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 <abhishek.nar...@iitdalumni.com> 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 > > ------------------------------------- > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. > ======================================== > > > > ------------------------------------------------------------------------------ > Want fast and easy access to all the code in your enterprise? Index and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! 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