Team
Josie Paris– Director 
Marche Polytechnic University, IT
Personal Page
Arrival: 03 January 2024, Departure: 20 January 2024
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: 04 January 2024, Departure: 20 January 2024
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: 03 January 2024, Departure: 20 January 2024
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
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Arrival: 04 January 2024, Departure: 20 January 2024
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
Uppsala University, SE and Universidad Politécnica de Madrid, ES
Personal Page
Arrival: 03 January 2024, Departure: 20 January 2024
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 1: 07 January 2024, Departure 1: 09 January 2024, Arrival 2: 18 January 2024
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: 15 January 2024, Departure: 20 January 2024
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 2024, Departure: 20 January 2024
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.
Vincenza Colonna
Institute of Genetics and Biophysics, IT
Personal Page
Arrival: 11 January 2024, Departure: 13 January 2024
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
Petr Daněček
Wellcome Trust Sanger Institute, UK
Arrival: TBC, Departure: TBC
With a background in computer science and PhD in biophysics, Petr Danecek works in methods development and data analysis. He is one of the lead developers of BCFtools/SAMtools/HTSlib and was involved in large-scale sequencing projects such as 1000 Genomes Project, UK10k, or Deciphering Developmental Disorders (DDD). His research interests are currently focused on investigating the genetic architecture of neurodevelopmental disorders.
Sonya Dyhrman
Columbia University, USPersonal Page
Arrival: 13 January 2024, Departure: 20 January 2024
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: 16 January 2024, Departure: 18 January 2024
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
Personal Page
Arrival: 18 January 2024
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
Personal Page
Arrival: 11 January 2024, Departure: 17 January 2024
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: 11 January 2024, Departure: 16 January 2024
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: 07 January 2024, Departure: 11 January 2024
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 2024, Departure: 14 January 2024
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 2024, Departure: 14 January 2024
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.
Oleg Simakov
University of Vienna, AUS
Personal Page
Arrival: TBC, Departure: TBC
Oleg researches major transitions in metazoan evolution from the perspective of the underlying genomic changes. Over the past years, the Simakov Lab has contributed to the broader sampling of metazoan genomes, revealing ancestral metazoan and bilaterian genomic architectures and their diversification patterns. Although many gene families can be traced back to the ancient metazoan ancestor, many of them are linked at both micro- (local gene cluster) and macro-syntenic (chromosomal) levels. Having a broad phylogenetic focus the Simakov Lab aims to (1) characterize and expand our knowledge of conserved and novel gene linkages and their associated (non-coding) elements across metazoans, (2) study their evolutionary dynamics through comparative genomics and modeling approaches, and (3) establish molecular tools for investigating their role during development and clade-specific innovation.
Fritz Sedlazeck
Baylor College of Medicine, US
Personal Page
Arrival: 11 January 2024, Departure: 13 January 2024
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
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Arrival: 12 January 2024, Departure: 18 January 2024
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: 14 January 2024, Departure: 20 January 2024
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.
Chris Wheat
Stockholm University, SE
Personal Page
Arrival: 11 January 2024, Departure: 20 January 2024
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
TBC
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.
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