Postdoc positions on context dependent cell signalling (wet and/or dry)

Why do some mutations cause cancer in some tissues and not others ? What happens to the cell signalling pathways during differentiation ? Why are some genes essential in some cell types and not others or why are some drugs more effective at killing some cell types than others ?

We think that this is a great time to be asking these questions of how the genetic background or tissue of origin changes cell states. More precisely for us, how this re-wires cell signalling. It has become routine to measure changes in phosphorylation across different conditions, including different cancer types. The Sanger and others are establishing panels of human cell lines that are being profiled with an increasing array of omics technologies with drug sensitivity and CRISPR based gene essentiality information. These panels offer a great opportunity to address these questions.

We want to combine the work we have been doing in studying human signalling with phosphoproteomic data, with variant effect predictors, microscopy based studies of cell signalling and network modelling to address this question of context dependent changes in cell signalling.

To support this research we have 2 postdoc positions available: one would be primarily computational and would involve image analysis and network modelling in collaboration with microscopy groups (see here for project and application); the second would be primarily experimental with a focus on microscopy. The latter would be available via the ESPOD fellowship scheme in collaboration with Leopold Parts group at Sanger (see here for project description and here to apply). The split between computational and experimental is open and wet/dry mixed candidates are encouraged as well to apply to both.

These projects complement existing work in the group using cancer Omics data to study the genetic determinants of changes in protein abundance and phosphorylation and will be in collaboration with work developed by the Petsalaki group at EBI that is also recruiting. Email me if you have any questions/concerns about the positions.

Positions available to study the functional relevance of protein phosphorylation

Photo by leg0fenris. Disclaimer: this photo should
not be taken as implicit support for the actions of the empire

In the past few years, thanks to advances in mass-spectrometry, tens to hundreds of thousands of phosphorylation sites have been discovered across different species. However, even for very well studied model organisms like yeast we known the function of only a very small number of these. Along with other groups, we have shown that these modifications can diverge quickly (Landry, Beltrao, Tan) leading to the hypothesis that some of these phosphorylation sites might even serve no purpose in extant species. Given these evolutionary observations and the large number of sites that are now routinely identified per study how do we go about identifying which ones are indeed functionally relevant ? In what environmental contexts ? How many might be "non-functional" ?  If these questions sound interesting then we have two posts (postdoc and technician) currently open to develop genetic approaches that we think are going to be important to answer these questions. The work will be conducted at the EMBL Genome Biology unit in Heidelberg (Germany) in collaboration with the Typas lab.

Answering these questions will take a combination of different approaches ranging from proteomics to genetics and bioinformatics. These positions, although focused on the genetics aspects, will offer the possibility to explore and learn from the other expertise. The deadline for application is the 17th of May. Additionally information about our group can also be seen at the EBI webpage and we welcome informal questions about the project and positions by email.

Collaborative postdoc fellowship opportunities

I interrupt this long blogging hiatus to point out two potential postdoc fellowship opportunities to work with our group at the EMBL-EBI. One is the EIPOD program that is an EMBL wide interdisciplinary program. For this fellowship the project is collaboration with Nassos Typas (genetics) and Jeroen Krijgsveld's (proteomics) groups at the EMBL in Heidelberg. Successful candidates would be studying how Salmonella uses post-translational modification effector proteins to regulate and subvert the host cell. It is important to note that EIPOD applicants must be interested in doing both the computational and experimental aspects of the project. Applicants are only expected to have experience in one of the areas (bioinformatics, proteomics, genetics) and an interest in learning about the others. The deadline for the EIPOD application in 11 of September.

The other fellowship opportunity is the newly created EBPOD program. This is a collaborative program set up between the EMBL‐EBI and the NIHR Cambridge Biomedical Research Centre (BRC). As described in the program webpage this is a program meant to explore and develop computational approaches for translational clinical research involving human subjects. Our project proposal (PDF link) aims to study and identify cell surface markers of primed/activated neutrophils obtained from patients with chronic inflammatory diseases. The project is a collaboration with Paul J Lehner and Edwin Chilvers. The applicant would be in charge of the computational analysis which would focus on proteomics data of protein composition changes in the membrane vs total cell (as in Weekes et al. Cell 2014). Prior expertise in protein related computational research would be ideal.

Sysbio postdoc fellowship: spatio-temporal control of cell-cycle regulation

Funding is available for a 3 year postdoctoral fellowship to study spatio-temporal control in cell-cycle regulation. This is a join project between our group at the EMBL-EBI and the Quantitative Cell Biology group headed by Silvia Santos at the MRC Clinical Sciences Centre in London. More information about the groups interests can be found in the respective webpages.

The main objective of this project will be to study how the spatial and temporal control of key cell-cycle proteins change in different biological contexts. Examples of these different contexts include different differentiation states and/or different species.


We are looking for candidates that are interested in doing both experimental and computational work and previous experience in  cell biology, microscopy, programming, image analysis and/or modelling of dynamical systems are all considered an asset. We will consider candidates that have a stronger expertise on either experimental or computational methods but are interested in learning and using both approaches. Additional information and application link is here with a closing date of 24 November 2013. We are available for further clarification in regards to suitability of background or information about the projects.

EBI-Sanger postdoctoral fellowship on Plasmodium kinase regulatory networks

I am happy to announce a call for applications for a EBI-Sanger postdoctoral fellowship to study the kinase regulatory networks in Plasmodium. This is one of four currently open calls in the the EBI–Sanger Postdoctoral (ESPOD) Programme and the call closes on the 26th of July. This interdisciplinary programme is meant to foster collaborations between the EBI and the Wellcome Trust Sanger Institute, both at the Genome Campus near Cambridge UK. Our project is a collaboration between myself (EBI), Jyoti Choudhary (mass-spectrometry group leader at Sanger) and Oliver Billker (group leader at Sanger studying malaria parasites). The postdoctoral fellow would have the opportunity to work at the interface between bioinformatics, mass-spectrometry (MS) and Plasmodium biology. A description of the project can be found online (PDF) but briefly the objective is to characterize kinase regulatory network of the malaria parasite by combining quantitative phosphoproteomics with computational analysis. There will be a strong emphasis on the computational analysis of the MS data and some prior computational experience is a plus. The ideal candidate would have prior experience in phosphoproteomics with a strong interest in learning the computational aspects required or prior experience in the relevant computational skills and interest in learning/performing some of the experimental work. Feel free to contact me if you require more information about the project or the ESPOD fellowship.