2017 Workshop on Genomics, Český Krumlov Instructors


Guy Leonard
University of Exeter, UK

Dr Leonard works with comparative genomics, phylogenomics and genome assembly with an interest in the evolutionary relationships of eukaryotes and the cellular & genomic innovations of the diversity of eukaryotic cells. This led him to specifically look at the prevalence of gene fusion & fission events. More recently he has been trying to understand the adaptations and evolutionary history of a oomycete-relative, Hyphochytrium catenoides and the fungal-eye complex of the chytrid fungus Blastocladiella emersonii.

Daniel McDonald
University of California San Diego, USA

Dr. McDonald is a bioinformatics scientist in the Knight Lab at the University of California San Diego, and his primary interest is in the study of the human microbiome in relation to health. Daniel’s graduate work was done under the mentorship of Dr. Rob Knight and focused on the development of the American Gut Project, Quantitative Insights into Microbial Ecology (QIIME), Greengenes 16S rRNA database, and the BIOM-format.

Josie Paris
University of Exeter, UK

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Josie’s interests are in population genomics, in particular the use of NGS methods in molecular ecology to aid conservation and management efforts. Josie is a final-year PhD student at the University of Exeter, supervised by Dr Jamie Stevens and Dr Eduarda Santos. She is using population genomics (RAD sequencing) to explore patterns of metal tolerance in populations of brown trout Salmo trutta.

Sophie Shaw
University of Aberdeen, UK

Sophie works as a Bioinformatician in the Centre for Genome Enabled Biology and Medicine. She provides analysis of numerous different data sets including differential expression analysis, transcriptomics, whole genome assembly and single cell genomics. Alongside this gives support to researchers analysing their own data. Previous to working in Aberdeen, she completed her PhD researching the functional impact of differential allele expression in Candida albicans. After this she worked as a post-doctoral researcher investigating transcriptional reprogramming in the fungus Trichoderma hamatum GD12 during biocontrol of the pathogen Sclerotinia sclerotiorum and plant growth promotion of lettuce.

Elin Videvall
Lund University, Sweden

Elin Videvall

Elin studies evolutionary genomics of host-microbe interactions. Her PhD project revolves around transcriptomes of birds and their malaria parasites and gut microbiomes of ostriches, supervised by Dr Charlie Cornwallis and Dr Olof Hellgren. Elin has experience working with RNA-seq, analysing differential gene expression and assembling transcriptomes de novo, and also with 16S-seq, microbiome analyses, genome assemblies and using various genomic tools.

Maria Pachiadaki
Bigelow Laboratory for Ocean Sciences, USA

maria

Maria’s research interests revolve around the genomics, eco-physiology and evolution of marine microorganisms. She is a postdoctoral investigator at Bigelow Laboratory for Ocean Sciences, where she uses multiple –omics tools and rate measurements to shed light into the microbial life of the aphotic realm, their activities and their impact on ecosystem-level processes through their roles in biogeochemical cycling.

Yoshiki Vazquez Baeza
University of California San Diego, USA

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I’m a fourth year graduate student in the Computer Science and Engineering department working with Rob Knight at the University of California, San Diego. I analyze longitudinal human datasets with Inflammatory Bowel Disease and other host-associated diseases.

Sarah Baldwin
McGill University, Montréal, Canada
Sarah Baldwin
Sarah uses genomics and populations genetics to study major evolutionary transitions in plants. She also loves statistics and using R! Her current work is evaluating genome-wide responses to increased inbreeding using RAD-sequencing, linkage mapping, and segregation distortion analysis in a non-model organism.

Anna Karnkowska
University of Warsaw, Poland

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Ania has just started an assistant professor position at the University of Warsaw. During her postdoctoral research at Charles University in Prague and at the University of British Columbia in Vancouver, she was working on diversity and evolution of microbial eukaryotes. Ania is using genomic and transcriptomic data to understand origin and fate of plastids and mitochondria. More recently she has been also working on uncultured divergent parasitic lineages of eukaryotes and trying to decipher their evolutionary origin and cellular traits.


Previous years Workshop on Genomics Instructors
2016
Guy Leaonard, University of Exeter
Sophie Shaw, University of Aberdeen
Josie Paris, University of Exeter
Lokeshwaran Manoharan, Lund University
Jan Provaznik, University of Southern Bohemia
Elin Videvall, Lund University

2015
Guy Leaonard, University of Exeter
Sophie Shaw, University of Aberdeen
Josie Paris, University of Exeter
Ludovic Dutoit, Uppsala University
Jordi Paps, Oxford University
Adam Bazinet, University of Maryland
Alper Kucukural, University of Massachusetts

2014
Guy Leaonard, University of Exeter
Sophie Shaw, University of Aberdeen
Adam Bazinet, University of Maryland
Anders Lanzén, Neiker-Tecnalia
Melanie Melendrez, Walter Reed Army Institute of Research
Daniel McDonald, University of Colorado
Dag Ahren, Lund University

2013
Adam Bazinet, University of Maryland
Daniel Ayres, University of Maryland
Daniel McDonald, University of Colorado
Kristina Cammen, Duke University
Peter Batzel, University of Oregon
Luke Ursell, University of Colorado

2012
Adam Bazinet, University of Maryland
Daniel McDonald, University of Colorado
Dag Ahren, Lund University
Lionel Guy, Uppsala University
Tejashwari Meerupati, Lund University
Matthew Conte, University of Maryland

2011
Adam Bazinet, University of Maryland
Daniel McDonald, University of Colorado
Giovanna Carpi, Fondazione Edmnund Mach
Daniel Ayres, University of Maryland
Henk den Bakker, Cornell University
Ted Gibbons, University of Maryland
Gerardo Nava, Washington University
Lionel Guy, Uppsala University