avin FA, Bhassu S, Tan YS, Shahbazi P, Vikineswary S., ScientificWorldJournal 2014(), 2014
PMID: 24587752
Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.
Op De Beeck M, Lievens B, Busschaert P, Declerck S, Vangronsveld J, Colpaert JV., PLoS One 9(6), 2014
PMID: 24933453
The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS.
Han J, Zhu Y, Chen X, Liao B, Yao H, Song J, Chen S, Meng F., Biomed Res Int 2013(), 2013
PMID: 23484151
Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy.
Pino-Bodas R, Martín MP, Burgaz AR, Lumbsch HT., Mol Ecol Resour 13(6), 2013
PMID: 23437908
Optimization of a real-time PCR assay for the detection of the quarantine pathogen Melampsora medusae f. sp. deltoidae.
Boutigny AL, Guinet C, Vialle A, Hamelin RC, Andrieux A, Frey P, Husson C, Ioos R., Fungal Biol 117(6), 2013
PMID: 23809649
Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project.
Osmundson TW, Robert VA, Schoch CL, Baker LJ, Smith A, Robich G, Mizzan L, Garbelotto MM., PLoS One 8(4), 2013
PMID: 23638077
Does anaerobic bacterial antibiosis decrease fungal diversity in oral necrobacillosis disease?
Antiabong JF, Boardman W, Adetutu EM, Brown MH, Ball AS., Res Vet Sci 95(3), 2013
PMID: 24091030
Target-based therapeutic matching in early-phase clinical trials in patients with advanced colorectal cancer and PIK3CA mutations.
Ganesan P, Janku F, Naing A, Hong DS, Tsimberidou AM, Falchook GS, Wheler JJ, Piha-Paul SA, Fu S, Stepanek VM, Lee JJ, Luthra R, Overman MJ, Kopetz ES, Wolff RA, Kurzrock R., Mol Cancer Ther 12(12), 2013
PMID: 24092809
Rapid and simple preparation of mushroom DNA directly from colonies and fruiting bodies for PCR
Izumitsu K, Hatoh K, Sumita T, Kitade Y, Morita A, Gafur A, Ohta A, Kawai M, Yamanaka T, Neda H, Ota Y, Tanaka C., Mycoscience 53(5), 2012
PMID: IND44735660
DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context.
Kelly LJ, Hollingsworth PM, Coppins BJ, Ellis CJ, Harrold P, Tosh J, Yahr R., New Phytol 191(1), 2011
PMID: 21434928
Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.
Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP., PLoS One 6(4), 2011
PMID: 21533038
Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera.
Aveskamp MM, de Gruyter J, Woudenberg JH, Verkley GJ, Crous PW., Stud Mycol 65(), 2010
PMID: 20502538
Microevolution and speciation in Thalassiosira weissflogii (Bacillariophyta).
Sorhannus U, Ortiz JD, Wolf M, Fox MG., Protist 161(2), 2010
PMID: 20018562
Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation.
Del-Prado R, Cubas P, Lumbsch HT, Divakar PK, Blanco O, de Paz GA, Molina MC, Crespo A., Mol Phylogenet Evol 56(1), 2010
PMID: 20399873
DNA barcoding of arbuscular mycorrhizal fungi.
Stockinger H, Krüger M, Schüssler A., New Phytol 187(2), 2010
PMID: 20456046
Exploring the use of cytochrome oxidase c subunit 1 (COI) for DNA barcoding of free-living marine nematodes.
Derycke S, Vanaverbeke J, Rigaux A, Backeljau T, Moens T., PLoS One 5(10), 2010
PMID: 21060838
An open source chimera checker for the fungal ITS region.
Nilsson RH, Abarenkov K, Veldre V, Nylinder S, DE Wit P, Brosché S, Alfredsson JF, Ryberg M, Kristiansson E., Mol Ecol Resour 10(6), 2010
PMID: 21565119
Quantifying microbial communities with 454 pyrosequencing: does read abundance count?
Amend AS, Seifert KA, Bruns TD., Mol Ecol 19(24), 2010
PMID: 21050295
High diversity of the fungal community structure in naturally-occurring Ophiocordyceps sinensis.
Zhang Y, Zhang S, Wang M, Bai F, Liu X., PLoS One 5(12), 2010
PMID: 21179540
A class-wide phylogenetic assessment of Dothideomycetes.
Schoch CL, Crous PW, Groenewald JZ, Boehm EW, Burgess TI, de Gruyter J, de Hoog GS, Dixon LJ, Grube M, Gueidan C, Harada Y, Hatakeyama S, Hirayama K, Hosoya T, Huhndorf SM, Hyde KD, Jones EB, Kohlmeyer J, Kruys A, Li YM, Lücking R, Lumbsch HT, Marvanová L, Mbatchou JS, McVay AH, Miller AN, Mugambi GK, Muggia L, Nelsen MP, Nelson P, Owensby CA, Phillips AJ, Phongpaichit S, Pointing SB, Pujade-Renaud V, Raja HA, Plata ER, Robbertse B, Ruibal C, Sakayaroj J, Sano T, Selbmann L, Shearer CA, Shirouzu T, Slippers B, Suetrong S, Tanaka K, Volkmann-Kohlmeyer B, Wingfield MJ, Wood AR, Woudenberg JH, Yonezawa H, Zhang Y, Spatafora JW., Stud Mycol 64(), 2009
PMID: 20169021

37 References

Daten bereitgestellt von Europe PubMed Central.

Development and validation of a diagnostic microbial microarray for methanotrophs.
Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A., Environ. Microbiol. 5(7), 2003
PMID: 12823189
Isolation of plant DNA from fresh tissue
Doyle, Focus 12(), 1990
Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring.
Hajibabaei M, Singer GA, Clare EL, Hebert PD., BMC Biol. 5(), 2007
PMID: 17567898
DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics.
Hajibabaei M, Singer GA, Hebert PD, Hickey DA., Trends Genet. 23(4), 2007
PMID: 17316886
GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
He, ISME Journal 1(), 2007
Biological identifications through DNA barcodes
Hebert, Proceedings. Biology Sciences/The Royal Society 270(), 2003
Phylogenetic relationships of Scenedesmus and Acutodesmus (Chlorophyta, Chlorophyceae) as inferred from 18S rDNA and ITS-2 sequence comparisons
Hegewald, Plant Systematics and Evolution 241(), 2003
CLUSTAL V: improved software for multiple sequence alignment.
Higgins DG, Bleasby AJ, Fuchs R., Comput. Appl. Biosci. 8(2), 1992
PMID: 1591615
Variance stabilization applied to microarray data calibration and to the quantification of differential expression.
Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M., Bioinformatics 18 Suppl 1(), 2002
PMID: 12169536
The diversity of Scenedesmus and Desmodesmus (Chlorophyceae) in Itasca State Park, Minnesota, USA
Johnson, Phycologia 46(), 2007
Integer linear programming approaches for non-unique probe selection
Klau, Discrete Applied Mathematics 155(), 2007
A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogens.
Kostic T, Weilharter A, Rubino S, Delogu G, Uzzau S, Rudi K, Sessitsch A, Bodrossy L., Anal. Biochem. 360(2), 2006
PMID: 17123456
Oligonucleotide microarray for identification of Enterococcus species.
Lehner A, Loy A, Behr T, Gaenge H, Ludwig W, Wagner M, Schleifer KH., FEMS Microbiol. Lett. 246(1), 2005
PMID: 15869972
Development of a DNA microarray for detection and identification of fungal pathogens involved in invasive mycoses.
Leinberger DM, Schumacher U, Autenrieth IB, Bachmann TT., J. Clin. Microbiol. 43(10), 2005
PMID: 16207946
Highly parallel microbial diagnostics using oligonucleotide microarrays.
Loy A, Bodrossy L., Clin. Chim. Acta 363(1-2), 2005
PMID: 16126187
Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment.
Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M., Appl. Environ. Microbiol. 68(10), 2002
PMID: 12324358
16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales".
Loy A, Schulz C, Lucker S, Schopfer-Wendels A, Stoecker K, Baranyi C, Lehner A, Wagner M., Appl. Environ. Microbiol. 71(3), 2005
PMID: 15746340
Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences.
Mitterer G, Huber M, Leidinger E, Kirisits C, Lubitz W, Mueller MW, Schmidt WM., J. Clin. Microbiol. 42(3), 2004
PMID: 15004052
Distinguishing species.
Muller T, Philippi N, Dandekar T, Schultz J, Wolf M., RNA 13(9), 2007
PMID: 17652131
Oligonucleotide microarray for identification of Bacillus anthracis based on intergenic transcribed spacers in ribosomal DNA.
Nubel U, Schmidt PM, Reiss E, Bier F, Beyer W, Naumann D., FEMS Microbiol. Lett. 240(2), 2004
PMID: 15522510
A generalized inverse for matrices.
Penrose, Proceedings of 51(), 1955

R, 2007
An optimal cutting-plane algorithm for solving the non-unique probe selection problem.
Ragle MA, Smith JC, Pardalos PM., Ann Biomed Eng 35(11), 2007
PMID: 17763962
Primer3 on the WWW for general users and for biologist programmers.
Rozen S, Skaletsky H., Methods Mol. Biol. 132(), 2000
PMID: 10547847
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota.
Schultz J, Maisel S, Gerlach D, Muller T, Wolf M., RNA 11(4), 2005
PMID: 15769870
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses.
Schultz J, Muller T, Achtziger M, Seibel PN, Dandekar T, Wolf M., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845103
Microcoding: the second step in DNA barcoding.
Summerbell, Philosophical Transactions of the Royal Society of London. Series B, Biology Sciences 360(), 2005
Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples.
Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J., BioTechniques 36(4), 2004
PMID: 15088384

White, 1990
High-density microarray of small-subunit ribosomal DNA probes.
Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL., Appl. Environ. Microbiol. 68(5), 2002
PMID: 11976131
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures.
Wolf M, Achtziger M, Schultz J, Dandekar T, Muller T., RNA 11(11), 2005
PMID: 16244129
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