Co-Directors
Josie Paris– Director 
Marche Polytechnic University, IT
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Arrival: 10 May 2023, Departure: 27 May 2023
Josie is an evolutionary biologist using analytical approaches in ecological genomics in order to integrate knowledge of adaptation into understanding the dynamics and conservation of wild animal populations. Her expertise is in population genomics (RADseq, whole-genome sequencing data), although she also plays with transcriptomics, genome assembly and annotation, and comparative genomics. Josie is currently a Marie Skłodowska-Curie Research Fellow working on rapid adaptation in King penguins. She is also working on the first genome of the European lobster, detecting balancing selection in the Trinidadian guppy, invasion genomics in bumblebees and conservation genomics of several Mediterranean reptile species.
Rayan Chikhi – Co-Director (Course Engineer)
Institut Pasteur, FR
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Arrival: 10 May 2023, Departure: 27 May 2023
Rayan’s research interests are focused on computational theory for de novo assembly of short DNA sequencing reads including algorithms and data structures, graph theory, high-performance computing, parallelism, and DNA sequencing.
Joan Ferrer Obiol – Co-Director (Faculty Liason)
University of Milan, IT
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Arrival: 10 May 2023, Departure: 27 May 2023
Joan is a postdoctoral researcher working with the University of Milan and the Movecolab (Movement ecology of colonial birds in Italy, https://movecolab.it/). His research interests are in using phylogenomics, comparative genomics and population genomics to learn more about the evolutionary history of birds with a particular interest in seabirds. He is particularly interested in investigating the genetic basis of complex traits such as migratory behaviour in birds combining genomics with ecological data.
Guy Leonard – Lead Developer
Oxford University, UK
Personal Page
Not present on-site
Guy 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 work has led him to specifically look at the prevalence of gene fusion & fission events across the eTOL. More recently he has been trying to understand the adaptations and evolutionary history of an oomycete-relative, Hyphochytrium catenoides and a fungal-eye complex present in chytrid fungi, specifically in Blastocladiella emersonii. He also supports other bioinformatics work within the group, providing; advice on sequencing, genome and transcriptome assembly, genome annotation, phylogenomic tree reconstruction, 18S amplicon analysis with DADA2, all along with mainting a set of web-based BLAST servers, this website, and an HPC environment for the group’s use!
Mercè Montoliu Nerín – Head Teaching Assistant
Uppsala University, SE
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Arrival: 10 May 2023, Departure: 27 May 2023
Mercè’s background is in evolutionary genomics, specially interested in organisms living in symbiosis, and genomic study design to study complex eukaryotric organisms. Related to that, her study has focused on de novo genome assembly, mixing of sequencing techniques, as well as single cell genomics. Furthermore, her research also focuses on comparative genomics and phylogenomics.
Scott Handley – Coordinator
Washington University, US
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Arrival: 21 May 2023, Departure: 27 May 2023
Dr. Handley is interested in how viral and bacterial communities impact health and disease in humans. His research program is split between investigating the gut virome and bacterial microbiome in either AIDS or IBD.
Faculty
David Barnett
Maastricht University, NL
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Arrival: 20 May 2023, Departure: 26 May 2023
David has expertise in applying data analysis and visualisation techniques to study the infant/child gut microbiome and child health and molecular epidemiology. He has developed the R package microViz for microbiome data analysis and visualization.
Aitor Blanco Miguez
University of Trento, IT
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Arrival: 22 May 2023, Departure: 26 May 2023
Dr. Aitor Blanco-Miguez is a postdoctoral fellow in the Laboratory of Computational Metagenomics (led by Prof. Nicola Segata) at the University of Trento, where he is currently developing methods for metagenomic data analysis. His research interests include the role of the yet-to-be characterized microbial species in the human microbiome and how the food-associated microbiomes interact with that of the host.
Francesco Cicconardi
University of Bristol, UK
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Arrival: 16 May 2023, Departure: 26 May 2023
Dr Cicconardi is an evolutionary biologist and a biodiversity scientist with research experience in different organisms including basal hexapods, insects, and mammals. He is particularly interested in the study of phylogeny, biodiversity and how species adapt and evolve. More recently, using comparative genomics approaches, he studied how species adapt to new environments and the genomic bases of adaptive radiations in Neotropical butterflies, such as Heliconiini and Ithominii (Lepidoptera: Nymphaids).
Sonya Dyhrman
Columbia University, US
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Arrival: 20 May 2023, Departure: 28 May 2023
Members of the Dyhrman group are broadly interested in how marine microbes interact with each other and their geochemical environment, looking at the interface of microbial physiology and the biogeochemical cycles of carbon, nitrogen and phosphorus. Much of their current work leverages ‘omics’ approaches to examine the physiological ecology of microbes that play a keystone role in marine ecosystems. Dr. Dyhrman is a member of the Workshop’s Scientific Advisory Board.
Evan Eichler
University of Washington, US
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Arrival: 24 May 2023, Departure: 26 May 2023
The long-term goal of Dr Eichler’s research is to understand the evolution, pathology and mechanism(s) of recent gene duplication and DNA transposition within the human genome. Their lab involves the systematic discovery of these regions, the development of methods to assess their variation, the detection of signatures of rapid gene evolution and ultimately the correlation of this genetic variation with phenotypic differences within and between species.
Rosa Fernández
Institute of Evolutionary Biology, ES
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Arrival: 22 May 2023, Departure: 25 May 2023
Dr Fernández is interested in understanding animal genome evolution at a macroevolutionary scale. Her group’s research focuses on phylogenomic approaches to understand (i) how animals are related to each other, (ii) how they reshaped their genomes to generate their inmense diversity and (iii) how they adapted to new environments – such as during terrestrialization or adaptation to life in caves.
Erik Garrison
University of Tennessee, US
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Arrival: 14 May 2023, Departure: 21 May 2023
Dr Garrison is a genomicist with a quantitative social science background. He is learned in the ways of free culture, sharing in the powers of free software and lover of commonwealths.
Brian Haas
Broad Institute, US
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Arrival: 20 May 2023, Departure: 24 May 2023
Brian Haas is a senior computational biologist at the Broad Institute. He is one of the authors of the well-known transcriptome assembler Trinity.
Katharina Hoff
University of Greifswald, DE
Personal Page
Arrival: 18 May 2023, Departure: 20 May 2023
Dr Hoff currently works at the Department of Mathematics and Computer Science and in the Center for Functional Genomics of Microbes at University of Greifswald (Germany). Katharina’s bioinformatics research is about genome, transcriptome and proteome analysis with a focus on genome annotation.
Antoine Limasset
Université de Lille & CNRS, FR
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Arrival: 15 May 2023, Departure: 21 May 2023
Dr. Limasset is a tenured research scientist at CNRS who works on genome assembly, read correction, graphs, and data structure.
Paolo Manghi
University of Trento, IT
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Arrival: 22 May 2023, Departure: 26 May 2023
Dr Manghi graduated in Bioinformatics cum laude at the Bologna university (Italy) in 2016 after a thesis about bi-directional recurrent neural networks in UCD (Dublin) under the supervision of Professors Piero Fariselli e Gianluca Pollastri. He joined the laboratory of Nicola Segata at the university of Trento in 2017, where he got his PhD in Biomolecular Sciences, with a thesis on the development of meta-analysis and machine-learning approaches for the integration of multiple metagenomic populations to discover links between microbiome and host’s phenotypes and conditions. He’s co-author and a maintainer of the curatedMetagenomicData 3 resource, under the supervision of Prof. Levi Waldron.
Camille Marchet
Université de Lille, FR
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Arrival: 15 May 2023, Departure: 21 May 2023
Dr. Marchet is a research associate working in BONSAI team (Lille, France). Her work focuses on methods and data structures in sequence bioinformatics, with applications to RNA in particular. After a MSc in Ecology and Evolution from Université Claude Bernard Lyon 1 and an engineering degree in Bioinformatics from INSA de Lyon, she worked as an engineer for two years before obtaining PhD funding in GenScale team (Rennes, France). Her postdoc was in Transipedia ANR with Rayan Chikhi and Mikaël Salson. Transipedia aims at being a transcriptome-encyclopedia, e.g., facilitating indexing, query and exploitation of the numerous publicly available RNA-seq data. She is mostly working on new data structures to index large collections of NGS datasets. Before and during her PhD, she worked on methods for transcriptomics, in particular for de novo variants discovery and RNA long read analysis.
Natalia Nensheva
University of Greifswald, DE
Personal Page
Arrival: 18 May 2023, Departure: 24 May 2023
As a first-year Ph.D. student at the University of Greifswald, I am currently developing new algorithm for annotating eukaryotic metagenomic data with Katharina Hoff and other colleagues from Mario Stanke’s team. During my academic career, which involved pursuing bachelor’s and master’s degrees in mathematical biology and bioinformatics at the Moscow Institute of Physics and Technology, I participated in various projects related to the analysis of genomic data. Subsequently, I gained professional experience by joining the esteemed companies, Boston Gene and Genotek, where I was involved in diverse projects, such as developing a heteroplasmy analysis pipeline for mitochondrial DNA data, processing chromatograms and Oxford Nanopore Sequencing data, and also creating an algorithm for identifying somatic mutations in genes carrying germline pathogenic mutations in cancer.
Fritz Sedlazeck
Baylor College of Medicine, US
Personal Page
Arrival: 17 May 2023, Departure: 17 May 2023
Dr Sedlazeck’s research focuses on the identification of coding and non-coding complex variations and their impact on evolution and diseases across a multitude of organisms but with a focus on human diseases. He is fascinated in how variable genomes are and investigating the impact of such variability. To assess these, he collaborated and initiated efforts to determine which technologies or methodologies were most appropriate to discover variations of different forms as well as the biases that they contain. This work just recently lead to novel insights in structural variations and their genotypic and phenotypic impact on cardiovascular, mendelian and neurological diseases and other organisms. His group is continuing to drive the understanding around SV and understanding better their impact on phenotypes in human diseases but also across other organisms.
Doug Scofield
Uppsala University, SE
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Arrival: 23 May 2023, Departure: 27 May 2023
Doug is a research bioinformatician at the Department of Ecology and Genetics, at Uppsala University, as well as, Application expert at the Uppsala Multidisciplinary Centre for Advanced Computational Science (UPPMAX).
Rachel Steward
Lund University, SE
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Arrival: 21 May 2023, Departure: 27 May 2023
Rachel is an evolutionary ecologist who has turned to genomics to better understand the molecular mechanisms underlying phenotypic plasticity and how it evolves, with a particular focus on plant-insect interactions. Rachel completed her PhD at the University of South Carolina, where she studied the eco-evolutionary dynamics of a native insect responding to an attractive but lethal novel host plant. As a postdoc, she has been investigating the role of alternative splicing in phenotypic plasticity and polyphenisms, specifically the consequences of splicing plasticity on genetic diversity. Additionally, she works on the genomic basis and gene expression underlying plastic and evolved differences in host plant use in different insect systems, including Pieris and Polygonia butterflies, and most recently, Tephritis peacock flies. Rachel is currently a postdoctoral researcher working with the Runemark lab in the Speciation, Adaptation and Coevolution group at Lund University.
Marcela Uliano-Silva
Wellcome Sanger Institute, UK
Personal Page
Arrival: 17 May 2023, Departure: 20 May 2023
Dr Marcela Uliano-Silva is a Senior Bioinformatician at the Wellcome Sanger Institute. She works with the Darwin Tree of Life Assembly Team, testing, creating and improving various assembly pipelines to yield chromosome-level genomes for all eukaryotic taxa occurring in Britain and Ireland. She is also part of the Vertebrate Genomes Project (VGP) and has joined the consortium with her work on the high-quality genome of the two-toed sloth Choloepus didactylus. This work was one of the goals of her Marie Skłodowska Curie PostDoc (IF-Horizon2020) at the Leibniz Institute for Zoo and Wildlife Research (IZW) and Berlin Center for Genomics in Biodiversity Research (BenGendiv), in Berlin, Germany, where she was before she joined the Sanger. Marcela is also a TED Fellow, with whom she promotes science to the general public and acts as an example of women in science. She is very passionate to bring education, safety and opportunities to developing countries especially through science education in conservation and evolutionary genomics. To help ensure the protagonism of scientists sequencing biodiversity in the global south, Dr Uliano-Silva co-chairs the committee in Justice, Equity, Diversity and Inclusion (JEDI) of the Earth Biogenome Project, which aims to produce genomes for all biodiversity on Earth.
Rob Waterhouse
University of Lausanne, CH
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Arrival: 20 May 2023, Departure: 23 May 2023
Dr Waterhouse’s group’s research is focused on elucidating interactions between gene evolution and gene function through developing computational approaches to interrogate evolutionary and functional genomics data. They are developing quantifications of gene evolutionary dynamics and functional properties to build models that link the underlying genetics to observable biological features. Their research projects focus on insects and other arthropods as their countless adaptations to exploit ecological niches mean that they are ideal for investigating how conservation or divergence of functional genomic elements give rise to the splendour of animal biology.
Chris Wheat
Stockholm University, SE
Faculty Page
Arrival: 19 May 2023, Departure: 27 May 2023
The Wheat lab investigates fundamental questions in evolutionary biology using a range of species and methods. While we primarily work upon butterflies, we also have collaborations with people working on mussels, dragonflies, beetles and fish. Although we extensively integrate OMICS data (whole genome sequencing, RNA-seq, Pool-seq, metabolomics), we also use butterfly nets, respirometers, and CRISPR. We investigate the genetics of diapause, immune performance, wing coloration, life history tradeoffs, plasticity and coevolutionary escalation. Professor Wheat is a member of the Workshop’s Scientific Advisory Board.
James Whiting
University of Calgary, CA
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Arrival: 20 May 2023, Departure: 26 May 2023
Dr Whiting is interested in the genomics of adaptation, and in particular the repeatable evolution in natural populations. He previously investigated these topics in three-spined stickleback (MacColl Lab, University of Nottingham, UK) and Trinidadian guppies (Fraser Lab, University of Exeter, UK), and is now researching the prevalence and processes governing repeatability in the genetic basis of adaptation to climate across diverse plant species. In addition to examining natural systems, he is also interested in generating and exploring hypotheses for adaptation and parallel/convergent evolution using simulations.
He has also been involved with the development of various R packages for analysis of genome sequencing data:
– AF-vapeR: Allele frequency vector analysis of parallel evolutionary responses (https://github.com/JimWhiting91/afvaper)
– GenotypePlot: exploratory visualisation tool for VCF/SNP data (https://github.com/JimWhiting91/genotype_plot)
Mike Zody
New York Genome Center, US
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Arrival: 13 May 2023, Departure: 17 May 2023
Dr. Zody is the Research Director of Computational Biology at the New York Genome Center, formerly Chief Technologist for the Broad Institute. He has been involved with a large number of whole-genome sequencing and comparative genomics projects.
Dag Ahrén
David Barnett
Kirsten Bos
Rayan Chikhi
Sonya Dyhrman
Malachi Griffith
Brian Haas
Scott Handley
Ilya Korunsky
Guy Leonard
Antoine Limasset
Camille Marchet
Josie Paris
Sophie Shaw
Emiliano Trucchi
Chris Wheat
Mike Zody
2020
Rayan Chikhi
Sonya Dyhrman
Evan Eichler
Kirk Gosik
Malachi Griffith
Brian Haas
Antoine Limasset
Camille Marchet
Christa Schleper
Emiliano Trucchi
Chris Wheat
Kelly Wrighton
Mike Zody
2019
Julian Catchen
Rayan Chikhi
Bill Cresko
Sonya Dyhrman
Malachi Griffith
Brian Haas
Daniel McDonald
Antonis Rokas
Zachary Skidmore
Jacob Steenwyk
Hannah Tavalire
Amy Willis
Mike Zody
2018
Julian Catchen
Rayan Chikhi
Bill Cresko
Sonya Dyhrman
Evan Eichler
Brian Haas
Sarah Hird
Eline Lorenzen
Daniel McDonald
Antonis Rokas
Karthik Shekhar
Mike Zody
2017
Julian Catchen
Rayan Chikhi
Bill Cresko
Sonya Dyhrman
Evan Eichler
Jennifer Gardy
Brian Haas
Daniel McDonald
Paul McMurdie
Ramunas Stepanauskas
Tobias Uller
Chris Wheat
Mike Zody
2016
Julian Catchen
Rayan Chikhi
Bill Cresko
Sonya Dyhrman
Evan Eichler
Toni Galbaldón
Brian Haas
Daniel McDonald
Paul McMurdie
Antonis Rokas
Gosia Trynka
Chris Wheat
Mike Zody