Claus Vogl

Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien,
Veterinärplatz 1, 1210, Wien

claus.vogl@vetmeduni.ac.at

Instead of a CV

My early work had been heavily influenced by my Ph.D. supervisor, Günter Wagner. But I had been too timid to follow his bold path---I have always needed concrete data. My first postdoc was with William Atchley at NCSU. There I learned about population and quantitative genetics. Back in Vienna I worked practically with rats and fish. Then I spent three years in Outi Savolainen's group in Oulu, Finland, working again in population and quantitative genetics. With Shizhong Xu, the bend was more theoretical. After a short time doing bioinformatics with Tao Jiang and Mike Clegg, I spent a year in Munich with Wolfgang Stephan, before returning to Vienna.

Expertise

Ever since I got in touch with Elja Arjas, I have been using the Bayesian approach to model various biological processes using probabilistic models. The idea has always been to subdivide a complex biological problem into manageable chunks, model these chunks conditional on key parameters from other chunks, and then put the whole into a Markov chain Monte Carlo (MCMC) integration scheme. Sounds maybe complicated, but is quite easy, much like playing with Lego blocks when I was a kid. I have applied this approach to data from population genetics problems, linkage-, QTL-, and TRDL-mapping, phylogenetic problems, and to gene expression chip analysis.

Programs

The programs are generally written in C++, compiled with the GNU C++ compiler, run on unix computers, and come with absolutely no warranty. Please contact me via e-mail, if you have questions or problems.

Anita: performs map construction, mapping of quantitative trait loci (QTL), and mapping of transmission ratio distorting loci (TRDL). A tarball with the program and documentation is here: anita.tar.gz.

Chips: performs a clustering analysis of transcriptomics chip data. A tarball with the program and documentation is here: chips.tar.gz.

coal_dipl: performs calculation of within and among population inbreeding coefficients. In contrast to the usual, individual inbreeding coefficients and populationwise Theta_p's are estimated. A tarball with the program and documentation is here: coal_dipl.tar.


Teaching

At the Ludwig-Maximilian Universität in Munich, I introduced beginning students of biology to probability and Bayesian statistics. The manuscript is in the German language and can be found here: PDF.

I used to offer a course in quantitative genetics and QTL mapping in the English language. The manuscript has evolved with my experience and with the students that enroll. The current version is here: PDF.

Material for a course in computer intensive methods (CIM), at the Institute of Statistics, University of Vienna (last held 2008), can be found here:
PDF

Material for the course "UK Biometrie" at the Institute of Statistics, University of Vienna (last held 2009), mainly on the coalescence and population genetic data analysis, can be found here:
PDF

Material for the course "Statistische Genetik und Bioinformatk" at the Institute of Statistics, University of Vienna (2009), mainly on hidden Markov models (HMM), can be found here:
preprint of an article on HMMs with Andreas Futschik
Homework until Jan. 11, 2009
hmm_aln_02.R: program to generate pairwise aligned data sets and a Viterbi algorithm for global alignment
hmm_02.R: program to generate a mock CpG data set and HMM analysis


Links

Please have a look at the Evolvienna intiative.

Publications

Schaljo B, Kratochvill F, Gratz N, Sadzak I, Sauer I, Hammer M, Vogl C, Strobl B, Müller M, Blackshear PJ, Poli V, Lang R, Murray PJ, Kovarik P (2009) Tristetraprolin is required for full anti-inflammatory response of murine macrophages to IL-10. Journal of Immunology 183:1197-206.

Stockinger S, Kastner R, Kernbauer E, Pilz A, Westermayer S, Reutterer B, Soulat D, Stengl G, Vogl C, Frenz T, Waibler Z, Taniguchi T, Rülicke T, Kalinke U, Müller M, Decker T (2009) Characterization of the interferon-producing cell in mice infected with Listeria monocytogenes. PLoS Pathog. 5:e1000355.

Hornberg A, Fernández SR, Vogl C, Vilcek S, Matt M, Fink M, Köfer J, Schöpf K (2008) Genetic diversity of pestivirus isolates in cattle from Western Austria. Vet microbiol. 135:205-13.

Radwan M, Miller I, Grunert T, Marchetti-Deschmann M, Vogl C, O'Donoghue N, Dunn MJ, Kolbe T, Allmaier G, Gemeiner M, Müller M, Strobl B (2008) The impact of tyrosine kinase 2 (Tyk2) on the proteome of murine macrophages and their response to lipopolysaccharide (LPS). Proteomics 8:3469-3485

Painz R, Walter I, Kolbe T, Rigler D, Vogl C, Steinborn R, Rülicke T, Helmreich M, Karaghiosoff M, Müller M (2008) Organ-specific and differential requirement of TYK2 and IFNAR1 for LPS-induced iNOS expression in vivo. Immunobiology 212:863-875

Costantino G, Egerbacher M, Kolbe T, Karaghiosoff M, Strobl B, Vogl C, Helmreich M, Müller M. (2007) Tyk2 and signal and stransducer and activator of transcription 1 contribute to intestinal I/R injury. Shock 29:238-244

Sauer I, Schaljo B, Vogl C, Gattermeier I, Kolbe T, Muller M, Blackshear PJ, and P. Kovarik. (2006) Interferons limit inflammatory responses by induction of tristetraprolin. Blood 107:4790-4797.

Leeb T, Vogl C, Zhu B, de Jong PJ, Binns MM, Chowdhary BP, Scharfe M, Jarek M, Nordsiek G, Schrader F, and H. Blocker (2006) A human-horse comparative map based on equine BAC end sequences. Genomics 87:772-776.

Vogl, C., Sanchez-Cabo, F., G. Stocker, S. Hubbard, S., Wolkenhauer, O., Trajanoski, Z. (2005) A fully Bayesian model to cluster gene expression profiles. Bioinformatics, 21:ii130-ii136

Karhu, A., Vogl, C., Moran, G.F., Bell, J.C., Savolainen, O. (2005) Analysis of microsatellite variation in Pinus radiata reveals effects of genetic drift but no recent bottlenecks. Journal of Evolutionary Biology, 19:167-175

Guo, Y.-P., Vogl, C., van Loo, M., Ehrendorfer, F., (2005) Hybrid origin of the tetraploid Achillea alpina and A. wilsoniana. Molecular Ecology, 15:133-144

Kuittinen, H., de Haan, A.A., Vogl, C., Oikarinen, S., Leppälä, J., Koch, M., Mitchell-Olds, T., Langley, C.H., Savolainen, O. (2004). Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana. Genetics 168:1575-1584.

Muir, G., Lowe, A.J., Fleming, C.C., Vogl C. (2004). Population structure and mating systems in remnants of Irish sessile oaks (Quercus petraea (Matt.) Liebl.). Annals of Botany 93:691-697.

Myburg, A, Vogl, C., Griffin, A.R., Sederoff, R.R., Whetten, R.W. (2004) Genetics of Postzygotic Isolation in Eucalyptus: Whole-Genome analysis of barriers to introgression in a wide interspecific cross of E. grandis and E. globulus. Genetics 166:1405-1418.

Vogl, C., Das, A., Beaumont, M., Mohanty, S. and Stephan, W. (2003) Population subdivision and molecular sequence variation: Theory and analysis of Drosophila ananassae data. Genetics 165:1385-1395.

Vogl, C., Badger, J., Kearney, P., Li, M., Clegg, A. and Jiang, T. (2003) Probabilistic analysis indicates discordant gene trees in chloroplast evolution. J. Mol. Evol. 56:330--340.

Vogl, C., Xu, S. (2002) QTL analysis in arbitrary pedigrees with incomplete marker information. Heredity 89:339--345.

Vogl, C., Karhu, A., Moran, G., Savolainen, O. (2002) High resolution analysis of mating systems: inbreeding in natural populations of Pinus radiata. J. Evol. Biol. 15:433--439.

Vogl, C., Xu, S. (2000) Multipoint mapping of viability and segregation distorting loci using molecular markers. Genetics 155:1439--1447.

Xu, S., Vogl, C. (1999) Maximum likelihood analysis of quantitative trait loci under selective genotyping. Heredity 84:525--537.

Vogl, C., Grillitsch, B., Wytek, R., Spieser, O.H., Scholz, W., (1999) Qualification of spontanous locomotory behavior of fish for sublethal toxicity testing. Part 1: Variability of measurement parameters under general test conditions. Environmental Toxicology and Chemistry 18(12):2736--2742.

Grillitsch, B., Vogl, C., Wytek, R., (1999) Qualification of spontanous locomotory behavior of fish for sublethal toxicity testing. Part 2: Variability of measurement parameters under toxicant-induced stress. Environmental Toxicology and Chemistry 18(12):2745.

Kärkkäinen, K., Kuittinen, H., van Treuren, R., Vogl, C., Oikarinen, S., Savolainen, O., (1999) Genetic basis of inbreeding depression in Arabis petrea. Evolution 53(5):1354--1365.

Fürnsinn, C., Neschen, S., Noe, Ch., Roden, M., Vogl, C., Waldhäusl, W.  (1997) Acute non-insulin-like stimulation of rat glucose metabolism by troglitazone in vitro. Br. J. Pharmacol. 122:1367-74

Schlötterer, C., Vogl, C., Tautz, D. (1997) Polymorphism and locus-specific effects at microsatellite loci in natural Drosophila melanogaster populations. Genetics 146:303--320.

Fürnsinn, C., Englisch, W., Ebner, K., Nowotny, W., Vogl, C., Waldhäusl, W.  (1996) Insulin-like vs. non-insulin-like stimulation of glucose metabolism by Vanadium, Tungsten, and Selenium compounds in rat muscle.  Life Sci. 53:1989--2000.

Schiesari, L., Grillitsch, B., Vogl C. (1996) Comparative morphology of phytotelmonous and pond-dwelling larvae of four neotropical treefrog species (Amphibia, Anura, Hylidae, Osteocephalus oophagus, O. taurinus, Phrynohyas resinifictrix, P.  venulosa). Alytes 13:109--139.

Vogl, C. (1995) Developmental Buffering and Selection. Evolution 50:1343--1346.

Vogl, C., Atchley, W.R. (1995) Hormone gradients and cartilage cell kinetics. Cell Proliferation 28:453--469. 

Vogl, C., Atchley, W.R., Cowley, D.E., Crenshaw, P., Murray, J.D., Pomp, D. (1994) The epigenetic influence of growth hormone on skeletal development. Growth, Development and Aging 57:163--182.

Vogl, C., Atchley, W.R., Xu, S. (1994) The ontogeny of morphological differences in the mandible in two inbred strains of mice. J. Craniofac. Genet.  Dev.  Biol. 14:97--110.

Atchley, W.R., Xu, S., Vogl C. (1994) Developmental quantitative genetic models of evolutionary change. Dev. Genet. 15:92--103.

Vogl, C. (1993) Theoretical enhancements of finite element scaling analysis (FESA) methodology. Syst.  Biol. 42:341--355.

Atchley, W.R., Cowley, D.E., Vogl, C., McLellan, T. (1992) Evolutionary divergence, shape change, and genetic correlation structure in the rodent mandible. Syst.  Biol. 41:196--221.

Vogl, C., Rienesl, J. (1991) Testing for developmental constraints: Carpal fusions in urodeles. Evolution 45:1516--1519.

Vogl, C., Wagner, G.P. (1990) Interspecific variability in random clades: models for testing hypotheses on the relative evolutionary flexibility of quantitative traits. Syst. Zool. 39:109-130.