Life at Earlham Institute
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Applications are open for this LongTREC PhD project in the Wilfried Haerty Group at the Earlham Institute.
LongTREC is a Doctoral Network of the Marie Sklodowska-Curie action program (MSCA-DN) that will develop methods and tools for the analysis of transcriptomic data obtained with the most recent single-molecule, long-reads sequencing technologies.
Project Description:
Nearly 95% of multiexonic genes in humans undergo alternative splicing, the process by which multiple isoforms are transcribed from a single gene through differential inclusion of exons and splice sites.
Alternative splicing is a highly regulated process with evidence for the developmental stage-, tissue-, and cell-specific isoforms. The development of long-read RNA sequencing has opened the unique opportunity to gather a much more comprehensive understanding of the existing transcript diversity and its regulation. Work by ourselves and others, mainly conducted at the tissue level demonstrated that the current transcript diversity in human is severely underestimated.
Although already extremely informative, this work was conducted on thousands to millions of cells, obfuscating transcripts that are found in specific cell types including rare cell types such as stem cells. Recent molecular developments by ourselves and others aiming to bring long-read sequencing to single cells already provided unique insights on transcript regulation but also fundamental events such as VDJ recombination. Methods so far have been suffering from relatively low throughput leading to the recovery of genes with mid to high expression. Additionally, there is limited availability of computational tools for their analysis and visualization.
We offer a highly collaborative PhD project between the Haerty (bioinformatics) Macaulay (molecular biology, technology development) groups. The main aim of the project is to develop protocols and computational solutions to further enable the applications of long-read RNA sequencing to single cells, with a specific focus on rare cell types such as hematopoietic stem cells, and genes fundamental to our physiology and of primary interest in disorders and diseases but expressed at low levels.
The student will work in a rapidly developing field and gain unique expertise in computational biology, large dataset analysis, genomics, transcriptomics, sequencing technologies, molecular biology, technology development, and therapeutic target identification.
The project will be conducted at the Earlham Institute, a UKRI-BBSRC strategically supported research centre of excellence for bioinformatics and sequencing technology development. In addition to the training offered through the LongTrec network, the student will have access to training and career development opportunities at EI and on Norwich Research Park.
Eligibility criteria:
We welcome applications from PhD candidates from any country fulfilling the following criteria:
Application and selection process
Applications must contain the following documents (in pdf):
Our work is primarily computational, focusing on comparative genomics and population genetics, as well as data integration, approaches to identify putative functional elements, characterise their evolution and assess the potential impact of their disruption.
We believe that our people are our greatest asset, and we want you to have the freedom to achieve your very best work here.
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The behaviours and communication skills we expect from candidates.