Posts by Rafal Marszalek

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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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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Methylating much?

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source: flickr, calciostreaming (CC BY)

Our readers might have gotten distracted this month by discussions on whether it is right or wrong for Illumina to limit researchers’ use of their kit, and so we are here to help you regain focus: after a deliberately thematic issue on the RBPome, we have just published an accidentally thematic issue on DNA methylation.

Useful tools

This month Genome Biology publishes three tools that many working on DNA methylation should find quite handy.

Mark Robinson (of edgeR, which he published together with another of this issue’s authors, Gordon Smyth) and company present a new method, BayMeth, for the effective quantification of data generated with DNA-methylation-capture-seq techniques (MBD-seq, MeDIP-seq and so on). So if you …

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Uniform diversity: a genome-wide study of PRC1 ortholog localization

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Poly-combs! /source: Sean McMenemy (CC BY)

Polycomb-group proteins are a well-characterized family of proteins involved in chromatin remodeling. In mammals, Polycomb-group proteins form two multiprotein complexes: Polycomb repressive complex 2 (PRC2), which represses gene expression, and PRC1.

PRC1, unlike its highly conserved sister, is a masterpiece of variety. It comprises the subunits Polycomb (Pc), Posterior sex combs (Psc), Polyhomeotic (Ph) and Sex combs extra (Sce) – but in humans there are five orthologs of Pc, six of Psc, three of Ph and two of Sce, which can, in theory, give rise to up to 180 different versions of PRC1. And while we don’t know for sure how many versions of PRC1 are to be found in human cells, one thing is clear: there doesn’t …

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Cancer progression Genome Biology special issue: call for papers

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cancer-prog-genome-biology_v6

Genome Biology would like to announce that we are now inviting Research, Method or Software manuscript submissions for publication in a special issue on cancer progression and heterogeneity, which is planned for late summer 2014.

Recent advances, such as single-cell sequencing technologies, are allowing us to study cancer genomics at a depth that was not previously possible. Now, Genome Biology wants to highlight the importance of this field by publishing a special issue with an emphasis on cancer progression and heterogeneity. We will consider Research, Method and Software manuscripts describing insights into, or developing methods for studying, all aspects of the genomics of cancer progression, including the clonal evolution of cancer, cancer heterogeneity, metastasis, single-cell …

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Buzz-phrase of the month: ‘insect genomes’ in the latest issue of Genome Biology

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source: Sajjad Fazel (CC BY-SA 3.0)

About one million insect species have been identified to date; however, many people believe that with this number we’re merely scratching the surface and there may exist five times as many species of this class in the world. Last year, Genome Biology started filling the gaps in our knowledge on these animals with the publication of only the second ever beetle genome.

In our latest issue, Genome Biology adds two more pieces to this buzzing puzzle: Dr Kocher and colleagues report a draft genome of the halictid bee Lasioglossum albipes, and Dr Xiao and colleagues present a genome of the fig wasp Ceratosolen solmsi. Both these insects exhibit very different but equally fascinating lifestyles.

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Fred Sanger: I think you should try harder

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Frederick_Sanger2

Genome Biology was sad to learn of Frederick Sanger’s death on Tuesday, November 19th. Although Sanger retired from scientific research 30 years ago, long before the journal Genome Biology ever started, it is safe to say that without his work we wouldn’t even be here.

The journal was launched in 2001, the same year that the completion of sequencing of the human genome was reported. The sequencing was done entirely using the method Sanger had devised for determining genetic sequences. Although his was not the first technique for reading DNA sequence, it was the first really practical one and, like many methods that revolutionize fields, it was an elegant and conceptually simple idea. Sanger had, in …

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Open-Phylo: give science back to the people

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open-phylo-screen

It seems that scientific research in the last two hundred years or so has made a full conceptual circle. In the good old days of the nineteenth century, any Englishman with a vaguely middle-class background, a source of modest income and an insatiable curiosity could treat research as an eccentric pastime. Whether that meant sea voyages and bird watching or hiking trips and rock collecting, what mattered first of all was the pursuit of the understanding of how the world works.

But times changed, and the world changed, and research moved from gentleman’s clubs to academic institutions. And although it gained more structure, and although, as hobbyists turned into professionals, scientific dillydallying turned into a rigorous process, we …

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Fear the bias no more: a novel technique for accurate microRNA quantification

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Inaccurate miRNA quantification has its source in the biased library construction/ source: Paul Lowry (CC BY)

It is estimated that in a single mammalian cell the median copy number of an mRNA is 17 molecules, with the dynamic range spread over four orders of magnitude. At the same time, an average microRNA can recognize as many as 400 target sites, and has to be able to do so equally effectively for both those mRNA species that have only a few copies and those that have a few thousand copies in the cell. Our understanding of this highly dynamic regulation network therefore depends to a high degree on our ability to accurately quantify microRNA.

Of the three major approaches to RNA quantification, microarrays and RT-PCR suffer from the same ailment: they are …

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Genome Biology’s July issue is brought to you by the letters R, N and A

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source: wiki; Bruce1ee; CC BY-SA 2.0

Following our spectacular special issue on plant genomics (which you can re-live here), July brought another set of amazing articles with a broad, if unintentional, underlying RNA-esque theme.

All tissues, all ages

We kicked off with a study from Alvis Brazma and colleagues, who analyze gene expression across 21 different human tissues and cell lines, finding that the majority of genes have only one dominant transcript. It seems that news about the death of the ‘one gene = one protein’ paradigm was greatly exaggerated.

The topic of tissue-specific expression returned in work from Nadav Ahituv and Katherine Pollard’s labs, in which the authors perform a smart in vivo screen of all 4,096 unique …

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