Dag Ahrén
Lund University, Sweden
Personal Page
Arrival: 20 May, Departure: 29 May
Dr. Ahrén’s primary interest is understanding genetic and genomic mechanisms related to fungal host interactions (parasitic as well as symbiotic). He works as a lecturer at Lund University and is the manager of the Microbiology, Immunology & Protein structure team at NBIS. He also has a keen interest in targeted metagenomics using custom made probes for targeting important ecological processes such as carbon turnover and methane synthesis and degradation. Dr. Ahrén along with Scott Handley, Rayan Chikhi, Sonya Dyhrman, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.
David Barnett
Maastricht University, NL
Personal Page
Arrival: 29 May, Departure: 4 June
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.
Kirsten Bos
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Personal Page
Arrival: 24 May, Departure: 26 May
Dr. Bos is the Research Group Leader for Molecular Palaeopathology at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Her team tackles historical questions relating to the changing landscape of infectious disease over time, host-pathogen coevolution, and the biological consequences of European and New World contact. She uses techniques in ancient DNA retrieval to sequence enough DNA from preserved archaeological tissues so that ancient pathogen genomes can be computationally reconstructed.
Rayan Chikhi
Institut Pasteur, France
Personal Page
Arrival: 22 May, Departure: 5 June
Dr. Chikhi’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. Dr. Chikhi along with Scott Handley, Dag Ahrén, Sonya Dyhrman, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.
Sonya Dyhrman
Columbia University, USA
Personal Page
Arrival: 20 May, Departure: 29 May
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 along with Scott Handley, Rayan Chikhi, Dag Ahrén, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.
Malachi Griffith
Washington University, USA
Personal Page
Arrival: 24 May, Departure: 29 May
Dr. Griffith is the assistant director of the McDonnell Genome Institute (MGI) at the University of Washington. His research is focused on the development of personalized medicine strategies for cancer using genomic technologies. Over the last 15 years, he has worked on developing methods in data mining, genomics, and bioinformatics for application to cancer precision medicine.
Brian Haas
Broad Institute, USA
Personal Page
Arrival: 25 May, Departure: 1 June
Brian Haas is a senior computational biologist at the Broad Institute. He is one of the authors of the well-known transcriptome assembler Trinity.
Scott Handley
Washington University, USA
Personal Page
Arrival: 22 May, Departure: 7 June
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. Dr. Handley along with Rayan Chikhi, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.
Ilya Korunsky
Brigham and Women’s Hospital and Harvard Medical School, USA
Personal Page
Arrival: 30 May, Departure: 2 June
Dr Korunsky’s lab develop algorithms and software packages to perform analysis of genomic data with complex study designs, particularly focusing on single cell analysis to carry out spatial mapping, temporal mapping, and cross disease comparisons.
Guy Leonard
University of Oxford, UK
Personal Page
Arrival: 19 May, Departure: 5 June
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. Dr. Leonard along with Rayan Chikhi, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Scott Handley and Josie Paris are the Workshop Co-directors.
Antoine Limasset
Université de Lille & CNRS, France
Personal Page
Arrival: 24 May, Departure: 30 May
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, France
Personal Page
Arrival: 24 May, Departure: 30 May
Dr. Marchet is a postdoc researcher working in BONSAI team (Lille, France), with Rayan Chikhi and Mikaël Salson. After a MSc in Ecology and Evolution from Université Claude Bernard Lyon 1 and an engineer 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 takes part in Transipedia ANR. 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.
Josie Paris
University of L’Aquila, Italy
Personal Page
Arrival: 18 May, Departure: 3 June
Dr. Paris is an evolutionary biologist using analytical approaches at the forefront of 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), transcriptomics, and de novo genome assembly. Josie is currently working on the genome assembly and epigenetics (RRBS) of the European lobster, balancing selection in the Trinidadian guppy, conservation genomics of Mediterranean reptiles and mitogenome analysis of oysters. Dr. Paris along with Rayan Chikhi, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Scott Handley and Guy Leonard are the Workshop Co-directors.
Sophie Shaw
All Wales Medical Genomics Service, Cardiff, UK
Personal Page
Arrival: 22 May, 25 May
Dr. Shaw works as a Clinical Bioinformatician at the All Wales Medical Genomics Service for the NHS in the UK. She develops and validates diagnostic and prognostic NGS sequencing tests for genetic conditions and cancer mutations. In her previous roles, she has worked for a bioinformatician within an academic setting providing analysis of numerous different data sets including differential expression analysis, transcriptomics, whole genome assembly and single cell genomics. She is involved in the running of numerous international workshops focused on genomics analysis as well as teaching within her institute. Dr. Shaw along with Rayan Chikhi, Sonya Dyhrman, Dag Ahrén, Guy Leonard, Scott Handley and Josie Paris are the Workshop Co-directors.
Emiliano Trucchi
Marche Polytechnic University, Italy
Personal Page
Arrival: 1 June, Departure: 18 June
Dr Trucchi enjoys researching the genomic revolution in molecular ecology and evolutionary biology. He is working on many great projects (in phylogeography and population genetics, genotype-phenotype mapping, landscape genetics, speciation genomics of species complexes,…) but his current hot research topic is epigenetics and its evolutionary potential. Dr. Trucchi is also a co-director for the Workshop on Population and Speciation Genomics.
Chris Wheat
Stockholm University, Sweden
Faculty Page
Arrival: 27 May, Departure: 4 June
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.
Mike Zody
New York Genome Center, USA
Personal Page
Arrival: 23 May, Departure: 26 May
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.
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