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PhD Scholarships

PhD studentship

Systematically defining new modes of ubiquitin binding within and/or beyond the DNA damage response

(A*STAR PROGRAMME)

University of Manchester Supervisors: Dr Christine Schmidt, Jim Warwicker. A*STAR Supervisor: Frank Eisenhaber (BII).

Posttranslational modification with ubiquitin is fundamental to most aspects of eukaryotic cell biology. This importance translates to human health, as defective ubiquitin networks are linked to diseases including cancer, neurodegeneration and immunodeficiency. Ubiquitin can be modified itself, leading to different ubiquitin topologies, collectively termed the ubiquitin code. Ubiquitin-modified substrates are recognised by specific receptors that translate the modifications into biochemical and cellular events, for instance to promote genome stability through the DNA damage response. Many thousands of ubiquitylation sites have been revealed. By contrast, only few receptors specific to different ubiquitin topologies are known. This drastically limits our ability for translating the ubiquitin code.

To address this challenge, the project will make use of novel comprehensive approaches to systematically define the proteomes binding to different ubiquitin topologies. The project integrates computational as well as biophysical, cellular and biochemical assays that will be combined to unique pipelines to identify novel ubiquitin-binding regions that will impact on multiple cell biology areas. Moreover, the work will provide the means for studying underexplored networks of other ubiquitin and ubiquitin-like topologies. Based on the cross-disciplinary techniques of this project, the work will lay the foundation for new areas of ubiquitin biology. Moreover, in the longer run, the findings have potential to aid the design of new therapeutic strategies to treat diseases associated with perturbed ubiquitin networks.

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The successful candidate will have a degree in biology, bioinformatics or any associated sciences, and an eagerness to cross the boundaries of traditional academic disciplines, especially between biology and computational sciences. Knowledge of a scripting language, such as Pearl and/or Python, will be advantageous but not essential.

Schmidt website: https://www.research.manchester.ac.uk/portal/christine.schmidt.html

Eisenhaber website: http://www.bii.a-star.edu.sg/research/biography/franke.php

Funding Notes

This project is available to UK/EU candidates. Funding covers fees (UK/EU rate) and stipend for four years. Overseas candidates can apply providing they can pay the difference in fees and are from an eligible country. Candidates will be required to split their time between Manchester and Singapore, as outlined on (https://www.bmh.manchester.ac.uk/study/research/astar/ ).

Applications should be submitted online and candidates should make direct contact with the Manchester supervisor to discuss their application directly. Applicants must have obtained, or be about to obtain, at least an upper second class honours degree (or equivalent) in a relevant subject.

References

1. C. K. Schmidt et al., Systematic E2 screening reveals a UBE2D–RNF138–CtIP axis promoting DNA repair. Nat. Cell Biol. 17, 1458–1470 (2015).

2. P. A. Knobel et al., USP28 is recruited to sites of DNA damage by the tandem BRCT domains of 53BP1 but plays a minor role in double-strand break metabolism. Mol. Cell. Biol. 34, 2062–74 (2014).

3. B. Eisenhaber et al., The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment. Methods Mol. Biol. 1415, 477–506 (2016). (F. Eisenhaber is last author on this paper).

4. W. A. Sherman et al., HPMV: Human protein mutation viewer — relating sequence mutations to protein sequence architecture and function changes. J. Bioinform. Comput. Biol. 13, 1550028 (2015). (F. Eisenhaber is last author on this paper).

Check out  3 PhD students (# of pos: 3)

5. W. Xi et al., Molecular Insights into Division of Single Human Cancer Cells in On-Chip Transparent Microtubes. ACS Nano. 10, 5835–5846 (2016). (C. Schmidt is co-corresponding author on this paper).

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PhD Scholarships

PhD positions at The University of Warwick : Biological Sciences/Synthetic biology (# of pos: 4)

Our group is offering PhD positions for 2018-2019 academic year.  These studentships are hosted by The University of Warwick Doctoral Training Centres 

 Details below

1) PhD project title: Engineering microbial chemical factories to produce renewable and modified biomaterials. 

PhD is hosted via MIBT Partnership

Research Area  : Synthetic biology, Organocatalysis, Structural biology and enzymology

Link :-  https://warwick.ac.uk/fac/cross_fac/mibtp/pgstudy/phd_opportunities/molecularandmetabolicengineering2018/biomaterials

2) PhD project title: Development of novel halogenase enzymes for biopharmaceutical applications.

PhD is hosted via MIBT Partnership

Research Area : Synthetic biology, Organocatalysis, Structural biology and enzymology

Link :- https://warwick.ac.uk/fac/cross_fac/mibtp/pgstudy/phd_opportunities/molecularandmetabolicengineering2018/applications

3) PhD project title: Expanding the genetic lexicon: Developing novel tools for non-natural amino acid incorporation in to therapeutic peptides and proteins.

PhD is hosted via SynBIO DTC 

Research Area : Synthetic biology, Organocatalysis, Structural biology and enzymology

Link :- https://www2.warwick.ac.uk/fac/sci/lifesci/study/pgr/studentships/synbiocdt

4) PhD project title:  Bioplastics from E. coli

PhD is hosted via SynBIO DTC

Research Area : Synthetic biology, Organocatalysis, Structural biology and enzymology

Link :- https://www2.warwick.ac.uk/fac/sci/lifesci/study/pgr/studentships/synbiocdt

Applications are encouraged from UK, EU and International students.

Please be aware that International (non EU) applicants are not eligible for EPSRC/BBSRC funded studentships.

To be eligible for a full EPSRC/BBSRC award (Tuition fees and Stipend) a student must have:

  • Settled status in the UK, meaning they have no restrictions on how long then can stay and
  • Been ‘ordinarily resident’ in the UK for 3 years prior to the start of the studentship. This means they must have been normally residing in the UK (apart from temporary or occasional absences) and
  • Not been residing in the UK wholly or mainly for the purpose of full-time education. (This does not apply to UK or EU nationals).
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To be eligible for an EPSRC/BBSRC tuition fees only award:

  • Students from EU countries other than the UK are generally eligible for a fees-only award. To be eligible for a fees-only award, a student must be ordinarily resident in a member state of the EU, in the same way as UK students must be ordinarily resident in the UK.

Interested students with research experience and qualification please contact us directly. 

https://warwick.ac.uk/fac/sci/lifesci/people/bmenon/

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France Scholarships

PhD position in quantum optimal control theory at the University of Bourgogne

This PhD project aims at applying innovative mathematical tools coming

from optimal control theory to improve theoretical and experimental techniques

in Nuclear Magnetic Resonance (NMR), in Electron Spin Resonance (ESR) and in NV

centers. This approach will allow us to explore and to experimentally reach the

physical limits of the corresponding spin dynamics in presence of typical

experimental imperfections and limitations. A first objective will be to

develop new optimal control algorithms able for an inhomogeneous ensemble of

spins to maximize the signal to noise ratio per unit time of the system. A

general problem is to generalize the Ernst angle solution used in NMR, which is

only valid for a homogeneous spin ensemble. This work will be done in

collaboration with the group of S. Glaser (TUM, Munich, Germany). This approach

will find different applications in NMR and ESR where the sensitivity of the

experiment is a crucial parameter. The student will focus on a specific

experimental setup in ESR used by the group of P. Bertet (CEA, Paris Saclay),

where an important goal is the maximization of the emitted signal of spins

coupled to a microwave resonator. The student will take into account in the

numerical computation specific constraints of this experimental setup. In the

same direction, the student will also use optimal control techniques to design

new CMPG sequences accounting for the coupling between the spins and the

cavity. The same types of control techniques will also be used for manipulating

NV ensembles in collaboration with the group of T. Debuisschert (Thalès,

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Paris). This will allow the improvement of the sensitivity of the corresponding

experiments. For a more fundamental point of view, the ESR will investigate the

numerical techniques used to design robust control fields with respect to

experimental imperfections. A first objective will be to understand the

efficiency of these methods and to prove the optimality (this concept will be

to define rigorously) of the control fields. The ESR will mainly study spin

systems but it is clear that the results of this project will not be restricted

to the physical systems investigated and the techniques developed during the

PhD could be applied to other physical systems with similar properties.

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Israel Scholarships

Marie Curie Innovative Training Network (ITN) META-CAN – PhD position in Computational biology to…

The Machine Learning for Healthcare and Life Sciences group at IBM Research – Haifa is a partner in the funded Marie Curie Innovative Training Network (ITN) META-CAN. The network is a pan-European interdisciplinary and intersectoral training programme for excellence.  It brings young researchers together with world-leading academics, clinicians, and industry personnel to focus on the connections of metabolism, immune response, and cancer.

We are looking for an enthusiastic and highly-motivated early stage researcher (ESR), with a background and experience in computational biology, machine learning and/or statistics and good programming skills (preferably in Python or R). This ESR will study towards a PhD degree and, under our guidance (and in collaboration with the Technion Integrated Cancer Center), will analyze comprehensive omics data to better understand the metabolic adaptations of cancer cells to the central nervous system niche.

The right candidate will enjoy a competitive salary and outstanding work environment.

For more details see http://metacan.eu/  or contact [email protected]

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