Steffen Klaere

Research Interests:

• Holistic analysis of agricultural ecosystems,
Modern sequencing methodology permit the phylogenetic identification of thousands of organisms and to taxonomically characterise an ecosystem. There are alternative methods that lead to a functional characterisation of the ecosystem at an increased cost. I am interested in building informative taxonomic and functional ecosystem models, and link these models to find ways to predict function from taxonomy. Further, in an agricultural environment we are interested in linking an ecosystem model to external factors and outcomes, which ideally inform management decisions and lead to a more sustainable industry.
• Evaluation of the goodness of fit for statistical tests in phylogeny,
I am interested in developing diagnostic tools to assess model-to-data fitness in phylogenetic inference. The goal is to develop exploratory and statistics to highlight regions of data for which the standard models do not adequately explain the signal.
• Quantitative measures of biodiversity
The use of phylogenetic information in the assessment of biodiversity is limited, depending strongly on the availability and quality of genetic and/or morphological data. I want to expand my horizon beyond phylogenetics and look into the multitude of measures available for the evaluation of the three parts of biodiversity: diversity, distribution, and abundance. My goal is to find a set of measures which is the cheapest to compute while retaining as much information as possible.
• Connecting variational linguistics with historical linguistics.
Methods from population genetics and phylogenetics have permeated into the research into language evolution. We want to take this approach further and classify the overlap between the fields and develop research topics that can provide a more detailed picture into human social behaviour through the development of language.

Teaching:

Lectures

No current teaching due to sabbatical.

Current Students

• Jelena Cosič is doing a PhD with me working on modelling ecosystems using Bayesian networks. Her work is part of the Vineyard Ecosystems Project and co-supervised by Bruno Feddrizzi and Mat Goddard.
• Paulina Giraldo Perez is doing a PhD with Mat Goddard assessing the impact of vineyard management techniques on the local ecosystem. I am providing support with regards to the statistical analysis of next generation sequencing data. Paulina is working within the Vineyard Ecosystems Project.
• Daisy Shepherd is doing a PhD with Russell Millar and me working on Diagnostic tools for phylogenetic inference.
• Jessica Suda is doing a PhD in Chemistry with Bruno Feddrizzi working on the impact of microbial communities on cheese quality. My supervision regards the statistical tools needed to link microbial profiles to cheese quality.

Short Vita:

Professional Experience:

• 2016-present: Senior Lecturer for Statistics at the Department of Statistics and the School of Biological Sciences;
• 2012-2016: Lecturer for Statistics at the Department of Statistics and the School of Biological Sciences;
• 2010-2011: Postdoctoral research fellow with Assoc. Prof. David Bryant at the Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand;
• 2009-2010: Postdoctoral research fellow with Assoc. Prof. David Bryant at the Computational Evolution Group, University of Auckland, New Zealand;
• 2005-2008: Postdoctoral research fellow with Prof. Arndt von Haeseler at the Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), Vienna, Austria;
• 2005: Postdoctoral research fellow with Prof. Arndt von Haeseler at the Institute of Bioinformatics, University of Düsseldorf, Germany;
• 2001-2005: Staff scientist at the Institute of Biomathematics and Biometry, Research Center for Environment and Health, Neuherberg, Germany

Education:

• 2001-2005: Ph.D. student at Ludwig-Maximilian-Universität Munich, Germany: Mathematics in Biology;
• 1995-2000: Studies at University of Jena, Germany: Mathematics in Economics;
• 1990-1994: Friedrich-Schiller-Gymnasium, Weimar, Germany;
• 1982-1990: Erich-Weinert-Gesamtschule, Legefeld, Germany.

Degrees:

• 'Dr. rer-nat.' (2005), Ludwig-Maximilian-Universität München
  Advisors: Prof. Dr. V. Liebscher, Prof. Dr. A. von Haeseler
  PhD-Thesis: Stochastic Models of Molecular Evolution: An Algebraical and Statistical Analysis
  (Accompanying files: Invariants for the Kimura 2ST model )
• 'Dipl. Math-oec.' (2000), Friedrich-Schiller-Universität Jena
  Advisors: Prof. Dr. K.-H. Fichtner, PD Dr. V. Liebscher
  Diploma-Thesis: Über eine Klasse stochastischer Differentialgleichungen ohne Adaptiertheitsforderung (in German)

Research Grants:

• 2018: Named Investigator on a University of Waterloo Water Institute Grant on Statistics in Metagenomics.
• 2015: Named Investigator on 7yr programme Resilient and Profitable Wine Industry funded by MBIE and NZ Winegrowers.
• 2013: FRDF New Staff Grant for project Phylogenetics with real confidence: Statistical selection of phylogenetic models
• 2007: One month stay at the Programme "Phylogenetics" at the Isaac Newton Institute, Cambridge, UK
• 2003: Three month Marie-Curie grant for Programme "Mathematique, Informatique et Genomique" at the Institut Henri Poincare, Paris, France.

Publications / Conference Contributions

• 2018
• Knight S, Klaere S, Morrison-Whittle P, Goddard M. Fungal diversity during fermentation correlates with thiol concentrations in wine. Australian Journal of Grape and Wine Research 24(1):105-112. doi: 10.1111/ajgw.12304;
• 2017
• Meyerhoff M, Klaere S. A case for clustering speakers and linguistic variables: Big issues with smaller samples in language variation, 23-46. In Language Variation - European Perspectives VI by I Buchstaller and B Siebenhaar (eds). Link: Book;
• Parish KJ, Herbst-Johnstone M, Bouda F, Klaere S, Fedrizzi B. Industrial scale fining influences the aroma and sensory profile of Sauvignon blanc. LWT - Food Science and Technology 80:423-429. doi: 10.1016/j.lwt.2017.03.003;
• Parish KJ, Herbst-Johnstone M, Bouda F, Klaere S, Fedrizzi B. Sauvignon Blanc aroma and sensory profile modulation from high fining rates. Australian Journal of Grape and Wine Research 23(3):359-367. doi: 10.1111/ajgw.12281;
• 2016
• Chernomor O, Klaere S, von Haeseler A, Minh BQ. Split diversity: measuring and optimising biodiversity using phylogenetic split networks, 173-195, In: Biodiversity Conservation and Phylogenetic Systematics: preserving our evolutionary heritage in an extinction crisis by Pellens R and Grandcolas P (editors). doi: 10.1007/978-3-319-22461-9_9;
• Jelley RE, Herbst-Johnstone M, Klaere S, Pilkington LI, Grose C, Martin D, Barker D, Fedrizzi B. Optimization of Ecofriendly Extraction of Bioactive Monomeric Phenolics and Useful Flavor Precursors from Grape Waste. ACS Sustainable Chemistry and Engineering 4(9):5060-5067. doi: 10.1021/acssuschemeng.6b01551
• Parish KJ, Herbst-Johnstone M, Bouda F, Klaere S, Fedrizzi B. Pre-fermentation fining effects on the aroma chemistry of Marlborough Sauvignon blanc press fractions. Food Chemistry 208:3236-335. doi: 10.1016/j.foodchem.2016.03.111
• 2015
• Fichtner K-H, Klaere S, Liebscher V. Solving a class of linear Skorokhod Stochastic Differential Equations. Communications on Stochastic Analysis 9(4):457-466. link: Full Contents;
• Knight S, Klaere S, Fedrizzi B, Goddard MR. Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir. Scientific Reports 5. doi: 10.1038/srep14233;
• Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger M, von Haeseler A Split diversity in constrained conservation prioritization using integer linear programming. Meth Ecol Evol 6(1), 83-91. doi: 10.1111/2041-210X.12299;
• 2014
• Sawaya S, Klaere S. The relationship between extinction of a branching process and moments of the offspring distribution. Journal of Statistical Distributions and Applications 1:10. doi: 10.1186/2195-5832-1-10;
• Gayevskii V, Klaere S, Knight S, Goddard M. ObStruct: A Method to Objectively Analyse Factors Driving Population Structure Using Bayesian Ancestry Profiles. PLoS One 9(1):e85196. doi: 10.1371/journal.pone.0085196;
• 2012
• Fischer M, Klaere S, Nguyen MAT, von Haeseler A. On the group theoretical background of assigning stepwise mutations onto phylogenies. Alg Math Biol 7:36. doi: 10.1186/1748-7188-7-36;
• Klaere S, Liebscher V. An algebraic analysis of the two-state Markov model on tripod trees. Math Biosci 237(1-2), 38-48. doi: 10.1016/j.mbs.2012.03.001;
• Bryant D, Klaere S. The link between segregation and phylogenetic diversity. J Math Biol 64(1-2), 149-162. doi: 10.1007/s00285-011-0409-5;
• 2011
• Nguyen MAT, Klaere S, von Haeseler A. MISFITS: Highlighting alignment patterns that do not fit. Mol Biol Evol 28(1), 143-152. doi: 10.1093/molbev/msq180;
• 2010
• Minh BQ, Klaere S, von Haeseler A. SDA*: A simple and unifying solution to recent bioinformatic challenges for conservation genetics. Proceedings of the 2nd International Conference on Knowledge and Systems Engineering - KSE 2010 (Hanoi, Vietnam), 33-37, IEEE Computer Society, Los Alamitos, CA, USA. (ISBN: 978-0-7695-4213-3). doi: 10.1109/KSE.2010.24;
• 2009
• Hanada R, Leibbrandt A, Hanada T, Kitaoka S, Furuyashiki T, Fujiwara H, Trichereau J, d Paolino M, Qadri F, Plehm R, Klaere S, Komnenovic V, Mimata H, Yoshimatsu H, Takahashi N, von Haeseler A, Bader M, Kilic SS, Ueta Y, Narumiya S, Pifl C, Penninger JM. Central control of fever and female body temperature by the osteoclast differentiation factors RANKL/RANK. Nature, 462(7272), 505-509. doi: 10.1038/nature08596;
• Minh BQ,Klaere S, von Haeseler A. Taxon selection under split diversity. Syst Biol, 58(6), 586-594 doi: 10.1093/sysbio/syp058;
• 2008
• Klaere S, Gesell T, von Haeseler A. The impact of single substitutions on multiple sequence alignments. Proc Roy Soc Lond B, 363(1512), 4041-4047. doi: 10.1098/rstb.2008.0140;
• Kupczok A, von Haeseler A, Klaere S. An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. J Comput Biol, 15(6), 577-591. doi: 10.1089/cmb.2008.0068;
• Minh BQ, Pardi F, Klaere S, and von Haeseler A. Budgeted Phylogenetic Diversity on Circular Split Systems. IEEE/ACM Trans Comput Bi. 6(1), 22-29. doi: 10.1109/TCBB.2008.54;
• 2006
• Minh BQ, Klaere S, von Haeseler A. Phylogenetic Diversity within Seconds. Syst Biol 55(5), 769-773. doi: 10.1080/10635150600981604.

Talks

• 2017
• Do your data fit your phylogenetic tree? Invited colloquium talk at School of Mathematics and Statistics, Victoria University Wellington, March 2017;
• Signal or Noise? When is a highly variable site actually noise? Annual New Zealand Phylogenetics Meeting, Onetangi, Waiheke Island, February 2017;
• 2015
• Holistic vineyard ecology Annual New Zealand Phylogenetics Meeting, Portobello NZ, February 2015;
• 2014
• How a blind man checks whether the fat man went to the lingerie store? The UTas Theoretical Phylogenetics Meeting, Hobart Tasmania, November 2014;
• Phylogenetic inference with real confidence? Mathematical and Computational Evolutionary Biology, Hameau de l'Etoile, France, June 2014; also GryPhylo, Greifswald, Germany, July 2014;
• 2013
• What drives (model-based) phylogenetic inference? Annual New Zealand Phylogenetics Meeting, Whakapapa village NZ, February 2013;
• 2012
• Do your data fit your phylogenetic tree? The UTas Theoretical Phylogenetics Meeting, Hobart Tasmania, November 2012; also Annual New Zealand Mathematics and Statistics Postgraduate Conference, Whangaparoa Peninsula NZ, November 2012, and NZSA 2012 Conference, Dunedin NZ, November 2012;
• Unfortunately ignored: Goodness of fit tests and Outlier detection in phylogenetics. Annual New Zealand Phylogenetics Meeting, Kaikoura NZ, February 2012;
• 2011
• Hadamard-type transforms for nonsymmetric models. The UTas Theoretical Phylogenetics Meeting, Hobart Tasmania, November 2011;
• Some thoughts on biodiversity conservation. Annual New Zealand Phylogenetics Meeting, Leigh by the Sea NZ, February 2011;

Conference Posters

• Phylogenetics with real confidence presented at SMBE Annual Meeting, July 2013, Chicago USA;
• Does your phylogenetic tree fit your molecular data? presented at SMBE Annual Meeting, June 2012, Dublin Ireland;
• Phylogenetic inference in the presence of horizontal transfer: Some properties. presented at SMBE Annual Meeting, July 2010, Lyon France;
• Il Buono, Il Brutto, Il Cattivo. presented at Phyloinformatics workshop, October 2007, Edinburgh UK;
• Phylogenetic Diversity on Split Systems. presented at MASAMB 2007 March 2007, Manchester UK;
• Stochastic Models of Molecular Evolution: An Algebraic Analysis. presented at Conference on the Mathematics of Evolution and Phylogeny, June 2005, Paris France.

Former Students

PhD Students

• Patricio Maturana Russel successfully defended his PhD thesis in Statistics introducing Nested Sampling to Bayesian Phylogenetic Inference in November 2017. He is now doing a PostDoc at the Department of Statistics, University of Auckland. The thesis was collaboratively supervised with Brendon Brewer.
• Katie Parish successfully defended her PhD thesis in Chemical Sciences on the impact of fining methods on wine quality in September 2017. Main supervisor was Bruno Feddrizzi.

Masters Students

• Daisy Shepherd did her MSc with Stephane Guindon and me in 2014. She investigated the utility of sliding window approaches for diagnostic tests in phylogenetic inference.
• Bradley Liu finished his MSc with me in 2014. He worked on influence measures in phylogenetic post inference.
• Rachel Harrison finished her MSc with me in 2014. She worked on fuzzy clustering algorithms in multivariate data analysis.

Honours Students

• Amy Doyle finished her BSc hons. with me in 2014. She worked on a data analysis in soil chemistry using the PLSR method.
• Crystal Ng did her BSc hons with me in 2013. She analysed confidence intervals for multinomial parameters.
• Nur Aqilah Ruslan did her BSc hons with me in 2013. She applied classical clustering methods to short tandem repeat (STR) data.
• Daisy Shepherd did her BSc hons with Stephane Guindon and me in 2013. She investigated the suitability of the invariant sites parameter in phylogenetic inference.

Summer students

• Eva Brammen from the University of Greifswald, Germany did her summer studentship with Miriam Meyerhoff me in 2016. She investigated how increasing a sample size in a speaker-centric dataset by simulating artificial speakers' profiles from the existing data.
• Jale Basten from the University of Greifswald, Germany did her summer studentship with me in 2016. She advanced the work of Ole Geldschläger on saturated sites in phylogenetic inference.
• Ole Geldschläger from the University of Greifswald, Germany did his summer studentship with me in 2015. He investigated the utility of combining saturation statistics to better identify saturated sites in phylogenetic inference.
• Bor-Kuan Song did his summer studentship with me in 2014. He investigated the biogeography of NZ birds and plants, a project that mostly revolved around finding and transforming appropriate data.
• Lily Trinh did her summer studentship with Miriam Meyerhoff and me in 2014. She worked on data analysis in sociolinguistics.
• Daisy Shepherd did her summer studentship with me in 2013. She investigated stability of the inferred topology in phylogenetic analysis.

Previous Teaching Experience

Lectures

• Semester 2, 2017: STATS 330, BIOSCI 322, and BIOSCI 733
• Semester 1, 2017: BIOSCI 209
• Semester 2, 2016: STATS 330, BIOSCI 322, BIOSCI 347, and BIOSCI 733;
• Semester 1, 2016: BIOSCI 209 and STATS 302;
• Semester 2, 2015: STATS 20x, STATS 330, BIOSCI 210, BIOSCI 347, and BIOSCI 733;
• Semester 1, 2015: BIOSCI 209;
• Semester 2, 2014: STATS 20x, STATS 330, BIOSCI 210, BIOSCI 347, and BIOSCI 733;
• Semester 1, 2014: STATS 20x;
• Semester 2, 2013: STATS 20x, STATS 330, and BIOSCI 347;
• Semester 1, 2013: STATS 20x;
• Semester 2, 2012: BIOSCI 347;
• Semester 1, 2012: STATS 210;
• Spezielle Statistik in der Biotechnologie, WiSe 2008/2009, Veterinary University Vienna;
• Spezielle Statistik in der Biotechnologie, WiSe 2007/2008, Veterinary University Vienna;
• Spezielle Bioinformatik in der Biotechnologie, WiSe 2007/2008, Veterinary University Vienna;
• Spezielle Statistik in der Biotechnologie, WiSe 2006/2007, Veterinary University Vienna;

Hobbies

• Seeing my boys grow;
• Hiking, cycling (MapMyRide), and ornithology (OSNZ);
• Competitive sports like basketball, volleyball, football, badminton, squash, or table tennis;
• Reading, watching movies, listening to music, playing computer and board games.

Addresses

S. Klaere - Last Change: December 17, 2012 .