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Article in Journal

Levy Karin E, Ashkenazy H, Wicke S, Pupko T, Mayrose I: TraitRateProp: A web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. Nucleic Acids Research accepted (Details)

Levy Karin E, Wicke S, Pupko T, Mayrose I: An integrated model of phenotypic trait changes and site-specific sequence evolution. Systematic Biology 2017, e-pub ahead of print (Details)

Röschenbleck J, Wicke S, Weinl S, Kudla J, Müller KF: Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae). Genome Biology and Evolution 2017, 9:64-76 (Details)

Wicke S, Müller KF, dePamphilis CW, Quandt D, Bellot S, Schneeweiss GM: Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants. Proceedings of the National Academy of Sciences of the United States of America 2016, 113:9045-9050 (Details)

Feng YL, Wicke S, Li JW, Han Y, Lin CS, Li DZ, Zhou TT, Huang WC, Huang LQ, Jin XH: Lineage-specific reductions of plastid genomes in an orchid tribe with partially and fully mycoheterotrophic species. Genome Biology and Evolution 2016, 8:2164?2175 (Details)

Bartelheimer M, Poschlod P: Ellenberg's water table experiment put to the test: species optima along a hydrological gradient. Oecologia 2016, 181:1163-1172 (Details)

Bartelheimer M, Poschlod P : Functional characterizations of Ellenberg Indicator Values - a review on ecophysiological determinants. Functional Ecology 2016, 30:506-516 (Details)

Cusimano N, Wicke S: Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae. New Phytologist 2016, 210:680-693 (Details)

Kilian N, Henning T, Plitzner P, Müller A, Güntsch A, Stöver BC, Müller KF, Berendsohn WG, Borsch T: Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens. Database 2015, 2015:bav094 (Details)

Höpfner I, Beyschlag W, Bartelheimer M, Werner C, Unger S : Role of mycorrhization and nutrient availability in competitive interactions between the grassland species Plantago lanceolata and Hieracium pilosella. Plant Ecology 2015, 216:887-899 (Details)

Szövényi P, Frangedakis E, Ricca M, Quandt D, Wicke S, Langdale JA: Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts. BMC Plant Biology 2015, 15:98 (Details)

Schmid C, Bauer S, Bartelheimer M : Should I stay or should I go? Roots segregate in response to competition intensity. Plant and Soil 2015, 391:283-291 (Details)

Bartelheimer M, Schmid C, Storf J, Hell K, Bauer S : Interspecific competition in Arabidopsis thaliana ? a knowledge gap is starting to close. Progress in Botany 2015, 76:303-319 (Details)

Fleischmann A, Michael T, Rivadavia F, Wang W, Temsch E, Greilhuber J, Müller KF, Heubl G: Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms. Annals of Botany 2014, 114:1651--1663 (Details)

Wicke S, Schäferhoff B, dePamphilis CW, Müller KF: Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae. Molecular Biology and Evolution 2014, 31:529-545 (Details)

Röschenbleck J, Albers F, Müller KF, Weinl S, Kudla J: Phylogenetics, character evolution and a subgeneric revision of the genus Pelargonium (Geraniaceae). Phytotaxa 2014, 159:31-76 (Details)

Wicke S, Müller KF, dePamphilis CW, Quandt D, Wickett NJ, Zhang Y, Renner SS, Schneeweiss GM : Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family. The Plant Cell 2013, 25:3711-3725 (Details)

Fischer E, Schäferhoff B, Müller KF: The phylogeny of Linderniaceae - The new genus Linderniella, and new combinations within Bonnaya, Craterostigma, Lindernia, Torenia and Vandellia. Willdenowia 2013, 43:209-238 (Details)

Testroet P, Quandt D, Santos-Guerra A, Müller KF, Lobin W: Population genetics and conservation of Sideroxylon canariense (Sapotaceae) on the Canary Islands. Vieraea 2013, 41:295-308 (Details)

Abedi M, Bartelheimer M, Poschlod P : Effects of substrate type, moisture and its interaction on soil seed survival of three Rumex species. Plant and Soil 2014, 374:485-495 (Details)

Bartelheimer M, Poschlod P : The response of grassland species to nitrate versus ammonium coincides with their pH optima. Journal of Vegetation Science 2014, 25:760-770 (Details)

Schmid C, Bauer S, Müller B, Bartelheimer M : Belowground neighbor perception in Arabidopsis thaliana studied by transcriptome analysis: roots of Hieracium pilosella cause biotic stress. Frontiers in Plant Science 2013, 4 (Details)

Müller B, Bartelheimer M : Interspecific competition in Arabidopsis thaliana: root hairs are important for competitive effect, but not for competitive response. Plant and Soil 2013, 371:167-177 (Details)

Damayanti L, Muñoz J, Wicke S, Symmank L, Shaw B, Frahm J-P, Quandt D: Common but new: Bartramia rosamrosiae, a 'new' widespread species of apple mosses (Bartramiales, Bryophytina) from the Mediterranean and western North America. Phytotaxa 2012, 73:37-59 (Details)

Abedi M*, Bartelheimer M* (*equally contributing), Poschlod, P : Aluminium toxic effects on seedling root survival affect plant composition along soil reaction gradients ? a case study in dry sandy grasslands. Journal of Vegetation Science 2013, 24:1074-1085 (Details)

Fischer E, Schäferhoff B, Müller KF: The new monotypic genus Bardotia (Orobanchaceae) from Madagascar and remarks on the phylogenetic relationships of the African and Madagascan genera Micrargeria, Parastriga, Radamaea, Rhamphicarpa and Sieversandreas. Phytotaxa 2012, 46:19-33 (Details)

Barniske A, Borsch T, Müller KF, Krug M, Worberg A, Neinhuis C, Quandt D: Phylogenetics of early branching eudicots: comparing phylogenetic signal accross chloroplast introns, spacers, and genes. Journal of Systematics and Evolution 2012, 50:85-108 (Details)

Naumann J, Symmank L, Samain M, Müller KF, Neinhuis C, dePamphilis CW, Wanke S: Chasing the hare - Evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level. BMC Evolutionary Biology 2011, 11:357 (Details)

Müller KF: McPherson S. (ed. by Fleischmann A. and Robinson A.): Carnivorous plants and their habitats. (Book review). Willdenowia 2011, 42:387-388 (Details)

Wicke S, Costa A, Muñoz J, Quandt D: Restless 5S: The re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants. Molecular Phylogenetics and Evolution 2011, 61:321-332 (Details)

Korotkova N, Borsch T, Quandt D, Taylor NP, Müller KF, Barthlott W: What does it take to resolve relationships and to identify species with molecular markers? An example from the epiphytic Rhipsalideae (Cactaceae). American Journal of Botany 2011, 98:1549-1572 (Details)

Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D: The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Molecular Biology 2011, 76:273-297 (Details)

Schäferhoff B, Fleischmann A, Fischer E, Albach DC, Borsch T, Heubl G, Müller KF: Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences. BMC Evolutionary Biology 2010, 10 (Details)

Simmons MP, Müller KF, Norton: Alignment of, and phylogenetic inference from, random sequences: the susceptibility of alternative methods to artifactual resolution and support. Molecular Phylogenetics and Evolution 2010, 57:1004-1016 (Details)

Preußing M, Olsson S, Schäfer-Verwimp A, Wickett NJ, Wicke S, Quandt D, Nebel M: New insights in the evolution of the liverwort family Aneuraceae (Metzgeriales, Marchantiophyta), with emphasis on the genus Lobatiriccardia. Taxon 2010, 59:1424-1440 (Details)

Fleischmann A, Schäferhoff B, Heubl G, Rivadavia F, Barthlott W, Müller KF: Phylogenetics and character evolution in the carnivorous plant genus Genlisea A. St.-Hil. (Lentibulariaceae). Molecular Phylogenetics and Evolution 2010, 56:768-783 (Details)

Simmons MP, Webb CT, Müller KF: The deterministic effects of alignment bias in phylogenetic inference. Cladistics 2010, 27:402-416 (Details)

Simmons MP, Zhang LB, Müller KF: Phylogenetic inference using non-redundant coding of dependent characters vs. alternative approaches when applied to protein-coding genes. Cladistics 2010, 27:186-196 (Details)

Stöver BC, Müller KF: TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 2010, 11 (Details)

Müller KF, Albach DC: Evolutionary rates in Veronica L. (Plantaginaceae): Disentangling the influence of life history and breeding system. Journal of Molecular Evolution 2010, 70:44-56 (Details)

Bartelheimer M, Gowing D, Silvertown J : Explaining hydrological niches: the decisive role of below-ground competition in two closely related Senecio species. Journal of Ecology 2010, 98:126-136 (Details)

Schäferhoff B, Müller KF, Borsch T: Caryophyllales phylogenetics: disentangling Phytolaccaceae and Molluginaceae and description of Microteaceae as a new isolated family. Willdenowia 2009, 39:209-228 (Details)

Wicke S, Quandt D: Universal primers for the amplification of the plastid trnK/matK region in land plants. Anales del Jardín Botánico de Madrid 2009, 66:285-288 (Details)

Simmons MP, Müller KF, Webb CT: The relative sensitivity of different alignment methods and character codings in sensitivity analysis. Cladistics 2008, 24:1039-1050 (Details)

Beck SG, Fleischmann A, Huaylla H, Müller KF, Borsch T: Pinguicula chuquisacensis (Lentibulariaceae), a new species from the Bolivian Andes, and first insights on phylogenetic relationships among South American Pinguicula. Willdenowia 2008, 38:201-212 (Details)

Wahrmund U, Rein T, Frahm, Müller KF, Groth-Malonek M, Knoop V: Fifty mosses on five trees: Comparing phylogenetic information in three types of non-coding mitochondrial DNA and two chloroplast loci. Plant Systematics and Evolution 2008, 282:241-255 (Details)

Bartelheimer M, Steinlein T, Beyschlag W : 15N-nitrate-labelling demonstrates a size symmetric competitive effect on belowground resource uptake. Plant Ecology 2008, 199:243-253 (Details)

Wall PK, Leebens-Mack J, Müller KF, Field D, Altman NS, dePamphilis CW: PlantTribes: A gene and gene family resource for comparative genomics in plants. Nucleic Acids Research 2007, 36:D970-D976 (Details)

Jansen RK, Cai Z, Daniell H, Raubeson L, DePamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee, Peery R, McNeal JR, Kuehl JV, Boore JL: Analysis of 81 Genes from 64 Chloroplast Genomes Resolves Relationships in Angiosperms and Identifies Genome-Scale Evolutionary Patterns. Proceedings of the National Academy of Sciences of the United States of America 2007, 104:19369-19374 (Details)

Barakat A, Müller KF, Sáenz de Miera: Molecular evolutionary analysis of the Arabidopsis L7 ribosomal protein gene family. Gene 2007, 403:143-150 (Details)

Simmons MP, Müller KF, Norton AP: The relative performance of indel-coding methods in simulations. Molecular Phylogenetics and Evolution 2007, 44:724-740 (Details)

Weigelt A, Schumacher J, Walther T, Bartelheimer M, Steinlein T, Beyschlag W : On the hyperbolic competition model ? Reply. Journal of Ecology 2007, 95:601-602 (Details)

Simmons MP, Zhang, Webb CT, Müller KF: A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference. Molecular Phylogenetics and Evolution 2007, 42:528-542 (Details)

Weigelt A, Schumacher J, Walther T, Bartelheimer M, Steinlein T, Beyschlag W : Identifying mechanisms of competition in multi-species communities. Journal of Ecology 2007, 95:53-64 (Details)

Müller K, Borsch T, Legendre L, Porembski S, Barthlott W: Recent progress in understanding the evolution of Lentibulariaceae. Plant Biology 2006, 8:748-757 (Details)

Greilhuber J, Borsch T, Müller KF, Worberg A, Porembski S, Barthlott W: Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biology 2006, 8:770-777 (Details)

Müller KF, Borsch T, Hilu KW: Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F and rbcL in basal angiosperms. Molecular Phylogenetics and Evolution 2006, 41:99-117 (Details)

Müller KF: Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution 2006, 38:667-76 (Details)

Müller KF, Borsch T: Multiple origins of a unique pollen feature: stellate pore ornamentation in Amaranthaceae. Grana 2005, 44:266-281 (Details)

Müller KF: The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support. BMC Evolutionary Biology 2005, 5:58 (Details)

Cieslack T, Polepalli, White A, Müller KF, Borsch T, Barthlott W, Steiger J, Marchand A, Legendre L: Phylogenetic Analysis of Pinguicula (Lentibulariaceae): Chloroplast DNA Sequences and Morphology Support Several Geographically Distinct Radiations. American Journal of Botany 2005, 92:1723-1736 (Details)

Bartelheimer M, Steinlein T, Beyschlag W : Aggregative root placement: a feature during interspecific competition in inland sand-dune habitats. Plant and Soil 2006, 280:101-114 (Details)

Borsch T, Löhne C, Müller KF, Hilu KW, Wanke S, Worberg A, Barthlott W, Neinhuis C, Quandt D: Towards Understanding Basal Angiosperm Diversification: Recent Insights Using Rapidly Evolving Genomic Regions. Nova Acta Leopoldina 92 2005, 342:85-110 (Details)

Müller KF, Borsch T: Phylogenetics of Amaranthaceae based on matK/trnK sequence data - evidence from parsimony, likelihood, and Bayesian analyses. Annals of the Missouri Botanical Garden 2005, 92:66-102 (Details)

Müller KF: SeqState - primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics 2005, 4:65-69 (Details)

Rahmanzadeh R, Müller KF, Fischer E, Bartels D, Borsch T: The Linderniaceae and Gratiolaceae (Lamiales) are further lineages distinct from Scrophulariaceae. Plant Biology 2005, 7:67-78 (Details)

Müller KF, Borsch T: Phylogenetics of Utricularia (Lentibulariaceae) and molecular evolution of the trnK intron in a lineage with high substitutional rates. Plant Systematics and Evolution 2005, 250:39-67 (Details)

Neinhuis C, Wanke S, Hilu KW, Müller KF, Borsch T: Phylogeny of Aristolochiaceae based on parsimony, likelihood, and Bayesian analyses of trnL-trnF sequences. Plant Systematics and Evolution 2004, 250:7-26 (Details)

Müller J, Müller KF: TreeGraph: automated drawing of complex tree figures using an extensible tree description format. Molecular Ecology Notes 2004, 4:786-788 (Details)

Müller KF, Borsch T, Legendre L, Porembski S, Theisen I, Barthlott W: Evolution of carnivory in Lentibulariaceae and the Lamiales. Plant Biology 2004, 6:477-490 (Details)

Müller KF: PRAP - computation of Bremer support for large data sets. Molecular Phylogenetics and Evolution 2004, 31:780-782 (Details)

Hilu KW, Borsch T, Müller KF, Soltis DE, Soltis PS, Savolainen V, Chase M, Powell M, Alice, Evans R, Sauquet H, Neinhuis C, Slotta, Rohwer, Campbell, Chatrou L: Angiosperm phylogeny based on matK sequence information. American Journal of Botany 2003, 90:1758-1776 (Details)

Quandt D, Müller KF, Huttunen S: Characterisation of the chloroplast DNA psbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions. Plant Biology 2003, 5:400-410 (Details)

Müller J, Müller KF: QuickAlign: A New Alignment Editor. Plant Molecular Biology Reporter 2003, 21:1-5 (Details)

Müller KF, Borsch T, Legendre L, Theisen I, Barthlott W: Evolution of carnivory in the Lentibulariaceae: considerations based on molecular, morphological, and physiological evidence. Proceedings of the 4th International Carnivorous Plant Conference, Tokyo, Japan 2002 2002, 63-73 (Details)

Frahm, Müller KF, Stech M: The taxonomic status of Eurhynchium crassinervium from river banks based on ITS sequence data. Journal of Bryology 2000, 22:291-306 (Details)

Book (Monograph)

Knoop V, Müller KF: Gene und Stammbäume: Ein Handbuch zur molekularen Phylogenetik. 2008, Spektrum Akademischer Verlag, 397 (Details)

Knoop V, Müller KF: Gene und Stammbäume. Ein Handbuch zur molekularen Phylogenetik. 2006, Spektrum Akademischer Verlag, 310 (Details)

Chapter in Book

Grimm J, Hoffmann M, Stöver BC, Müller KF, Steinhage V: Image-Based Identification of Plant Species Using a Model-Free Approach and Active Learning. In Friedrich G, Helmert M, Wotawa F: KI 2016: Advances in Artificial Intelligence, 2016, Springer International Publishing; 169-176 (Details)

Wicke S: Genomic evolution in Orobanchaceae. In Joel DM, Gressel J, Musselman LJ: Parasitic Orobanchaceae - Parasitic Mechanisms and Control Strategies , 2013, Springer; Chapter 15 (Details)

Poschlod P, Abedi M, Bartelheimer M, Drobnik J, Rosbakh S, Saatkamp A : Seed Ecology and Assembly Rules in Plant Communities . In Van der Maarel, E, Franklin, J: Vegetation Ecology, 2013, Wiley; 164-202 (Details)

Müller KF: Biodiversität und Evolution. In Behler J, Fischer S, Funke A, Hartmann B, Heimhofer U, Martens W, Müller KF, Schmidt K, Schuchart C, Spehr M, Trapp O, Wagner M, Zwierlein C: Perspektiven - Forschungsfragen der Zukunft, 2011, Verlag Ferdinand Schöningh; 1-10 (Details)

Quandt D, Müller KF, Stech M, Hilu KW, Frey W, Frahm J-P, Borsch T: Molecular evolution of the chloroplast trnL-F region in land plants. In Goffinet B, Hollowell V, Magill R: Molecular Systematics of Bryophytes, 2004, Missouri Botanical Garden Press; 13-37 (Details)

Huttunen S, Ignatov MS, Müller KF, Quandt D: The phylogeny and evolution of epiphytism in three moss families Meteoriaceae, Brachytheciaceae, and Lembophyllaceae. In Goffinet B, Hollowell V, Magill R: Molecular Systematics of Bryophytes, 2004, Missouri Botanical Garden Press; 328-364 (Details)

Wicke S, Schneeweiss GM: Next generation organellar genomics: Potentials and pitfalls of high-throughput technologies for molecular evolutionary studies and plant systematics. In Hörandl E; Appelhans M: Next generation sequencing in plant systematics, 2015, Koeltz Scientific Books; Chapter 1 (Details)

Conference abstract (poster)

Wiechers S, Müller KF, Stöver BC: Increasing data accessibility and reuse in phylogenetics by employing externally defined ontologies. 6th annual Symposium of the Münster Graduate School of Evolution; Münster, Germany; 2017 (Details)

Stöver BC, Wiechers S, Müller KF: JPhyloIO - A Java library for event-based reading and writing of different alignment and tree formats through one common interface. European Conference on Computational Biology (ECCB); The Hague, The Netherlands; 2016 (Details)

Wiechers S, Müller KF, Stöver BC: New comparison and annotation methods of the phylogenetic tree editor TreeGraph 2. 5th annual Münster Graduate School of Evolution Symposium; Münster, Germany; 2015 (Details)

Stöver BC, Wiechers S, Müller KF: Recent development of the phylogenetic tree editor TreeGraph 2. German Conference on Bioinformatics (GCB); Dortmund, Germany; 2015 (Details)

Stöver BC, Müller KF: LibrAlign - A powerful Java GUI library for MSA and attached raw and meta data. IPAM Multiple Sequence Alignment Workshop; Los Angeles, USA; 2015 (Details)

Stöver BC, Müller KF: AlignmentComparator - Comparing and annotating alternative alignments of the same data set. IPAM Multiple Sequence Alignment Workshop; Los Angeles, USA; 2015 (Details)

Stöver BC, Müller KF: LibrAlign - A Java library with powerful GUI components for multiple sequence alignment and attached raw and meta data. German Conference on Bioinformatics (GCB); Bielefeld, Germany; 2014 (Details)

Stöver BC, Müller KF: AlignmentComparator - A GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments. 4th annual Münster Graduate School of Evolution Symposium; Münster, Germany; 2014 (Details)

Stöver BC, Müller KF: LibrAlign - A GUI library for displaying and editing multiple sequence alignments and attached data. BioDivEvo 2014; Dresden, Germany; 2014 (Details)

Stöver BC, Müller KF: Software in the BioInfWeb project. 2nd annual Münster Graduate School of Evolution Symposium; Münster, Germany; 2012 (Details)

Stöver BC, Quandt D, Müller KF: Complex mutations and multiple sequence alignment - Example: Hairpin-initiated repeats (HIRs). 2nd annual Münster Graduate School of Evolution Symposium; Münster, Germany; 2012 (Details)


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