Lab Members: Frank Kauff

Frank Kauff (Postdoctoral Research Associate)

Ph.D., Biology, Duke University

2002 Ph. D. (Biology), University of Kaiserslautern, Germany

1997 Diploma (= M.S., Biology), University of Kaiserslautern, Germany

Research Interests
Phylogenetics, and all that’s related
Python, esp. Biopython

Current Research
WASABI: Bioinformatics of AFTOL (check Science or our website for a description of WASABI)
Development of a simulation framework for host-parasite coevolution (cooperation with Daniel Henk)
Fungal genomics (cooperation with Jason Stajich and Cymon Cox)

Grants and Awards
2006 – Tuckerman Award for the best lichen paper in The Bryologist 2005.
2005 – Deep Hypha Traval Award (NSF Research Coordination Network: A Phylogeny for Kingdom
2001 – Visiting Scholarship Grant of the Field Museum of Natural History, Chicago, USA
2000 – Visiting Lichenologist Program, Michigan State University Herbarium, East Lansing (MI), USA
1997 – Dissertation fellowship “Landesgraduiertenförderung Rheinland-Pfalz”, Germany

Kauff F, Cox CJ, Lutzoni F. 2007. WASABI: An automated sequence processing system for multi-gene phylogenies. Syst. Biol. (in press)

Hofstetter V, Miadlikowska J, Kauff F, Lutzoni F. 2006. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: A case study of the Lecanoromycetes (Ascomycota). Mol. Phylogen. Evol. (in press)

Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J, Reeb V, Hodkinson BP, Kukwa M, Lücking R, Hestmark, Garcia-Otalora M, Rauhut A, Büdel B, Scheidegger C, Timdal E, Stenroos S, Brodo I, Perlmutter GB, Ertz D, Diederich P, Lendemer JC, Tripp E, Yahr R, May P, Gueidan C, Spatafora JW, Schoch C, Arnold AE, Robertson C, Lutzoni F. 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia, in press.

Geiser DM, Gueidan C, Schoch C, Hofstetter V, Fraker E, Untereiner WA, Miadlikowska J, Lutzoni F, Kauff F, Aptroot A, 2006. Eurotiomycetes: Eurotiomycetidae + Chaetothyriomycetidae. Mycologia, in press.

James TY, Kauff F, Schoch C, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch T, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung G-H, Johnson D, O’Rourke B, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schüßler A, Longcore JE, O’Donnell K, Mozley-Standridge K, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lücking R, Büdel B, Geiser DM, Aptroot A, Buck WR, Cole MS, Diederich P, Printzen C, Schmitt I, Schultz M, Yahr R, Zavarzin A, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R. (2006). Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443:818-822.

Kauff F, Büdel B, (2005). Ascoma ontogeny and apothecial anatomy in the Gyalectaceae (Ostropales, Ascomycota) support the reestablishment of the Coenogoniaceae. Bryologist 108(2): 272-281.

Lutzoni F, Kauff F, Cox C, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung GH, Lücking R, Lumbsch T, O’Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hall B, Hansen K, Harris RC, Hosaka K, Lim YW, Liu Y, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R, (2004). Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Amer. J. Bot. 91: 1446-1480.

Kauff F, Lutzoni F, (2002). Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Mol. Phylogen. Evol. 25: 138-156.

Kauff F, Rudall P, Conran J, (2000). Systematic root anatomy of Asparagales and other monocotyledons. Plant Syst. Evol. 223: 139-154.

Related Articles
Fungal trees grow faster with computer help. Science, Vol 309, Issue 5733, 374 , 15 July 2005

Selected Abstracts
Kauff F, Büdel B, Lutzoni F, (2003). Ascoma ontogeny and apothecial anatomy in the Gyalectaceae (Ostropales, Ascomycetes) and the restoration of the Coenogoniaceae. Inoculum 54(3):29.

Hofstetter V, Kauff F, Vilgalys R, (2003). Phylogeny of the Lyophyllae (Agaricales, Basidiomycetes): Systematic vs. ecological transitions in Basidiomycota. Inoculum 54(3):25.

Kauff F, Lutzoni F, Büdel B, (2002). Phylogeny of Ostropales and Gyalectales – evidence from molecular and ontogenetical data. 7th International Mycological Congress 7, Oslo, Norway.

Kauff F, Cox CJ, Lutzoni F, (2004). Bioinformatics of AFTOL (Assembling the Fungal Tree of Life). Evolution 2004, Fort Collins, USA.

Cox CJ, Kauff F, (2004). Of Snakes and mushrooms: The use of (Bio)Python in the AFTOL project. Inoculum 55(4).

Cox CJ, Kauff F, Lutzoni F, (2004). A data management framework for the AFTOL project. – In: Randlane, T/Saag, A (eds.): Book of Abstracts of the 5th IAL Symposium. Lichens in Focus. Tartu University Press, pp. 77.

Hofstetter V, Miadlikowska J, Gueidan C, Reeb V, Arnold AE, Kauff F, Cox CJ, Yahr R, Lutzoni F, (2004). What do protein-coding genes (ATP6, EF1-Alpha and RNA polymerase II) bring to molecular systematics of lichens?. – In: Randlane, T/Saag, A (eds.): Book of Abstracts of the 5th IAL Symposium. Lichens in Focus. Tartu University Press, pp. 16.

Test for tree compatibility: COMPAT
Kauff F, Lutzoni F. 2002. Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Mol. Phyl. Evol. 25: 138-156

Ambiguous Regions Coding: ARC
Miadlikowska, Lutzoni, Goward, Zoller, Posada (2003) “New approach to an old problem: Gap-rich regions from ITS and rDNA large-subunit are incorporated into phylogenetic analyses to resolve the Peltigera canina species complex.”, Mycologia 95(6):1181-1203.

Random Tree Sampling: RT
Simple python script to sample a subset of trees from a given treefile.