• Articles
• Books (Monographs)
• Theses (Doctoral or Postdoctoral)

Articles

Research Articles (Journals)

• Fischer, Eberhard; Killmann, Dorothee; Gerlach, Johanna; Schütte, Claudia; Leh, Burkhard; Müller, Kai; Quandt, Dietmar. 2024. ‘Hoefkenia hunsrueckensis, a New Genus and Species from Europe, and the Identity of Virescentia vogesiaca (F.W.Schultz ex Skuja) Necchi, D.C.Agostinho & M.L.Vis (Batrachospermales, Rhodophyta).’ Diversity 16, № 8: 473. doi: 10.3390/d16080473.
• Wolf, Magnus; Greve, Carola; Schell, Tilman; Janke, Axel; Schmitt, Thomas; Pauls, Steffen U; Aspöck, Horst; Aspöck, Ulrike;. 2023. ‘The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils .’ The Journal of heredity 115, № 1: 112–119. doi: 10.1093/jhered/esad074.
• Wiechers S; Kösters LM; Quandt D; Borsch T; Wicke S; Müller KF. 2023. ‘BarKeeper – A versatile web framework to assemble, analyze, and manage DNA barcoding data and metadata.’ Methods in Ecology and Evolution Early View. doi: 10.1111/2041-210X.14047.
• Wolf, M; Zapf, K; Gupta, DK; Hiller, M; Árnason, Ú; Janke, A. 2023. ‘The genome of the pygmy right whale illuminates the evolution of rorquals.’ BMC Biology 21, № 79. doi: 10.1186/s12915-023-01579-1.
• Wolf, M; de Jong, M; Halldórsson, SD; Árnason, Ú; Janke, A;. 2022. ‘Genomic Impact of Whaling in North Atlantic Fin Whales.’ Molecular Biology and Evolution 39, № 5. doi: 10.1093/molbev/msac094.
• Mašková T, Phartyal SS, Abedi M, Bartelheimer M, Poschlod P. 2022. ‘Soil moisture level and substrate type determine long-term seed lifespan in a soil seed bank.’ Plant and Soil 477: 475–485. doi: 10.1007/s11104-022-05449-7.
• Bathe M, Bartelheimer M, Asshoff R. 2021. „Alltagsvorstellungen zum Platzen von Kirschen im Kontext der Modellkompetenz.“ MNU Journal 74: 50–53.
• Ordon K, Bartelheimer M, Asshoff R. 2021. ‘Biology student teachers’ interest and self-efficacy in planning and conducting field trips after participation in a university course.’ Environmental Education Research 27: 88–109. doi: 10.1080/13504622.2020.1849565.
• Kösters LM, Wiechers S, Lyko P, Müller KF, Wicke S. 2021. ‘WARPP - web application for the research of parasitic plants.’ Plant Physiology 185: 1374–1380. doi: 10.1093/plphys/kiaa105.
• Asshoff R, Bartelheimer M, Kullmann H, Kurtz J, Meyer E I, Müller K, Scharsack J, Schütz H-U. 2020. „Studierende in der Rolle von Exkursionsleiterinnen und Exkursionsleitern – Auswirkungen auf Interesse, Einstellungen und Selbstwirksamkeit.“ Natur und Landschaft 6-2020: 269–275.
• Reisch C, Meier S, Schmid C, Bartelheimer M. 2020. ‘Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients.’ PeerJ — the Journal of Life and Environmental Sciences 8, № e8887. doi: 10.7717/peerj.8887.
• Schlesak S, Hedenäs L, Nebel M, Quandt D. 2019. ‘Addendum to Hypnum subcomplanatum Hedenäs, Schlesak, D. Quandt.’ Bryophyte Diversity and Evolution 41, № 1: 1–1.
• Stöver BC, Wiechers S, Müller KF. 2019. ‘JPhyloIO: A Java library for event-based reading and writing of different phylogenetic file formats through a common interface.’ BMC Bioinformatics 20, № 1: 402. doi: 10.1186/s12859-019-2982-3.
• Aly R, Lati R, Abu-Nassar J, Ziadna H, Achdari G, von Muenchow CS, Wicke S, Bari VK, Eizenberg H. 2019. ‘The weedy parasite Phelipanche aegyptiaca attacks Brassica rapa var. rapa L. for the first time in Israel.’ Plant Disease 2019: 1. doi: 10.1094/PDIS-02-19-0285-PDN.
• Maul K, Krug M, Nickrent DL, Müller KF, Quandt D, Wicke S. 2018. ‘Morphology, geographic distribution, and host preferences are poor predictors of phylogenetic relatedness in the mistletoe genus Viscum L.’ Molecular Phylogenetics and Evolution 131: 106–115. doi: 10.1016/j.ympev.2018.10.041.
• Schlesak S, Hedenäs L, Nebel M, Quandt D. 2018. ‘Cleaning a taxonomic dustbin: placing the European Hypnum species in a phylogenetic context!’ Bryophyte Diversity and Evolution 40, № 2: 37–54. doi: 10.11646/bde.40.2.3.
• Borsch T, Flores-Olvera H, Zumaya S, Müller KF. 2018. ‘Pollen characters and DNA sequence data converge on a monophyletic genus Iresine (Amaranthaceae, Caryophyllales) and help to elucidate its species diversity.’ Taxon 67: 944–976. doi: 10.12705/675.7.
• Poppinga S, Westermeier AS, Fleischmann A, Müller KF, Speck T. 2018. ‘Evolution of a sucker: Functional principles of traps in carnivorous bladderworts (Utricularia, Lentibulariaceae).’ Atlas of Science 1.
• Barrett CF, Wicke S, Sass C. 2018. ‘Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex.’ New Phytologist 218, № 3: 1192–1204. doi: 10.1111/nph.15072.
• Sattler J, Bartelheimer M. 2018. ‘Root responses to legume plants integrate information on nitrogen availability and neighbour identity.’ Basic and Applied Ecology 27: 51–60. doi: 10.1016/j.baae.2018.01.001.
• Wang Y-H, Wicke S, Wang H, Jin J-J, Chen S-Y, Zhang S-D, Li D-Z, Yi T-S. 2018. ‘Plastid genome evolution in the early-diverging legume subfamily Cercidoideae (Fabaceae).’ Frontiers in Plant Science 8: 138. doi: 10.3389/fpls.2018.00138.
• Westermeier AS, Fleischmann A, Müller K, Schäferhoff B, Rubach C, Speck T, Poppinga S. 2017. „Trap diversity and character evolution in carnivorous bladderworts (Utricularia, Lentibulariaceae).“ Scientific Reports 7: 12052. doi: 10.1038/s41598-017-12324-4.
• Araya Y, Bartelheimer M, Valle C, Crujeiras R, García-Baquero, G. 2017. ‘Does functional soil microbial diversity contribute to explain within-site plant beta-diversity in an alpine grassland and a dehesa meadow in Spain?’ Journal of Vegetation Science 28: 1018–1027. doi: 10.1111/jvs.12557.
• Noben S, Kessler M, Quandt D, Weigand A, Wicke S, Krug M, Lehnert M. 2017. ‘Biogeography of the Gondwanan tree fern family Dicksoniaceae—A tale of vicariance, dispersal and extinction.’ Journal of Biogeography 44, № 11: 2648–2659. doi: 10.1111/jbi.13056.
• Barré P, Stöver BC, Müller KF, Steinhage V. 2017. ‘LeafNet: A computer vision system for automatic plant species identification.’ Ecological Informatics 40: 50–56. doi: 10.1016/j.ecoinf.2017.05.005.
• Levy Karin E, Ashkenazy H, Wicke S, Pupko T, Mayrose I. 2017. ‘TraitRateProp: A web server for the detection of trait-dependent evolutionary rate shifts in sequence sites.’ Nucleic Acids Research 45, № 1: W260–W264. doi: 10.1093/nar/gkx288.
• Levy Karin E, Wicke S, Pupko T, Mayrose I. 2017. ‘An integrated model of phenotypic trait changes and site-specific sequence evolution.’ Systematic Biology 66, № 6: 917–933. doi: 10.1093/sysbio/syx032.
• Röschenbleck J, Wicke S, Weinl S, Kudla J, Müller KF. 2017. ‘Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae).’ Genome Biology and Evolution 9, № 1: 64–76. doi: 10.1093/gbe/evw271.
• Geiger, M. F.; Astrin, J. J.; Borsch, T.; Burkhardt, U.; Grobe, P.; Hand, R.; Hausmann, A.; Hohberg, K.; Krogmann, L.; Lutz, M.; Monje, C.; Misof, B.; Morinière, J.; Müller, Kai F.; Pietsch, S.; Quandt, Dietmar; Rulik, B.; Scholler, M.; Traunspurger, W.; Haszprunar, G.; Wägele, W. 2016. ‘How to tackle the molecular species inventory for an industrialized nation-lessons from the first phase of the German Barcode of Life initiative GBOL (2012-2015).’ Genome 59: 661–670.
• Wicke S, Müller KF, dePamphilis CW, Quandt D, Bellot S, Schneeweiss GM. 2016. ‘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 113, № 32: 9045–9050. doi: 10.1073/pnas.1607576113.
• Feng YL, Wicke S, Li JW, Han Y, Lin CS, Li DZ, Zhou TT, Huang WC, Huang LQ, Jin XH. 2016. ‘Lineage-specific reductions of plastid genomes in an orchid tribe with partially and fully mycoheterotrophic species.’ Genome Biology and Evolution 8, № 7: 2164–2175. doi: 10.1093/gbe/evw144.
• Bartelheimer M, Poschlod P. 2016. ‘Ellenberg's water table experiment put to the test: species optima along a hydrological gradient.’ Oecologia 181: 1163–1172. doi: 10.1007/s00442-016-3624-3.
• Bartelheimer M, Poschlod P. 2016. ‘Functional characterizations of Ellenberg Indicator Values - a review on ecophysiological determinants.’ Functional Ecology 30: 506–516. doi: 10.1111/1365-2435.12531.
• Cusimano N, Wicke S. 2016. ‘Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae.’ New Phytologist 210, № 2: 680–693. doi: 10.1111/nph.13784.
• Bitard-Feildel, Tristan; Heberlein, Magdalena; Bornberg-Bauer, Erich; Callebaut, Isabelle. 2015. ‘Detection of orphan domains in Drosophila using "hydrophobic cluster analysis".’ Biochimie 119. doi: 10.1016/j.biochi.2015.02.019.
• Kilian N, Henning T, Plitzner P, Müller A, Güntsch A, Stöver BC, Müller KF, Berendsohn WG, Borsch T. 2015. ‘Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens.’ Database 2015: bav094. doi: 10.1093/database/bav094.
• Höpfner I, Beyschlag W, Bartelheimer M, Werner C, Unger S. 2015. ‘Role of mycorrhization and nutrient availability in competitive interactions between the grassland species Plantago lanceolata and Hieracium pilosella.’ Plant Ecology 216: 887–899. doi: 10.1007/s11258-015-0476-6.
• Szövényi P, Frangedakis E, Ricca M, Quandt D, Wicke S, Langdale JA. 2015. ‘Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts.’ BMC Plant Biology 15: 98. doi: 10.1186/s12870-015-0481-x.
• Schmid C, Bauer S, Bartelheimer M. 2015. ‘Should I stay or should I go? Roots segregate in response to competition intensity.’ Plant and Soil 391: 283–291. doi: 10.1007/s11104-015-2419-3.
• Milutinović B, Fritzlar S, Kurtz J. 2014. ‘Increased Survival in the Red Flour Beetle after Oral Priming with Bacteria-Conditioned Media.’ Journal of Innate Immunity 6, № 3: 306–314. doi: 10.1159/000355211.
• Bartelheimer M, Schmid C, Storf J, Hell K, Bauer S. 2015. ‘Interspecific competition in Arabidopsis thaliana – a knowledge gap is starting to close.’ Progress in Botany 76: 303–319. doi: 10.1007/978-3-319-08807-5_12.
• Fleischmann A, Michael T, Rivadavia F, Wang W, Temsch E, Greilhuber J, Müller KF, Heubl G. 2014. ‘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 114, № 8: 1651–1663. doi: 10.1093/aob/mcu189.
• Wicke S, Schäferhoff B, dePamphilis CW, Müller KF. 2014. ‘Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae.’ Molecular Biology and Evolution 31, № 3: 529–545. doi: 10.1093/molbev/mst261.
• Röschenbleck J, Albers F, Müller KF, Weinl S, Kudla J. 2014. ‘Phylogenetics, character evolution and a subgeneric revision of the genus Pelargonium (Geraniaceae).’ Phytotaxa 159, № 2: 31–76.
• Wicke S, Müller KF, dePamphilis CW, Quandt D, Wickett NJ, Zhang Y, Renner SS, Schneeweiss GM. 2013. ‘Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family.’ The Plant Cell 25: 3711–3725. doi: 10.1105/tpc.113.113373.
• Fischer E, Schäferhoff B, Müller KF. 2013. ‘The phylogeny of Linderniaceae - The new genus Linderniella, and new combinations within Bonnaya, Craterostigma, Lindernia, Torenia and Vandellia.’ Willdenowia 43: 209–238. doi: 10.3372/wi.43.43201.
• Testroet P, Quandt D, Santos-Guerra A, Müller KF, Lobin W. 2013. ‘Population genetics and conservation of Sideroxylon canariense (Sapotaceae) on the Canary Islands.’ Vieraea 41: 295–308.
• Abedi M, Bartelheimer M, Poschlod P. 2014. ‘Effects of substrate type, moisture and its interaction on soil seed survival of three Rumex species.’ Plant and Soil 374: 485–495. doi: 10.1007/s11104-013-1903-x.
• Bartelheimer M, Poschlod P. 2014. ‘The response of grassland species to nitrate versus ammonium coincides with their pH optima.’ Journal of Vegetation Science 25: 760–770. doi: 10.1111/jvs.12124.
• Schmid C, Bauer S, Müller B, Bartelheimer M. 2013. ‘Belowground neighbor perception in Arabidopsis thaliana studied by transcriptome analysis: roots of Hieracium pilosella cause biotic stress.’ Frontiers in Plant Science 4: 296. doi: 10.3389/fpls.2013.00296.
• Müller B, Bartelheimer M. 2013. ‘Interspecific competition in Arabidopsis thaliana: root hairs are important for competitive effect, but not for competitive response.’ Plant and Soil 371: 167–177. doi: 10.1007/s11104-013-1675-3.
• Damayanti L, Muñoz J, Wicke S, Symmank L, Shaw B, Frahm J-P, Quandt D. 2012. ‘Common but new: Bartramia rosamrosiae, a 'new' widespread species of apple mosses (Bartramiales, Bryophytina) from the Mediterranean and western North America.’ Phytotaxa 73: 37–59.
• Abedi M*, Bartelheimer M* (*equally contributing), Poschlod, P. 2013. ‘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 24: 1074–1085. doi: 10.1111/jvs.12016.
• Fischer E, Schäferhoff B, Müller KF. 2012. ‘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 46: 19–33.
• Barniske A, Borsch T, Müller KF, Krug M, Worberg A, Neinhuis C, Quandt D. 2012. ‘Phylogenetics of early branching eudicots: comparing phylogenetic signal accross chloroplast introns, spacers, and genes.’ Journal of Systematics and Evolution 50: 85–108. doi: 10.1111/j.1759-6831.2012.00181.x.
• Naumann J, Symmank L, Samain M, Müller KF, Neinhuis C, dePamphilis CW, Wanke S. 2011. ‘Chasing the hare - Evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level.’ BMC Evolutionary Biology 11: 357. doi: 10.1186/1471-2148-11-357.
• Müller KF. 2011. ‘McPherson S. (ed. by Fleischmann A. and Robinson A.): Carnivorous plants and their habitats. (Book review).’ Willdenowia 42: 387–388.
• Wicke S, Costa A, Muñoz J, Quandt D. 2011. ‘Restless 5S: The re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants.’ Molecular Phylogenetics and Evolution 61, № 2: 321–332. doi: 10.1016/j.ympev.2011.06.023.
• Korotkova N, Borsch T, Quandt D, Taylor NP, Müller KF, Barthlott W. 2011. ‘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 98, № 9: 1549–1572. doi: 10.3732/ajb.1000502.
• Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D. 2011. ‘The evolution of the plastid chromosome in land plants: gene content, gene order, gene function.’ Plant Molecular Biology 76, № 3-5: 273–297. doi: 10.1007/s11103-011-9762-4.
• Schäferhoff B, Fleischmann A, Fischer E, Albach DC, Borsch T, Heubl G, Müller KF. 2010. ‘Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences.’ BMC Evolutionary Biology 10. doi: 10.1186/1471-2148-10-352.
• Simmons MP, Müller KF, Norton. 2010. ‘Alignment of, and phylogenetic inference from, random sequences: the susceptibility of alternative methods to artifactual resolution and support.’ Molecular Phylogenetics and Evolution 57, № 3: 1004–1016. doi: 10.1016/j.ympev.2010.09.004.
• Preußing M, Olsson S, Schäfer-Verwimp A, Wickett NJ, Wicke S, Quandt D, Nebel M. 2010. ‘New insights in the evolution of the liverwort family Aneuraceae (Metzgeriales, Marchantiophyta), with emphasis on the genus Lobatiriccardia.’ Taxon 59, № 5: 1424–1440.
• Fleischmann A, Schäferhoff B, Heubl G, Rivadavia F, Barthlott W, Müller KF. 2010. ‘Phylogenetics and character evolution in the carnivorous plant genus Genlisea A. St.-Hil. (Lentibulariaceae).’ Molecular Phylogenetics and Evolution 56, № 2: 768–783. doi: 10.1016/j.ympev.2010.03.009.
• Simmons MP, Webb CT, Müller KF. 2010. ‘The deterministic effects of alignment bias in phylogenetic inference.’ Cladistics 27, № 4: 402–416. doi: 10.1111/j.1096-0031.2010.00333.x.
• Simmons MP, Zhang LB, Müller KF. 2010. ‘Phylogenetic inference using non-redundant coding of dependent characters vs. alternative approaches when applied to protein-coding genes.’ Cladistics 27, № 2: 186–196. doi: 10.1111/j.1096-0031.2010.00327.x.
• Stöver BC, Müller KF. 2010. ‘TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses.’ BMC Bioinformatics 11: 7. doi: 10.1186/1471-2105-11-7.
• Müller KF, Albach DC. 2010. ‘Evolutionary rates in Veronica L. (Plantaginaceae): Disentangling the influence of life history and breeding system.’ Journal of Molecular Evolution 70, № 1: 44–56. doi: 10.1007/s00239-009-9307-5.
• Bartelheimer M, Gowing D, Silvertown J. 2010. ‘Explaining hydrological niches: the decisive role of below-ground competition in two closely related Senecio species.’ Journal of Ecology 98: 126–136. doi: 10.1111/j.1365-2745.2009.01598.x.
• Schäferhoff B, Müller KF, Borsch T. 2009. ‘Caryophyllales phylogenetics: disentangling Phytolaccaceae and Molluginaceae and description of Microteaceae as a new isolated family.’ Willdenowia 39: 209–228.
• Wicke S, Quandt D. 2009. ‘Universal primers for the amplification of the plastid trnK/matK region in land plants.’ Anales del Jardín Botánico de Madrid 66, № 2: 285–288. doi: 10.3989/ajbm.2231.
• Simmons MP, Müller KF, Webb CT. 2008. ‘The relative sensitivity of different alignment methods and character codings in sensitivity analysis.’ Cladistics 24, № 6: 1039–1050. doi: 10.1111/j.1096-0031.2008.00230.x.
• Beck SG, Fleischmann A, Huaylla H, Müller KF, Borsch T. 2008. ‘Pinguicula chuquisacensis (Lentibulariaceae), a new species from the Bolivian Andes, and first insights on phylogenetic relationships among South American Pinguicula.’ Willdenowia 38: 201–212.
• Wahrmund U, Rein T, Frahm, Müller KF, Groth-Malonek M, Knoop V. 2008. ‘Fifty mosses on five trees: Comparing phylogenetic information in three types of non-coding mitochondrial DNA and two chloroplast loci.’ Plant Systematics and Evolution 282: 241–255. doi: 10.1007/s00606-008-0043-x.
• Bartelheimer M, Steinlein T, Beyschlag W. 2008. ‘15N-nitrate-labelling demonstrates a size symmetric competitive effect on belowground resource uptake.’ Plant Ecology 199: 243–253. doi: 10.1007/s11258-008-9429-7.
• Wall PK, Leebens-Mack J, Müller KF, Field D, Altman NS, dePamphilis CW. 2007. ‘PlantTribes: A gene and gene family resource for comparative genomics in plants.’ Nucleic Acids Research 36, № IS 1: D970–D976. doi: 10.1093/nar/gkm972.
• 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. 2007. ‘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 104, № 49: 19369–19374. doi: 10.1073/pnas.0709121104.
• Barakat A, Müller KF, Sáenz de Miera. 2007. ‘Molecular evolutionary analysis of the Arabidopsis L7 ribosomal protein gene family.’ Gene 403: 143–150. doi: 10.1016/j.gene.2007.08.002.
• Simmons MP, Müller KF, Norton AP. 2007. ‘The relative performance of indel-coding methods in simulations.’ Molecular Phylogenetics and Evolution 44: 724–740. doi: 10.1016/j.ympev.2007.04.001.
• Weigelt A, Schumacher J, Walther T, Bartelheimer M, Steinlein T, Beyschlag W. 2007. ‘On the hyperbolic competition model – Reply.’ Journal of Ecology 95: 601–602. doi: 10.1111/j.1365-2745.2007.01260.x.
• Simmons MP, Zhang, Webb CT, Müller KF. 2007. ‘A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference.’ Molecular Phylogenetics and Evolution 42: 528–542. doi: 10.1016/j.ympev.2006.08.008.
• Weigelt A, Schumacher J, Walther T, Bartelheimer M, Steinlein T, Beyschlag W. 2007. ‘Identifying mechanisms of competition in multi-species communities.’ Journal of Ecology 95: 53–64. doi: 10.1111/j.1365-2745.2006.01198.x.
• Müller K, Borsch T, Legendre L, Porembski S, Barthlott W. 2006. ‘Recent progress in understanding the evolution of Lentibulariaceae.’ Plant Biology 8: 748–757. doi: 10.1055/s-2006-924706.
• Greilhuber J, Borsch T, Müller KF, Worberg A, Porembski S, Barthlott W. 2006. ‘Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size.’ Plant Biology 8: 770–777. doi: 10.1055/s-2006-924101.
• Müller KF, Borsch T, Hilu KW. 2006. ‘Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F and rbcL in basal angiosperms.’ Molecular Phylogenetics and Evolution 41, № 1: 99–117. doi: 10.1016/j.ympev.2006.06.017.
• Müller KF. 2006. ‘Incorporating information from length-mutational events into phylogenetic analysis.’ Molecular Phylogenetics and Evolution 38, № 3: 667. doi: 10.1016/j.ympev.2005.07.011.
• Müller KF, Borsch T. 2005. ‘Multiple origins of a unique pollen feature: stellate pore ornamentation in Amaranthaceae.’ Grana 44: 266–281. doi: 10.1080/00173130500477787.
• Müller KF. 2005. ‘The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support.’ BMC Evolutionary Biology 5: 58. doi: 10.1186/1471-2148-5-58.
• Cieslack T, Polepalli, White A, Müller KF, Borsch T, Barthlott W, Steiger J, Marchand A, Legendre L. 2005. ‘Phylogenetic Analysis of Pinguicula (Lentibulariaceae): Chloroplast DNA Sequences and Morphology Support Several Geographically Distinct Radiations.’ American Journal of Botany 92: 1723–1736. doi: 10.3732/ajb.92.10.1723.
• Bartelheimer M, Steinlein T, Beyschlag W. 2006. ‘Aggregative root placement: a feature during interspecific competition in inland sand-dune habitats.’ Plant and Soil 280: 101–114. doi: 10.1007/s11104-005-2612-x.
• Borsch T, Löhne C, Müller KF, Hilu KW, Wanke S, Worberg A, Barthlott W, Neinhuis C, Quandt D. 2005. ‘Towards Understanding Basal Angiosperm Diversification: Recent Insights Using Rapidly Evolving Genomic Regions.’ Nova Acta Leopoldina 92 342: 85–110.
• Müller KF, Borsch T. 2005. ‘Phylogenetics of Amaranthaceae based on matK/trnK sequence data - evidence from parsimony, likelihood, and Bayesian analyses.’ Annals of the Missouri Botanical Garden 92, № 1: 66–102.
• Müller KF. 2005. ‘SeqState - primer design and sequence statistics for phylogenetic DNA data sets.’ Applied Bioinformatics 4: 66–69.
• Rahmanzadeh R, Müller KF, Fischer E, Bartels D, Borsch T. 2005. ‘The Linderniaceae and Gratiolaceae (Lamiales) are further lineages distinct from Scrophulariaceae.’ Plant Biology 7, № 1: 67–78. doi: 10.1055/s-2004-830444.
• Müller KF, Borsch T. 2005. ‘Phylogenetics of Utricularia (Lentibulariaceae) and molecular evolution of the trnK intron in a lineage with high substitutional rates.’ Plant Systematics and Evolution 250: 39–67. doi: 10.1007/s00606-004-0224-1.
• Neinhuis C, Wanke S, Hilu KW, Müller KF, Borsch T. 2004. ‘Phylogeny of Aristolochiaceae based on parsimony, likelihood, and Bayesian analyses of trnL-trnF sequences.’ Plant Systematics and Evolution 250: 7–26. doi: 10.1007/s00606-004-0217-0.
• Müller J, Müller KF. 2004. ‘TreeGraph: automated drawing of complex tree figures using an extensible tree description format.’ Molecular Ecology Notes 4: 186–788. doi: 10.1111/j.1471-8286.2004.00813.x.
• Müller KF, Borsch T, Legendre L, Porembski S, Theisen I, Barthlott W. 2004. ‘Evolution of carnivory in Lentibulariaceae and the Lamiales.’ Plant Biology 6: 477–490. doi: 10.1055/s-2004-817909.
• Müller KF. 2004. ‘PRAP - computation of Bremer support for large data sets.’ Molecular Phylogenetics and Evolution 31, № 2: 780–782. doi: 10.1016/j.ympev.2003.12.006.
• 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. 2003. ‘Angiosperm phylogeny based on matK sequence information.’ American Journal of Botany 90: 1758–1776. doi: 10.3732/ajb.90.12.1758.
• Quandt D, Müller KF, Huttunen S. 2003. ‘Characterisation of the chloroplast DNA psbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions.’ Plant Biology 5: 400–410. doi: 10.1055/s-2003-42715.
• Müller J, Müller KF. 2003. ‘QuickAlign: A New Alignment Editor.’ Plant Molecular Biology Reporter 21: 1–5. doi: 10.1007/BF02773390.
• Müller KF, Borsch T, Legendre L, Theisen I, Barthlott W. 2002. ‘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 : 63–73.
• Frahm, Müller KF, Stech M. 2000. ‘The taxonomic status of Eurhynchium crassinervium from river banks based on ITS sequence data.’ Journal of Bryology 22: 291–306.

Research Article (Book Contributions)

• Müller KF. 2022. ‘Magnoliopsida (Angiosperms) p.p. Subclass Rosidae p.p. (Trochodendranae to Saxifraganae).’ In Syllabus of Plant Families - Part 5/1, edited by Frey W, 215–255. Stuttgart: Borntraeger.
• Müller KF, Fischer, E. 2022. ‘Magnoliopsida (Angiosperms) p.p. Subclass Rosidae p.p. (Rosanae to Berberidopsidanae).’ In Syllabus of Plant Families - Part 5/1, edited by Frey W, 255–615. Stuttgart: Borntraeger.
• Grimm J, Hoffmann M, Stöver BC, Müller KF, Steinhage V. 2016. ‘Image-Based Identification of Plant Species Using a Model-Free Approach and Active Learning.’ In KI 2016: Advances in Artificial Intelligence, edited by Friedrich G, Helmert M, Wotawa F, 169–176. Basel : Springer International Publishing. doi: 10.1007/978-3-319-46073-4_16.
• Wicke S, Schneeweiss GM. 2015. ‘Next generation organellar genomics: Potentials and pitfalls of high-throughput technologies for molecular evolutionary studies and plant systematics.’ In Next generation sequencing in plant systematics, edited by Hörandl E; Appelhans M, Chapter 1. Oberreifenberg / Koenigstein: Koeltz. doi: 10.14630/000002.
• Wicke S. 2013. ‘Genomic evolution in Orobanchaceae.’ In Parasitic Orobanchaceae - Parasitic Mechanisms and Control Strategies , edited by Joel DM, Gressel J, Musselman LJ, 267–286. Düsseldorf: Springer VDI Verlag. doi: 10.1007/978-3-642-38146-1_15.
• Poschlod P, Abedi M, Bartelheimer M, Drobnik J, Rosbakh S, Saatkamp A. 2013. ‘Seed Ecology and Assembly Rules in Plant Communities .’ In Vegetation Ecology, edited by Van der Maarel, E, Franklin, J, 164–202. 2^nd Ed. New York City: John Wiley & Sons. doi: 10.1002/9781118452592.ch6.
• Müller KF. 2011. ‘Biodiversität und Evolution.’ In Perspektiven - Forschungsfragen der Zukunft, edited by 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, 1–10. 1^st Ed. Paderborn: Ferdinand Schöningh.
• Quandt D, Müller KF, Stech M, Hilu KW, Frey W, Frahm J-P, Borsch T. 2004. ‘Molecular evolution of the chloroplast trnL-F region in land plants.’ In Molecular Systematics of Bryophytes, edited by Goffinet B, Hollowell V, Magill R, 13–37. St. Louis: Missouri Botanical Garden Press.
• Huttunen S, Ignatov MS, Müller KF, Quandt D. 2004. ‘The phylogeny and evolution of epiphytism in three moss families Meteoriaceae, Brachytheciaceae, and Lembophyllaceae.’ In Molecular Systematics of Bryophytes, edited by Goffinet B, Hollowell V, Magill R, 328–364. St. Louis: Missouri Botanical Garden Press.

Non-Scientific Contributions (Journals)

• Asshoff, Roman; Dankbar, Julia; Bartelheimer, Maik. 2024. „Pflanzliche Gipfelstürmer - Bedroht der Klimawandel die alpine Flora?“ Unterricht Biologie 495: 32–38.
• Asshoff, R., Dankbar, J., Bartelheimer, M. 2019. „Licht und Schatten. Mathematisieren im Biologieunterricht im Kontext einer ökologischen Freilandübung.“ Der mathematisch-naturwissenschaftliche Unterricht 72, № 03: 222–228.

Books (Monographs)

• Knoop V, Müller KF. 2008. Gene und Stammbäume: Ein Handbuch zur molekularen Phylogenetik. 2^nd Ed. Heidelberg: Spektrum Akademischer Verlag.
• Knoop V, Müller KF. 2006. Gene und Stammbäume. Ein Handbuch zur molekularen Phylogenetik. 1^st Ed. Heidelberg: Spektrum Akademischer Verlag.

Theses (Doctoral or Postdoctoral)

• Stöver, BC. 2018. Software components for increased data reuse and reproducibility in phylogenetics and phylogenomics Dissertation thesis, WWU Münster. Münster.
• Bartelheimer M. 2013. Ecophysiology of root interactions and plant niche differentiation Habilitation thesis, University of Regensburg.
• Müller, Kai. 2005. Evolution of Amaranthaceae - A case study integrating molecular phylogenetics and pollen data Dissertation thesis, Rheinische Friedrich-Wilhems-Universität Bonn. Bonn.
• Bartelheimer M. 2005. Pflanzliche Interaktionen in ressourcenarmen Sandökosystemen: Die Bedeutung funktioneller und morphologischer Wurzelparameter für die unterirdische Konkurrenzfähigkeit Dissertation thesis, University of Bielefeld.