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Wednesday, 7 October 2015

4-Year PhD programme

4-Year PhD programme overview
Students spend the first eight months of the programme undertaking three rotation projects in different research groups. This ensures exposure to different disciplines in genomics, and allows the students to gain a better overall picture of the scientific nature of the Institute and the different technologies that are available. In particular, all students are required to carry out at least one informatics rotation and one experimental laboratory rotation. This helps students to develop wide ranging skills both at the bench and in data analysis. Students are required to write a short report or prepare a poster and make a presentation to the group at the end of each project. Selection of the final PhD project laboratory is by mutual consent between the student and supervisor and takes place during the third rotation period.

Wellcome Trust Sanger Institute

  • Monitoring of each student's progress is achieved through the submission of a project report or the preparation of a poster for each rotation, their first year report and by thesis committee meetings which take place every 6 months.
  • During their PhD, students are expected to attend training courses in transferable and general research skills, participate in the students' journal club, present their work regularly and attend seminars.
  • Students offered one of our 4-year PhD programme studentships will obtain full financial support, including tuition fees, regardless of nationality. At least ten studentships will be available across all our research areas. Since Sanger Institute studentships are extremely competitive, we also encourage you to seek your own funding. Any students with their own funding should still apply to the 4-year PhD Programme in the usual way.
  • For information on how to make an application to our 4-year PhD Programme please go to How to apply.

How to apply

If you have any questions about the application process, please look at the FAQs. If you need further assistance, contact the Graduate Programme Office. Please note that the Graduate Programme Office is unable to comment on whether you are a suitable candidate for our 4-year PhD programme.

Academic requirements

  • Candidates are expected to hold, or be about to achieve, a 1st or an upper 2nd class degree or an equivalent overseas qualification. If overseas (non-UK, non-EU) applicants, who have not studied in a EU country, have GRE scores, they should include them in their application, as the results from this standardised test enable us to more easily compare applicants from different countries.

Competence in English

  • If your first language is not English you will need to meet the University of Cambridge's English languagerequirements, although you do not have to fulfil this requirement before submitting your on-line application to the Wellcome Trust Sanger Institute. However, if you are offered a place on our programme, you will need to fulfil this requirement before you can be admitted to the University of Cambridge.

Application procedure

  • You need to complete the Wellcome Trust Sanger Institute on-line application.
  • Closing date for applications for the 2016 intake: Tuesday 1st December 2015 (23.59 GMT)

When completing the on-line application form you will need to:

  • Provide details of your academic qualifications
  • Provide details of two academic referees
  • Outline your research interests and indicate how these fit with the research interests of the Sanger Institute (max 200 words)
  • Outline any relevant work experience (max 200 words)
  • Write a personal statement on your research experience, research interests and career goals, explaining why you wish to pursue graduate training at the Sanger Institute (max 400 words)
  • Upload your University transcript(s) (and GRE scores if available) as a PDF file
You should request and receive your transcript(s) from your institution before you begin your application so that you have them ready to upload. If you are currently studying you should upload a transcript with the marks you have obtained so far.
Once you have completed the first page of the application form, a URL with a unique identifier will be generated, which you should bookmark. If you want to continue the application process at a later time you can use this URL to return to your incomplete form.

Once you have submitted your completed application form:

  • You will receive a confirmation email
  • Your chosen referees will receive an email asking them to submit an on-line reference for you
Please ensure that you have provided the correct institutional email address for your referees and that they have agreed to provide a reference for you. Once a referee has submitted their reference:
  • Your referee will receive a confirmation email
  • You will receive a confirmation email
It is your responsibility to ensure your referees have submitted their reference by Tuesday 8th December 2015 (23.59 GMT) at the latest.
The final deadline for the receipt of references is only one week after the application deadline. Therefore, please do not leave your application until the last minute as this does not leave much time for your referees to respond.

Please note that without references your application will not be processed.

  • If you are unable to upload your transcript(s), please contact the Graduate Programme Office and include your URL/unique identifier in the email.
  • Should you have any difficulties in submitting your on-line application, or you do not receive an email confirming that your submission has been successful, please contact the Graduate Programme Office and include your URL/unique identifier in the email.
  • Shortlisted candidates will be invited to attend our PhD Open Day on 25th January 2016 at the Wellcome Trust Sanger Institute in Hinxton, where they will have three interviews with individual Sanger Institute Faculty members and one panel interview with three Sanger Institute Faculty members. If overseas applicants are unable to attend the PhD Open Day, they can be interviewed via a series of Skype or telephone interviews (during the two weeks before the Open Day).
  • If you have not heard from us by 8th January 2016 you should assume that you have not been shortlisted for interview.
  • The studentships will be allocated on a competitive basis after the PhD Open Day. All students who are offered a studentship on our 4-year PhD programme will obtain full financial support, including tuition fees, regardless of nationality.
  • Sanger studentships are extremely competitive, and we encourage you to seek your own funding. Any students with their own funding should still apply to our 4-year PhD Programme via the online application form.
  • Once a student has been selected for the 4-year PhD programme they have to apply for admission to theUniversity of Cambridge using the University's on-line GRADSAF (Graduate Admission and Scholarship Application Form). A student cannot take up our award unless they are also successful in securing admission to the University.
  • Please note that if you wish to be considered for the University of Cambridge's funding competitions you will need to submit a GRADSAF before the relevant deadline, in addition to making an application to our 4-Year PhD Programme.

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Bioinformatics: Devices of the future

As the medical field progresses, Beulah Pereira talks to Dr. Ragavendra Baliga, Associate Director, Division of Cardiovascular Medicine, Ohio, about devices that will replace traditional treatments
What are bioinformatic devices? Bioinformatics is an application of computer technology, which mainly deals with management of biological information of patients. From gathering, storing, analysing and integrating biological and genetic information, this can then be applied to gene-based drug discovery and development, which is a relatively new concept.

Future Computing: DNA Hard Drives | Nick Goldman

Why do we need them?

  • Today, we still use traditional medical treatments like antibiotics, vaccines and physical surgeries to deal with illnesses and diseases. However, with the medical field progressing at a faster-than-ever pace, new devices and treatment methods may help a great deal. While talking about the idea and the need for bioinformatic-powered devices, Dr. Ragavendra Baliga, Associate Director, Division of Cardiovascular Medicine, Ohio, says,
“Such devices will be both diagnostic and therapeutic giving the patient more control over their health, and that too at their fingertips.” No longer will patients have to line up at hospitals to constantly check for diabetes, blood pressure or even their heart rate. “These devices will allow patients to track important parameters such as blood sugar, heart rate and blood pressure. In fact, companies like Target are offering this facility to their employees,” he adds.

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Bioinformatics research underpins development of precision medicine

In his 2015 State of the Union address, President Barack Obama announced the launch of the Precision Medicine Initiative, a new research effort to revolutionize how we improve health and treat disease.
“Doctors have always recognized that every patient is unique, and doctors have always tried to tailor their treatments as best they can to individuals,” the president said. “You can match a blood transfusion to a blood type — that was an important discovery. What if matching a cancer cure to our genetic code was just as easy, just as standard?”

President Obama Speaks on the Precision Medicine Initiative

  • Cathy Wu, the Unidel Edward G. Jefferson Chair of Bioinformatics and Computational Biology at the University of Delaware, has devoted her career to improving how new scientific data generated by the scientific community is stored, organized, indexed, viewed, and analyzed.
  • She’s especially intrigued by proteins, which are important players in biological processes and may be the key that opens the precision medicine door.
  • Wu recently received two major grants to support this work.
  • The first is a $2.8 million renewal grant from the National Institutes of Health (NIH) to further develop the Protein Ontology (PRO), a virtual reference library for proteins developed by Wu and her colleagues.
  • The NIH PRO grant will allow researchers to capture and accurately represent scientific knowledge for ontology mapping — the process of finding connections between concepts — and semantic integration of gene-disease-drug information.

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Saturday, 3 October 2015

Bioinformatics Algorithms reveal Genomic Inconsistency in STAP Study


“The scientific process requires replicating and extending existing data,” said George Q. Daley, HMS professor of biological chemistry and molecular pharmacology at Boston Children’s and co-senior author on both papers addressing the STAP controversy.

  • Tremendous controversy erupted in early 2014 when two papers published inNature described how a technique called “stimulus-triggered acquisition of pluripotency,” or STAP, could quickly and efficiently turn ordinary cells into pluripotent stem cells, that is, stem cells capable of developing into all the tissues in the body.
  • The simplicity of the approach — subjecting the cells to particular stresses like mild acid exposure — seemed too good to be true. And it was.

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Next generation sequencing Online Workshop


From October 13th to October 23rd, NCBI will present the first iteration of NCBI NOW, a free online experience aimed at those new to next generation sequencing (NGS) analysis. Enrollment in this course is limited to the first 1,000 participants who sign up through the ORAU Portal. Since enrollment is on a first-come, first-served basis, please only sign up for this educational opportunity if you will be able to participate fully.

Learners will watch 6-7 videos (average video duration: 45-60 minutes) online during the first 7 days of the course. These videos will cover the basics of NGS data, preprocessing, quality control and alignment strategies for both DNA-Seq and RNA-Seq, as well as a brief discussion of downstream analysis. Additionally, we will demonstrate how to leverage BLAST tools for NGS analysis.

  • Next, participants will apply a selection of RNA-Seq alignment algorithms over three days (1-2 hours per day), mapping RNA-Seq data to GRCh38 chromosome 20. Finally, participants will compare the results of these mappers for specific genes. Throughout the course, participants will be able to post questions at Biostars; experts from NCBI and elsewhere will be available online to answer questions.
  • Learners will emerge from the course equipped to map their own RNA-Seq or DNA-Seq data to the human genome, understand the options for downstream analysis, and use their understanding of the basic steps of data processing to interact more effectively with bioinformatician collaborators.
  • A note about registration: When registering for an account, you will be prompted for a partition. Please ensure that NCBI is selected, as this will provide access to the proper materials for this workshop. However, if you have already created an account without selecting this option, there is no need to create a second account. Your account has been reassigned to the NCBI partition.

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Thursday, 1 October 2015

International Ph.D. student position @ DCRC


The Danish Cancer Society is looking for a Ph.D. student to join the Cell Death and Metabolism (CDM) unit in the Danish Cancer Society Research Center (DCRC).

We offer a Ph.D. student position in an international environment with a strong record in generating new discoveries within the field of cancer biology. You will work under the supervision of senior scientist Kenji Maeda, on the research topics at the interface of cancer biology and lipid metabolism. You will participate in an international project taking place at the CDM unit, lead by Prof. Professor Marja Jäättelä, and in close collaboration with the European Molecular Biology Laboratory in Heidelberg (EMBL-Heidelberg), Germany. The student will be enrolled in an appropriate program under the Graduate School of Health and Medical Sciences, University of Copenhagen.

Work tasks

  • To systematically investigate the regulations of lipid metabolism in human cancer cells and their pathological consequences
  • To develop a novel, generic strategy to quantitatively measure lipid species at the sub-cellular levels using mass spectrometry

Education required

  • Master degree in biomedicine, biology, biochemistry, human biology, or relevant discipline


  • Experience with molecular and cellular biology-based techniques and in cancer biology, lipid metabolism, or membranes is an advantage
  • Fluent communication in English
  • High level of motivation and clear career goals
  • Ability to work in a team

Additional information

  • More information can be obtained directly from senior scientist Kenji Maeda, e-mail

Work place

  • The laboratories are located in a pleasant, smoke-free environment recently completely renovated and with modern interior equipped with state-of-the-art technology. We have plenty of room for social interactions and activities, and have several benefits for the personnel, such as health conscious canteen and a daily selection of free fruit, well-functioning sports activities, and an inspiring art society. The everyday working language is English.
    We offer a position with 37 hours a week with lunch break included. Salary will be provided according to the current agreements between the Danish Cancer Society and the relevant trade union.

Application and closing date for applications

Deadline for application is October 20, 2015. The selected candidates will be invited for a personal interview. The position is available from 1 January 2016.

  • The application should be written in English including a letter of motivation, CV, and at least one reference from previous working place.
  • The application labelled ‘Cell Death and Metabolism’ should be submitted through the electronic form at the Danish Cancer Society’s homepage:
  1. Go to the homepage:
  2. Click the link for the appropriate position at the Danish Cancer Society Research Center
  3. Click the link: Apply for position.

Then enter your contact information and attachments. Please note that attached documents must be either Word (doc/docx) or Adobe (pdf).

Apply for position


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Wednesday, 30 September 2015

Early stage researcher/PhD student positions


Early stage researcher/PhD student positions available in the European Training Network Brain Barriers Training – BtRAIN

The European Training Network Brain Barriers Training – BtRAIN invites applications for 12 positions for Early Stage Researchers (ESR)/PhD students.

The following BtRAIN projects are available

Project 1: In vitro models of the blood brain-barrier (BBB) and applications in pharmacological and toxicological screenings
Project 2: In vitro models of the blood-brain and blood- cerebrospinal fluid (CSF) barriers using an integrated microfluidic device
Project 3: Comparison of mouse and zebrafish cerebral endothelial cell transcriptomes and functional investigation of conserved pathways governing brain angiogenesis and BBB formation
Project 4: Integrative meta-analysis of public and novel vertebrate BBB omics data and establishment of the BBBhub platform
Project 5: Role of the orphan G-protein-coupled receptor Gpr126 signalling in the development of the blood-brain barrier
Project 6: Age-induced changes in gene and microRNA expression at the mouse blood-brain barrier
Project 7: Blood-brain barrier derived non-conding RNAs as functional biomarkers for the aging BBB versus the BBB in Alzheimer’s Disease
Project 8: Brain endothelial mechanisms directing the cellular pathway of T cell migration across the BBB
Project 9: Contribution of the BBB in amyloid-b biology in Alzheimer’s disease
Project 10: Exploring CD4+ T cells as carriers to mediate transport of drugs across the blood-brain barrier
Project 11: Role of different receptors in promoting pathogen and leukocyte migration across the brain cerebrospinal fluid barrier (BCSFB) in meningitis
Project 12: Molecular control of the human brain barriers in health and neuroinflammation

Eligibility Criteria

BtRAIN is a research fellowship programme for ‚Early Stage Researchers (ESR)’. If you intend to do your PhD and you have less than 4 years research experience, you might apply for a fellowship. Applicants will have to meet the Marie Sklodowska-Curie eligibility criteria ( p40-41).

Pre-requisites for the candidates

  • University Master Degree in any discipline in the Life Sciences, Medical Sciences, or in Biomedical Engineering, Chemistry or Bioinformatics, depending on the project applied for
  • Mobility during the program to fulfill the requirements for secondments
  • Ability to work in an international team and to meet deadlines
  • Ability to analyze, integrate and communicate large amounts of data
  • Ability to multi-task

Submit your application now:

Read More/Apply Online

15 international PhD fellowships in AFib-TrainNet

15 international PhD fellowships in Atrial Fibrillation – AFib-TrainNet consortium (EU Marie Curie ITN actions) : Copenhagen, Denmark
The AFib-TrainNet ETN ( is currently advertising 15 PhD fellowships at 7 partner institutions all over Europe. This doctoral training network consists of top research institutions and highly specialized biotech companies with the complementary competences needed to produce both outstanding research results and an excellent training environment for early stage researchers (ESRs). In the Network, all 15 ESRs from the partner institutions will enroll simultaneously (March 2016), and together benefit from an extensive web of training events. AFib-TrainNet also features a number of longer secondment periods to additional partners within the Network.

Introduction to the University of Copenhagen

  • This coordinated research exchange reflects our focus on top-level interdisciplinary science, and ensures that ESRs have the opportunity to forge strong relationships cross-network and reap the benefits of the world-class, highly interdisciplinary team of collaborating partners.

The following positions are now open:

Objectives of AFib-TrainNet

The AFib-TrainNet project are working towards four objectives. Our objectives are to:
  • Train the next generation of excellent researchers for interdisciplinary careers in basic, applied and translational cardiovascular and pharmacological research.
  • Develop cutting-edge technologies and methods for AF research by bringing together eminent experts from both industry and academia, including biologists, physiologists, pharmacologists, computational scientist and clinicians.
  • Pursue key biological targets, all the way from early stage to pre-clinical investigation.
  • Build a high-impact structure ensuring multi-level dissemination and exploitation of all results.
If interested, please follow the link to the AFib-TrainNet homepage for further information about individual ESRprojects, for contact information, and to apply.

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