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Acknowledgements (Additional) (Charles Chiu, 02 October 2015)

This study is made possible in part by the generous support of the American people through the United States Agency for International Development (USAID). The contents are the responsibility of the authors and do not necessarily reflect the views of USAID or the United States Government. read full comment

Comment on: Greninger et al. Genome Medicine, 7:99

Translational bioinformatics in the cloud (sara sota, 20 August 2015)

 There has been a little talk about cloud computing on Bioinformatics at the BackupMag. We highlight some fundamental issues of translational bioinformatics and the potential use of cloud computing in NGS data processing for the Translational bioinformatics.       read full comment

Comment on: Dudley et al. Genome Medicine, 2:51

Correction: Corresponding author email address (Ross Hopkins, 01 July 2015)

Professor Fredrik Wikund's email address is The email address displayed in the article was inserted in error during the publication process.   read full comment

Comment on: Wiklund Genome Medicine, 2:45

Confusion between false positives and read throughs in Table 2 (Matt Zhaohui, 10 June 2015)

Actually, the column "False Positives" from Table 2 shows which tools report read throughs (i.e. SOAPfuse, deFuse, FusionCatcher) and which tools do NOT report read throughs (i.e. JAFFA, TopHat-Fusion). Basically, in Table 2, the read throughs are counted as false positives even that in Table 1 they are not. Therefore Table 2 does not show any discovery rate for any of the tools presented as it is claimed in the article (quote: "JAFFA also demonstrated excellent sensitivity and a very low false discovery rate on 250 bp reads simulating a MiSeq dataset (Table 2"). The datasets used in Table 2 contains reads simulated by BEERS tool which the authors acknowlege in the article that it generates read-throughs which are actually fusion... read full comment

Comment on: Davidson et al. Genome Medicine, 7:43

Appreciation of special susceptibility through metabolomics (Heikki Savolainen, 10 July 2012)

Dear... read full comment

Comment on: Robinette et al. Genome Medicine, 4:30

Thumbs up for the authors, but you overlooked ... (Kristina Spiller, 04 August 2011)

...there is actually already one such data sharing model, known as GISAID ( It successfully addresses all the principles & procedures suggested here. Based on a collaboration of bonafide researchers from various disciplines and coordinated/backed by the vision of an influential media executive, the most significant influenza sharing platform proves fittingly the viability of all 7 principles prescribed by the authors. Now hosted by the federal office for agriculture & food in Germany it has emerged into a public-private partnership supported by international cooperation. We need more of these examples to move science forward. The days of public-domain databases as we know them, and their failure to provide transparency of access and usage and accountability are... read full comment

Comment on: Knoppers et al. Genome Medicine, 3:46

Complementary publication (cloud computing for comparative genomics) (Dennis Wall, 02 September 2010)

Nice paper! Have you seen this read full comment

Comment on: Dudley et al. Genome Medicine, 2:51

sample sizes (James Timmons, 19 April 2010)

I would like to thank Dr Bossola for their interesting comments. When studies using the same approach we did find strong evidence that ICU patients - patients with severe imobillity and inflammation - that the pathways mentioned by Dr Bossola were indeed activated as described. In contrast, using the same technology we did not find such pathways activated in this type of cancer related cachexia (Frederikson et al PLos One 2008). Thus we know the technology is... read full comment

Comment on: Stephens et al. Genome Medicine, 2:1

Role of ubiquitin-proteasome in cancer cachexia (Maurizio Bossola, 17 March 2010)

we read with much interest the article by Sthepens et al recently published in Genome Medicine (1) that shows, among other results, that the mRNA expression of the E3 ligases MURF1 and MAFbx, examined by qRT-PCR, was not related with weight loss in the skeletal muscle of patients with cancer of the upper gastrointestinal tract. According to the authors, this result would suggest that the ubiquitin E3 ligases do not play the same role in human cancer cachexia as that previously demonstrated in animal and cell studies and that any support to the findings of previous human studies (2-4) could be found. Indeed, few studies have investigated the ubiquitin-proteasome pathway in the skeletal muscle of cancer patients (2-5), but none of these have assessed the expression of E3 ligases. In our... read full comment

Comment on: Stephens et al. Genome Medicine, 2:1

Response to Dr. Tarynn M. Witten's comment (Peter Csermely, 27 January 2010)

We would like to thank for the comment of Dr. Witten to our paper. First, we would like to apologize for Dr. Witten for not citing any of the listed contributions. Indeed, the 1984 Mech. Aging Dev. paper represents one of the first uses of network theory in aging, which deserves citation, as we will do in our later papers. This work is extended by its sequel, the 1985 Mech. Aging Dev. paper. In 1984 the complex network structure of the cell was obviously unknown, and therefore, the centrality of the critical elements defined by Witten is rather a general central position of a systems theory-type network than the refined versions of betweenness and other types of centralities of the interactome or metabolic type networks attracting the focus of research today. Obviously at that time Witten┬┐s... read full comment

Comment on: Simkó et al. Genome Medicine, 1:90

sodium control problems common to bipolar disorder and schizophrenia (Gregory Marlow, 08 December 2009)

One should considered that the genes responsible for the sodium level control system may be the ones responsible for bipolar disorder and schizophrenia. Both these illness have a ten fold higher frequency of hospital admissions with hyponatremia compared to hyponatremia in all other admissions. I believe that most hyponatremia in psychiatric patients is incorrectly attributed to polydipsia. Instead it should be looked at as a possible underlying cause. Patients with hyponatremia can display many mental symptoms common to bipolar disorder and schizophrenia. In addition there is a mechanism that links sodium to the circadian rhythm. In the evening the body lowers blood sodium levels in preparation for sleep. If the individual already has a low level due to some hormone problem, the evening... read full comment

Comment on: Carroll et al. Genome Medicine, 1:102

History of Research in Aging Networks (Tarynn Witten, 04 December 2009)

While an interesting paper, this paper ignores the significant previous literature in the field of aging networks, reliability theoretic applications to aging networks and purports to be the first to generate the ideas of using hubs and other network concepts to understand the behavior of aging processes. Unfortunately, the ignored literature significantly overlaps the results in this paper.... read full comment

Comment on: Simkó et al. Genome Medicine, 1:90