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Students

Elif Bozlak

PI Barbara Wallner
funding by FWF DK

Research area

My love and curiosity about nature directed me to study Molecular Biology and Genetics. During my bachelor studies, I realized the importance of organizing and analyzing experimental data and developing new tools to produce meaningful results from experiments. This led me to continue my studies in Bioinformatics, which is a fascinating field for me. In my master thesis, I analyzed whole-genome sequencing data to calculate the mutation rate per generation for modern horses in a collaboration with Vetmeduni Vienna.

In my Ph.D. project I try to analyze Y-chromosomal sequences of different mammals such as horses, sheep, and goats, to investigate male-driven demography and finding selection patterns. I will construct Y-chromosomal assemblies when needed and reconstruct Y-chromosomal haplotypes from NGS data. I will use both modern and ancient samples in my studies to better understand the geographic replacement of populations during time and space. 

Claire Burny

PI Christian Schlötterer
funding by FWF DK and Vetmeduni Vienna

Research area

In December 2014 I got a diploma in Bioinformatics engineering from the National Institute of Applied Sciences in Lyon (France), which I complemented with a Master degree in Biostatistics at the University of Lyon. During my Master thesis I developed a model-based classification method of longitudinal data to identify groups of typical biomarker trajectories. I worked then as research assistant in the quantitative genetics research group at the Ecole Normale Superieure of Lyon, headed by Dr. Gaël Yvert, which studies the ability of a phenotypic traits to vary and to adapt. I have been involved in a diverse set of research projects, one of them focused on small-effect genetic factors on complex traits at the single cell level taking advantage of the accessibility of flow-cytometry measurements in S. cerevisiae yeast.

I am happy to join the Vienna Graduate School of Population Genetics to dive into the field of Population Genetics. During my PhD, I will study adaptive QTLs, with particular focus on the inference of selection signatures from time series SNP allele frequency data (e.g. Barghi et al., 2018). The goal of my PhD is to develop methods to identify and characterize targets of selection, using state of the art statistical methods including machine learning.

Howard Chen

PI Andreas Futschik
funding by FWF DK

Research area

I studied actuarial science during my bachelor at the London School of Economics, and statistics during my master's at the University of Warwick. My master's dissertation was based on Hamiltonian Monte Carlo (HMC), at developing a new method of HMC that is able to overcome some of the difficulties of the original algorithm, for example the struggle to sample from multi-modal distributions. This was achieved by using an idea of physics, called metadynamics, coupled with the active subspace method and importance sampling in order to apply this method to statistics.

During my PhD I will be working to construct a model that is able to simulate the migration path of freshwater fish in Japan during the last few million years, first focusing on single species, and hopefully incorporating multiple species into a single model later during my studies. The migration path is particularly interesting in Japan due to the tractable ice ages and migration from Korea during these times, as well as the rapid changing geography on the archipelago giving more complexity.

Mimmi Eriksson

PI Ovidiu Paun
funding by FWF DK

Research area

I first started to study biology due to an interest in conservation biology, therefore, this was the focus of my studies towards my bachelor’s degree. All throughout my studies I found population genetics and population dynamics to be fascinating and when I began my master’s degree I choose to focus on population genomics and evolution. I have undertaken both my bachelor's and master's degree at the University of Gothenburg, Sweden, where I graduated in June 2017. For my master thesis I used the allotetraploid weed Capsella bursa-pastoris to investigate the accumulation of deleterious alleles across the species range. The aims were to test whether the two ancestral genomes differed in this respect and if the accumulation could be explained by a recent range expansion.

During my PhD, I will study the role of transposable elements (TE) in local adaptation after whole genome duplication (WGD). The orchid genus Dactylorhiza will be used as a study system due to the possibility to investigate arrays of sibling, but ecologically-divergent allopolyploids. First, the difference in relative abundance of classes and subclasses of TEs will be evaluated using low-coverage whole genome sequencing across allopolyploids of different ages, together with representatives of their diploid parents. This is expected to provide information on the TEs dynamics through time after allopolyploidization. Further work will test the relevance of these dynamics for the ecological divergence of the polyploids, focusing on the regulatory influence of TEs on neighbouring genomic regions.

Hannah Götsch

PI Reinhard Bürger
funding by FWF DK

Research area

During my bachelor’s degree program in mathematics at the University of Vienna I discovered my fascination for applied mathematics. Therefore, I decided to complete the master’s degree program in mathematics with a specialization in biomathematics. This led me to seminars and lectures in the biomathematics area, which brought me to discover my fascination and enjoyment for dealing with problems in mathematical population genetics. Thus, it was natural to decide to write also my master’s thesis about a topic in population genetics. With the help of computer simulations, I studied the architecture of a quantitative trait in a structured population under selection and different genetic and environmental assumptions. Furthermore, I aimed to derive analytical approximations to predict the distribution of the allele frequencies.

The aim of my Ph.D. project is to develop and analyze various deterministic and stochastic models for the adaptation of complex ecological traits in a spatially structured population by looking at the dynamics of individual gene loci.

Clara Groot Crego

PI Ovidiu Paun
funding by FWF DK

Research area

Evolution in all its shapes and forms fascinates and intrigues me: from
the shaping of the tree of life to short time scale changes in
populations. In a very broad sense, I would like to understand the
forces and dynamics which explain the fantastic diversity of the natural
world, be it in plants, animals, fungi or prokaryotes.

I did my Bachelor in General Biology at the KULeuven, Belgium, and my
Master in the EU-funded MEME programme (Master of Excellence and
Mobility in Evolutionary Biology) at the LMU in Munich, Germany, and the
University of Montpellier, France. It was during my master that I got to
work with genomic data for the first time and ask interesting
evolutionary questions.

At the moment, I’m focusing on understanding the evolutionary forces
that drive adaptive radiations. In my PhD project (Group Lexer), I’m
using genomic data to disentangle the demographic history and selection
regime of a radiated clade of tillandsioid bromeliads, a neotropical
plant group from the Americas.

Christina Hedderich

PI Ovidiu Paun
funding by FWF-DK

Research area

I studied Life Sciences at the University of Potsdam with the specialisation in organismic biology, including evolutionary biology. During my undergraduate studies, I developed a strong enthusiasm for evolutionary botany. I followed my interest by starting my MSc studies in Plant Sciences at the University of Technology in Graz. For my master's thesis I collaborated with the University of Vienna and investigated the origin of the endemic subspecies Erigeron glabratus subsp. candidus by analysing the genomic population structure of E. glabratus in the Eastern Alps with RADseq data.

As a member of the Vienna Graduate School of Population Genetics and during my PhD at the University of Vienna, I will focus on understanding the drivers of the adaptive radiation of persimmons on New Caledonia, a biodiversity hotspot. The aim of the project is to use genomic data to disentangle potential sources of adaptive variation after long-distance dispersal, and to test the hypothesis that adaptive genome evolution can be a by-product of structural variation.

Tejashwini Hegde

PI Christian Schlötterer
funding by Vetmeduni Vienna and FWF-DK

Sheng-Kai Hsu

PI Christian Schlötterer
funding by FWF-DK

Research area

I was awarded both my bachelor and master degree by the department of Agronomy at National Taiwan University (NTU). During my undergraduate study, I started a research project investigating the genetic architecture of anaerobic germination in rice and I continued working on this project for my master thesis. Using approaches in both genomics and transcriptomics, we associated natural variation during the anaerobic germination trait to the variation in genomic haplotypes and crucial gene expression. After that, I spent a year as a research assistant, involved in several research projects including a study on the diversity of the mitochondrial genome in rice as well as a population genetic study on the plumage coloration of bulbuls, a native Taiwanese bird species.

My research experience motivated me in pursuing further knowledge in the field of genetics. Therefore, I joined the Vienna Graduate School of Population Genetics and jumped into the world of population genetics of Drosophila. I’m sure that I can broaden my view in this field during my PhD, studying the sexually antagonistic evolution in experimentally evolved populations. Due to their different roles in reproduction, males and females could have opposing trait optima for a given phenotype, leading to sexual conflict in selection and resulting in sexual dimorphism at both transcriptomic and phenotypic levels. Evidence of this sexual dimorphism was widely observed in a  number of organisms. However, the resolving mechanisms of the sexual conflict remain obscured. The main goal of my PhD project is to unveil this mystery, taking advantage of a special design in experimental evolution. By investigating the evolution of the transcriptomes of both sexes in experimentally evolved populations, we are able to acquire direct evidence on how evolution works in the population and we aim to obtain novel insights into how sexual conflict is resolved during  evolution.

Wei-Yun Lai

PI Christian Schlötterer
funding by Vetmeduni Vienna and FWF DK

Research area

I received my bachelor's degree from the department of Agronomy at Nation Chung Hsing University (NCHU) and my master's degree from the department of Agronomy at National Taiwan University. During undergraduate study, I worked on the identification of alternative splicing events caused by Ds transposon family during abiotic stresses in maize. This study was focusing effort into the detailed influence of Ds transposition on the transcriptomic flexibility in response to abiotic stresses in maize. As a research assistant in the Institute of Information Science at Academia Sinica, I developed an analytical pipeline aiming to identify potential trait- associated regulators over multiple traits in yeast. 

During my PhD the Vienna Graduate School of Population Genetics, I’m going to study the evolution of gene expression variance in Drosophila simulans. The major aim of my project is to identify the genes showing significant changes in their expression variance during the evolution, and we anticipate to unveil the underlying evolutionary forces and fitness benefits.

Anna Maria Langmüller

PI Christian Schlötterer
funding by Vetmeduni Vienna and FWF DK

Research area

I completed my bachelor's degree in Ecology and Biodiversity at the University of Salzburg. For my master's degree I decided to shift toward bioinformatics and graduated in March 2015. In my master thesis I detected and investigated copy number variations in low coverage sequencing data of the human genome using a newly developed algorithm cn.MOPS.

During my master studies I developed an interest in population genetics. Therefore, I am grateful for the opportunity to do my PhD at the Vienna Graduate School of Population Genetics. The main goal of my PhD project is to explore and understand the genomic response of Drosophila simulans populations evolving in a hot fluctuating environment. Because of the special experimental design and possible comparisons to populations developing under different environmental conditions, I am optimistic that I can demystify some dynamics of adaption.

Dan Liu

PI Christian Schlötterer
funding by Vetmeduni Vienna and FWF DK

Research area

I got my bachelor and master degree in computer science specializing in computational biology and machine learning. I developed a novel logistic matrix factorization with neighborhood regularization algorithm on heterogeneous networks to predict potential virus-host associations, apply Bayesian matrix factorization to find unknown associations between microbes and diseases, and to visualize microbe networks by statistical analysis.

During my PhD at the Vienna Graduate School of Population Genetics, I will analyze highly replicated Drosophila populations adapting to a novel temperature regime for more than 100 generations. Our aim is to develop suitable summary statistics for Approximate Bayesian Computation to estimate the adaptation architecture. We will take advantage of a nested design of founder genotypes to investigate polygenic adaptation traits by QTL-check experiments.

Marta Pelizzola

PI Andreas Futschik
funding by FWF DK

Research area

I studied Applied Mathematics, with a master degree in Stochastics and Data Science at the University of Torino that I took in October 2017. My master thesis was focused on stochastic modelling and processes, and computational methods. I studied the relationship between longitudinal and time-to-event data applied to a dementia dataset in the elderly. I have always been interested in applications and for my PhD I decided to focus on the natural science field.

During my PhD project I will work on models for data from experimental evolution. As a first task I will evaluate existing methods and then, as a second stage, I will work on the development of new ones. The goal then will be to increase the available tools to understand the response to selection, for example in the case of populations adapting to environmental changes (like temperature changes).

Rahul Pisupati

PI Magnus Nordborg
funding by FWF DK and Gregor Mendel Institute

Research area

I received my master's degree from Indian Institute of Technology (IIT) Kharagpur, India. I am enthusiastic about genome architecture and gene regulation. I study these topics using tools from computational biology and mathematics. Recently I have developed a tool called SNPmatch (web application at https://arageno.gmi.oeaw.ac.at) to genotype samples from even very low-coverage sequencing data for given SNP databases.

For my PhD project with Magnus Nordborg I will try to address several interesting research questions on methylation in the genome of the plant model A. thaliana.

Lara Radović

PI Barbara Wallner
funding by Vetmeduni Vienna

Research area

I enrolled in the Faculty of Agriculture of the University of Zagreb for the love of natural sciences. The field of Agricultural Economics seemed ideal for me and in 2017, I was awarded with a Bachelor´s degree. Throughout my undergraduate studies I got more and more interested in genetics so I decided to shift toward Animal Genetics and Breeding. I made my diploma with highest honors and defended my master thesis entitled “Variability analysis of the whole goat mitogenoma" in 2019. For my thesis, I retrieved a large number of complete goat mitogenomes from the whole-genome data stored in public depositories and analysed their variability, in addition to performing phylogenetics.

Curiosity, previous experience and economical background helped shape my research interests, particularly in the field of population genetics. I am very happy that I joined the Vienna Graduate School of Population Genetics and that I have an opportunity to broaden my knowledge.

In my PhD project, I will focus on the dynamic but still enigmatic Y chromosome. Several features make Y chromosome interesting: strictly male-limited transmission, absence of recombination, degeneration of Y-linked genes during evolution and accumulation of genes responsible for maleness and reproduction. Therefore, my project aims to better understand the evolutionary dynamics of mammalian Y chromosomes by studying several species groups with similar divergence as humans and apes (2-20 mya). I will infer lineage-specific as well as shared evolutionary constraints of the Y chromosomal genes and will study the extent to which different types of selection act to maintain genes within this unique genomic environment.

Dagny Asta Runarsdottir

PI Christian Schlötterer
funding by Vetmeduni Vienna and FWF DK

more info coming, soon

Florian Schwarz

PI Robert Kofler
funding by FWF stand-alone and FWF DK

Research area

After I received my bachelor’s degree in 2015 I continued my studies at the Ludwig-Maximilians-University (LMU) in my hometown Munich with the master program ‘Evolution, Ecology and Systematics’. There, I focused on studies of evolutionary biology and population genetics and their applications in bioinformatics. During my master's thesis I got familiar with the effect of meiotic drive, a process that can lead to a conflict of selection on different levels (‘selfish’ chromosome vs the host organism carrying it), which further deepened my pre-existing interest about the various evolutionary forces shaping DNA and their impact on the respective organism.

For my PhD I will work on the evolution of Transposable Element (TE) activity in Drosophila. TEs can be grouped in different classes and are repetitive parts of the genome able to ‘selfishly reproduce’ (transpose) and reinsert themselves at different positions, independent from the ‘functional’ genome. These elements can have all kinds of evolutionary implications on their host genome, including adaptive advantages as well as deleterious effects, ranging between e.g. only slightly raised metabolic costs to induction of sterility for offspring in certain crosses (hybrid dysgenesis).

I will first contribute to establish a reliable lab protocol for the extraction and the sequencing of long-read DNA sequence data with the MinION sequencing technology. Afterwards, I will
establish a bioinformatic pipeline to identify and categorize the different classes and families of Transposons. Ultimately, by applying this method to certain strains of Drosophila melanogaster, I hope to obtain datasets and analysis tools with which I can contribute to unravel more details about TE evolution and TE-induced evolutionary phenomena like hybrid dysgenesis.

Divya Selvaraju

PI Robert Kofler
funding by FWF stand-alone

Research area

As I was constantly motivated and driven by scientific discoveries, I always wanted to stay in science. I completed my Bachelor's in Information Technology where I learned how the technological improvement in computing power is dramatically changing the world of science. Later, during my Master's in Bioinformatics and Biotechnology, I trained in data analysis as a part of my coursework which expanded my knowledge how to mine omics data and bring out hidden information from it.

Invention of new sequencing technologies created a whole new dimension to how we study a particular biological question. I developed an interest in genome evolution and always wondered about the manipulation of the four bases (A, T, G, C) which generated diverse live forms on earth. One of the key players contributing to genome evolution are transposable elements, also known as selfish DNA, that occupy large parts of the genome in higher eukaryotes. They play a significant role in shaping the genome size and they are involved in many disease conditions by disrupting genes and regulatory regions. So, shedding light on the long-term trends of transposable elements would give a better understanding of their propagation in the genome. For my PhD project I will combine experimental evolution, molecular biological methods and a bioinformatic analysis approach to unravel the evolutionary dynamics of transposable elements in Drosophila species. 

Krzysztof Stankiewicz

PI Joachim Hermisson
funding by FWF DK

Research area

I was awarded my Bachelor's degree in biomedical engineering from the University of Minnesota in May 2016, and my Master's degree in Bioinformatics and Theoretical Systems Biology from Imperial College London in the fall of 2017. During my undergraduate studies, I developed an HMM-based method to identify introgression between a selfing/outcrossing pair of the Capsella genus, and used my results to study barriers against gene flow in recently diverged species. My Master's work focused on pedigree analysis and recombination rate mapping in the African mosquito A. gambiae, as well as developing a package to analyze topological sensitivity in ODE networks fit to empirical data.

My research experience spurred in me a fascination for population genetics and the interplay between various biological forces in creating and maintaining species diversity. In my PhD project I will work on the signatures of post-speciation gene flow and long-term balancing selection, primarily using data from the Arabidopsis thaliana 1001 genomes project.

Aglaia Szukala

PI Ovidiu Paun
funding by FWF DK

Research area

Evolutionary biology and ecology stimulated my interest the most during my undergraduate studies. For my master thesis in the field of plant phylogenetics, I worked on montane and alpine plants of the genus Jurinea (Compositae) in the Caucasus and was very fascinated by the population ecology of the endemics in this region.

To further develop this interest, I started my PhD in October 2016 under the supervision of Ovidiu Paun. The project focuses on understanding the processes leading to speciation, as exemplified by the reiterate occurrence of ecotypes within the plant species Heliosperma pusillum. The analysis of whole transcriptomes and genomes of individuals from natural populations, common garden and transplantations will allow us to clarify the processes driving to ecotype divergence in this species.

Xiaomeng Tian

PI Christian Schlötterer
funding by Vetmeduni Vienna and FWF DK

more info coming, soon

Lauri Törmä

PI Kirsten-André Senti / Christian Schlötterer
funding by Vetmeduni Vienna

Research area

I studied genetics and physiology at the University of Turku in Finland. My interest in evolutionary developmental biology drove me to study eye development in Drosophila melanogaster with former PopGen Vienna faculty member Dr. Alistair McGregor at Oxford Brookes University (UK). During my time working with Alistair, I realised how crucial population genetics is to understand evolution. Before finishing my master’s I also investigated the cytology of spindle formation in D. melanogaster at University of Turku.

In my project at the Vienna Graduate School of Population Genetics I am using CRISPR-Cas9 to functionally validate loci linked to temperature adaptation during experimental evolution in Drosophila simulans. After validation, my aim is to understand how these alleles make the flies fitter in hot temperature.

Filip Wierzbicki

PI Robert Kofler
funding by FWF stand-alone

Research area

I obtained the master’s degree in Molecular Biotechnology at the University of Applied Sciences “FH Campus Wien”. The study program covers a wide range of life sciences and provides a good basis for research in modern biology. My strong interest in evolution and my passion for the tiniest components of life led me to population genetics. In my opinion, taking advantage of mathematics, informatics and technology in biology is the best way to describe living systems. So I joined the group of Robert Kofler at the Institute of Population Genetics to write my master thesis. I investigated the evolution of the small RNA composition in Drosophila and focused on the control of transposable elements (TE) by small RNAs. During this time I developed a strong interest in the co-evolution between TEs and their hosts.

For my Ph.D., I continue to work in the field of TE biology. I will study TE invasions and track the co-evolution between hosts and parasites over generations. To investigate the dynamics of TE invasions, I will employ techniques of molecular biology and bioinformatics. The project aims to shed light on factors that lead to the establishment of TE control.

Benjamin Wölfl

PI Joachim Hermisson
funding by FWF DK

Research area

I obtained my master's degree in Bioinformatics and Systems Biology at the University and the Free University of Amsterdam in The Netherlands. The involvement in a variety of research projects made me appreciate the importance of mathematical and computational methods in biology. For example, I was inspired by how evolution shapes the metabolic network of microbes. For my master thesis I worked on polygenic adaptation supervised by Joachim Hermisson.

During my PhD studies, I will continue to work on models of polygenic adaptation. We employ mathematical and computational methods in order to better understand how polygenic adaptation proceeds and which genetic footprints it leaves.

Burçin Yıldırım

PI Claus Vogl
funding by FWF DK

Research area

I have completed my bachelor’s degree in Molecular Biology and Genetics at the Boğaziçi University (Turkey). However, my appreciation of biology has further flourished as my understanding of evolution grew. That’s why, during my master studies, I directed my focus towards more comprehensive research in evolutionary biology. More specifically, my master's project was concentrated on understanding the selective forces causing speciation on hybridizing populations and resolving deep splitting lineages using computational methods in population genetics and phylogenetics.

For my PhD I wanted to stay in this field while improving my knowledge on the theoretical part and therefore joined the Vienna Graduate School of Population Genetics in September 2019. In a broad sense, for my PhD project, I will try to optimize methods for the inference of population genetics parameters.

Fond zur Förderung der wissenschaftlichen Forschung
vetmed uni vienna
Gregor Mendel Institute of Molecular Plant Biology
Universität Wien