Posts tagged: Genome Biology

John Rinn and Jernej Ule: Guest Editors for Genome Biology RBPome issue

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Genome Biology is very pleased to announce the Guest Editors of our special issue on the RBPome as John Rinn and Jernej Ule. The issue will be published in late 2013.

RNA binding proteins and their recognition elements within the transcriptome
The issue will focus on RNA binding proteins (RBPs), and the RNA molecules and motifs to which they bind: it is this RNA landscape, sculpted by RBPs, that we believe to be a particularly exciting and fast-moving area of research at the present time.

Or, as John puts it: "Almost all RNA genes function through protein interactions - with the ongoing explosion of RNA genes …

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Complex consensus: PRDM9 binding to DNA is unusually complicated

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repaired chromosome

Taking into account the importance of the role that genetic recombination plays in evolution, adaptation, survival, and – perhaps most importantly – sex, we know surprisingly little about the molecular foundations of this phenomenon. What we do know is that genetic recombination is not a completely random process; that it follows a pattern. Some chromosomal regions are more, and some less, likely to be affected by double-stranded breaks – and the recombination events that follow. Areas with a high frequency of recombination have been appropriately dubbed ‘recombination hotspots’.

Now, recombination hotspots are a bit of an enigma themselves: for a long time no one could put their finger on how these hotspots are defined – or chosen. But, as it …

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Diamonds in the rough: DNA60 in Genome Biology

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dna xray small

One of the most wonderful things about science, to my mind, is the way its fundamental principles are simultaneously both universal and personal. Quantum physics helps to explain the nature of grandiose concepts such as time and space, but it also applies to the insignificant particles that make up my own cells. Equally, within these very cells, at any moment, biological processes newly reported in the literature are taking place, as are those that have yet to be discovered.

Life's secret
For this reason, when I look at one of the beautiful X-ray diffraction photos taken by Rosalind Franklin and her PhD student Ray Gosling in the early 1950s, from painstaking work performed on calf thymus samples in gloomy …

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Genome Biology at Non-coding RNA, epigenetics and transgenerational inheritance 2013

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Genome Biology

This year's Abcam conference on 'non-coding RNAs, epigenetics and transgenerational inheritance' had a distinct Lamarckian flavor with conference Chair and 2013 Hooke medal recipient, Eric Miska, recommending Arthur Koestler's 'The case of the midwife toad' as extracurricular reading. In addition to his literary recommendations Miska discussed his recently published observations on the ability of piRNA phenotypes to be inherited through generations in C. elegans. The nematode and RNAi theme was continued in Scott Kennedy's talk, which focused on his recently published work on identifying genes required for RNAi inheritance in C. elegans. He identified such genes through screening for mutants defective in transmitting RNAi phenotypes to the next generation, but which are still able …

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The Genome Biology special DNA60 Bioinformatics Challenge is nearly upon us: starts Monday!

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Stand by for an important update on Genome Biology's highly anticipated, ultra-tricky, ultra-cool, *supreme* DNA60 Bioinformatics Challenge with a truly amazing prize…

Recently, we excited informatics enthusiasts with the prospect of a special Genome Biology Bioinformatics Challenge in honor of DNA60, but we were lamentably low on the detail. Here, we are putting that right.

So what is this Challenge all about then?
DNA60 celebrates the sixtieth anniversary of the publication of Watson and Crick's Double Helix, and Genome Biology will be marking the occasion, April 25th, with some special content. But we also wanted to have some fun, and to give away some prizes, so we decided to …

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Camus enters the clinic: Genome Biology at Genomic Disorders 2013

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Genome Biology

It is not unusual per se for Nobel laureates to be quoted at genomics conferences, but it is perhaps a little out of the ordinary when the Nobel Prize in question is for Literature. But, then again, the Wellcome Trust's 'Genomic Disorders 2013: From 60 years of DNA to human genomes in the clinic' was not your run-of-the-mill conference; instead, a mesh of current research and historical (and futuristic) perspective paid tribute to the 60th anniversary of Watson and Crick's discovery of the double helix.

So it was not entirely out of keeping with expectations when philosopher (and former candidate for Slovene of the year) Renata Salecl stepped onto the podium and asked:

'Should I kill myself, or have

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Cowabunga, dude!: the hidden secrets of the western painted turtle genome

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wiki; CC BY 2.0

There is something amazingly captivating about turtles: those slow, long-living, hard-shelled creatures, which look very much like how you’d expect a miniature version of some dinosaur to look. They have inspired artists for many years, and continue to do so, from the Mock Turtle in Lewis Caroll’s Alice’s Adventures in Wonderland, through the impressive, world-carrying Great A’Tuin in Terry Pratchett novels, to the symbols of late 20th century pop-culture that are the Teenage Mutant Ninja Turtles. Turtles are enigmatic and elegant, reason enough for their study; with many turtle species on the brink of extinction, however, the need to capture the full scope of their biology becomes more urgent. It is perhaps surprising, therefore, that turtles …

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Beetlemania

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Credit: Ward Strong, B.C. Ministry of Forests, Lands, and Natural Resource Operations.

JBS Haldane famously remarked that the Creator appears to be inordinately fond of beetles – with over 400,000 species described, they make up over a quarter of all known animal species. This enthusiasm has not been shared by genomicists. Only a single beetle genome has been completed, that of the red flour beetle, Tribolium castaneum. Now, a new publication in Genome Biology DOUBLES our knowledge of beetle genomes, by describing the sequencing and assembly of the genome of the mountain pine beetle, Dendroctonus ponderosae.

D. ponderosae is a species of bark beetle native to North America. The beetles lay eggs under the bark of various species of pine trees and then release pheromones to attract more beetles. When the eggs …

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A special bioinformatics challenge for DNA Day – open to all

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That's one small step for a man, a giant leap for mankind – a quote infamous for two reasons: the first words uttered by a man on the moon, and the answer to the feared 'Bioinformatics Challenge' at the most recent incarnation of Beyond The Genome, a conference run annually by Genome Biology and our sister journal Genome Medicine.

The challenge, run each year on the conference's Informatics day, involves the deciphering of a hidden code within a package of sequence data, using all the computational biology skills that the participants can muster. It's a race against the clock, and the winner is awarded with what we describe in all modesty as a truly awesome prize.

A special

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Chicken or the egg: comprehensive annotation of the chicken W sex chromosome

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wiki commons; M.Karim (GNU FDL)

Looking at the problem of sex determination from our anthropocentric perspective, it is easy to forget that the world doesn’t revolve around the Y chromosome. Some animals determine their sex simply by changing the number of X chromosomes (BFF of many Genome Biology readers, C. elegans, belongs to this group). For others, like crocodiles and some turtles, the sex will be determined by the temperature at which the egg incubates. The platypus has 10 sex chromosomes, but, surprisingly, seems to lack the sex-determining SRY gene. And then there is the ZW sex chromosome system in birds, in which the sex of the offspring depends on the ovum and not the sperm.

This is not the only difference between us and …

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