The Gilbert Group
Our research heavily exploits the ongoing developments in DNA sequencing technology, with a particular interest in applying such methods to non-model systems. Our research themes include:
Adaptive, Comparative and Speciation Genomics
What is the genomic basis of change, whether at the intra- or inter-specific level? What are the limits of our current understandings of how genomes work? How messy is speciation, and what is the relative role of genomics vs other factors as this speciation happens?
Conservation and Population Genomics
Using both reduced representation as well as full genome resequencing data, we are studying the population structure of a range of animals and plants across both the local and global scale.
Using ancient DNA and associated biomolecules we are studying the timing and tempo of change of the genetic transitions that domestic species underwent as humans transformed them from their wild relatives.
Many of the techniques we implement in our other research has perhaps surprising relevance for industry. This includes deciphering the microbial interactions during fermentation processes, through to elucidating the genomic basis of desirable phenotypes.
Hologenomics and Metagenomics
What role do our microbial passengers play in the adaptation of plants and animals to new environments? And what is the interplay between the host’s genome and that of the associated microbes?
Metabarcoding is the massively parallel amplicon sequencing of complex biological materials with an aim of reconstructing the taxonomic variation in such materials. We develop and apply such techniques to a wide range of questions, spanning the diagnostic to the auditing of biodiversity.
Ancient DNA studies have finally entered the era in which the datasets recoverable from degraded materials can be studied at the genomic scale. Many technical challenges remain, whether relating to the most efficient recovery and analysis of such data, as well as outlining the realistic limits to the contributions of aDNA to our understanding of life. We work on attempting to overcome some of these challenges through the development and validation of new methods, as well as apply aDNA datasets to a range of the above questions.
‘Extinction Genomics - Exploring and exploiting the potential of extinct genome sequencing’
This is a project funded through an ERC Consolidator Grant award (681396) to Tom Gilbert, that started on April 1st 2016. Through this funding we have been able to build a small research team whose goals are to explore what exactly the limits are on genome reconstruction from extinct or otherwise historic/ancient materials. Read more...
Our research is only possible thanks to generous funding from a number of key sources. These include the Marie Sklodowska Curie Actions (in particular the training networks ArchSci2020 and Microwine, as well as numerous Individual Fellowships), the European Research Council (Consolidator Grant 681396-Extinction Genomics), the Lundbeck Foundation, Carlsberg Foundation and Villum Foundation, the Danish Council for Independent Research, the Danish National Research Foundation and the Innovationsfonden.
Members of the group
Morten Limborg (Assistant Professor), salmon hologenomics
Antton Alberdi (Assistant Professor), dietary adaptation in insectivorous bats
Ashot Margaryan (Assistant Professor), human palaeogenomics
Shyam Gopalakrishnan (Assistant Professor), history of wolves and dogs
Miyako Kodama (postdoc), salmon hologenomics
Marcela Sandoval Velasco (postdoc), extinction genomics
Ostaizka Aizpurua (postdoc), metagenomic plasticity in fishing bats
Christian Carøe (postdoc), wine and cheese transcriptomics
Glenn Dunshea (postdoc), Antarctic eDNA
Åshild Vågene (postdoc), Pathogen palaeogenomics
Sarah Mak, Laboratory manager
Anna Fotakis, Holofood coordinator
Sen Li, Bioinformatics Manager
Christina Lynggaard (PhD student), eDNA and environmental regeneration
Jonas Niemann (PhD student), extinct genome reconstruction
Fatima Sanchez Barreiro (PhD student), rhinoceros conservation genomics
Anne Marie Eriksen (PhD student), microbial diagenesis of bone
Martin Ellegaard (PhD student), human palaeogenomics
Marta Ciucani (PhD student), wolf genomics
Lara Puetz (PhD student), fish metagenomics
Mandy Pittman (PhD student), vertebrate metagenomics
Martin Nielsen (PhD student), insect community genomics
Adam Koziol (PhD student), vertebrate hologenomics
Vanessa Iurif (visiting PhD student), bioethanol metagenomics
Josh Evans (visiting PhD student), fermentation metagenomics
Emily Cavill (visiting MSc student), Seychelles Magpie Robin genomics
Mads Lund (Msc student), maize hologenomics
Mads Bjørnsen (MSc student), Greenland Sledge Dog hologenomics
Daniel Øksnebjerg (MSc student), Ugandan coffee plantation insect diversity
Frederik Leerhøi (MSc student),Ugandan coffee plantation insect diversity
Søren Christensen (MSc student), Ugandan coffee plantation insect diversity
Max Ramsøe (Research Assistant), FoodTranscriptomics Project
Meng Zhao (Research Assistant), African great lake sedimentary DNA
Camilla Hjorth Scharff-Olsen (Research Assistant), Wolf genomics projects
Sarai Reyes Avila (intern), Palaeogenomics