Thank you Peter
I think you are right that the discussion at Seqanswer forum is more
appropriate http://seqanswers.com/forums/showthread.php?t=32156 . However,
there was no fruitful outcome out there and so I thought of taking another
opinion in this bioinformatics mailing forum .
Abhishek
On Sat, Aug 2, 2014 at 4:16 PM, Peter Cock <[email protected]>
wrote:
> I do not think this is not an appropriate use of the samtools mailing list.
>
> It might be better to continue any discussion on this thread on SEQanswers:
>
> http://seqanswers.com/forums/showthread.php?t=32156
>
> Peter
>
> On Sat, Aug 2, 2014 at 7:24 AM, Abhishek Narain Singh
> <[email protected]> wrote:
> > Dear Bioinformaticians
> >
> > These days it has become an increasingly common issue where all the
> ideas,
> > analysis and results are reported by bioinformatician, whereas his name
> is
> > missing from the paper submitted. This has happened with me in the
> 'Genome
> > of The Netherlands' GoNL project where after having worked in the project
> > for 7 months with providing various kinds of inputs and results, my name
> was
> > not included in any conference or journal publications! The list of
> authors
> > attached with this mail clearly mentions me in several of the minutes of
> the
> > meetings (which can be provided if and when needed) Here are the
> publication
> > details:
> >
> > Laurent C Francioli, Androniki Menelaou, Sara L Pulit, Freerk van Dijk,
> Pier
> > Francesco Palamara, Clara C Elbers, Pieter B T Neerincx, Kai Ye, Victor
> > Guryev, Wigard P Kloosterman,et al. Whole-genome sequence variation,
> > population structure and demographic history of the Dutch population. The
> > Genome of the Netherlands Consortium. Nat Genet. 2014 Jun 29. doi:
> > 10.1038/ng.3021.
> >
> > Kiezun A, Pulit SL, Francioli LC, van Dijk F, Swertz M, al., Genome of
> the
> > Netherlands Consortium, (2013) Deleterious Alleles in the Human Genome
> Are
> > on Average Younger Than Neutral Alleles of the Same Frequency. PLoS Genet
> > 9(2): e1003301. doi:10.1371/journal.pgen.1003301 (as member of GoNL
> analysis
> > team) [pdf] (As member of the GoNL data analysis team)
> >
> > K.Ye, V.Guryev, W.Kloosterman, L.Francioli, J.Y.Hehir-Kwa, E.Lameijer,
> > A.Abdellaoui, J. de Ligt, V. Koval, N. Amin, F. van Dijk, L.C. Karssen,
> H.
> > Mei, Genome of the Netherlands consortium, Analysis of structural
> variation
> > in the Genome of the Netherlands (GoNL) project, ASHG, San Francisco, Nov
> > 2012 (As member of the GoNL data analysis team)
> >
> > V. Guryev, W. Kloosterman, L. Francioli, J. Y. Hehir-Kwa, E. Lameijer, A.
> > Abdellaoui, J. de Ligt, V. Koval, N. Amin, F. van Dijk, L. C. Karssen, H.
> > Mei, K. Ye, Genome of the Netherlands consortium, Analysis of structural
> > variation in the Genome of the Netherlands (GoNL) project, ESHG,
> Nurnberg,
> > June 2012 (As member of the GoNL data analysis team)
> >
> > Laurent C. francioli, Kiran V. Garimella, Mark A. dePristo, Paul I.W. de
> > Bakker on behalf of Genome of the Netherlands Project, Trio-aware SNP
> > discovery and genotyping in low coverage whole genome sequencing,
> Genetica
> > Retraite, 15-16 March 2012, Maastricht, The Netherlands (As member of the
> > GoNL data analysis team)
> >
> > The Genome of the Netherlands Consortium. Whole-genome sequence
> variation,
> > population structure and demographic history of the Dutch population. Nat
> > Genet. 2014 Jun 29. doi: 10.1038/ng.3021.
> > http://www.ncbi.nlm.nih.gov/pubmed/24974849
> >
> > Deelen P, Menelaou A, van Leeuwen EM, Kanterakis A, van Dijk F,
> Medina-Gomez
> > C, Francioli LC, Hottenga JJ, Karssen LC, Estrada K, Kreiner-Møller E,
> > Rivadeneira F, van Setten J, Gutierrez-Achury J, Westra HJ, Franke L, van
> > Enckevort D, Dijkstra M, Byelas H, van Duijn CM; Genome of the
> Netherlands
> > Consortium, de Bakker PIW, Wijmenga C, Swertz MA. Improved imputation
> > quality of low-frequency and rare variants in European samples using the
> > "Genome of The Netherlands". Eur J Hum Genet. 2014 Jun 4. doi:
> > 10.1038/ejhg.2014.19. http://www.ncbi.nlm.nih.gov/pubmed/24896149
> >
> > Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, Karssen LC, Abdellaoui
> A, Ye
> > K, Guryev V, Vermaat M, van Dijk F, Francioli LC, Hottenga JJ,Laros JF,
> Li
> > Q, Li Y, Cao H, Chen R, Du Y, Li N, Cao S, van Setten J, Menelaou A,
> Pulit
> > SL, Hehir-Kwa JY, Beekman M, Elbers CC, Byelas H,de Craen AJ, Deelen P,
> > Dijkstra M, den Dunnen JT, de Knijff P, Houwing-Duistermaat J, Koval V,
> > Estrada K, Hofman A, Kanterakis A, van Enckevort D, Mai H, Kattenberg M,
> van
> > Leeuwen EM, Neerincx PB, Oostra B, Rivadeneira F, Suchiman EH,
> Uitterlinden
> > AG, Willemsen G, Wolffenbuttel BH, Wang J, de Bakker PIW, van Ommen GJ,
> van
> > Duijn CM. The Genome of the Netherlands: design, and project goals. Eur J
> > Hum Genet. 2014 Feb;22(2):221-7. doi:
> > 10.1038/ejhg.2013.118.http://www.ncbi.nlm.nih.gov/pubmed/23714750
> >
> >
> > I got it written from my employer as an email from his authentic
> > institutional email account that authorship will be awarded for work,
> and I
> > need not worry about it. However, he did not stood by his words!
> >
> >
> > This also happened with me while I was working in Toronto and gave 2
> > presentations to my SickKids employer reporting that the human genome
> does
> > not look like 99.9% similar but reasonably less. I compared Celera
> genome (
> > this has 60% J Craig Venter's genome) and NCBI genomes. Few months after
> I
> > left the job after giving the reports to my boss, a highly cited paper
> got
> > published reporting the same findings that the human genomes are only
> about
> > 99.5% similar comparing J Craig Venter genome and NCBI genome, and it did
> > not have my name in it. I could have well left the employment without
> giving
> > a presentation! However, I did ask my boss if I should present my work
> and
> > if he would be able to attend the presentation, for which he gave me
> > confirmatory email reply by his authentic institutional email account
> that
> > he would be present in my talk, and that he would look at the prospects
> of
> > publishing the work after some experimental confirmation is done, as the
> > results are only computationally predicted. He did not stood by his words
> > after he got experimental confirmation, and did not list me anywhere.
> Here
> > is the publication:
> >
> > Levy S, Sutton G, Ng PC, Feuk L, Halpern AL et al. (2007) The Diploid
> Genome
> > Sequence of an Individual Human. PLoS Biol 5(10): e254.
> > doi:10.1371/journal.pbio.0050254 (worked in the project) .
> >
> >
> > I did inform the conference steering committee and the journal editors
> about
> > the issues, but they do not seem to be interested in resolving the
> issues.
> > Any suggestions regarding how to tackle this unethical practice in
> science
> > would be appreciated, where bioinformatics are hired to get results and
> not
> > being put as co-author, if not the first author, in the resulting
> > discoveries.
> >
> > Well there are even more gross unethical practices in science that happen
> > such as your supervisor takes your findings and sells those to results to
> > another group for exchange of cash or other benefits. The other group
> which
> > may be in another country, publishes the work or even patents it on its
> own
> > name. However, such cases are I guess very difficult to prove and so I
> drop
> > out from going into details of it. Is there a central global biological
> > sciences or bioinformatics legal body where I can raise my voice? Else,
> such
> > incidents only serves as examples set for promoting more such
> malpractices
> > in science for future. My supervisor kicked me from lab in Cambridge
> > University in June , and 2 months later in August my ideas are then
> > submitted as a patent priority application by another group in Europe for
> > vitamin B5 overproduction
> http://patentscope.wipo.int/search/en/WO2010018196
> > . You will see clearly in my PhD thesis submission
> > https://1c4016a7-a-7221ba2e-s-sites....attredirects=0 , which is before
> in
> > July 2008 than this priority date, that I have given the same ideas . Is
> > there a way to act on this and authorship cases legally ?
> >
> >
> > Regards,
> >
> > Abhishek Narain Singh
> >
> > -------------------------------------
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