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Showing posts from 2017

PhD studentship in my group: Detecting novel cancer subtypes in The Cancer Genome Atlas datasets using Bayesian...

PhD studentship in my group: Detecting novel cancer subtypes in The Cancer Genome Atlas datasets using Bayesian clustering methods. Application deadline 31/01/18. Start date Oct 2018. https://goo.gl/uMnFAH
https://goo.gl/uMnFAH

Day 30. The final outing for the beast. http://mobro.co/dbrewer


Day 30. The final outing for the beast. http://mobro.co/dbrewer

Day 16. The beast is getting thick. Excuse the crazy hair. Please consider donating. http://mobro.co/dbrewer


Day 16. The beast is getting thick. Excuse the crazy hair. Please consider donating. http://mobro.co/dbrewer

It's November, so it's moustache growing time again!


It's November, so it's moustache growing time again!

http://mobro.co/dbrewer

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

I've just noticed that the final version of a manuscript based on work by one of my ex-PhD students while under my supervision has finally been published. This is an interesting look at the mechanisms of gene loss (and gain) in prostate cancers. The main mechanism in cancer is a two-hit method where one allele is knocked out by one mutation (substitution, indel, breakpoint, or copy number deletion) and the other allele by a different mutation. In prostate cancer this work hints that this might not be the case for the majority of drivers.

This one was a lot of work but we got there in the end.
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007001

Garmin connect final lets you import gpx from other sources as courses.

Garmin connect final lets you import gpx from other sources as courses. Whoop. That saves the faff of adding time stamps, importing as an activity, converting to a course, then deleting the activity.

Along with weighting routes according to how popular they are like Strava does, this is a real step forward.
http://connect.garmin.com

I've got two PhD positions available. The deadline for applications is midnight!

I've got two PhD positions available. The deadline for applications is midnight!

Details here:
https://goo.gl/2IvDhU
https://goo.gl/NRXn6K
https://goo.gl/NRXn6K

Biomarker Data Analysis: Development of a Test for Prostate Cancer : PhD Studentship @ UEA, Norwich

Biomarker Data Analysis: Development of a Test for Prostate Cancer : PhD Studentship @ UEA, Norwich

Prostate cancer (PCa) is extremely common and has been detected in 30% of 40 year-old men, rising to 65% in 70 year olds. However, only a small proportion of these cancers will become clinically apparent and only ~20% of these will progress and kill the patient. Deciding which men to treat and which not is a major problem for patients and the NHS. Our research is designed to develop new clinical tests to aid in these decisions.

Due to the interconnected plumbing of the human urinary system, prostate biomarkers can be harvested from urine samples. We have just completed a 3-year Movember funded study run from UEA involving 12 collaborating teams in 7 different countries. This study looked at urine as a source of biomarkers for prostate cancer diagnosis and prognosis examining: Microvesicular-RNA expression, DNAmethylation, Proteins, and Mass Spectrometry, generating ~150,000 data points. Initial analysis has revealed PCa biomarkers that are over-expressed in aggressive disease. The PhD student will fully analyse this unique data to reveal the optimal combination of markers for diagnosis, prognosis, and response to therapy. The data readout will be developed into a clinically implementable test to aid patient therapy.

This is a bioinformatics/data analysis based PhD. During the PhD you will gain knowledge on how to deal with big data, statistical analyses, machine learning and model building. You will be part of the Cancer Genetics team at the Norwich Medical School, which is an interdisciplinary team comprising a mixture of bioinformaticians and lab-based scientists. We have a broad interest in translational cancer based molecular studies with a particular focus on prostate cancer. Research includes urine based biomarker studies, whole genome sequencing studies, subtype detection studies and bacteria in cancer studies.

https://goo.gl/2IvDhU

Closing Date: 2nd June 2017
Starting Date: July 2017
https://goo.gl/2IvDhU

Hunting for Human Infectious Agents in Cancer using data from Genomics England’s 100,000 genome project : PhD...

Hunting for Human Infectious Agents in Cancer using data from Genomics England’s 100,000 genome project : PhD Studentship @ UEA, Norwich

Infectious agents, such as bacteria and viruses, are involved in the development of a variety of human cancers such as cervical, liver, stomach and bladder cancer. We hypothesise that other infectious agents are directly linked to cancer development, but as yet remain unidentified. We have developed an analytic pipeline (SEPATH) that identifies infectious agents in whole genome sequencing data. This pipeline is already in place, working and currently being improved. Through a competitive process we have been awarded access to apply SEPATH to the whole genome sequence data of 40,000 cancer genomes from Genomics England’s 100,000 Genome project. Genomics England’s 100,000 Genome project is a large-scale initiative, backed by the UK government, to sequence samples from 100,000 patients including 40,000 from a range of different cancer types. The aim of this PhD studentship is to run SEPATH on this data and search for new infectious agents associated with cancer in a range of different types. In addition links between cancer aggression and the structure of the microbiome will be examined as well as potentially identifying new bacteria linked to cancer.

This is a bioinformatics/data analysis based PhD. During the PhD you will gain knowledge on how to deal with big data, statistical analyses, machine learning and model building. You will be part of the Cancer Genetics team at the Norwich Medical School, which is an interdisciplinary team comprising a mixture of bioinformaticians and lab-based scientists. We have a broad interest in translational cancer based molecular studies with a particular focus on prostate cancer. Research includes urine based biomarker studies, whole genome sequencing studies, subtype detection studies and bacteria in cancer studies.

https://goo.gl/NRXn6K

Closing Date: 2nd June 2017
Starting Date: October 2017
https://goo.gl/NRXn6K

Broccoli’s cancer prevention mechanism found to work on “non-coding RNA” to prevent formation of tumors –...


http://www.naturalnews.com/2017-03-27-broccoli-cancer-prevention-mechanism-found-to-work-on-non-coding-rna-to-prevent-formation-of-tumors.html

PhD opportunity in cancer pathogen bioinformatics.

PhD opportunity in cancer pathogen bioinformatics. Closing date Thursday 24/03/17. https://www.uea.ac.uk/study/-/hunting-for-human-infectious-agents-in-cancer-using-data-from-genomics-england-s-100-000-genome-project
https://www.uea.ac.uk/study/-/hunting-for-human-infectious-agents-in-cancer-using-data-from-genomics-england-s-100-000-genome-project

In September 2017 I will be taking on a massive ride, cycling from Land's end to John O'Groats in nine days in aid...

In September 2017 I will be taking on a massive ride, cycling from Land's end to John O'Groats in nine days in aid of Prostate Cancer UK and the WizzyBug Loan scheme. Please consider sponsoring me at the link below. Prostate Cancer UK Designability
https://goo.gl/TSmZnJ

#BeBoldForChange


#BeBoldForChange

The LPD paper, the research that got some publicity last week, is finally up at the publishers website.

The LPD paper, the research that got some publicity last week, is finally up at the publishers website. http://dx.doi.org/10.1016/j.euf.2017.01.016
http://dx.doi.org/10.1016/j.euf.2017.01.016

Hunting for Human Infectious Agents in Cancer using data from Genomics England's 100,000 genome project : PhD...

Hunting for Human Infectious Agents in Cancer using data from Genomics England's 100,000 genome project : PhD Studentship @ UEA, Norwich

This is an exciting PhD opportunity in my group. Deadline 24/03/17.

https://www.uea.ac.uk/study/-/hunting-for-human-infectious-agents-in-cancer-using-data-from-genomics-england-s-100-000-genome-project
https://www.uea.ac.uk/study/-/hunting-for-human-infectious-agents-in-cancer-using-data-from-genomics-england-s-100-000-genome-project

The Daily Express has got in the act.

The Daily Express has got in the act.
http://shr.gs/gG5WlId

This is a brilliant interactive visual website for explaining basic statistics.

This is a brilliant interactive visual website for explaining basic statistics.

http://students.brown.edu/seeing-theory/
http://students.brown.edu/seeing-theory/

Finally, local press coverage of the research.

Finally, local press coverage of the research.
http://www.edp24.co.uk/news/health/scientists_praised_by_champion_jockey_after_developing_test_to_stop_cancer_patients_get_unnecessary_treatment_which_can_cause_impotence_1_4910722?utm_source=Google_Plus&utm_medium=Social_Icon&utm_campaign=in_article_social_icons

New test distinguishes 'tigers' from 'pussycats' in prostate cancer


https://medicalxpress.com/news/2017-02-distinguishes-tigers-pussycats-prostate-cancer.html

The Times coverage on our research published today.

The Times coverage on our research published today.
http://www.thetimes.co.uk/article/prostate-test-picks-out-the-worst-cancers-20fdnlbbr

Coverage in The Sun on our research due to be published today.

Coverage in The Sun on our research due to be published today.
https://www.thesun.co.uk/living/2980640/breakthrough-test-tells-medics-if-prostate-cancer-is-tiger-or-pussycat-tumour-and-if-itll-turn-deadly/

A short piece on the ITV News website on our research looking at a new subtype of prostate cancer.

A short piece on the ITV News website on our research looking at a new subtype of prostate cancer.
http://www.itv.com/news/2017-03-01/a-new-test-could-save-prostate-cancer-sufferers-unnecessary-treatment/

Coverage in The Mirror on our research looking at a new subtype of prostate cancer.

Coverage in The Mirror on our research looking at a new subtype of prostate cancer.
http://www.mirror.co.uk/science/thousands-prostate-cancer-sufferers-could-9938339#ICID=sharebar_googleplus

This is the UEA press release on our research looking into a new classification for prostate cancer.

This is the UEA press release on our research looking into a new classification for prostate cancer.
https://www.uea.ac.uk/about/-/new-test-distinguishes-prostate-cancer-tigers-from-pussycats-

Some important results from my group is due to be published today.

Some important results from my group is due to be published today. We think we might have discovered a new subtype of prostate cancer. Here's a video about it. More stuff to follow.
https://www.youtube.com/watch?v=5MuJs6pkXDA&feature=player_embedded

Great bit of technology for extracting tables from PDFs.

Great bit of technology for extracting tables from PDFs.
http://tabula.technology/