Posts tagged: Genome Biology

How can ‘conservation genomics’ help the recovery of the most endangered species?

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Crested Ibis 6. Credit Ningshan branch of State Forestry Administration China

Cheng Cheng is from the School of Life Science & Technology at Xi’an Jiaotong University, China, and Jun Yu is from the Beijing Institute of Genomics, Chinese Academy of Sciences. They are authors of an article published in Genome Biology which has revealed the genomic ‘signatures’ of extinction events in birds. In this post they talk about how these new insights could be used to help conservation efforts of the endangered Crested Ibis in China, and prevent the extinction of other species.

Birds play important roles in ecological balance. They are found everywhere around the globe, with their species numbering nearly twice that of mammals. Unfortunately, the rate of their extinction appears to have increased in the past millennium. …

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A ticking time bomb? Ebola and the neglected tropical diseases

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600px-Ebola_virus_particles

Ripudaman K Bains is the Assistant Editor of Genome Biology, and the in-house editor of the journal’s special issue on the ‘genomics of infectious diseases

In recent months, infectious diseases have been at the forefront of public attention. The deepening Ebola crisis in West Africa has now claimed nearly 6,000 lives, and although the international response is increasing the disease continues to strain already overextended medical infrastructure in affected countries.

It is perhaps surprising that Ebola is officially classed as a ‘neglected tropical disease’. The 2014 outbreak is the worst on record; between 1976 and 2013 there were 26 outbreaks of the virus, almost all of which occurred in sub-Saharan African nations, resulting in a total of 1,716 …

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House fly genome could reveal insights into insecticide resistance

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A global team of researchers, led by Jeffrey Scott at Cornell University, have successfully sequenced the house fly genome, published today in Genome Biology. In this guest post, Professor Scott tells us more about why the research represents a significant scientific advance.

An optimist is a fellow who believes a housefly is looking for a way to get out

George Jean Nathan

 House flies are responsible for a great deal of human misery. They transmit over one hundred human diseases, including antibiotic resistance strains. Fly transmitted trachoma alone causes 6 million cases of childhood blindness each year. We hope that the house fly genome will open new opportunities for controlling this pest.

House fly larvae also live in a virtual sea …

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Reading the new map of breast cancer

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Dr Nick Peel of Cancer Research UK on the classification of breast cancer

Research published today in Genome Biology could improve treatments, and the targeting of treatments, for breast cancer. In this guest post, Cancer Research UK’s Dr Nick Peel describes the history of the findings and what they could mean for future research.

Just over two years ago a landmark study took our knowledge of breast cancer to a new level.

An international team of scientists, led by Professor Carlos Caldas and his team at the Cancer Research UK Cambridge Institute, mapped the genetic landscape of breast cancer in unprecedented detail, redefining it as 10 distinct diseases.

But as with many of these vast genetic explorations, the study revealed as much unexplored terrain as it mapped – exposing the complexity …

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‘Prostate cancers’ not ‘prostate cancer’ – revealing the many faces of ‘one’ disease

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Iain Frame

New research published today in Genome Biology shows that RNA sequencing could lead the way towards more personalized treatments for prostate cancer. In this guest post, Dr Iain Frame, Director of Research at Prostate Cancer UK discusses what this could mean for patients and health services, and what more is needed to provide effective support and treatment for men with prostate cancer.

We are used to hearing and talking about prostate cancer as a single disease.  Albeit a disease with its tigers and pussycats – the tigers being the aggressive cancers that move out of the prostate gland to other parts of the body, and the pussycats being those cancers that may never cause any harm and won’t go …

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On a personal note: cancer genomics and personalized medicine

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Special issue GB cover-page-001

When I was three years old my grandma passed away after a long fight with cancer. I should disclaim quickly: it never affected me greatly, since I was too young to remember anything. I know, though, that that experience was a gruelling one for my mum, who cared for our grandma during the therapy – battle with cancer ain’t pretty in general, and it was even worse then.

It would of course be easy to blame the health system of the communist regime in which we lived at the time but the truth is that the treatment strategy was pretty much the same all over the place: surgery, radiotherapy, chemotherapy. It doesn’t work? Let’s try harsher treatment. And the understanding …

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Microbial monitoring: health forensics for the modern age

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Metadata plot

A new paper published in Genome Biology today uses smartphone tracking and additional observations to piece together a staggering amount of information about the research subjects and their individual microbiomes. In this guest post, Jack A Gilbert, Associate Professor at the University of Chicago and Group Leader at Argonne National Laboratory, delves into this promising new avenue of research and data collection.

At the beginning of September 2013 I weighed about 205lbs (92kg). I decided to do something about my weight, for my health and for the sake of my family and of course I approached this plan as a scientist. For me that meant parameterizing my inputs and outputs so I could control what I was doing to …

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Word of caution: a new method to study RNA-seq biases

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Shaury Nash CC BY-SA

As next generation sequencing methods quickly become ubiquitous tools of genomics, more and more effort is directed to understand what are the limitations of these approaches. These limitations present themselves quite often in the form of coverage biases.

Last year Genome Biology published a study from David Jaffe and colleagues that looked at coverage biases in DNA sequencing. The authors used a suite of computational tools for bias assessment and applied them to a number of commonly used technologies. It turned out that, for instance, PacBio coverage is the least biased; and that high- and low-CG regions and long runs of homopolymers are very prone to coverage biases. They emphasized that the presence of such biases may lead to …

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Genome regulation: it’s the geometry, stupid!

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Transcription factories (from Cope et al.)

The emerging realization that cells modify the three dimensional arrangement of DNA in order to regulate the genome is changing the way that scientists think about how and when genes are expressed. A new study in Genome Biology goes so far as to show that information about the shape of the genome is sufficient on its own to accurately classify cells according to leukemia subtype.

Traditional genomics studies have examined the genome as a linear DNA sequence. According to this viewpoint, each gene is surrounded by adjacent sequence – in particular the region of the genome immediately upstream – that regulates its expression: when the gene is turned off and on, and to what degree.

It has long been known that …

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It’s in your genes: a new method for cancer drug response prediction

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source: flickr;  viZZZual.com (CC BY)

One of the greatest challenges of current medicine is predicting how a patient will respond to a given drug. In an ideal world, where time, money and – most importantly – the patient’s well-being and survival are not an issue, we would simply either keep trying different treatments until hitting the jackpot, or perhaps harvest the patient’s cells and try a range of treatments in vitro. The problem is, of course, that the world is not ideal and such in vitro testing is usually not practical and, in general, especially in the case of many of the most debilitating diseases, patients often don’t have time to waste.

It is then not really surprising that many researchers have been …

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