Irimia Lab

Irimia LabIrimia Lab

Systems and Synthetic Biology

Irimia Lab
Transcriptomics of vertebrate development and evolution
Group leader

Irimia Lab

Transcriptomics of vertebrate development and evolution
Group leader
We are offering a fully-funded PhD position in our lab
From Dec 2018: ICREA Research professor.
From June 2014: Group Leader at the Centre for Genomic Regulation (CRG), Barcelona, Spain.
2011-2014: Postdoc in the laboratory of Prof. Blencowe, University of Toronto, Toronto, Canada.
2011-2011: Postdoc in the laboratory of Prof. Fraser, Stanford University, USA.
2006-2010: PhD in Genetics in the laboratory of Prof. Garcia-Fernandez, Universitat de Barcelona, Barcelona, Spain.
2005-2006: Postgrad researcher in the laboratory of Prof. Penny, Massey University, Parlmerston North, New Zealand.
2004-2005:  Postgrad researcher in the laboratory of Prof. Arctander, University of Copenhagen, Copenhagen, Denmark.
2000-2004: Diploma studies in Genetics, Universidad Complutense de Madrid, Madrid, Spain


Seasonal and circadian genetic variation charted across the human body (13/02/2023)
A research team at the CRG have published research in PLOS Biology which details how the circadian and circannual cycles influence humans at the molecular level by measuring changes to the activity of genes inside cells across different types of tissues. 

‘Tiny but mighty’ gene fragments are crucial for maintaining blood sugar levels (09/02/2023)
A research team at the CRG has now discovered that microexons are also found in another type of cell that carries out highly-specialised functions within complex tissues and organs – endocrine cells in the pancreas.

Tiny gene fragments revealed as crucial new players in retinal development and vision (13/07/2022)
Researchers at the CRG reveal that Srrm3 is a master regulator gene crucial for the development of photoreceptors, cells in the back of the retina which capture and process light, sending signals to the brain that enable vision.

Act of sabotage determines mammalian embryonic development (12/04/2022)

Researchers at the Centre for Genomic Regulation (CRG) in Barcelona made the discovery after creating an atlas of splicing events during the early development of cows, humans and mice.
Uncovering the mysterious role of microexons in human disease (14/12/2020)
Manuel Irimia, ICREA Research Professor at the Centre for Genomic Regulation (CRG) has been awarded an ERC Consolidator Grant
The genomic keys to the origin of the vertebrates (21/11/2018)
An international team of scientists co-led by CRG researcher Manuel Irimia reports how more complex and specialised gene regulation proved to be pivotal in the origin of the vertebrates.
This change, a random error in the evolutionary process that occurred over 700 million years ago, facilitated the connection of the gene networks involved in animal embryogenesis.
Manuel Irimia, CRG junior group leader, has been elected EMBO Young Investigator. He is one of the two researchers elected in Spain.
A new study revises the development and evolutionary origin of the vertebrate brain (28/04/2017)
Researchers have made the first detailed map of the regions into which the brain of one of the most closely-related organisms to the vertebrates is divided and which could give us an idea of what our ancestor was like.
'Yin and Yang' Switch Lies at the Heart of Animal Stem Cells (09/08/2016)
A molecular switch that flips between different versions of genes could be crucial for maintaining stem cells across all animals from simple flatworms to humans, according to a study from scientists at the Centre for Genomic Regulation (CRG) in Barcelona, published today, in the journal eLife.


How does a single genome sequence encode the information to build the enormous complexity of cell types and structures of an adult animal? How are changes in this sequence translated into morphological differences during evolution? These two exciting questions have always been the center of my research. In my lab, we approach these topics focusing on cell and tissue type specific transcriptomes: How are they encoded in the genome? How are they generated during embryogenesis? How do they impact cell function in adult organisms? How do they evolve and how they impact evolution? To answer these questions, we not only study transcriptional regulation, but also other mechanisms that expand transcriptomic diversity, such as alternative splicing and gene duplication.

In particular, we focus on two highly contrasting systems: (i) early mammalian embryogenesis and (ii) vertebrate neural development. These two developmental contexts have radically distinct characteristics. On the one hand, early embryogenesis captures in vivo pluripotency and the first cell fate decisions, involves relatively simple morphogenetic processes, and shows particularly high evolutionary rates. On the other hand, vertebrate brains are extremely complex systems of highly differentiated cell types that develop through very specialized processes (e.g., neuritogenesis, axon guidance, migration, etc.). Furthermore, neural-specific isoforms are exceptionally conserved. Thus, by combining both biological systems we aimed at obtaining highly complementary insights into the roles of transcriptome specificity and diversification in development and evolution. Moreover, these two systems are key to understand two evolutionary transitions we are fascinated about: the origin of vertebrates and the origin of mammals.

To tackle these questions, we combine computational approaches (comparative bulk and single-cell transcriptomics and functional genomics) with experiments using in vitro and in vivo systems (zebrafish, mouse and fruitfly) to investigate how these mechanisms impact embryonic development, adult function, disease and evolution.


Database, Webservice

Atlas of alternative splicing profiles across animal tissues, cell types and developmental stages.

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