Team
Josie Paris– Director 
Marche Polytechnic University, IT
Personal Page
Arrival: 02 January 2025, Departure: 18 January 2025
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 de novo genome assemblies of the King penguin, the European lobster, and the white perch, detecting balancing selection in the Trinidadian guppy, invasion genomics in bumblebees and conservation genomics of several Mediterranean reptile species.
Rayan Chikhi – Course Engineer
Institut Pasteur, FR
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Arrival: 06 January 2025, Departure: 18 January 2025
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 – Faculty Liaison
University of Milan, IT
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Arrival: 02 January 2025, Departure: 18 January 2025
Joan is a postdoctoral researcher working with the Bird Genoscape Project at Colorado State University (https://www.birdgenoscape.org/). His research interests are in using population genomics and phylogenomics to learn more about the evolutionary history of birds with a particular interest in seabirds. He is particularly interested in investigating local adaptation and 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
Arrival: 03 January 2025, Departure: 18 January 2025
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 – Equality, Diversity & Outreach
Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid, ES
Personal Page
Arrival: 02 January 2025, Departure: 18 January 2025
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.
Miloš Duchoslav – Content support and local operations liaison
Charles University in Prague, CZ
Personal Page
Arrival: 02 January 2025, Departure: 18 January 2025
Miloš did his PhD in molecular biology of plants, focusing on photosynthesis. As a postdoc, he moved to the field of ecological genomics of plants. He is studying adaptation of plants to toxic soils and parallelism in evolution.
Scott Handley – Coordinator
Washington University, US
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Arrival 1: 05 January 2025, Departure: 18 January 2025
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
Dag Ahrén
Lund University, SE
Personal Page
Arrival: 13 January 2025, Departure: 18 January 2025
Dag is interested in microbial interactions between microorganisms and their environment, either in host-parasite systems or on a ecosystem-wide scale. His research is primarily using genome assembly /annotation, single cell genomics, metagenomics and transcriptomics to study population genomics and adaptations to new environmental conditions. He is also head of a team of bioinformaticians supporting researchers in the fields of microbiology, immunology and structural biology
David Barnett
Maastricht University, NL
Personal Page
Arrival: 14 January 2025, Departure: 18 January 2025
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.
Francesco Cicconardi
University of Bristol, UK
Personal Page
Arrival: 10 January 2025, Departure: 18 January 2025
Francesco Cicconardi is a Senior Research Assistant at the University of Bristol, working in the EBAB lab. Driven by a passion forunderstanding how evolution shapes biodiversity, he has focus on the comparative genomics ofArthropoda, including Collembola and Hymenoptera, although his primary research revolves around Lepidoptera. His current work centres on brain evolution in the adaptive radiation of Heliconiini, a fascinating group of Neotropical butterflies, where he explores various aspects of functional genomics for the understanding of the genetic underpinnings of the evolution of cognition and neural circuitry. To unravel these evolutionary processes, Francesco employs an array of cutting-edge methodologies, including genome assembly and annotation, OMICS data integration, bulk and single-cell RNA sequencing, ATAC-seq, and methylation analysis.
Vincenza Colonna
Institute of Genetics and Biophysics, IT
Personal Page
Arrival: 07 January 2025, Departure: 14 January 2025
Vincenza is a genomicist and an expert in human evolutionary and population genomics and bioinformatics. She has been part of the international consortium 1000 Genomes where she led contributions to two specific aspects. First, she contributed to develop FunSeq, a tool that integrates non-coding information from relevant biological databases for the functional characterization of non-coding variants. Second, she led a genome-wide scan to identify genomic regions with exceptionally high levels of population differentiation demonstrating that these regions are enriched for positive selection events and that one half may be the result of classic selective sweeps. Findings from both sub-projects have since been applied to demographic inference and the molecular diagnosis of cancer and myeloid malignancies, and to deeper studies on positive selection at the ABCA12 gene. During her PhD she worked on human isolated populations contributing to characterize several isolated populations, describing the genomic consequences of isolation, contributing to genetic association studies and to characterize rare variation. She founded and led OBiLab, a project on training in Bioinformatics
Sonya Dyhrman
Columbia University, US
Personal Page
Arrival: 10 January 2025, Departure: 18 January 2025
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
Personal Page
Arrival: 12 January 2025, Departure: 14 January 2025
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.
Erik Garrison
University of Tennessee, US
Personal Page
Arrival: 07 January 2025, Departure: 14 January 2025
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
Personal Page
Arrival: 10 January 2025, Departure: 15 January 2025
Brian Haas is a Principal Computational Scientist 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: 07 January 2025, Departure: 10 January 2025
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
Personal Page
Arrival: 08 January 2025, Departure: 12 January 2025
Dr. Limasset is a tenured research scientist at CNRS who works on genome assembly, read correction, graphs, and data structure.
Camille Marchet
Université de Lille, FR
Personal Page
Arrival: 08 January 2025, Departure: 12 January 2025
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.
Valentina Peona
Swedish Natural History Museum, Stockholm, SE
Personal Page
Arrival: 11 January 2025, Departure: 18 January 2025
Valentina is interested in understanding how transposable elements and other repetitive elements shape the evolution of eukaryotic genomes, sex chromosomes and centromeres. She currently studies how transposable elements can contribute to the evolution and reinforcement of reproductive barriers. She has expertise in assembling genomes, structural variants and pangenomes.
Fritz Sedlazeck
Baylor College of Medicine, US
Personal Page
Arrival: 09 January 2025, Departure: 10 January 2025
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.
Rachel Steward
Lund University, SE
Personal Page
Arrival: 12 January 2025, Departure: 18 January 2025
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 an independent researcher affiliated with the Speciation, Adaptation, and Coevolution (SPACE) group at Lund University
Marcela Uliano-Silva
Wellcome Sanger Institute, UK
Personal Page
Arrival: 13 January 2025, Departure: 18 January 2025
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.
Olga Vinnere Pettersson
SciLifeLab, Uppsala University, SE
Personal Page
Arrival: 06 January 2025, Departure: 12 January 2025
Olga is a sequencing technology consultant / project coordinator at the National Genomics Infrastructure, a part of Genomics Platform of SciLifeLab: the center of excellence in molecular biosciences in Sweden. Currently, Olga is leading the SciLifeLab – Uppsala University involvement in the Biodiversity Genomics Europe (BGE) consortium, an initiative founded by the EU Horizon Europe program. Together with the Sanger institute, we are leading the effort of sequencing reference genomes of the European eukaryotic biodiversity and creating a de-centralized infrastructure to carry out this work on our continent. Vice-chair of ERGA, member of ERGA SSP and EBP Sampling Committee.
Chris Wheat
Stockholm University, SE
Personal Page
Arrival: 06 January 2025, Departure: 12 January 2025
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.
Mike Zody
New York Genome Center, US
Personal Page
Arrival: 04 January 2025, Departure: 10 January 2025
Dr. Zody is the Scientific 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
Vincenza Colonna
Petr Daněček
Sonya Dyhrman
Evan Eichler
Rosa Fernández
Erik Garrison
Brian Haas
Katharina Hoff
Antoine Limasset
Camille Marchet
Fritz Sedlazeck
Oleg Simakov
Rachel Steward
Marcela Uliano-Silva
Chris Wheat
Mike Zody
2023
David Barnett
Aitor Blanco Miguez
Francesco Cicconardi
Sonya Dyhrman
Evan Eichler
Rosa Fernández
Erik Garrison
Brian Haas
Katharina Hoff
Antoine Limasset
Paolo Manghi
Camille Marchet
Natalia Nensheva
Fritz Sedlazeck
Doug Scofield
Rachel Steward
Marcela Uliano-Silva
Rob Waterhouse
Chris Wheat
James Whiting
Mike Zody
2022
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