Mouse brain sections labeled for cortical neuronal subtypes (left) and glial subtype (right). Image credit: Omer Bayraktar
Our Research and Approach
We seek to explore the vast cellular diversity in the human body.
To understand human cellular diversity, we aim to (i) create single-cell level 3D maps of human organs using large-scale spatial transcriptomics and (ii) uncover the specialized functions of brain cell types using large-scale in vitro screens and mouse models.
We focus on studying neural cell type diversity in the human cerebral cortex.
Without the cerebral cortex, we would not have complex thought and behavior. The cortex also plays major roles in many neurodevelopmental and psychiatric disorders including autism spectrum disorders (ASDs) and schizophrenia. To precisely understand cortical function and determine how it goes awry in disease, we need to classify more than 16 billion neurons and 60 billion glial cells across this complex brain structure.
Our team will work on three major research directions:
Large-scale spatial transcriptomics for mapping human tissues: We will establish automated histology and imaging pipelines to map human tissues at single cell resolution at scale. We will use and develop highly-multiplexed single molecule fluorescent in situ hybridization (smFISH) methods to identify molecular cell types. We will extensively collaborate with Human Cell Atlas (HCA) and other teams at Sanger on diverse tissue applications and to develop automated image data analysis pipelines.
Cortical cell type diversity in health and disease: We will use single cell sequencing and large-scale spatial transcriptomics to map neuronal and glial subtypes in the developing and adult human cerebral cortex. We will further utilize spatial transcriptomics to identify cellular pathways involved in neurodevelopmental disorders such as ASD.
Large-scale screens to discover human glial function: Glia represent the majority of cells in the human cerebral cortex, but we know little about their biology. We will perform large-scale protein interaction screens and imaging-based cellular assays to discover glial molecular pathways that regulate neuronal development. We will also study glia-neuron interactions in vivo using mouse models. In our initial studies, we will focus on the role of human astrocytes in synapse development.
Research positions available
Postdoc, imaging specialist and PhD student positions available and will be posted on Sanger jobs soon. Please contact Omer (sanger email) if interested.
Omer's research aims to explore human brain cellular diversity using large-scale approaches. His team will harness spatial transcriptomics, imaging and functional screening to study neural diversity in health and disease.
Omer is fascinated by the cellular complexity of the brain. His research team is interested in using large-scale approaches to map brain cell types, to identify how glial cells shape neuronal circuits and to discover cellular pathways affected in neurodevelopmental disorders.
The International Human Cell Atlas initiative aims to create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human health and diagnosing, monitoring, and treating disease.
Programmes, Associate Research Programmes and Facilities
We are focused on using single-cell approaches, so called “cell atlas” technologies and understanding human genetics at the cellular level. The team combine cutting-edge techniques in wet and dry lab and are applying these methodologies for further understanding of human health, development and disease.
The Cellular Generation and Phenotyping (CGaP) core facility provides central cell biology support to the Sanger Institute. CGaP takes a unique approach at the institute by partnering with faculty groups in order to deliver the scale-up of existing protocols to facilitate 'Science at Scale'. We function as a contract research group for the institute, running multiple, distinct cell biology based projects. The facility has expertise in cell derivation from primary tissue, iPSC and organoid derivation, cellular differentiation, CRISPR library screening, functional bioassays, phenotypic assays and end point analysis (e.g. Immunocytochemistry).
In collaboration with our colleagues in Cellular Operations and Stem Cell Informatics, our work focuses on supporting and delivering the gene editing requirements of the Institute's faculty and research programmes. Through the adoption and implementation of modern genome editing techniques, we tailor our technical experience to help answer biological questions. We optimise, develop and democratise the delivery of genome editing tools and platforms for the Institute’s research programmes. For our collaborating partners we provide an agile, project focused, cost effective and efficient service as well as develop and provide biological resources, technical support and training for research groups and their staff.
Our goal is to understand how genetic background influences outcome of mutations. To do so, we measure, model, and modulate cell state across healthy and disease-relevant human genetic diversity. In the lab, we develop tools for genetic perturbations, and use genome engineering and synthetic biology to create cell lines for screening cellular traits. In the office, we develop probabilistic models as well as software tools to accurately and efficiently analyse the readouts.
The Vento Lab uses genomics and computational tools to reconstruct immune environments. The main areas of focus are: Immunogenomics - Immune responses against infection, Reproductive atlas - Reconstructing dynamic maps of reproductive organs, and Cellular networks - Cell-cell communication