Tag Archives: UCL

Cancer Bioinformatics Jobs in London

Couple of London-based Bioinformatics positions available:

Senior Bioinformatician in the  Gene Function Team, Inst. of Cancer Research, Chelsea, London led by Professor Alan Ashworth.

The Gene Function Laboratory currently houses over 30 scientists and runs a wide-ranging portfolio of projects including basic cancer biology and drug development programmes. As part of these projects, the laboratory interacts with a diverse range of collaborators, contract research organisations, pharmaceutical companies and funding charities.

We are seeking an experienced and motivated Senior Bioinformatician to support high- throughput cell-based screening and Next Generation Sequencing based projects within the Breakthrough Centre. The successful post holder will perform statistical analyses and quality control reporting on screen data, using publicly available packages and commercial software to facilitate the prompt and efficient transfer of data into scientific publications. The postholder will also perform next generation sequencing data analysis including read alignment and variant calling.

Experience in the analysis of RNA interference or cell-based drug screens is essential, as is the ability to apply existing third-party tools to the analysis of Next Generation Sequencing and microarray data sets.

Applicants should hold a PhD or equivalent qualification in a relevant subject, have scripting experience in R and Perl and will ideally hold a post-graduate qualification in bioinformatics.

The starting salary will be in the range £40,725 – £43,119 p.a. inclusive and the position will be offered initially on a fixed-term contract of one year.

Informal enquiries are welcome and can be made to Dr Chris Lord (chris.lord@icr.ac.uk). Please note – this address is for enquiries only and you should not send your application to this email address; CV, pdf copies of your best 3 publications over the last 5 years and covering letter must be submitted online at http://www.icr.ac.uk/jobsearch. Job Ref. No. 1279843

Closing date: 16 October 2012

Postdoctoral Research Fellow Position available in Cancer Bioinformatics at  UCL Cancer Institute and CR-UK London Research Institute

A fellowship position is available in the UCL Cancer Institute and CR-UK London Research Institute in the Swanton laboratory
To study mechanisms of cancer genome instability, intratumour heterogeneity and drug resistance using genome wide cancer sequencing and trasncriptomic datasets in breast cancer, funded by the BCRF, building on recent work (Gerlinger et al New England Journal of Medicine 2012 and Yap and Swanton Science Translational Medicine 2012). Potential candidates will be expected to have an interest in oncology and translational research and be proficient in ‘R’ or equivalent and have a strong statistical background. Competitive London PDRF salary will be offered to the successful applicant.

Please make informal inquiries with a CV and covering letter to charles.swanton@cancer.org.uk


Joint UCL Computational Biology / CoMPLEX Seminar

3D Protein Structure Predicted from Evolutionary Sequence Variation

Chris Sander, Debora S. Marks

3pm 1st July 2011, University College London



The trajectory of an evolving protein through sequence space is constrained by the need to maintain structure and function. Residues in spatial proximity tend to co-evolve, yet attempts at inverting the evolutionary record to derive proximity constraints have so far been inadequate. Here we use constraints inferred from evolution to predict de novo3D protein structures, without use of homology modeling or fragments from known structures. Our evolutionary constraints tackle the major obstacle in state-of-the-art de novo prediction: the ability to sample 3D conformational space. The predicted constraints are calculated with a method borrowed from statistical physics using maximum entropy which solves the inverse problem of inferring spatial proximity from patterns of co-evolution. We report prediction for 12 proteins ranging from 20-220 residues in size at a Ca-RSMD of 2.8 – 5.1 Å. The predicted structures have excellent topological agreement with experimentally determined structures, with structural elements well placed in 3D space, suggesting they can be refined further. In this era of massive genomic sequencing across many species, the evolutionary record captured in sequence alignments provides an increasingly powerful source of predictive information, in particular for protein families that have resisted experimental structure determination.


Medawar Lankester Lecture Theatre – behind Foster Court

UCL Cruciform Building

Conference: Enabling Systems Biology

11th-14th April 2011 – University College London

The conference will gather the current expertise in data integration and systems biology approaches to tackle four domains of research: cell cycle, cellular signaling, metabolism and stem cells.
A workshop will allow participants to practice various bioinformatics tools aimed at analyzing and integrating biological data

UCL Computational Biology Launch

A Symposium to launch UCL Computational Biology will be held on Tuesday 15th February 2011 from 9.15am to approximately 5.30pm, in the Christopher Ingold Auditorium, Department of Chemistry, University College London. A poster session and post-Symposium Reception from 6.00pm, will be held in North Cloisters, Wilkins building.

Register for this event at http://uclcomputationalbiology.eventbrite.com

The closing date for registration is Tuesday February 1st. Registration on the day will take place outside the Christopher Ingold Auditorium, Department of Chemistry, from 8.45am.

UCLBioinformatics / Molecular Bio PostDoc

Posted on LBF-Discuss mailing list by Elia Stupka:

an exciting and challenging opportunity for a post-doc position within a very interdisciplinary EU funded project, Dopaminet ( http://www.dopaminet.eu ) is now available in my new lab at UCL, so we are seeking high caliber candidates, please forward to those who might be interested (and ready for the challenge!), deadline September 15th. Please note that although not mandatory, preference will be given to candidates who have laboratory experience (besides the mandatory bioinformatics experience)

The successful candidate will work in conjunction with renowned international laboratories across Europe and Japan (including the Riken Institute, Karolinska Institute and SISSA) as part of the EU funded Dopaminet project ( http://www.dopaminet.eu/ ). The aim of the project is to understand the molecular signatures and networks of dopaminergic neurons from large genomics and imaging datasets.

The candidate will focus in particular on the analysis (and possibly the generation) of next-generation sequencing technologies datasets with CAGE, RNASeq and ChipSeq protocols on samples obtained from ex-vivo cells as well as differentiated stem cells.

The candidate will work within the laboratory lead by Elia Stupka, whose general aim is to decipher functional elements of the genome and their role in disease using functional and comparative genomics approaches. The laboratory is located within the medical genomics group lead by Stephan Beck at the UCL Cancer Institute, and has strong ties to other next-generation sequencing laboratories across London.

Candidates should have:

* Prior experience with the analysis of genomics data (ideally with next-generation sequencing data)
* Experience in common bioinformatics packages such as Bioconductor and Bioperl
* Good track record in internationally peer-reviewed publications is mandatory

Beneficial, but not required:

* Prior experience with comparative genomics and model organisms
* Candidates with laboratory experience will have the opportunity to conduct their own experiments within the framework of the project, besides analysing datasets from other laboratories in the project.

Further details on the post and application forms on our website:

Details/application: http://www.ucl.ac.uk/cancer/vacancies/ES0709/index.htm