Retraction Watch

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Award-winning plant researcher correcting several papers critiqued on PubPeer

with 137 comments

Olivier Voinnet

Olivier Voinnet

Olivier Voinnet, a researcher at ETH in Zurich and the winner of the 2013 Rössler Prize, is correcting a number of papers following critiques of more than a dozen of his studies on PubPeer.

The work appears in journals including Cell and PNAS. Voinnet’s co-author on several of the papers, David Baulcombe, who is also highly decorated, left this comment on relevant PubPeer entries:

This response is from David Baulcombe – corresponding author on this paper. I first became aware of the problem with this paper just before Christmas when I received an anonymous email. Since then I have been investigating the problem and have now notified the editor. I recognize that I should have detected the error before the article was submitted and I apologise for the error.

Voinnet gave a similar statement to Retraction Watch:

I have become aware of potential problems with several papers just before Christmas when I received an anonymous email. Since then, I have been investigating the problems with the main co-authors of these papers and have now taken action with the respective journal editors. I apologise for not seeing these errors earlier.

The two researchers left a more detailed joint comment on one entry, for a Cell paper cited 462 times:

This response is from David Baulcombe – corresponding author on this paper and Olivier Voinnet who carried out the experiment and drafted the figure. We accept that the figure legends were incomplete because they did not point out that Figure 3 (panel D, right hand panel lane 4) and Figure 5 (panel D lane 1) are the same image. This duplication is not an error because the Northern experiments for these figures were carried out at the same time, exposed on the same autoradiograph and both used the same negative control sample (Mock: M). Neither of these images was spliced but the two figures show parts of the same autoradiograph, with the overlap across the negative control track (M). We have the original autoradiograph.

We apologise for the lack of clarity and have asked the journal editor for the opportunity to publish a clarification statement.

Written by Ivan Oransky

January 9th, 2015 at 11:28 am

Comments
  • Leonid Schneider January 9, 2015 at 2:32 pm

    It is always good to have authors replying to such accusations. It would be better though to have a verdict from a more independent source, like the respective journal’s editorial office. But we are talking about Cell here, so fat chance. There are however many journals involved, so maybe one of them will make a move first? PNAS or EMBO J, maybe?

  • irre January 9, 2015 at 2:41 pm

    Extract from Pubpeer’s FAQ:

    Q: Are authors alerted when a comment is posted on their paper? Yes, as soon as new comments are submitted the authors of the paper are alerted of the comment.

    These papers have been getting comments since September. Amazing that both authors had to wait for an anonymous email late in December to be informed.

    • Leonid Schneider January 9, 2015 at 2:57 pm

      the anonymous e-mail probably went to the journal as well 😉 Actually, are the journals informed automatically about PubPeer comments as well?

      • Bobo January 10, 2015 at 12:07 am

        No. I have emailed editors about comments that I’ve made there.

        Editors/journals should be informed, but it’s probably hard to automate such a thing, since corresponding editor emails are not available for most papers. The only way to handle it would be to send it to the editorial office or EoC of the journal, which would just create an overwhelming amount of email for some editors, and they’d likely just delete it.

        • Leonid Schneider January 10, 2015 at 6:34 am

          It still should be sent to journals’ editorial offices, PubPeer comments are generally relevant enough not to be treated as spam.

  • Irritated Researcher January 9, 2015 at 5:54 pm

    This is bad for Baulcombe, as a good fraction of his most-cited work is with Voinnet and is impacted

    http://scholar.google.co.uk/citations?user=NPrjUiYAAAAJ

    This is much worse for Voinnet, as he has 11 papers with fairly serious-looking issues on PubPeer (and one for which a possibly convincing explanation may have been offered; see below). They span almost his whole career. He is first or last author of quite a number and he is author on all of the Baulcombe papers on PubPeer. Of course, somebody may have been specifically targeting Voinnet’s papers, but as things stand all of Baulcombe’s problem papers have Voinnet as co-author but Voinnet has a bunch without Baulcombe.

    Baulcombe offers a precise explanation for one of the issues and claims that original data exists to back up that claim (so why not post it?). He also says that he should have noticed the issue.

    Meanwhile, in an apparently symmetrical statement, Voinnet claims to be trying to resolve his issues with his co-authors. The great thing about being PI is that there will always be some junior researcher to carry the can. But that still leaves the issue of the older papers where Voinnet himself will be in pole position.

    It will be interesting to see how Cell and PNAS deal with problems in such classic papers.

  • Elijah January 9, 2015 at 9:49 pm

    The e-mail alert system on pubpeer was not working for quite a while but has recently been fixed. So the “anonymous e-mail” they referred to might simply have been the system finally working again.

    • Hajile January 9, 2015 at 11:39 pm

      I think not.

  • Voinnet and Baulcombe queries January 10, 2015 at 1:45 pm

    A critical update, which reflects that all members of these groups are now coordinating very carefully (apparently) to correct the literature. Credit should be given for addressing the issues publically, on PubPeer, promising to deal with the concerns, and also promising to correct the literature. What is curious is that several of the first authors appear to have been instructed to deal with “their” papers, presumably by Voinnet (personally, I would have liked to see Voinnet himself come forward, as Baulcomb did, to make the comments on PubPeer). Notice how all of the comments are almost identical, pasted below as verbatim quotes from PubPeer, suggesting that indeed the notice was not from PubPeer, but instead a coordinated notice which arrived, as Baulcomb states, just prior to Christmas. If so, then this suggests that PubPeer’s automatic alert system is NOT working.

    Now for the update.

    First, a new paper being questioned, the 12th:
    https://pubpeer.com/publications/6B1389A9C7399D5843485C325BA5ED#fb20987
    doi: 10.1101/gad.1908710
    Genes & Development (2010) 24: 904-915
    Copyright © 2010 by Cold Spring Harbor Laboratory Press
    Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein
    Jacinthe Azevedo1, Damien Garcia1, Dominique Pontier2, Stephanie Ohnesorge1, Agnes Yu1, Shahinez Garcia1, Laurence Braun3, Marc Bergdoll1, Mohamed Ali Hakimi3, Thierry Lagrange2 and Olivier Voinnet1,4,5
    1Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 67084 Strasbourg Cedex, France;
    2Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique/Institut de Recherche et Développement/Université de Perpignan, 66860 Perpignan, France;
    3Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR, F-38042 Grenoble Cedex 9, France
    http://genesdev.cshlp.org/content/24/9/904
    http://genesdev.cshlp.org/content/24/9/904.full.pdf+html (open access)

    Now for some new responses by the Voinnet group that entered PubPeer in the past 24 hours:

    https://pubpeer.com/publications/F5BA8FE3EF8860205332839D02BBDD#fb20983
    Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing
    Patrice Dunoyer, Charles-Henri Lecellier, Eneida Abreu Parizotto, Christophe Himber, Olivier Voinnet, Plant Cell, 16 (2004)
    Written by Peer 2: “This response is from Patrice Dunoyer. I am the first author on this paper and became aware of potential problems with this paper when I recently received an anonymous email. Since then, I have been actively working to address the issues and the corresponding author, Olivier Voinnet, is currently contacting the journal editor. Our apologies for any inconvenience caused.”

    https://pubpeer.com/publications/FD08039FB188E781A80C1C469FFFAB#fb21017
    Isoprenoid biosynthesis is required for miRNA function and affects membrane association of ARGONAUTE 1 in Arabidopsis
    Peter Brodersen, Lali Sakvarelidze-Achard, Hubert Schaller, Mehdi Khafif, Grégory Schott, Abdelhafid Bendahmane, Olivier Voinnet, Proc. Natl. Acad. Sci. U.S.A., 109 (2012)
    Written by Peer 1: “This response is from Peter Brodersen. I am the first author on this paper and became aware of a mistake in the way a sub-panel of Figure 5C was assembled when the corresponding author of the paper recently received an anonymous email. I am addressing the issue and the corresponding author, Olivier Voinnet, is currently contacting the journal editor. We apologize for not having seen the error earlier.”

    https://pubpeer.com/publications/358DABD0BE713B03950C76D7652140#fb21008
    Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity
    Derrick J Gibbings, Constance Ciaudo, Mathieu Erhardt, Olivier Voinnet, Nat. Cell Biol., 11 (2009)
    Written by Peer 2: “This response is from Derrick Gibbings. I am the first author on this paper and became aware of potential problems with this paper when I recently received an anonymous email. Since then, I have been actively working to address the issue and the corresponding author, Olivier Voinnet, is currently contacting the journal editor. Our apologies for any inconvenience caused.”

    https://pubpeer.com/publications/E2451CF219109D92E4BFAD59410425#fb21007
    Selective autophagy degrades DICER and AGO2 and regulates miRNA activity
    Derrick Gibbings, Serge Mostowy, Florence Jay, Yannick Schwab, Pascale Cossart, Olivier Voinnet, Nat. Cell Biol., 14 (2012)
    Written by Peer 1: “This response is from Derrick Gibbings. I am the first author on this paper and became aware of potential problems with this paper when I recently received an anonymous email. Since then, I have been actively working to address the issue and the corresponding author, Olivier Voinnet, is currently contacting the journal editor. Our apologies for any inconvenience caused.”

    https://pubpeer.com/publications/C9E1F1DE1F0367633BCD9F0D21588D#fb20882
    Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation
    Constance Ciaudo, Nicolas Servant, Valérie Cognat, Alexis Sarazin, Emmanuelle Kieffer, Stéphane Viville, Vincent Colot, Emmanuel Barillot, Edith Heard, Olivier Voinnet, PLoS Genet., 5 (2009)
    Written by Unregistered Submission: “This response is from Constance Ciaudo. I am the first author on this paper and became aware of potential problems with this paper when I recently received an anonymous email. Since then, I have been actively working to address the issue and the corresponding author, Olivier Voinnet, is currently contacting the journal editor. Our apologies for any inconvenience caused.”

    No doubt for queries about 12 papers to suddenly land in a person’s inbox must undoubtedly be extremely traumatic, especially when the careers appear to be peaking. However, queries were posted publically, the groups are investigating, and they have taken public responsibility of addressing the literature. The ball is in their park but we need to watch these cases carefully. In addition, the wider literature of both groups (Baulcombe and Voinnet) needs to be tracked as an in-depth post-publication peer review.

  • Voinnet and Baulcombe queries January 10, 2015 at 5:15 pm

    A gel in a 14th paper is being queried at PubPeer:

    https://pubpeer.com/publications/817C7239C8FD3063013B8C258BF473#fb21031
    http://www.ncbi.nlm.nih.gov/pubmed/12198169
    http://emboj.embopress.org/content/21/17/4671.long
    http://emboj.embopress.org/content/embojnl/21/17/4671.full.pdf
    The EMBO Journal (2002) 21, 4671-4679
    Two classes of short interfering RNA in RNA silencing
    Andrew Hamilton 2, Olivier Voinnet 2, Louise Chappell 1, David Baulcombe 1
    1 The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
    2 Present address: Department of Pathology, Glasgow University, Western Infirmary, Glasgow, G11 6NT, UK
    DOI 10.1093/emboj/cdf464 | Published online 02.09.2002
    A. Hamilton and O. Voinnet contributed equally to this work

  • blatnoi January 11, 2015 at 1:28 am

    So, I’m not in the field, but I took a look at four of the papers on PubPeer out of curiosity, chosen pretty randomly (except for unconscious bias). Most of the ones I looked at, that’s three, had duplicated control bands and it seems that the authors can easily get out of this with the same response as in this post, by saying that several experiments were performed at the same time and the control was for all of them. Then it’s only a matter of re-labeling the figure. That really takes care of most of the papers if my small sampling experiment extends to all of them. The fourth one had some of those blotty things flipped or whatever, and the problem looked to be not in the control; that might be more troublesome.

    Am I on the right track here in thinking that this one is not so bad as other cases and the authors can get out of this mostly by corrections that relabel figures?

    • astroturfer January 11, 2015 at 5:57 am

      I think it is worse than that. There are some examples where loading controls have been fully replicated (suggesting they weren’t done in the first place), wild type/control samples have been used for treatment samples, and complete duplication of lanes. There are ~13 suspect papers and they all have one common element, Voinnet. Seems hard to understand how all of the other authors were all inappropriately arranging figures. I notice one paper (is it in PLoS Genetics?) where the legend says the experiments were repeated three times. I find that hard to believe if they are having to duplicate lanes. Unless of course, they got the same “anomalous” result three times. Perhaps those sorts of statements should be backed up in supp data with copies of all the experimental repeats?

      This sort of thing really needs to be investigated properly. I am concerned that because these are big people, they will be able to brush it away as inadvertent mistakes during figure preparation, they do not affect the conclusions of the paper etc etc. Except that they completely undermine the reader’s confidence in the results.

      What bugs me is that there are honest scientists out there who are struggling, really trying to get past that post-doc glass ceiling, when who knows how many spivs there are who cut corners and publish fast papers in top journals, and then scoop the jobs and the funding. One also has to think of the damaged careers of junior people along the way.

    • JB January 11, 2015 at 9:49 am

      Well, as you said, there are some cases for concern in the results bands of some of the papers but, yeah, I think it’d be fair to say that if we’ve seen the full extent of any ambiguities, then the implications may not be that severe for the overall conclusions of the papers.

      However, even assuming that least worst scenario, reusing gel controls for multiple experiments is basic sloppiness (I won’t go into the technical reasons, but it makes any results less reliable) that deals a blow to the contract of trust that exists between authors and readers. The papers are asking us to trust them about the conclusions of some fairly complex experiments: molecular biology controls are often non-trivial to get so, if there are doubts about the basic control experiments, then how much faith should we have that the complex experiments were done properly and that inadvertent errors didn’t creep into those as well?

      And that’s a question that’s likely to be asked even if the root cause *does* turn out to be completely innocent mild incompetence in either experimental design or manuscript preparation.

      To draw a very crude analogy, it’s like somebody saying that they’re a racing car driver and offering, as proof, a picture of themselves doing 200 in a fancy car. You’d want to see evidence that they can actually use the brakes before you hire them.

  • Irritated Researcher January 11, 2015 at 3:08 pm

    “Am I on the right track here in thinking that this one is not so bad as other cases and the authors can get out of this mostly by corrections that relabel figures?”

    Check out a larger sample, blatnoi. It’s not the case that “only controls” [sic] are concerned and I don’t see how relabelling is going to solve most of the issues, except maybe for inattentive and credulous journal editors.

    What is striking about many of the cases highlighted is that they are going to be difficult to pass off as simple errors. Only a small minority of the cases could plausibly be explained by the wayward pasting of a distinct gel region. And some of those include mirroring or rotation, which is already problematic. However, many cases give the apperance of being continuous gels that in fact contain visually undetectable duplications of regions that should never be processed separately.

    It’s a real dilemma: if the modification is done so as to be difficult to detect, it is harder to pass off as a mistake when it is discovered.

  • Voinnet and Baulcombe queries January 11, 2015 at 3:51 pm

    Update: A gel in a 15th paper is being queried at PubPeer:
    https://pubpeer.com/publications/7354A08C358C6D27839217949FE706#fb21101
    Published Online June 1 2006
    Science 7 July 2006: Vol. 313 no. 5783 pp. 68-71
    DOI: 10.1126/science.1128214
    Research Article
    Hierarchical Action and Inhibition of Plant Dicer-Like Proteins in Antiviral Defense
    Angélique Deleris 1, Javier Gallego-Bartolome 1, Jinsong Bao 2, Kristin D. Kasschau 2, James C. Carrington 2, Olivier Voinnet 1,*
    -Author Affiliations
    1 Institut de Biologie Moléculaire des Plantes, CNRS Unité Propre de Recherche (UPR) 2357, 12, rue du Général Zimmer, 67084 Strasbourg Cedex, France.
    2 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
    http://www.sciencemag.org/content/313/5783/68
    http://www.ncbi.nlm.nih.gov/pubmed/16741077

    This now brings in a new high-profile institute that did not exist in the other 14 queried papers, at Oregon State University, of Prof. James Carrington, who should be alerted immediately to this case:
    http://carringtonlab.org/publications/48
    http://cgrb.oregonstate.edu/core

    • Leonid Schneider January 12, 2015 at 4:47 pm

      Jim Carrington has replied on Pubpeer, and it does not look like he is happy about how this collaboration went:
      “This message is from Jim Carrington, collaborator/coauthor on the paper in question. This is the second of two papers that we coauthored with the Voinnet group and that has been identified here as having duplicated or suspicious-looking data. As with the other paper, I and the colleagues (3rd and 4th authors) I supervised for this work were surprised, and deeply concerned, to learn of the problem that was posted yesterday. As I noted for the other paper, we are committed to determining the cause, and to correcting the literature in the most appropriate and transparent way possible.”
      https://pubpeer.com/publications/7354A08C358C6D27839217949FE706#fb21241

    • Leonid Schneider January 13, 2015 at 1:48 am

      Comment by Deleris, which also leaves unclear who assembled the very problematic Figure 2A:
      “I am Angelique Deleris, the first author on this particular study. These revelations were surprising (I found out today) and I eagerly want to rectify and clarify the problems noted. I would also like to add my personal comments:

      Figure 2A – 2nd row (blue box): It appears the loading control seems to be repeated in two parts of the same figure. It should be noted that this result recapitulated a previously published finding, therefore the interpretation should not be questioned and the community should remain assured about the science. However, if a mistake occurred during construction of the figure, I apologize for not noticing it. I hope to track down the original loading control used for this experiment.

      Figure 2A – 3rd row (green box): I agree with the second commenter. The signal from the western blot was very strong, even after many attempts to reduce it. What may have appeared to be “erasure” according to the commenter 1 is actually due to adjustment of the contrast. I do not believe that the figure was manipulated apart from that.”
      https://pubpeer.com/publications/7354A08C358C6D27839217949FE706#fb21260

  • Ouch! January 11, 2015 at 4:37 pm

    There are two issues about Prof. James C. Carrington:
    1. He is no longer at the Center for Genome Research and Biocomputing, Oregon State University: http://cgrb.oregonstate.edu/main/people
    2. He is, instead, at the Donald Danforth Plant Science Center, where he is President and Principal Investigator:
    http://carringtonlab.org/members

    RW readers may recall that the Donald Danforth Plant Science Center was the center of a separate case, on cassava, revolving around Claude Fauquet:
    http://retractionwatch.com/2012/09/14/plos-one-gmo-cassava-paper-retracted-after-data-could-not-be-found/
    http://retractionwatch.com/2012/10/09/the-domino-effect-more-retractions-of-papers-that-cited-retracted-plos-one-gmo-cassava-study/

    Although both institutes and both cases are completely unrelated, this begins to paint a picture of how one error can now start to affect multiple research institutes. Unfortunately, OSU needs to be alerted to this issue since its name is associated with the paper being questioned.

  • Voinnet, Carrington queries January 12, 2015 at 2:27 am

    A gel in a 16th paper is being queried at PubPeer:
    https://pubpeer.com/publications/99D465D980ABB74F58439A9CD16219#fb21153

    Science 14 May 2010: Vol. 328 no. 5980 pp. 912-916
    DOI: 10.1126/science.1185880
    Small RNA Duplexes Function as Mobile Silencing Signals Between Plant Cells
    Patrice Dunoyer 1,*, Gregory Schott 1, Christophe Himber 1, Denise Meyer 1, Atsushi Takeda 2, James C. Carrington 2, Olivier Voinnet 1,*
    1 Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg 12 rue du Général Zimmer, 67084 Strasbourg cedex, France.
    2 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.

    http://imgur.com/aBdtw4Z

    • Leonid Schneider January 12, 2015 at 5:29 pm

      A reply by Jim Carrington:
      “This is Jim Carrington, a collaborator/coauthor on the paper in question. I was very surprised to learn, through PubPeer posts, about the duplications noted. Neither I, nor the postdoctoral scientist (5th author listed) in my group, were aware of the problems prior to these posts. I am committed to determining, with the corresponding authors, how these errors occurred and to correct the literature in the most appropriate and transparent way. I regret that I did not recognize the duplications prior to submission and publication.”
      https://pubpeer.com/publications/99D465D980ABB74F58439A9CD16219#fb21239

  • Voinnet queries January 12, 2015 at 2:30 am

    A 13th paper by the Voinnet group in question:

    https://pubpeer.com/publications/CCBC961A3F8AD01640A9C056C5A16D#fb21034
    http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003435
    Extreme Resistance as a Host Counter-counter Defense against Viral Suppression of RNA Silencing
    Raphaël Sansregret, Vanessa Dufour, Mathieu Langlois, Fouad Daayf, Patrice Dunoyer, Olivier Voinnet, Kamal Bouarab
    Affiliations:
    Raphaël Sansregret, Vanessa Dufour, Mathieu Langlois, Kamal Bouarab
    Centre SEVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
    Fouad Daayf
    Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
    Patrice Dunoyer, Olivier Voinnet
    Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
    Olivier Voinnet Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
    Published: June 13, 2013
    DOI: 10.1371/journal.ppat.1003435

    Fouad Daayf is another really big name in plant science.

    • Leonid Schneider January 12, 2015 at 4:51 pm

      A rather peculiar comment by Patrice Dunoyer, which actually, does take the biscuit:
      “This response is from Patrice Dunoyer. I am the fifth author on this paper and contributed to this figure. I became aware that I used a figure that was not meant to be published. Since then, I have been actively working to address the issue and the corresponding authors, Olivier Voinnet and Kamal Bouarab, are currently contacting the journal editor. Our apologies for any inconvenience caused”.
      https://pubpeer.com/publications/CCBC961A3F8AD01640A9C056C5A16D#fb21237

  • Voinnet queries January 12, 2015 at 7:53 am

    There are two corrections for this paper:
    Science 4 June 2010:
    Vol. 328 no. 5983 pp. 1229
    DOI:10.1126/science.328.5983.1229-c
    http://www.sciencemag.org/content/328/5983/1229.3
    “Small RNA duplexes function as mobile silencing signals between plant cells” by P. Dunoyer et al. (14 May, p. 912). References 19 to 22 are incorrect in the reference list, although they are cited with the correct numbers in the text. Reference 22 by P. Dunoyer et al. should be reference 19, and references 19 to 21 should instead be 20 to 22, respectively.

    Science 15 April 2011:
    Vol. 332 no. 6027 pp. 306
    DOI:10.1126/science.332.6027.306-c
    http://www.sciencemag.org/content/332/6027/306.3
    “Small RNA duplexes function as mobile silencing signals between plant cells” by P. Dunoyer et al. (14 May 2010, p. 912). The image in Fig. 3B (center panel) was previously published as Fig. 1e in P. Dunoyer et al., Nat. Genet. 39, 848 (2007).

  • blatnoi January 12, 2015 at 8:06 am

    Thanks everyone for the info (including some comments after this thread). That explains it a bit more for me, that these are not simple controls and they had to get them right. It seems like you really have to be in the field to know the level of seriousness of a problem, although too much image manipulation is always a red flag. I guess the nanochopsticks was a bit too obvious.

    I guess for me there is a gradient of problems. In a sub-field of catalysis in which I sometimes work, if someone’s exhaggerates a yield, which you can’t disprove anyways, or it’s blatantly obvious that it cannot be 99% isolated yield on a small scale since a few percent is always stuck to the extraction flask walls, then it’s not that big of a problem as opposed to a reaction not working as advertised, and the former I would be okay with not censuring as much (although it definitely does not make me happy that this is so prevelant). Even if a person says they ran a control for heterogeneity, but it turns out they were too lazy and five years later someone figures out heterogenous particles formed in situ were responsible, I would be okay with an apologetic correction. The reaction still works.

    I like reading these stories on RW, but I always try to figure out the level of seriousness of the problems, as in a field that I’m not familiar with, and initial comments being damning as they usually are, it’s hard to get a handle on things.

    • JB January 12, 2015 at 10:16 am

      To add: one issue is that, in a lot of molecular biology work, there often isn’t a single killer experiment that proves the whole title of the paper. It’s more a case of building up circumstantial evidence: ‘If A is true and B is true and C is true, then the most likely explanation is X.’ But if A is true and B is true and C is *false*, then the most likely explanation could be very different, so minor tweaks here and there can have big effects.

      My guess would be that many of the co-authors on these papers are now looking at exactly that: they’ll be checking whether the ambiguities actually invalidate the papers (= v.v. bad), or whether this is ‘tidying up’ that looks worse than it is (= still bad, but not the other people’s career hammer that this might otherwise end up as). One old fallback is, of course, the ‘well, the cut and pastes were just *helping* the data towards a conclusion that we knew – intuitively – to be true’. If the coauthors are lucky, then many of the conclusions in the papers in questions will already have been shown to be essentially correct by other groups, in which case lucky escapes all around.

      If, if, if…

  • Voinnet queries January 12, 2015 at 9:34 am

    A gel in a 17th paper is being queried at PubPeer (it is related to the 16th paper):
    https://pubpeer.com/publications/77E787DC1D67A2BABBC5EEF82030DD#fb21154
    Nature Genetics 39, 848 – 856 (2007)
    Published online: 10 June 2007 | doi:10.1038/ng2081
    Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways
    Patrice Dunoyer 1, Christophe Himber 1, Virginia Ruiz-Ferrer 1, Abdelmalek Alioua 1, Olivier Voinnet 1
    Institutions not visible (paywall)
    http://www.nature.com/ng/journal/v39/n7/full/ng2081.html
    Supplementary material
    http://www.nature.com/ng/journal/v39/n7/suppinfo/ng2081_S1.html

    http://imgur.com/aBdtw4Z

  • Focus on Baulcombe January 12, 2015 at 1:48 pm

    Additional facts about Baulcombe, including from a publically available CV, some of which is not available on the Wikipedia page:
    http://www.ae-info.org/attach/User/Baulcombe_David/CV/1112%20cv

    a) According to http://en.wikipedia.org/wiki/David_Baulcombe, as stated by the Royal Society: “David Baulcombe has made an outstanding contribution to the inter-related areas of plant virology, gene silencing and disease resistance. He discovered a specific signalling system and an antiviral defence system in plants. This led to the development of new technologies that promise to revolutionize gene discovery in plant biology.”

    b) http://www.theguardian.com/environment/2014/mar/14/europe-gm-crop-regulations
    http://www.plantsci.cam.ac.uk/research/davidbaulcombe/pdfs-dcb/current-biology.pdf
    Baulcombe is a rather influential position regarding GMOs, and their regulation, in the EU. Note the Voinnet-Carrington link.

    c) Both Baulcombe (1999-) and Voinnet serve on the advisory editor board of EMBO Journal. One of the papers that is being queried is precisely in this journal: http://emboj.embopress.org/editors How will their editorial positions going to be affected? This may serve as an important precedent for other (plant) science journals.

    d) Baulcombe serves on the advisory editor board of EMBO Reports (1999-):
    http://embor.embopress.org/content/editors

    e) Baulcombe and Carrington are on the editor board of PNAS (2009-):
    http://nrc88.nas.edu/pnas_search/memberDetails.aspx?ctID=20010085

    f) Baulcombe is on the editor board of f1000Prime (2001-):
    http://f1000.com/prime/thefaculty/member/496860677317811

    g) Baulcombe is on the editor board of Genome Biology (2005-):
    http://genomebiology.com/about/edboard

    h) Baulcombe is on the editor board of Cell Host and Microbe (2005-):
    http://www.journals.elsevier.com/cell-host-and-microbe (not visible, but listed on CV)

    i) Baulcombe is on the editor board of Cell (2009-):
    http://www.journals.elsevier.com/cell/ (not visible, but listed on CV)

    j) Baulcombe and Carrington on the science advisory board of the Two Blades Foundation:
    http://2blades.org/science-advisory-board.php
    From http://2blades.org/:
    “Incorporated in 2004, the Two Blades Foundation (2Blades) is a US based charitable organization that supports programs of research and development on durable disease resistance.”

    k) Baulcombe is on the scientific advisory board of the Donald Danforth Plant Science Center (2011-):
    http://www.danforthcenter.org/about/leadership/scientific-advisory-board
    Prof. James C. Carrington became President of the Donald Danforth Plant Science Center in 2011.

    l) Baulcombe is a trustee of Lawes Agricultural Trust (2009-):
    http://opencharities.org/charities/208228

    m) Baulcombe is on the Pepsico Science Advisory Board (2010-)(not visible, but listed on CV)
    http://www.pepsico.com/
    PepsiCo is the parent company of Pepsi, Frito-Lay, Tropicana, Gatorade, and Quaker

    n) Baulcombe: Biotechnology and Biological Sciences Research Council (BBSRC; Member, 2009-2013) and Strategy Advisory Board (Member 2010 -2013) (based on his CV).
    In an interview with the BBSRC, it is stated:
    http://www.bbsrc.ac.uk/news/people-skills-training/2014/140905-f-gb-bioscience-pioneers-david-baulcombe.aspx
    “How has BBSRC supported you throughout your career?
    “BBSRC has been a great sponsor through various responsive mode grants which have enabled both myself and my team to continue our pioneering work.””
    The BBSRC is the largest UK public funder of non-medical bioscience:
    http://en.wikipedia.org/wiki/Biotechnology_and_Biological_Sciences_Research_Council

    o) Baulcombe is on the Board of the National Institute of Agricultural Botany (NIAB) (2009-):
    http://www.farmersguardian.com/david-baulcombe-joins-niab-board/22131.article

    p) Fellow of the Academy of Medical Sciences (2010):
    http://www.acmedsci.ac.uk/fellows/fellows-directory/ordinary-fellows/professor-sir-david-baulcombe/

    q) Baulcombe is winner of the 2002 Ruth Allen Award, by The American Phytopathological Society (APS):
    http://www.apsnet.org/members/awards/RuthAllen/Pages/DavidCharlesBaulcombe.aspx
    Incidentally, there are 26 Molecular Plant Microbe Interactions papers, published by the APS, being queried at PubPeer.

    r) Co-Editor-in-Chief of Silence (2009-2011):
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835995/
    Silence ceased publication in 2013 (about 50 papers published):
    http://www.silencejournal.com/
    http://www.silencejournal.com/content

    Other prizes, based on the Wikipedia page, including the 2009 knighthood:
    • 2001 elected Fellow of the Royal Society (FRS)[3]
    • 2002 elected Member of the Academia Europaea
    • 2002 recipient of the Kumho Science International Award in Plant Molecular Biology and Biotechnology, awarded by the Kumho Cultural Foundation, Korea
    • 2003 co-recipient (with Craig Mello, Andrew Fire and Thomas Tuschl) of the Wiley Prize in the Biomedical Sciences, awarded by Rockefeller University
    • 2004 recipient of the M. W. Beijerinck Virology Prize, awarded by the Royal Netherlands Academy of Arts and Sciences
    • 2005 elected Foreign Associate Member of the National Academy of Sciences
    • 2005 co-recipient (with Craig Mello and Andrew Fire) of the Massry Prize, awarded by the Massry Foundation and the University of Southern California
    • 2006 recipient of the Royal Society’s Royal Medal
    • 2008 co-recipient of the Benjamin Franklin Medal in Life Science, awarded by the Franklin Institute [1]
    • 2008 co-recipient (with Victor Ambros and Gary Ruvkun) of the Albert Lasker Award for Basic Medical Research
    • 2008 appointed Fellow of Trinity College, Cambridge
    • 2009 knighted by Queen Elizabeth II in the 2009 Birthday Honours List for services to plant science.
    • 2009 recipient of the Harvey Prize, granted by the Technion Israeli Institute for Technology.
    • 2010 recipient of the Wolf Prize in Agriculture.
    http://www.wolffund.org.il/index.php?dir=site&page=winners&cs=49&language=eng
    http://www.wolffund.org.il/index.php?language=eng
    • 2012 Balzan Prize [30] for Epigenetics

    On the PubPeer page related to the EMBO Journal paper, Baulcombe wrote, about 2 hours ago:
    https://pubpeer.com/publications/817C7239C8FD3063013B8C258BF473#fb21194
    “This is David Baulcombe – the corresponding author of this paper. I will notify the editors of this irregularity immediately. As with the other points in papers for which I was corresponding author – I apologise for not having picked up the problems when the papers were submitted. I am investigating the extent of the problems in other papers.”

    I think the community needs to exercise patience here and give the authors breathing space to study the situation. The scientific community would be enriched if more whose papers were being questioned at PubPeer and RW would step forward as Baulcombe and Voinnet are doing, to address the public’s concerns. So, give them time. They understand that the community is watching now.

    The post-publication peer review will undoubtedly, step by step, expand to the vast repertoire of publications:
    http://scholar.google.co.uk/citations?user=NPrjUiYAAAAJ (Baulcombe) h-index = 93
    http://scholar.google.co.uk/citations?user=a1D7YVUAAAAJ&hl=ja (Voinnet) h-index = 55

  • Irritated Researcher January 12, 2015 at 5:24 pm

    There’s a nice profile of Voinnet by Science here:

    http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2009_05_29/caredit.a0900071

    Some choice quotes:

    “Many of us were very surprised that the work that he did didn’t earn a share of the Nobel Prize.” –Timothy Hunt.

    By the time Voinnet obtained his Ph.D., he had published 13 papers, half of them in top journals. He had also “established the existence of a systemic signal of silencing and the notion that most if not all plant viruses produce suppressors of silencing,” Baulcombe writes. “This work has really changed plant virology, had a broad impact in plant biology, and influence[d] thinking more generally about silencing.”

    But Voinnet, Baulcombe writes, also showed “hard work and [the] ability to focus on the important scientific issues to the exclusion of everything else, including the real world.”

    That year, he was a winner of the Amersham Biosciences and Science Prize in an essay competition. In 2004, he obtained a Young Investigator award from the European Molecular Biology Organization (EMBO). He received a Starting Independent Researcher Grant last year from the European Research Council. And this year, he won the EMBO Gold Medal…

    Voinnet says. “You’re not there just to make papers. You’re there also to bring the next generation on the way to be as good, if not much better, than you.”

    Voinnet has one big weakness, his colleagues say. “He was well known for filling a bench/desk/glasshouse space with debris from one experiment and then moving on to another … clear area for the next. When he left we isolate[d] new species of fungus from some of the stuff that he left behind,” Baulcombe jokes. Still, “I think his skill as an experimentalist was one of his greatest strengths,” Hamilton says.

  • Voinnet queries January 13, 2015 at 2:58 am

    The following just got posted for the 2006 Science paper:
    https://pubpeer.com/publications/7354A08C358C6D27839217949FE706#fb21260

    “I am Angelique Deleris, the first author on this particular study. These revelations were surprising (I found out today) and I eagerly want to rectify and clarify the problems noted. I would also like to add my personal comments:

    Figure 2A – 2nd row (blue box): It appears the loading control seems to be repeated in two parts of the same figure. It should be noted that this result recapitulated a previously published finding, therefore the interpretation should not be questioned and the community should remain assured about the science. However, if a mistake occurred during construction of the figure, I apologize for not noticing it. I hope to track down the original loading control used for this experiment.

    Figure 2A – 3rd row (green box): I agree with the second commenter. The signal from the western blot was very strong, even after many attempts to reduce it. What may have appeared to be “erasure” according to the commenter 1 is actually due to adjustment of the contrast. I do not believe that the figure was manipulated apart from that.”

  • Voinnet queries January 13, 2015 at 3:06 am

    A gel in an 18th paper is being queried at PubPeer:
    https://pubpeer.com/publications/FD2739B27FAE4C8BFF703A069F1422#fb21265
    http://imgur.com/BAja87G
    Nature Genetics 38, 258 – 263 (2006)
    Published online: 22 January 2006 | doi:10.1038/ng1722
    Induction, suppression and requirement of RNA silencing pathways in virulent Agrobacterium tumefaciens infections
    Patrice Dunoyer, Christophe Himber, Olivier Voinnet
    http://www.nature.com/ng/journal/v38/n2/full/ng1722.html

  • Patrice Donoyer queries January 13, 2015 at 3:54 am

    4 papers with Patrice Donoyer are being questioned at PubPeer, either directly, or with links to Voinnet:
    https://pubpeer.com/publications/F5BA8FE3EF8860205332839D02BBDD#fb20469
    https://pubpeer.com/publications/CCBC961A3F8AD01640A9C056C5A16D#fb21034
    https://pubpeer.com/publications/99D465D980ABB74F58439A9CD16219#fb21153
    https://pubpeer.com/publications/FD2739B27FAE4C8BFF703A069F1422#fb21265

    Patrice Donoyer is the PhD. Group leader in UPR 2357 – IBMP CNRS:
    http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=7
    http://ibmp.u-strasbg.fr/index.php?id=46&no_cache=1&L=1&id=46&no_cache=1&tx_labstructdef_pi1%5BshowUid%5D=180&tx_labstructdef_pi1%5BviewType%5D=member&type=98
    A list of publications may be found here:
    http://labex-ibmc.u-strasbg.fr/NetRNA/publis.php

    Under “Publications funded by the Labex NetRNA” (listed under Donoyer) at http://labex-ibmc.u-strasbg.fr/NetRNA/publis.php:
    2 papers listed in 2014:
    • Garcia D., Garcia S. and Voinnet O. (2014) Nonsense-mediated decay serves as a general viral restriction mechanism in plants Cell Host & Microbe 16:391-402.
    • Uddin M.*, Dunoyer P.*, Schott G., Akhter S., Shi C., Lucas W., Voinnet O. and Kim J.Y. (2014) The protein kinase TOUSLED facilitates RNAi in Arabidopsis Nucleic Acids Research 42:7971-7980.
    3 papers listed in 2013 (listed under Donoyer):
    • Incarbone M. and Dunoyer P. (2013) RNA silencing and its suppression: novel insights from in planta analyses Trends in Plants Science 18:382-392.
    • Romon M., Soustre-Gacougnolle I., Schmitt C., Perrin M., Burdloff Y., Chevalier E., Mutterer J., Himber C., Zervudacki J., Montavon T., Zimmermann A., Elmayan T., Vaucheret H., Dunoyer P. and Masson J.E. (2013) RNA silencing is resistant to low-temperature in grapevine PLoS One 8:e82652.
    • Sansregret R., Dufour V., Langlois M., Daayf F., Dunoyer P., Voinnet O. and Bouarab K. (2013) Extreme resistance as a host counter-counter defense against viral suppression of RNA silencing. PLoS Pathog. 9(6):e1003435.
    1 paper listed in 2012 (listed under Donoyer):
    • Schott G., Mari-Ordonez A., Himber C., Alioua A., Voinnet O. and Dunoyer P. (2012) Differential effects of Viral Silencing Suppressors on siRNA and miRNA loading support the existence of two distinct cellular pools of ARGONAUTE1. EMBO J. 31:2553-2565.

    Under “Other papers” (listed under Donoyer) at http://labex-ibmc.u-strasbg.fr/NetRNA/publis.php:
    1 paper listed in 2014:
    • Boccara M, Sarazin A, Thiébeauld O, Jay F, Voinnet O, Navarro L, Colot V. (2014) The Arabidopsis miR472-RDR6 silencing pathway modulates PAMP- and effector-triggered immunity through the post-transcriptional control of disease resistance genes. PLoS Pathog. 10(1):e1003883.
    10 papers listed in 2013 (listed under Donoyer):
    • Ciaudo C, Jay F, Okamoto I, Chen CJ, Sarazin A, Servant N, Barillot E, Heard E, Voinnet O. (2013) RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet. 9(11):e1003791.
    • Dunoyer P, Melnyk C, Molnar A, Slotkin RK. (2013) Plant mobile small RNAs. Cold Spring Harb. Perspect. Biol. 5(7):a017897.
    • Gibbings D, Mostowy S, Voinnet O. (2013) Autophagy selectively regulates miRNA homeostasis. Autophagy 9(5):781-3.
    • Maillard PV, Ciaudo C, Marchais A, Li Y, Jay F, Ding SW, Voinnet O. (2013) Antiviral RNA interference in mammalian cells. Science 342(6155):235-8.
    • Marí-Ordóñez A, Marchais A, Etcheverry M, Martin A, Colot V, Voinnet O. (2013) Reconstructing de novo silencing of an active plant retrotransposon. Nat. Genet. 45(9):1029-39.
    • Pumplin N, Voinnet O. (2013) RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat. Rev. Microbiol. 11(11):745-60.
    • Schwab R, Speth C, Laubinger S, Voinnet O. (2013) Enhanced microRNA accumulation through stemloop-adjacent introns. EMBO Rep. 14(7):615-21.
    • Voinnet O. (2013) MicroRNA and autophagy–C. elegans joins the crew. EMBO Rep. 14(6):485-7.
    • Voinnet O. (2013) How to become your own worst enemy. Nat. Immunol. 14(4):315-7.
    • Yu A, Lepère G, Jay F, Wang J, Bapaume L, Wang Y, Abraham AL, Penterman J, Fischer RL, Voinnet O, Navarro L. (2013) Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc. Natl. Acad. Sci. U S A 110(6):2389-94.
    11 papers listed in 2012 (listed under Donoyer):
    • Brodersen P., Sakvarelidze-Achard L., Schaller H., Khafif M., Schott G., Bendahmane A. and Voinnet O. (2012) Isoprenoid biosynthesis is required for miRNA function and affects membrane association of ARGONAUTE 1 in Arabidopsis. Proc. Natl. Acad. Sci. U S A 109(5):1778-1783.
    • Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C, Barillot E. (2012) ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics 28(23):3147-9.
    • De Luis A, Markmann K, Cognat V, Holt DB, Charpentier M, Parniske M, Stougaard J, Voinnet O. (2012) Two microRNAs linked to nodule infection and nitrogen-fixing ability in the legume Lotus japonicus. Plant Physiol. 160(4):2137-54.
    • Garcia D, Garcia S, Pontier D, Marchais A, Renou JP, Lagrange T, Voinnet O. (2012) Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions. Mol. Cell 48(1):109-20.
    • Gibbings D, Mostowy S, Jay F, Schwab Y, Cossart P, Voinnet O. (2012) Selective autophagy degrades DICER and AGO2 and regulates miRNA activity. Nat. Cell Biol. 14(12):1314-21.
    • Gibbings D., Leblanc P., Jay F., Pontier D., Michel F., Schwab Y., Alais S., Lagrange T. and Voinnet O. (2012) Human prion protein binds Argonaute and promotes accumulation of microRNA effector complexes. Nat. Struct. Mol. Biol. 19(5):517-524.
    • Luna AP, Morilla G, Voinnet O, Bejarano ER. (2012) Functional analysis of gene silencing suppressors from Tomato yellow leaf curl disease viruses. Mol. Plant Microbe Interact. 25(10):1294-306.
    • Marrocco K., Criqui M.C., Zervudacki J., Schott G., Eisler H., Parnet A., Dunoyer P. and Genschik P. (2012) APC/C-mediated degradation of dsRNA-binding protein 4 (DRB4) involved in RNA silencing. PloS One 7(4):e35173.
    • Pontier D, Picart C, Roudier F, Garcia D, Lahmy S, Azevedo J, Alart E, Laudié M, Karlowski WM, Cooke R, Colot V, Voinnet O, Lagrange T. (2012) NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol. Cell 48(1):121-32.
    • Rodrigo G, Carrera J, Ruiz-Ferrer V, del Toro FJ, Llave C, Voinnet O, Elena SF. (2012) A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS One 7(7):e40526.
    • Toedling J. , Servant N., Ciaudo C., Farinelli L., Voinnet O., Heard E. and Barillot E. (2012) Deep-Sequencing protocols influence the results obtained in small-RNA sequencing. PloS One 7(2):e32724.
    5 papers listed in 2011 (listed under Donoyer):
    • Bennasser Y., Chable-Bessia C., Triboulet R., Gibbings D., Gwizdek C., Dargemont C., Kremer E.J., Voinnet O. and Benkirane M. (2011) Competition for XPO5 binding between Dicer mRNA pre-miRNA and viral RNA regulates human Dicer levels. Nat. struct. Mol. Biol. 18(3):323-327.
    • Brosnan C.A. and Voinnet O. (2011) Cell-to-cell and long-distance siRNA movement in plants: mechanisms and biological implications. Curr. Opin. Plant Biol. 14(5):580-7.
    • Jay F., Wang Y., Yu A., Taconnat L., Pelletier S., Colot V., Renou J.P. and Voinnet O. (2011) Misregulation of auxin response factor 8 underlies the developmental abnormalities caused by three distinct viral silencing supressors in Arabidopsis. PLoS Pathog. 7(5):e1002035.
    • Suffert G., Malterer G., Hausser J., Viiliiäinen J., Fender A., Contrant M., Ivacevic T., Benes V., Gros F., Voinnet O. , Zavolan M., Ojala P.M., Haas J.G. and Pfeffer S. (2011) Kaposi’s Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis. PLoS Pathog. 7(12):e1002405.
    • Voinnet O. (2011) Micro-balancing innate immunity to Salmonella. EMBO J. 30(10):1877-9.
    5 papers listed in 2011 (listed under Donoyer):
    • Azevedo J., Garcia D., Pontier D. , Ohnesorge S., Yu A. , Garcia S. , Braun L. , Bergdoll M. , Hakimi M.A., Lagrange T. and Voinnet O. (2010) Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein. Genes Dev. 24:904-915.
    • Bourc’his D. and Voinnet O. (2010) A small-RNA perspective on Gametogenesis fertilization and early zygotic development. Science 330:617-622.
    • Braun L. , Cannella D. , Ortet P. , Barakat M. , Sautel C. F. , Kieffer S., Garin J., Bastien O. , Voinnet O. and Hakimi M. H. (2010) A complex small RNA repertoire is genereted by a plant/fungal-lide machinery and effected by a metazoan-like argonaute in the single-cell human parasite Toxoplasma gondii. PLoS Pathog. 6:1-20.
    • Chow J.C., Ciaudo C., Fazzari M.J., Mise N., Servant N., Glass J.L., Attreed M., Avner P., Wutz A., Barillot E., Greally J.M., Voinnet O. and Heard E. (2010) LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 141:956-969.
    • Dunoyer P., Brosnan C., Schott G., Wang Y., Jay F., Alioua A., Himber C. and Voinnet O. (2010) An endogenous systemic RNAi pathway in plants. Embo J. 29:1699-1712.
    • Dunoyer P., Schott G., Himber C., Meyer D., Takeda A., Carrington J.C. and Voinnet O. (2010) Small RNA duplexes function as mobile silencing signals between plant cells Science 328:912-916.
    • Gibbings D. and Voinnet O. (2010) Control of RNA silencing and localization by endolysosomes. Trends Cell Biol. 20:491-501.
    • Schulze S., Schäfer B.N., Parizotto E.A., Voinnet O. and Theres K. (2010) LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems. Plant J. 64:668-678.
    • Schwab R. and Voinnet O. (2010) RNA silencing amplification in plants: Size matters. Proc. Natl. Acad. Sci. U S A 107:14945-14946.
    • Toedling J., Ciaudo C., Voinnet O., Heard E. and Barillot E. (2010) girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. Bioinformatics 26:2902-2903.

    All papers require systematic post-publication peer review.

  • Voinnet queries January 13, 2015 at 6:37 am

    Voinnet has apparently provided a response to most of the PubPeer papers, as follows:
    “This response is from Olivier Voinnet -corresponding author on this paper. Through an anonymous email, I have become recently aware of a potential problem with this paper describing work conducted under my supervision. Since then, I have been investigating the problem and have notified the editors. My apologies for not having detecting this error before the paper was submitted.”

    Two gels in a 19th paper is being queried at PubPeer:
    https://pubpeer.com/publications/1E80001715C88F23AAC7DE7E1BCD41#fb21225
    http://imgur.com/rMdzqCA
    http://imgur.com/McDqCTw
    Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins
    Guillaume Moissiard, Eneida Abreu Parizotto, Christophe Himber, Olivier Voinnet
    Published in Advance June 25, 2007
    doi: 10.1261/rna.541307
    RNA 2007. 13: 1268-1278
    http://rnajournal.cshlp.org/content/13/8/1268
    http://rnajournal.cshlp.org/content/13/8/1268.full.pdf+html (open access)

  • Leonid Schneider January 13, 2015 at 7:52 am

    There are is a remarkable degree in personnel exchange between the Voinnet lab and that of Steve Jacobsen, UCLA: https://www.mcdb.ucla.edu/Research/Jacobsen/LabWebSite/P_LabMembers.shtml
    May be a coincidence, but here are the names of former or current Jacobsen lab members associated with PubPeer-annotated Voinnet papers:
    Javier Gallego-Bartolome, Angelique Deleris, Guillaume Moissiard

  • Leonid Schneider January 13, 2015 at 9:52 am

    Another Dunoyer/Voinnet paper questioned on Pubpeer:
    https://pubpeer.com/publications/5973C87C5EC3AC9590FE8531BFB2C0#fb21301
    “An endogenous, systemic RNAi pathway in plants”
    Patrice Dunoyer, Christopher A Brosnan, Gregory Schott, Yu Wang, Florence Jay, Abdelmalek Alioua, Christophe Himber, Olivier Voinnet, EMBO J., 29 (2010)

    Regardless if this applies to the paper in question:
    Some people believe, image manipulation of loading controls is not a big thing. This is absolutely wrong and a very dangerous assumption! By choosing to hide the original loading controls and replace them with manipulated ones, authors create the illusion that the lanes were equally loaded, which may actually be not the case at all, in order to create a certain message for the “relevant” signals. Without proof of equal loading, the entire figure becomes useless!

  • Neuroskeptic January 13, 2015 at 10:01 am

    This is spiralling out of control. It’s a veritable Blotterdämmerung.

    • JB January 14, 2015 at 2:12 pm

      ;D

  • Tapping the mouse with my index finger January 13, 2015 at 11:59 am

    Leonid, a good update. Things are evolving quickly so the community needs to follow carefully, and with precision. A few additional facts about that paper, and some “light” interpretation:

    a) “Acknowledgements: Research in OV’s laboratory is funded by a prize from the Bettencourt Foundation for Life Science Research and a starting grant from the European Research Council ‘Frontiers of RNAi’ ERC 210890. PD and GS are also supported by a research grant from Agence National pour la Recherche (ANR-08-JCJC-0063-01). We thank J Mutterrer for help with image acquisition, R Wagner’s team for plant care and members of OV’s laboratory and Emily McCallum for critical reading of the paper.”

    I count 20 papers being questioned. This is no random issue. It is time to start asking the following questions as well about the papers, ALL of them:
    1) Exactly who did what? We need to compile a list of, paper by paper, the authorship responsibilities of each paper. A pattern will emerge, no doubt, from all 20.
    2) What funding and support did each paper and each author receive?

    b) This is now the third Voinnet EMBO Journal paper being questioned. Voinnet also is on the editor board of EMBO Journal. The EMBO web-site of the paper you point out has this diamond symbol that states: “Transparent process”:
    http://emboj.embopress.org/content/29/10/1699
    That said, EMBO Journal should indicate exactly who conducted peer review, indicate peers’ names publically, as f1000Research and Frontiers journals do, and, ultimately, release the peer reports publically. Such information would be essential for all other papers being questioned as well to determine the individuals (“peers”) and editors who approved the publication of at least 20 papers without having picked up on what appears to be wide-scale band manipulation.

    Ideally, we would like to know if the position of Voinnet on this editor board, or of Baulcombe, had any influence on the acceptance process.

    c) “By choosing to hide the original loading controls and replace them with manipulated ones, authors create the illusion that the lanes were equally loaded, which may actually be not the case at all, in order to create a certain message for the “relevant” signals. Without proof of equal loading, the entire figure becomes useless!”

    This is an absolutely relevant point. As you say, some will say, “it’s only the control” no problem, we can recycle it among different gels. 100% wrong! Recycling control bands is absolutely unacceptable, and even if acceptable, should always be indicated in the figure legend that it was used elsewhere, with a suitable explanation. Authors who try and save their hide use such excuses as “it’s not a big thing”. One analogous comparison is not adding inverted commas to a direct quote, but then claiming that that is not plagiarism.

    d) The issue of precision. Please observe this paper carefully:
    http://emboj.embopress.org/content/embojnl/29/10/1699.full.pdf
    This is a wonderfully classical plant science paper of the highest possible caliber, and with such near-perfect precision. If, in fact, the claims of band (control or otherwise) are true, then this is nothing less than a disaster for the plant science community. Because it indicates – without trying to sound melodramatic – that we can trust almost nothing in the plant science literature.

    Those who are not plant scientists cannot appreciate the seriousness of these 20 allegations being put forward at PubPeer. This is not only about what is likely the top tier of scientists in plant science. It is about the most powerful among them. It is about big business. It is about powerful relationships and the interlink between powerful, high-profile journals like Nature Genetics, EMBO Journal, PNAS and others and an elite that has come to represent their editor boards. It is about the perception (false perhaps) that just because these journals carry high impact factors that they are untouchable. It is about the perception that when one wins a science prize for apparent perfection, then one may be in line to win a whole lot more, and with them, lots of money as well.

    This case trumps – many fold – the Ben Scheres
    http://retractionwatch.com/2014/03/21/i-am-deeply-saddened-and-disturbed-co-author-of-retracted-nature-paper-reveals-how-problems-came-to-light/

    Claude Fauquet
    http://retractionwatch.com/2012/09/14/plos-one-gmo-cassava-paper-retracted-after-data-could-not-be-found/

    and Jorge Vivanco cases:
    http://retractionwatch.com/2013/10/30/image-manipulation-leads-to-fifth-retraction-for-plant-research-group/

    Let us not forget the issue of image tampering in plant science:
    http://retractionwatch.com/2013/03/26/hefty-correction-in-jbc-for-gmo-researchers-in-image-tampering-case/#more-13302

    The plant science community has reached an important cross-road: is any image manipulation unethical, or not? The American Journal of Botany* seems to be taking the issue seriously, and so should the world’s pool of plant scientists. This case will no doubt spur a massive post-publication peer review campaign related to gel images.

    * TRUST AND SCIENTIFIC PUBLICATION: AJB POLICY FOR DIGITAL IMAGES
    JUDY JERNSTEDT, EDITOR-IN-CHIEF
    Department of Plant Sciences, University of California, Davis, One Shields Ave., Davis, California 95616-8780 USA
    http://www.amjbot.org/content/early/2014/12/02/ajb.1400499.full.pdf+html

  • Voinnet queries January 13, 2015 at 12:12 pm

    Another paper (by my count, the 21st) being questioned by the Voinnet group, including Dunoyer:
    https://pubpeer.com/publications/E29974117BADC0677B7D6300BC9156
    Science 22 April 2005: Vol. 308 no. 5721 pp. 557-560
    DOI: 10.1126/science.1108784
    Report
    A Cellular MicroRNA Mediates Antiviral Defense in Human Cells
    Charles-Henri Lecellier 1,*, Patrice Dunoyer 1, Khalil Arar 2, Jacqueline Lehmann-Che 3, Stephanie Eyquem 4, Christophe Himber 1, Ali Saïb 3, Olivier Voinnet1,*
    1 CNRS Unité Propre de Recherche (UPR) 2357, Institut de Biologie Moléculaire des Plantes, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France.
    2 Proligo, Paris, France.
    3 CNRS UPR9051, Hôpital St-Louis, Paris, France.
    4 INSERM U462, Hôpital St-Louis, Paris, France.
    http://www.sciencemag.org/content/308/5721/557 (Pay-walled)

    The number of affected institutions has once again expanded.

  • Gel manipulation in plant science January 13, 2015 at 12:31 pm

    The timing of this case is precious. A pin-pointed post-publication peer review of the literature in Molecular Plant-Microbe Interactions (see the link to Baulcombe and the Ruth Allen Award) that covered all papers in 2013 was completed precisely one week ago. 26 papers were identified with a range of issues, and these cases were all documented elsewhere at RW. Concerns were sent to the MPMI editorial board. Days later, the senior author (David Gilmer) of one of the papers (the first public response among 26) comes forward publically, to indicate, in plain English, that the gels of two images were in fact manipulated (without in fact having indicated this in the manuscript itself):
    https://pubpeer.com/publications/6FE390E2E6887DBB23CAEC8736204E#fb21312

    “Hello this is David Gilmer, corresponding author and supervisor of the paper cited. There is indeed a vertical line between lanes 3 and 4 for GF and also for P and RNA (Fig4G). This figure was assembled from 2 gels and 2 blots. Fig 6A, the figure was cutted to remove the sample present on the left of 1+2 (lane 2) RNA loading corresponds to a parallel loading on a dedicated gel. Regards David Gilmer”

    February 2013, Volume 26, Number 2 Pages 168-181
    http://dx.doi.org/10.1094/MPMI-06-12-0142-R
    The Benyvirus RNA Silencing Suppressor Is Essential for Long-Distance Movement, Requires Both Zinc-Finger and NoLS Basic Residues but Not a Nucleolar Localization for Its Silencing-Suppression Activity
    Sotaro Chiba,1,2 Kamal Hleibieh,1 Alice Delbianco,1,3 Elodie Klein,1 Claudio Ratti,3 Véronique Ziegler-Graff,1 Salah Bouzoubaa,1 and David Gilmer1
    1 Institut de Biologie Moléculaire des Plantes, Laboratoire Propre du CNRS (UPR 2357) Conventionné avec l’Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France;
    2 Institute of Plant Science and Resources, Okayama University, 2-20-1 Kurashiki, Japan;
    3 Università di Bologna, Dipartimento di Scienze e Tecnologie Agroambientali Area Patologia Vegetale, Viale G. Fanin, 40, II piano 40127, Bologna, Italy

    Some points to ponder:
    a) The similar theme between this paper and the Voinnet papers.
    b) The issue of manipulating figures without declaring such manipulations in a paper.
    c) The public responses, and quickly at that, of these cases in particular.

  • Leonid Schneider January 14, 2015 at 8:15 am

    Voinnet once said: “You’re not there just to make papers. You’re there also to bring the next generation on the way to be as good, if not much better, than you.”

    http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2009_05_29/caredit.a0900071

    Several first authors on the queried Voinnet papers are professors and group leaders by now:
    Dunoyer: http://www.ibmp.cnrs.fr/index.php?id=33&no_cache=1&no_cache=1&tx_labstructdef_pi1%5BviewType%5D=member&tx_labstructdef_pi1%5BshowUid%5D=180&L=1
    Ciaudo: http://www.mhs.biol.ethz.ch/Research/Ciaudo
    Gibbins: http://www.med.uottawa.ca/Nsc/eng/gibbings.html
    Brodersen: http://www1.bio.ku.dk/english/research/bi/rna_biologi/brodersen/
    Deleris (won HFSP start-up grant): http://www.hfsp.org/sites/www.hfsp.org/files/HFSP-2014CDA press release-19032014.pdf

  • Dave Fernig January 14, 2015 at 12:39 pm

    I have been following this from a distance. There do seem to be rather a lot of problems and I concur with @neuroskeptic “This is spiralling out of control. It’s a veritable Blotterdämmerung.”.

    It will be interesting if one line of defence is that of “it was OK at the time”, which is echoed at times in comments on PubPeer and also in the PubPeer blog Topic on gel/blot splicing:
    https://pubpeer.com/topics/1/A9C1A3DBF6649CC62871AA7DC87B17#fb17420

    My own view is that this is never defensible, something I recently posted about
    https://ferniglab.wordpress.com/2015/01/06/why-gel-splicing-is-not-ok/

    I look forward to updates.

  • Leonid Schneider January 14, 2015 at 1:09 pm

    First Voinnet paper from his new lab at ETH Zurich questioned on PubPeer:
    https://pubpeer.com/publications/2B8BFCFD515DBFCAAF0DE5858F4134
    “RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells”
    Constance Ciaudo, Florence Jay, Ikuhiro Okamoto, Chong-Jian Chen, Alexis Sarazin, Nicolas Servant, Emmanuel Barillot, Edith Heard, Olivier Voinnet, PLoS Genet., 9 (2013)

    The first author is now professor at ETH as well, her two earlier papers with Voinnet are already flagged.

  • Baulcombe January 14, 2015 at 1:27 pm

    From: http://www.theguardian.com/environment/2014/mar/14/europe-gm-crop-regulations
    Baulcombe writes:
    “The emerging GM technologies are described in a report that I and a small working group prepared for the UK’s Council for Science and Technology. The report is the technical annex to a letter from the CST to David Cameron, the prime minister, about GM.”

    “A global strategy for agriculture that accepts diversity and that integrates the best of biotechnology with that of traditional and organic practice would also help. Such a strategy would account for the needs of large and small farmers and it would be based on evidence. Food and agriculture are too important to be held up behind a red flag. We need minds that are open to new technology in agriculture and an end to the Punch and Judy of GM. It’s time to start talking seriously about a new way forward for crops and how we grow them.”

    “Prof Sir David Baulcombe is an expert on plant disease resistance at Cambridge University”

  • Voinnet queries January 14, 2015 at 1:35 pm

    Another paper (22nd?) being questioned by the Voinnet group:
    https://pubpeer.com/publications/2B8BFCFD515DBFCAAF0DE5858F4134#fb21421
    Constance Ciaudo
    Affiliations: Swiss Federal Institute of Technology Zurich, Department of Biology, Chair of RNA biology, Zurich, Switzerland, Institut Curie, CNRS UMR3215, Paris, France
    Current address: Swiss Federal Institute of Technology Zurich, Department of Biology, Chair of RNAi and Genome Integrity, Zurich, Switzerland
    Florence Jay
    Affiliations: Swiss Federal Institute of Technology Zurich, Department of Biology, Chair of RNA biology, Zurich, Switzerland, Life Science Zurich Graduate School, Plant Sciences program, University of Zurich, Zurich, Switzerland
    Ikuhiro Okamoto
    Affiliation: Institut Curie, CNRS UMR3215, Paris, France
    Current address: Kyoto University, Kyoto, Japan
    Chong-Jian Chen
    Affiliations: Institut Curie, CNRS UMR3215, Paris, France, Institut Curie, Paris, France
    Alexis Sarazin
    Affiliation: Swiss Federal Institute of Technology Zurich, Department of Biology, Chair of RNA biology, Zurich, Switzerland
    Nicolas Servant
    Affiliations: Institut Curie, Paris, France, INSERM U900, Paris, France, Mines ParisTech, Fontainebleau, France
    Emmanuel Barillot
    Affiliations: Institut Curie, Paris, France, INSERM U900, Paris, France, Mines ParisTech, Fontainebleau, France
    Edith Heard
    Affiliation: Institut Curie, CNRS UMR3215, Paris, France
    Olivier Voinnet
    Affiliation: Swiss Federal Institute of Technology Zurich, Department of Biology, Chair of RNA biology, Zurich, Switzerland, Life Science Zurich Graduate School, Plant Sciences program, University of Zurich, Zurich, Switzerland
    RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells.
    PLoS Genet 9(11): e1003791.
    doi:10.1371/journal.pgen.1003791
    http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003791
    http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1003791&representation=PDF

    The number of affected institutions has once again expanded, including now France, Japan and Switzerland.

  • SWISSPLANT 2015 Symposium invitation January 14, 2015 at 8:51 pm

    Perhaps Prof. Olivier Voinnet can explain, at least to his Swiss colleagues, as a seed speaker at the forthcoming SWISSPLANT 2015 Symposium, 28–30 January 2015 in Leukerbad, Valais (Lindner Hotel), these issues in his 23 papers being questioned at PubPeer, spanning almost 18 years:
    https://swissplantscienceweb.ch/research/swissplant-2015-symposium/

    • girasol January 30, 2015 at 7:55 pm

      So, Mr SWISSPLANT, did you get what you were after?

  • Leonid Schneider January 15, 2015 at 2:52 am

    Another major publication featuring Voinnet and Dunoyer questioned on Pubpeer:
    “A plant miRNA contributes to antibacterial resistance by repressing auxin signaling”
    Lionel Navarro, Patrice Dunoyer, Florence Jay, Benedict Arnold, Nihal Dharmasiri, Mark Estelle, Olivier Voinnet, Jonathan D G Jones, Science, 312 (2006)
    https://pubpeer.com/publications/EEB1AA81B4DCCF9C5B5A3DBADF07B2

    • Leonid Schneider January 16, 2015 at 12:39 pm

      Last author and first author state the image was indeed faulty and originated from Voinnet:

      “Dear PubPeer colleagues
      Thank you for alerting us to the duplication of the rRNA ethidium bromide-stained bands in Fig. 2A of Navarro et al (2006). As the author list reveals, we collaborated with the Voinnet Lab, who conducted the small RNA Northern Blot and prepared Fig. 2A. We still regard the biological conclusion of Fig. 2A (miR393 is induced by flg22) as sound because (i) the PAMP-insensitive miR171 was additionally used as internal control in this experiment and the blot was conducted by stripping and reprobing the same membrane that was first probed with miR393 (ii) several other publications have subsequently verified that miR393 is induced by bacterial PAMPs (e.g. Li et al Plant Phys (2010); Fahlgren et al., PLoS One (2007)). We will shortly contact the journal to notify them of this problem and will seek to publish a correction as soon as possible, and we are asking to see the original data from the Voinnet lab.

      We apologize for this error.

      Lionel Navarro and Jonathan Jones.”
      https://pubpeer.com/publications/EEB1AA81B4DCCF9C5B5A3DBADF07B2#fb21697

  • Leonid Schneider January 15, 2015 at 8:27 am

    Second Voinnet paper from his new lab at ETH Zurich is flagged on PubPeer:
    “Reconstructing de novo silencing of an active plant retrotransposon”
    Arturo Marí-Ordóñez, Antonin Marchais, Mathilde Etcheverry, Antoine Martin, Vincent Colot, Olivier Voinnet, Nat. Genet., 45 (2013)
    https://pubpeer.com/publications/AFABCD7C4C5C26E9590E8231DE9B17

    • Voinnet queries January 15, 2015 at 12:22 pm

      Note kindly the details about the authors and their affiliations.

      Lionel Navarro 1,2, Patrice Dunoyer 2, Florence Jay 2, Benedict Arnold 3, Nihal Dharmasiri 4, Mark Estelle 4, Olivier Voinnet 2,*,†, Jonathan D. G. Jones 1,*,†
      1 The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
      2 Institut de Biologie Molèculaire des Plantes du Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France.
      3 John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
      4 Department of Biology, Indiana University, Bloomington, IN 47405, USA.

    • Leonid Schneider January 18, 2015 at 12:56 pm

      There is a strange argument going on between Peer 2 and Peer 3 on the article’s PubPeer site. Peer 2 repeatedly claims the alleged manipulations are nothing but compression artefacts and sees therefore no urgency in authors’ responses. Peer 3 still disagrees. Both Peers’ views are supported or slammed by various “unregs”. So far, none of the authors took stand, at least not by revealing themselves as such. The original image was also not offered so far.

  • Bree January 15, 2015 at 12:23 pm

    Voinnet, Carrington queries
    A gel in a 16th paper is being queried at PubPeer: https://pubpeer.com/publications/99D465D980ABB74F58439A9CD16219#fb21153Science 14 May 2010: Vol. 328 no. 5980 pp. 912-916 DOI: 10.1126/science.1185880 Small RNA Duplexes Function as Mobile Silencing Signals Between Plant Cells Patrice Dunoyer 1,*, Gregory Schott 1, Christophe Himber 1, Denise Meyer 1, Atsushi Takeda 2, James C. Carrington 2, Olivier Voinnet 1,* 1 Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg 12 rue du Général Zimmer, 67084 Strasbourg cedex, France. 2 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.http://imgur.com/aBdtw4Z

    This one is especially bad!

  • Voinnet queries January 15, 2015 at 1:44 pm

    https://pubpeer.com/publications/CCBC961A3F8AD01640A9C056C5A16D#fb21557
    Prof. Fouad Daayf, of Canada, states:
    “This is Fouad Daayf. I am the 4th co-author on this paper. I just received an email that made me aware of an issue with Figure 6 in this paper. As I did not contribute any material to this figure, I contacted one of the two corresponding authors, who assured me that the issue is being investigated and that they will address it once they receive all the needed materials from the co-author(s) who prepared the figure. It is very important that this is addressed properly and promptly.”

  • Leonid Schneider January 16, 2015 at 4:43 am

    A Cell paper from Edith Heard lab (CNRS/INSERM, Paris) is flagged on Pubpeer. It features as key collaborators Voinnet and Ciaudo:
    “LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation”
    Jennifer C Chow, Constance Ciaudo, Melissa J Fazzari, Nathan Mise, Nicolas Servant, Jacob L Glass, Matthew Attreed, Philip Avner, Anton Wutz, Emmanuel Barillot, John M Greally, Olivier Voinnet, Edith Heard, Cell, 141 (2010)
    https://pubpeer.com/publications/166EEB0054C230E0B622EB2AF77F66

    • Voinnet queries January 16, 2015 at 7:02 am

      It is important to emphasize how more and more research institutes are being affected. The complete list of institutions is:

      Jennifer C. Chow,1,2,3 Constance Ciaudo,1,2,3,4 Melissa J. Fazzari,5 Nathan Mise,6,7 Nicolas Servant,1,8,9 Jacob L. Glass,5 Matthew Attreed,5 Philip Avner,6 Anton Wutz,10 Emmanuel Barillot,1,8,9 John M. Greally,5 Olivier Voinnet,4 and Edith Heard1,2,3,*

      1 Institut Curie, Paris F-75248, France
      2 CNRS UMR3215
      3 INSERM U934
      4 Institut de Biologie Mole´ culaire des Plantes du CNRS UPR2357, Universite´ de Strasbourg, Strasbourg 67084 Cedex, France
      5 Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
      6 URA1968 Institut Pasteur, Paris 75015, France
      7 Department of Pharmacology, Jichi Medical University, Tochigi 329-0431, Japan
      8 INSERM U900
      9 Mines ParisTech, Fontainebleau F-77300, France
      10 The Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge CB2 1QN, UK

    • Edith Heard + Voinnet link January 17, 2015 at 3:28 am

      Leonid, that is a very acute observation. Prof. Heard shares the following 6 papers with Voinnet, 3 of which are flagged on PubPeer. RW readers may wish to note that Prof. Heard is at the historical Curie Institute:
      http://en.wikipedia.org/wiki/Curie_Institute_(Paris)
      described on Wikipedia as “one of the leading medical, biological and biophysical research centres in the world”

      1) Ciaudo C, Jay F, Okamoto I, Chen CJ, Sarazin A, Servant N, Barillot E, Heard E, Voinnet O. (2013) RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet. 9(11):e1003791.
      https://pubpeer.com/publications/2B8BFCFD515DBFCAAF0DE5858F4134

      2) Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C, Barillot E. (2012) ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics 28(23):3147-9.

      3) Toedling J. , Servant N., Ciaudo C., Farinelli L., Voinnet O., Heard E. and Barillot E. (2012) Deep-Sequencing protocols influence the results obtained in small-RNA sequencing. PloS One 7(2):e32724.

      4) Chow J.C., Ciaudo C., Fazzari M.J., Mise N., Servant N., Glass J.L., Attreed M., Avner P., Wutz A., Barillot E., Greally J.M., Voinnet O. and Heard E. (2010) LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 141:956-969.
      https://pubpeer.com/publications/166EEB0054C230E0B622EB2AF77F66

      5) Toedling J., Ciaudo C., Voinnet O., Heard E. and Barillot E. (2010) girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. Bioinformatics 26:2902-2903.

      6) Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation
      Constance Ciaudo, Nicolas Servant, Valérie Cognat, Alexis Sarazin, Emmanuelle Kieffer, Stéphane Viville, Vincent Colot, Emmanuel Barillot, Edith Heard, Olivier Voinnet, PLoS Genet., 5 (2009)
      https://pubpeer.com/publications/C9E1F1DE1F0367633BCD9F0D21588D

    • Edith Heard responds January 17, 2015 at 11:21 am

      Edith Heard responds to one of her papers flagged at PubPeer (the last sentence is most interesting):
      https://pubpeer.com/publications/166EEB0054C230E0B622EB2AF77F66#fb21763

      “Edith Heard: as corresponding author of the Chow et al, 2010 paper I am responding to this comment. There is no error in Figure 2C – we purposefully showed the Rrm1 control gel twice in the lower two panels of Figure 2C in order to facilitate the reader’s assessment of each RT sample’s control Rrm1 RT PCR, below the corresponding L1-specific primer RT PCR. The RT-PCRs correspond to a single experiment that was run on a multirow gel – one row corresponding to the Rrm1 controls the other two rows to the L1 element Gf RT-PCRs. I hope this clarifies the issue, which has never been raised before by scientists interested in this paper, who have also used the primers and approach to investigate L1 expression subsequently. Finally I would like to point out that these experiments were performed by Jen Chow in my lab, not in Olivier Voinnet’s lab.”

      • Leonid Schneider January 17, 2015 at 2:10 pm

        While it is likely to have been only a misunderstanding in the case of this particular figure, the following last sentence by Dr. Heard speaks volumes:
        “Finally I would like to point out that these experiments were performed by Jen Chow in my lab, not in Olivier Voinnet’s lab.”

  • Leonid Schneider January 16, 2015 at 5:03 am

    Yet another Voinnet paper from ETH Zürich is flagged on PubPeer:
    “Two microRNAs linked to nodule infection and nitrogen-fixing ability in the legume Lotus japonicus”
    Ana De Luis, Katharina Markmann, Valérie Cognat, Dennis B Holt, Myriam Charpentier, Martin Parniske, Jens Stougaard, Olivier Voinnet, Plant Physiol., 160 (2012)
    https://pubpeer.com/publications/50BCC3BB622CF1A6EC16564E61EEA8

    • Voinnet queries January 16, 2015 at 7:07 am

      Denmark and Germany are now also affected:

      Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, 67084 Strasbourg, France (A.D.L., V.C., O.V.); Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, DK–8000 Aarhus C, Denmark (K.M., D.B.H., J.S.); Biozentrum Martinsried, Ludwig Maximilians University Munich, D–82152 Martinsried, Germany (M.C., M.P.); and Swiss Federal Institute of Technology Zurich, Department of Biology, 8092 Zurich, Switzerland (O.V.)

  • Voinnet queries January 16, 2015 at 7:33 am

    A new gel queried in yet another Voinnet paper:
    https://pubpeer.com/publications/85E5AD84F30EDF9042A96AD79ADE07#fb21657

    Published Online May 15 2008
    Science 30 May 2008: Vol. 320 no. 5880 pp. 1185-1190
    DOI: 10.1126/science.1159151
    Research Article
    Widespread Translational Inhibition by Plant miRNAs and siRNAs
    Peter Brodersen1, Lali Sakvarelidze-Achard1, Marianne Bruun-Rasmussen1, Patrice Dunoyer1, Yoshiharu Y. Yamamoto2, Leslie Sieburth3, Olivier Voinnet1,*
    1 Institut de Biologie Moléculaire des Plantes du CNRS, Unité Propre de Recherche 2357, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France.
    2 Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya Aichi, 464-8602, Japan.
    3 Department of Biology, University of Utah, Salt Lake City, UT84112, USA.
    http://www.sciencemag.org/content/320/5880/1185 (paywall)

  • girasol January 16, 2015 at 1:22 pm

    I have looked at all the PubPeer entries. The nature and scale of the problems are truly staggering. What are we to make of the fact that (at least so far) the common factor seems to be Voinnet himself? I see several commenters are leaning toward the view that much of this may be “minor” in the sense that it (probably) does not affect interpretations and results overall. But how would we know? Especially where some of the instances of apparent manipulation involve experimental rather than control lanes.

    The other thing it leaves me musing on is how can this happen? Either the culture in the lab is so lax that this kind of thing has run rampant of its own accord and Voinnet is oblivious/neglectful, or the practice is deliberately encouraged/permitted by him. Or he has assembled all the problematic figures himself? Something you would think unlikely as it is hard to imagine how it could be done without complicity of all the different co-authors responsible for the figure. All very strange.

    In any case I sincerely hope that the same standards are applied in investigation and response to this as in the case of Dhonoukshe, despite the even higher profile of OV. However, something …maybe it is all the prizes, grants and connections…makes me fear this may not happen. At the least, I suspect that there will be a more sophisticated “defense”.

    • Leonid Schneider January 16, 2015 at 2:07 pm

      As I already posted above:

      Some people believe, image manipulation of loading controls is not a big thing. This is absolutely wrong and a very dangerous assumption! By choosing to hide the original loading controls and replace them with manipulated ones, authors create the illusion that the lanes were equally loaded, which may actually be not the case at all, in order to create a certain message for the “relevant” signals. Without proof of equal loading, the entire figure becomes useless!

  • Voinnet queries: Jones responds January 16, 2015 at 2:51 pm

    Jonathan Jones, senior author, has clarified who the responsible party is, at least in the Science 2006 paper. He states, in a comment posted in the past 12 hours:

    “Dear PubPeer readers

    Thank you for alerting us to the duplication of the rRNA ethidium bromide-stained bands in Fig. 2A of Navarro et al (2006). As the author list reveals, we collaborated with the Voinnet Lab, who conducted the small RNA Northern Blot and prepared Fig. 2A. We still regard the biological conclusion of Fig. 2A (miR393 is induced by flg22) as sound because (i) the PAMP-insensitive miR171 was additionally used as internal control in this experiment and the blot was conducted by stripping and reprobing the same membrane that was first probed with miR393 (ii) several other publications have subsequently verified that miR393 is induced by bacterial PAMPs (e.g. Li et al Plant Phys (2010); Fahlgren et al., PLoS One (2007)). We will shortly contact the journal to notify them of this problem and will seek to publish a correction as soon as possible, and we are asking to see the original data from the Voinnet lab.

    Lionel Navarro and I apologize for this error.

    Jonathan Jones.”

    Despite this, he has the courtesy of issuing an apology, and of promising to correct the literature and provide the original gels from the Voinnet laboratory.

  • The Voinnet-Baulcombe-Carrington-Jones link January 16, 2015 at 4:04 pm

    From the comments above:

    “j) Baulcombe and Carrington on the science advisory board of the Two Blades Foundation:
    http://2blades.org/science-advisory-board.php
    From http://2blades.org/:
    “Incorporated in 2004, the Two Blades Foundation (2Blades) is a US based charitable organization that supports programs of research and development on durable disease resistance.””

    A careful examination of the Jones laboratory in the UK also reveals 4 scientists working at The Sainsbury Laboratory:
    http://www.tsl.ac.uk/staff/

    This then is the common link between Voinnet, Baulcombe, Carrington and Jones.
    Jones is co-author of one paper being questioned at PubPeer.
    Carrington is co-author of two papers being questioned at PubPeer.
    Baulcombe is co-author of seven papers being questioned at PubPeer.

    How is it possible that all the senior authors, linked by a common thread, did not observe any problems?

  • Voinnet queries January 16, 2015 at 5:16 pm

    More gels queried in yet another Voinnet paper, the 4th in Science:
    https://pubpeer.com/publications/C85CBFD2BB7258CC038990DB6E5F6A#fb21727
    http://imgur.com/S0IwHH3
    Science 15 August 2008: Vol. 321 no. 5891 pp. 964-967
    DOI: 10.1126/science.1159505
    Report
    Suppression of the MicroRNA Pathway by Bacterial Effector Proteins
    Lionel Navarro1, Florence Jay1, Kinya Nomura2, Sheng Yang He2, Olivier Voinnet1,*
    1 Institut de Biologie Moléculaire des Plantes, CNRS UPR 2353–Université Louis Pasteur, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France.
    2 Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
    http://www.sciencemag.org/content/321/5891/964 (paywall)

    This expands the institutes being affected by the Voinnet case to:
    Michigan State University

  • Keystone Symposium Feb 21 2015 January 16, 2015 at 8:16 pm

    After attending the SWISSPLANT 2015 Symposium, 28–30 January 2015 in Leukerbad, Switzerland, where Swiss plant scientists no doubt have ample queries about the 29 papers being questioned at PubPeer, Voinnet may also answer queries from the plant RNA Silencing in Plants specialists on February 21, 2015, at the Keystone Resort, Keystone, Colorado, USA:
    https://www.keystonesymposia.org/index.cfm?e=web.Meeting.Program&meetingid=1363

    At the meeting, Prof. David Baulcombe, Dr. James C. Carrington and a few other co-authors of some of the papers being questioned. It promises to be a challenging meeting.

    May I recommend a small worshop on figure and gel manipulation, how to prevent it and how to detect it through post-publication peer review.

    Incidentally, how many of the questioned papers’ results were presented at previous Keystone Symposia?
    http://www.keystonesymposia.org/index.cfm?e=web.Meeting.Program&meetingid=1299
    2014
    http://www.keystonesymposia.org/index.cfm?e=web.Meeting.Program&meetingid=1239
    2013
    http://www.keystonesymposia.org/12B1
    2012
    http://www.keystonesymposia.org/11C7
    2011

    The links between so many papers, meetings, institutes, continents, countries and journals is astonishing.

    • Keystone Symposium Feb 21 2015 January 17, 2015 at 3:15 am

      A tad more detail.

      Papers by several of the Keystone Symposium speakers are being questioned at PubPeer, namely those by:
      David C. Baulcombe, University of Cambridge, UK (Keynote address)
      James C. Carrington, Donald Danforth Plant Science Center, USA
      Olivier Voinnet, Swiss Federal Institute of Technology, Zürich, Switzerland
      Thierry Lagrange, Centre National pour la Recherche Scientifique, France
      Vincent Colot, École Normale Supérieure, France

      There is one other of Voinnet’s co-authors who is not in papers currently being questioned at PubPeer, but who is also making an oral presentation at the meeting:
      Sascha Laubinger, University of Tübingen, Germany

  • Voinnet queries January 17, 2015 at 3:34 pm

    There seems to be some misunderstanding in the broader plant science community about the purpose of PubPeer in this – and in fact any other – case. PubPeer serves as an online forum of discussion of papers, much the same way that scientists converge around a table during a journal club discussion, or intra-lab discussion, to debate a paper’s methodology or results. Discussion about issues is healthy, and although some members of the public, or even associates of Voinnet may be defensive, the basal premise of queries about papers, or aspects within those papers, is always academic. Most likely what spurred a surge in queries of the Voinnet papers in the past 7-10 days, rising dramatically from about half a dozen in late 2014 to almost 30 in less than 2 weeks within 2015, was not so much that all of them had proven errors, but the fact that some concerns in select papers resulted some red flags and thus an increase in scrutiny of Voinnet’s papers.

    Most likely such scrutiny would never have occurred if some initial red flags had not appeared at PubPeer. Most likely more papers might not have been analyzed had the papers with “issues” not been in such high-ranking journals. The hawks among those analyzing Voinnet papers need to tone back the rhetoric, however, and give the authors ample breathing space to assess their original gels.

    At this point, looking at the case from an external perspective, I wish to make a suggestion. Hopefully, Voinnet and colleagues can silence the voice of their critics by providing/creating an open access library of ALL gels from all papers related to transgene silencing experiments dating back as far as the mid to late 1990s. This is the ideal scenario, and Voinnet and colleagues, many of whom are in well-financed and highly reputable institutes, could easily set a very positive historical precedent in plant science research by making an open access “library” of high resolution images of all original gels. Such a library would thus allow scientists to independently examine the originals and then make their own conclusions. It would also save the community the hassle of having to track down each and every gel associated with potentially hundreds of figures spread out over potentially dozens of journals and publishers. So, such an effort would be an incredibly positive service to plant science, despite the undoubtedly tremendous effort that such an open access data-base would require. If such an open access data-base could be established, then it could serve as the role model for all other molecular studies in plant science, future and past, and journals could easily adapt a policy that would require such an open access data-base to exist, independent of the publisher’s site.

    Voinnet might ask, why should he be responsible for doing something like that? I think the reason is quite obvious: there is currently a high level of intrinsic doubt, uncertainty and distrust. Unfortunately, plant science (and other sciences) seems to have evolved to a point where everything said and published needs to be verified and proven, rightly so. So even a whisk of doubt needs thorough investigation and proof. The scale, breadth and depth of reach of the papers appearing at PubPeer is, as I indicated above, quite remarkable and this case is affecting a lot of individuals and institutes, all of whom have the right to know that such papers are being examined. At least until all doubt has been dispelled.

    May I suggest that the authors be given a fair chance to provide the support to disprove any incorrect and doubtful claims on PubPeer. If Voinnet and co-authors can disprove their critics wrong, with proof, then this then highlights that the channels of healthy discussion in science are functional. Science is not about a traditional peer review that is case closed, it is about a continuous and arduous path of discovery that will always meet with analysis, doubt and controversy. This has, and will hopefully always continue to be the basis of scientific discovery and debate. In that sense, the plant science community should be thankful to have sites like PubPeer or Retraction Watch, that allow that debate to take place. Such a possibility did not exist 10 or even 5 years ago, and this may be the reason why so many plant scientists appear to be shocked (see the buzz taking place at Twitter, for example).

  • josh p January 17, 2015 at 6:39 pm

    I consider myself to be on the side of waiting for all evidence to come in before grabbing the pitchforks and torches, however this collectively looks pretty bad and isnt an “oops” incident. I did northern blots all the time during my PhD and a single air bubble or blemish can cost you a whole week quantifying these bands. It will be very telling to see a few notebook pages of raw data blot film that backs this up as a mistake (not computer images). Its possible to generate 20 images from one sample by adjusting the exposure and repostioning film slightly in the dark room after exposures. We will need to see what bands were cropped and ensure they were from the correct lanes and from the same piece of film.

    On a personal note, we live in a collaborative funding era where everyone is slapped in as middle authors by doing one piece of a larger story (in this case the northern blots). First authors say “it wasn’t me!” Everyone pads their resume with more pubs on their CV. I personally believe less collaboration and more ownership avoids this blame game.

    This particular issue spans across the ENTIRE small RNA developmental field, there are some major papers being called into question. This rasies doubts, if you can be “caught” duplicating/doctoring images…..what does this say about your raw excel data and bar graphs? I really hope this ends well for all sides involved but I dont think it will.

  • The issue of authorship + responsibility January 17, 2015 at 10:24 pm

    As indicated above by Leonid, the rather revealing statement by Dr. Heard* that only a single individual, Jennifer C. Chow conducted the experiments, and not Voinnet or anyone in his laboratory, actually seems to have raised more questions than answers, even if the gels are OK.

    That issue pertains to authorship, author responsibilities and author contributions. A detailed analysis of all Voinnet papers that appear on PubPeer needs to be made to examine:
    a) who did what, exactly?
    b) who supervised what, exactly?
    c) who supervised who, exactly (or, maybe more appropriately, who was supervised by whom)?
    d) are exact functions indicated clearly in an authorship contributor statement? If yes, then these need to be examined. If no, is this because of a journal policy? Most top-ranking journals require such statements, and most of the Voinnet papers are in such top-ranking journals, so it is rather surprising to not see one for this paper (unless its online somewhere?).
    e) Considering this to be a bio-medical journal, and considering that many publishers apply the ICMJE rules of authorship, how woud the authorship of each paper abide by such regulations / requirements?
    f) Do all papers questioned on PubPeer, and those not questioned on PubPeer, contain a conflict of interest (or lack thereof) statement? Given the high-ranking links among many top-notch institutes, the narrow field of exploration of this topic – which appears to be dominated by precisely the Voinnet group and associates around the world (one can see this by the high % of co-authors who will be presenting at the Keystone Symposium in February, 2015) – the chances of COIs are not small.

    It is likely that these questions would not have been raised had no papers appeared at PubPeer. Now it seems that all angles need to be examined more closely, not only those pertaning to gel banding and/or potential image manipulation.

    * “Finally I would like to point out that these experiments were performed by Jen Chow in my lab, not in Olivier Voinnet’s lab.”

    • astroturfer January 18, 2015 at 5:15 am

      Well to be fair, Chow may only have been responsible for the figures in question, not the entire paper.

      • irre January 18, 2015 at 6:12 am

        As first author she carries a lot of responsibility for the entire paper.

        • The issue of authorship + responsibility January 18, 2015 at 6:25 am

          astroturfer, I am sure that Dr. Heard would have said “Jen Chow was responsible for the figures” if that’s what she wanted to say. But that’s not what she said. She said, really clearly, “these experiments were performed by Jen Chow”. That’s pretty clear. irre, what are you suggesting exactly? That the remaining 13 individuals in the team did almost nothing? Precisely the reason why we need to know what each one did. You can’t have 13 captains to a ship, can you?

  • Voinnet queries January 19, 2015 at 5:06 am

    Gels in another 5th Science paper by the Voinnet group being questioned at PubPeer:
    https://pubpeer.com/publications/E29974117BADC0677B7D6300BC9156#fb22061
    Science 22 April 2005: Vol. 308 no. 5721 pp. 557-560
    DOI: 10.1126/science.1108784
    Report
    A Cellular MicroRNA Mediates Antiviral Defense in Human Cells
    Charles-Henri Lecellier 1,*, Patrice Dunoyer 1, Khalil Arar 2, Jacqueline Lehmann-Che 3, Stephanie Eyquem 4, Christophe Himber 1, Ali Saïb 3, Olivier Voinnet 1,*
    1 CNRS Unité Propre de Recherche (UPR) 2357, Institut de Biologie Moléculaire des Plantes, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France.
    2 Proligo, Paris, France.
    3 CNRS UPR9051, Hôpital St-Louis, Paris, France.
    4 INSERM U462, Hôpital St-Louis, Paris, France.
    http://www.sciencemag.org/content/308/5721/557

  • Voinnet queries January 19, 2015 at 3:21 pm

    Voinnet has just provided four more public guarantees:

    https://pubpeer.com/publications/EEB1AA81B4DCCF9C5B5A3DBADF07B2#fb22177
    “This response is from Olivier Voinnet co-corresponding author on this paper. Through an anonymous email, I have become recently aware of a potential problem with this paper describing work conducted partially under my supervision. Since then, inspection of the the original raw data has allowed identification of the mistake, which will be corrected shortly through editorial contact . My apologies for not having detecting this error before the paper was submitted.”

    https://pubpeer.com/publications/80DD1F3E653159C8F89739FF7C7129#fb22180
    “This response is from Olivier Voinnet -corresponding author on this paper. Through an anonymous email, I have become recently aware of potential problems with this paper describing work conducted under my supervision. Since then, all original raw data have now been retrieved and appropriate notifications will be mad to the editors.”

    https://pubpeer.com/publications/7354A08C358C6D27839217949FE706#fb22175
    “This response is from Olivier Voinnet -co-corresponding author on this paper. Through an anonymous email, I have become recently aware of potential issues with this paper describing work conducted under my supervision. Since then, we have recovered all original raw data to investigate any potential problems and will shortly notify the editors as required.”

    https://pubpeer.com/publications/AFABCD7C4C5C26E9590E8231DE9B17#fb22174
    “This response is from Olivier Voinnet -corresponding author on this paper. Through an anonymous email, I have become recently aware of potential problems with this paper describing work conducted under my supervision. Since then, I have been investigating the problem with all original raw data and will be shortly notifying the editors. My apologies for not having detecting the problems before the paper was submitted.”

  • Leonid Schneider January 20, 2015 at 4:10 am

    Another Dunoyer/Voinnet paper queried on PubPeer:
    “Induction, suppression and requirement of RNA silencing pathways in virulent Agrobacterium tumefaciens infections”
    Patrice Dunoyer, Christophe Himber, Olivier Voinnet, Nat. Genet., 38 (2006)
    https://pubpeer.com/publications/FD2739B27FAE4C8BFF703A069F1422

    • Voinnet queries January 20, 2015 at 9:14 am

      Corrigendum. This is not new (see above): it was reported at RW on January 13, 2015 at 3:06 am (scroll above). However, a new part of Fig 5 is being questioned.

  • Voinnet queries January 20, 2015 at 9:10 am

    A new gel queried in yet another Voinnet paper, the second at Genes and Development:
    https://pubpeer.com/publications/4E966F257E4623AA5B14821D353DEC#fb22261
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC517516/
    http://genesdev.cshlp.org/content/18/18/2237.full.pdf

    In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA
    Genes and Development 18(18): 2237-2242
    Eneida Abreu Parizotto, Patrice Dunoyer, Nadia Rahm, Christophe Himber, and Olivier Voinnet
    Institut de Biologie Moleculaire des Plantes du CNRS, 67084 Strasbourg Cedex, France
    Received May 6, 2004; revised version accepted July 22, 2004.
    DOI: 10.1101/gad.307804

  • Voinnet queries January 20, 2015 at 9:21 am

    The Leonid Schneider editorial of LabJournal on the Voinnet story is out (in German):
    http://laborjournal.de/editorials/906.lasso

  • Leonid Schneider January 21, 2015 at 11:29 am

    The accusations are being taken very seriosuly, this speaks for itself:

    “This response is from Cyril Zipfel, Head of The Sainsbury Laboratory (TSL):
    TSL has been made aware recently of irregularities reported on PubPeer concerning several papers authored by a previous researcher in the laboratory. As a leading institution in the field of molecular plant-microbe interactions, we are taking this situation extremely seriously. Together with the Head of our Scientific Council, we are actively discussing with all other institutions concerned to define the best way forward to co-ordinate efforts to clarify how these irregularities occurred and to take appropriate measures. I would like to acknowledge the immediate actions taken by Senior scientists at TSL, both past and present, to address concerns reported on PubPeer in relation to previous papers published by them.”
    https://pubpeer.com/publications/A090AEA18BF0DDC626CEB413174345#fb22352

  • Leonid Schneider January 21, 2015 at 1:04 pm

    Another Dunoyer/Voinet paper flagged on PubPeer:
    “Identification, subcellular localization and some properties of a cysteine-rich suppressor of gene silencing encoded by peanut clump virus”
    Patrice Dunoyer, Sébastien Pfeffer, Christiane Fritsch, Odile Hemmer, Olivier Voinnet, K E Richards, Plant J., 29 (2002)
    https://pubpeer.com/publications/7E72477BFA031E54D5D452B7E0BF6D

  • Leonid Schneider January 22, 2015 at 8:00 am

    Another ETH-Zürich paper by Voinnet in Science flagged:
    “Antiviral RNA interference in mammalian cells”
    P V Maillard, C Ciaudo, A Marchais, Y Li, F Jay, S W Ding, Olivier Voinnet, Science, 342 (2013)
    https://pubpeer.com/publications/4AB03F8F78506FAEB6B8F5B311C6CA

    • J January 22, 2015 at 11:21 am

      I’ve already commented on Pubpeer about this: if this paper has issues, it’s a big, big, deal, because it claims an RNA antiviral mechanism in mammals and a lot of people already doubt that story for biological reasons (see: http://www.cell.com/cell-reports/pdf/S2211-1247(14)00884-5.pdf).

      But: the images queried in Pubpeer are very low resolution and I don’t think they contain anything that can’t be easily explained away as a compression artefact.

      So, in this case at least, I think the current posting on Pubpeer doesn’t have a case (and I think a lot of the other postings do have a case, by the way).

    • Voinnet queries January 22, 2015 at 11:35 am

      This is the 6th Science Voinnet paper being flagged. Some additional details to the above:
      Science 11 October 2013: Vol. 342 no. 6155 pp. 235-238
      DOI: 10.1126/science.1241930
      Report
      Antiviral RNA Interference in Mammalian Cells
      P. V. Maillard1,*, C. Ciaudo1,*, A. Marchais1, Y. Li2, F. Jay1, S. W. Ding2, Olivier Voinnet1,†
      – Author Affiliations
      1 Department of Biology, Swiss Federal Institute of Technology Zurich (ETH-Z), 8092 Zurich, Switzerland.
      2 Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.
      ↵* These authors contributed equally to this work.
      http://www.sciencemag.org/content/342/6155/235

      This might very well be the first Voinnet paper involving UC Davis.

  • Leonid Schneider January 22, 2015 at 8:22 am

    A Voinnet paper with Dunyoer as last author is flagged:
    “Differential effects of viral silencing suppressors on siRNA and miRNA loading support the existence of two distinct cellular pools of ARGONAUTE1”
    Gregory Schott, Arturo Mari-Ordonez, Christophe Himber, Abdelmalek Alioua, Olivier Voinnet, Patrice Dunoyer, EMBO J., 31 (2012)
    https://pubpeer.com/publications/FFC9896ACDEE9C64A90CD05595D874

  • Unacceptable harassment of coauthors and others January 22, 2015 at 12:29 pm

    I understand the interest in Voinnet just now. But there is a difference between someone doing PPPR by commenting on gel artefacts and someone undertaking an email campaign of harassment, innuendo and character assassination.

    And it IS harassment to send anonymous emails to ALL the PIs at numerous institutes simply because someone there has once published with Voinnet. If anything, it is an even more egregious form of harassment to bombard people through the Keystone organisation.

    All of the following is fair:

    Commenting on the work in PPPR forums
    Contacting the authors with your concerns
    Contacting the journals with your concerns
    Contacting the appropriate person (Department Head; Dean; Research ethics officer, etc.) at the institute with your concerns

    In such a complex case as this one, with multiple papers published over many years, it is going to take quite some time for institutional investigations to be concluded. The institutes are obliged to conduct investigations in camera. It is a legal requirement. Coauthors are very likely to find themselves being told to not publicly comment and certainly not to provide juicy details to rubberneckers who are behaving like the worst sort of yellow press.

    Due process takes time. At this moment, you do not have the right to know arbitrary details of who did what just because your salacious cravings need to be satisfied. Many people are taking collateral damage. They are all hurting. Stop the persecution.

    What I expect from the anonymous person who has been conducting this harassment is that you now email an apology to your victims with the appropriate pseudonym that you used. And you tell them that you will never behave like this again. You will henceforth use your anonymity to protect yourself, but not as a cover for reckless spamming and harassment.

    It is important that people learn how to behave appropriately. Perhaps I should start a Topic at PubPeer on harassment where I would illustrate the problem by collecting the full set of harassing emails in order to lay bare the extent of someone’s obsessive and incorrect behaviour?

    • CR January 22, 2015 at 2:00 pm

      I completely agree with the necessity of creating such a topic. Anonymity is powerful; with greater power comes greater responsibility. Anonymous whistleblowers must learn how to take advantage of their position as to take positive action, resisting the temptation of abusing or pushing people because of their own frustration. Abusing anonymity only compromises the practice and will do more harm than good.

    • researcher January 23, 2015 at 2:10 am

      I also fully agree. I also received weird e-mails pointing to discussions on both pubpeer and retraction watch which claimed to be created by an “automatic alert service” but still contained some rather personal remarks…..leaving the impression that somebody tries to make the most of the affair…..because he/she profits from the case?

      • researcher2 January 23, 2015 at 9:24 am

        How can anybody possibly profit from such a case, unless the direct competition? Smear campaigns do not sound like the correct option. Strange how nobody seems to recognize that anonimity is the reason why 35+ Voinnet papers are currently being closely examined. I have seen no praise to PubPeer for raising awareness. Had there not been any e-mails to xyz individuals, would there have been any knowledge of the issues pointed out at PubPeer? Perhaps those seeking to demonize the messenger should instead focus on the message. The individual above also claims to have received e-mails. So what? One receives dozens of spam e-mails every day from the predatory publishers but we don’t see the proponents of this case raising their voices in anger over those e-mails, do we? Whistle-blowers, anonymous ones, are important. Perhaps you (and the individual above – Unacceptable harassment of coauthors and others) could release publically, and anonymously (using your anonymous RW handles), the content of those e-mails for the whole plant science community to judge your assessmet of the content of those e-mails. Without a copy of those e-mails in the public sphere, they remain mere references to ghosts. In the meatime, the plant science community awaits anxiously for the full set of gels published in those papers, as promised publicly by Voinnet and several of his co-authors at PubPeer.

  • Curious January 22, 2015 at 2:59 pm

    “I understand the interest in Voinnet just now.” Could you elaborate more on this comment? Indeed, the links between Voinnet and the Keystone Organization are established (Keystone Symposium), and one could understand their irritation in having one of their meetings disrupted by an academic investigation of several of its participating scientists. The image of the Keystone Organization is important given its high-profile Board of Trustees:
    https://www.keystone.org/about-us-the-keystone-center/board-of-trustees.html

    It would be extremely important to start a discussion at PubPeer, and most definately an unedited copy of such e-mails should be made public. That would allow the discussion to be fair and balanced and to provide all angles of the story. Also, since there are no apparent established and written rules on this issue, perhaps this could lead to a concise understanding among scientists. Your initiative at PubPeer is awaited.

    • Curious January 22, 2015 at 3:14 pm

      It seems as if the commentator above may have referred incorrectly to the Keystone organization, in his/her comment above. The Symposium where Voinnet and several co-authors will be making presentations is organized by Keystone Symposia on Molecular and Cellular Biology, whose web-site states: “Keystone Symposia is a 501(c)(3) nonprofit organization directed and supported by the scientific community.” And its Board of Directors seems to be different to that of the board of trustees of the Keystone Organization:
      http://keystonesymposia.org/index.cfm?e=Web.BoD&show=currentBoD

      Could the above commentator please clarify if he/she is referring to the Keystone Organization or to Keystone Symposia? This distinction is extremely important.

  • Unacceptable harassment of coauthors and others January 23, 2015 at 12:01 pm

    CR commented above “resisting the temptation of abusing or pushing people because of their own frustration”. This is exactly right.

    Guidelines with a list of do’s and don’ts might well be rather important now if this PPPR activity is not to become discredited and lose whatever support it has within the research community.

    Things that I am particularly concerned about as of this week that should go on the don’t list

    (1) No STALKING
    (2) No SPAMMING
    (3) Never, ever, pressure a researcher to publicly DENOUNCE a neighbour or colleague
    (4) Do not apply undue pressure to FORCE a researcher to comment. They have the right of silence and they may well not be able to comment on institutional and/or legal grounds. No respectable scientist should make unsound inferences based on their silence

    In democratic societies, we usually consider that the end does not justify the means. Alone, or in combination, some of the activities listed above have the potential to trigger a criminal investigation. Being found out as a stalker is certainly terminal to the career of a person doing it. Please think about this.

  • researcher2 January 23, 2015 at 1:08 pm

    Quite aggressive messages – if I may say – for someone who is trying to promote a peaceful solution to PPPR. What PPPR needs is understanding, calm and rational debate. Understanding cannot exist if there is no knowledge of an issue. Knowledge comes about through the message. The message seems to have come across and it seems that all responsible individuals are acting upon that. This seems to be the correct path of action, and Voinnet is applauded for taking that path.

    It’s quite interesting the defensive terminology that tends to appear when one is being examined, validly, in the public domain, i.e., PubPeer: “harassment”, “witch-hunting”, “stalking”, are but a few to have emerged from the camp of plant scientists whose work has been questioned or challenged recently. One thing is delivering an anonymous message. It is a whole different ball game associating terminology (and the implication of that terminology) as has been done above. Instead of veiled threats, perhaps that energy would be better channelled into creating a positive, pro-active PPPR base that supports PubPeer? Most likely Voinnet was not forced to investigate himself, or forced to do anything, by anyone, or was he? He appears to have made that choice voluntarily, he and several of his co-authors. One simply has to read the responses that were posted on PubPeer and then followed up above to understand this. It appears as if these individuals have gone into some sort of damage control mode, which is understandable. And of course, as researchers of the institutes where they are, surely they must know the protocol involved with an academic investigation? So, it seems unlikely that any external individuals could “force” Voinnet or anyone associated with him and his papers being questioned to do, or say, anything against his will.

    One has to praise Voinnet, in fact, because he did what Fazlul Sarker did not do, for example. He, in the light of public concerns at PubPeer, came forward to address them. It appears, from the time-line of the story, that comments existed back in September. It also seems as if Voinnet and those who were associated wth him, including his research institutes, failed to address those queries at PubPeer. Could this not have been the impulse for alerting the individuals you refer to above? Baulcombe and Voinnet and several others all refer to e-mails prior to Christmas.

    Unacceptable harassment of coauthors and others, could you be so kind as to post that e-mail – which you promised to post – you are referring to publicly, please, at RW, or at PubPeer, because it is important for the general public to ascertain if that e-mail is in fact as malicious as you claim it to be. The plant science community can surely judge for themselves? Would you be breaking any laws in your country by anonymously posting the content of that e-mail at RW, provided that all e-mails were redacted?

  • Carrington speaks January 23, 2015 at 1:16 pm

    Carrington has stated the following, January 23, 2015:
    https://pubpeer.com/publications/7850A6E12550CB11D8E88A65D37546#fb22632
    “During a systematic self-study of data integrity and accuracy (see below) in publications over the past 15 years from my group, we identified an error that needs to be corrected in Garcia-Ruiz et al. (www.plantcell.org/cgi/doi/10.1105/tpc.109.073056), which was published in The Plant Cell in 2010. On January 20, 2015 we discovered that the immunoblot panel in Figure 3A was incorrect. The published panel actually corresponds to a blot from a different sample set that was used for Figure 3B. In tracking down the cause of the error, we determined that it occurred inadvertently during final figure preparation by mistakenly inserting a similar-looking, but wrong, panel into the figure. We maintained all data from these experiments, which were done in 2008, so correcting the error with the proper panel was relatively straightforward. A correction, including a new Figure 3 with the correct blot and corresponding quantitation from the same blot, was sent to The Plant Cell editors on January 21, 2015. The corrected Figure 3, along with original immunoblot images, are posted on Figshare:
    http://figshare.com/articles/Garcia_Ruiz_et_al_2010_correction/1293020

    My coauthors and I were surprised and embarrassed to discover this mistake, and we sincerely regret that the paper was published with the wrong panel.

    As a side note, I initiated the review of published data produced in my laboratory because of recent questions and concerns about the integrity and accuracy of published figures in a number of papers from the plant biology and RNA silencing fields. The concerns highlight the need for all of us to ensure that our work is reported accurately and transparently. The review was a step to assure that our published work is free of systematic deficiencies or misleading practices, and to pinpoint ways in which internal practices can improve to better prevent inadvertent errors such as the one reported in this post.

    Jim Carrington”

    This implies that PubPeer has served an extremely important function in post-publication peer review in plant science, that in fact errors have already started to emerge, and that, unlike what is being suggested above, the proponents being questioned have not considered this an act of harassment, instead, an opportunity of self-evaluation and correction of the literature.

    Dr. Carrington is to be applauded for his honesty and frankness. But he does need to also acknowledge that this self-correction would not have been possible had it not been for two aspects: a) anonymity; b) PubPeer.

  • Unacceptable harassment of coauthors and others January 24, 2015 at 6:58 am

    For the commenter who is desperate for evidence that this harassment by email exists, it turns out that a recipient has now supplied some additional information at PubPeer.

    https://pubpeer.com/topics/1/877A42B12A198A44306771E0D80AB8

    “Here’s my experience with PubPeer. Recently a paper on which a faculty member from my Institution was a minor author was mentioned PubPeer. The issue, such that it was, was ‘ambiguous’ gel splicing. An email was sent to all faculty and academic staff at my Dept, ostensibly from one ‘Travis Brown’ on behalf of PubPeer from a Yahoo.com mailbox. Apparently having a paper mentioned on PubPeer ‘directly affects the researchers at, and the profile of, [my institution].’ Furthermore ‘any public commentary you can provide…would be welcomed.’

    I’m sorry, but this is utter BS, foot-jammed-in-the-door methodology. The issue does not ‘directly affect’ anyone within my Dept. Talk about overstepping the mark. Quite rightly, the email was ignored, and no response was given. Why wrestle with pigs?”

    I googled for the pseudonym used, Travis Brown. Apparently several such persons exist, one being a cyclist, another an author. Is it such a good idea to impersonate living people in spam emails?

  • Leonid Schneider January 24, 2015 at 9:16 am

    Another Voinnet paper (cautiously) flagged, Peer1 however uncertain if the errors are not compression artefacts after all. I however agree with Peer1, in such situation, where much of trust in the entire body of Voinnet’s research is at stake, authors should also investigate a false alarm.
    “Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions”
    Damien Garcia, Shahinez Garcia, Dominique Pontier, Antonin Marchais, Jean Pierre Renou, Thierry Lagrange, Olivier Voinnet, Mol. Cell, 48 (2012)
    https://pubpeer.com/publications/E9E2575F177DB45828F26B92842567

    • Unacceptable harassment of coauthors and others? January 24, 2015 at 1:46 pm

      And most definately, those who are associated with this paper should be notified, of course. If you were a co-author on a paper that was being examined publicly, would you not like to be notified? And would your institute and related academic affiliations not deserve to know that your paper was being scrutinized? After all, it’s not as if this is some redundant group working on some arbitrary soil microbe in the Bahamas. This is work that is being questioned in over 35 papers, certainly not a random number (unless this is serial and professional targeting), and in the world’ top rank of plant scientists, so individuals who are related in any way have the absolute right to know about this fact. This is not a matter of caution, it is a matter of fundamental trust.

    • researcher January 25, 2015 at 7:06 am

      It is wrong to say that “the entire body of Voinnet’s research is at stake”, the problem is about mistakes in papers (that I do not excuse), but Voinnet’s discoveries were confirmed in many independent laboratories. Don’t mix up the reality and its representation.

      • Reality check January 26, 2015 at 8:10 am

        In science a discovery has only been made if your data show that you made it. If it is found your data show something else, you simply did not make that discovery. It follows that no one can ever “confirm” a discovery that has not been made. This is the simple reality.

        • Irritated Researcher January 26, 2015 at 12:40 pm

          I think that statement could be nuanced a bit. There are fields where a theory or a conjecture can have a great influence, even in the absence of proof. Think Higgs boson, Fermat’s theorem, etc. Even in biology, a clear hypothesis can be extremely important. However, where we agree is that there should be no misrepresentation. If you are proposing a theory, that should be stated. If you say you have proved it, your data need to back that up.

  • researcher2 January 25, 2015 at 12:38 pm

    In response to researcher’s rebuttal to Leonid, I would say that this is a valid comment, and at this stage of the story, all opinions are simply opinions that will undoubtedly invoke strong doubt, and equally strong defense by the Voinnet et al. camp. Fortunately, in a balanced and moderated forum, both sides have this right to debate the issue, even if they are not directly involved with the proponents. Of course, the discussion raging on this page at RW and at PubPeer are all still completely hypothetical because the scientific community has yet to see the results of the internal investigations, and the resulting corrections of the literature, if any. Voinnet and some of his co-authors have publicly confirmed, in some cases (not all) that there are problems and that these would be corrected. It is most likely these public promises that may have spurred this story to emerge at RW. And validly so, because this could be the turning point of PPPR in plant science, so the case is being watched extremely closely to see exactly what all proponents – and those associated with them – do, and say.

    One should also note that promises to look into queries related to some papers stopped receiving public confirmations by Voinnet and/or co-authors for the past 5-10 (a rough count based on my observations of PubPeer entries being updated here at RW) papers being questioned at PubPeer. I am not sure what this says, but this is also a signifant change in the PR status of this case’s PPPR. However, it does the say the following: there was an initial stage (approximately 10 days in January) of active PR at PubPeer in which Voinnet and several co-authors gave personal guarantees at PubPeer that they were looking at the issues and claims. This was followed by relative silence, but as suggested by “Unacceptable harassment of coauthors and others”, this might be related to limitations by related parties as to what can, or cannot, be said in public with ongoing investigations.

    So, at minimum, one could expect a handful (?) of errata to emerge. If indeed there are a handful of errata, this could – once again, hypothetically – call into question several issues (but these will again not be discussed yet, because they could be interpreted as being premature). Perhaps what the commentator above was suggesting was that at this extremley high level of science (the highest in plant science), even minor errors can be interpreted as being quite a serious negative sign. Indeed, one cannot call into question the integrity of a person’s entire career, or literature although, all too often (erroneously or not), that association can occur in the minds of scientists, even if they wish to remain objective, as appears to be the case with “researcher”. It is my understanding – from what I have read at PubPeer and from the chatter I have seen on several web-sites, Twitter, etc. – that many people related to Voinnet – and even many who are not related to Voinnet – are in deep shock about the cases listed at PubPeer. Least of which are Voinnet and his many associates that have accumulated over the years, over several continents, and over several highly reputable research institutes. The mere existence of questions about their papers at PubPeer has sent a very chilling message throughout the spine of plant science researchers globally. Simply because of the potential perceived negative aspects, and their possible (unavoidable?) future implications.

    Even though we may discuss these issues anonymously, we have the responsibility of giving Voinnet et al. the time and support to investigate this situation. It appears as if all parties are aware of these papers, including the relevant journals. There is no doubt that the papers are now being handled at the highest possible levels. In the meantime, the plant science community has the responsibility of staying alert to new notices that appear at PubPeer, and to report them here at RW. For one simple reason, at the moment, there are only two web-sites that are focusing on this case to any level of depth: PubPeer and RW.

    It is a pity, however, to see such few commentators on this page. One would expect a much wider input, discussion and feedback, given the incredible repurcussions that this case will have on so many aspects of plant science, and publishing-related issues (at least related to plant science).

  • Irritated Researcher January 25, 2015 at 12:45 pm

    You have to question the work of someone who has made such a large number of mistakes over such a period of time. So far we have been shown zero original data, which hardly increases trust. Maybe the underlying science is right, but even if it is, that may not be thanks to the disputed work.

    I would also be a bit wary of replications of work that nobody suspected had any problems. I doubt they are carried out or examined with the same zeal as if the result were in doubt.

    It would be interesting for commenters to address the situation of individual results/papers on PubPeer in the light of the mistakes, as here.

    https://pubpeer.com/publications/358DABD0BE713B03950C76D7652140

    • Who is not irritated? January 25, 2015 at 4:48 pm

      This is a really excellent observation. Even though we see many anonymous comments, we can already begin to differentiate on which side of the fence they lie: scrutiny vs defense. I wish to point out one very important curiosity of the web-page you indicate at PubPeer. On January 12, 2015, Peer 4 writes, on behalf of Voinnet: “This response is from Olivier Voinnet -corresponding author on this paper. Through an anonymous email, I have become recently aware of a potential problem with this paper describing work conducted under my supervision. Since then, I have been investigating the problem and have notified the editors. My apologies for not having detecting this error before the paper was submitted.” The original concerns were posted on September 11th, 2014. PubPeer claims to contact the authors automatically. This indicates that for 3 months Voinnet and co-authors were silent. Or did they not receive the PubPeer notice? Either way, one fact is absolutely clear: had it not been for that anonymous email, a whole chain of events spanning a mere 2 weeks would not have been in place.

      As for “So far we have been shown zero original data.” Give it some time. We are dealing with papers spanning from 1998-2013, at least those being questioned at PubPeer, so this is undoubtedly a daunting task since Voinnet appears to have changed research institute a few times in that period, and has worked with umpteen leading scientists who are – despite what the protagonists would like the public to believe – directly affected by this.

  • Dani Zamir January 25, 2015 at 5:26 pm

    The anonymous sharp-eyed scientists, who identified copy pasted bands in papers coauthored by Olivier Voinnet, demand an immediate confession – right now!
    When they publish a paper don’t they use the best gels they have? And when the controls don’t look that good don’t they run the gel again “for the Figure?” And if they copy paste a control band does this invalidate all their findings? Science is a humane undertaking – we need to express our views with patience and compassion particularly when a colleague is hurting.

    • Copy pasta January 25, 2015 at 5:59 pm

      “And if they copy paste a control band does this invalidate all their findings?”

      i) It invalidates trust. Also, see above for why loading controls exist.

      ii) While the honest scientist is rerunning the gel (and establishing its reproducibility), the dishonest one has moved on to photoshopping those for the next paper. It’s hard to compete with that kind of productivity.

      iii) In this case there is a good deal more than one “control band” at stake (unless you mean the one that appears in three papers).

      iv) If you think rerunning a gel is the same as copy-pasting a control band…

    • Leonid Schneider January 26, 2015 at 1:42 am

      Dani, see comments by “Copy pasta” and my explanation about loading controls above. Also, scientists re-run a gel to achieve an equal loading, not to achieve a result they like and then copy-paste a nice image of equal loading from elsewhere.

    • J January 26, 2015 at 3:12 am

      “When they publish a paper don’t they use the best gels they have?”
      Yes, they do.

      “And when the controls don’t look that good don’t they run the gel again “for the Figure?”
      No, they’d run the gel again “for the replicates”. And if the controls run badly in all of their gels, then no, they wouldn’t run it again “for the Figure”. They’d stop and think about whether they’re wrong.

      “And if they copy paste a control band does this invalidate all their findings?”
      Yes, it does. If I sell you a car and say that everything works, and everything does work except the brakes, which fail the first time you go around a corner, would you happily get straight back into that car to drive from New York to Albuquerque? Or would you want your money back? Yeah, me too. And then I’d call the car vendor dishonest.

      ‘we need to express our views with patience and compassion’
      Really, not everybody is at it. I know good postdocs who’ve lost their jobs because experiments didn’t work, even though they really, really wanted them to. And I know mediocre scientists who’ve got grants and promotions from what I strongly suspect was misconduct. Which of those two groups do you think is more in need of ‘patience and compassion’?

  • Leonid Schneider January 26, 2015 at 1:37 pm

    Irritated Researcher
    There are fields where a theory or a conjecture can have a great influence, even in the absence of proof. Think Higgs boson, Fermat’s theorem, etc. E.

    at the risk of digressing, your examples are theories based on solid and peer-reviewable mathematics (this is why Higg’s boson was eventually detected etc), not obscure philosophical pondering. In molecular cell biology, math-based theories are rare, and otherwise you need some solid data, otherwise you theory is not a “theory”, but a philosophical construct or a fancy hypothesis. In a way, this is what creationism/intelligent design is all about.

  • Voinnet queries January 27, 2015 at 4:01 pm

    Gels in another Voinnet paper being questioned at PubPeer:
    https://pubpeer.com/publications/BBCA038B5E2EC75F15E8922FBCD8F1#fb23167
    Molecular Plant-Microbe Interactions
    October 2012, Volume 25, Number 10 Pages 1294-1306
    http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-04-12-0094-R
    http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-04-12-0094-R

    http://dx.doi.org/10.1094/MPMI-04-12-0094-R
    Functional Analysis of Gene-Silencing Suppressors from Tomato Yellow Leaf Curl Disease Viruses
    Ana P. Luna,1 Gabriel Morilla,2 Olivier Voinnet,2 and Eduardo R. Bejarano1

    1 Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Genética, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071 Málaga, Spain;
    2 Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France

  • Leonid Schneider January 28, 2015 at 3:12 am

    Another Voinnet paper flagged, and as it features several recurrent names (Dunyoer, Moissiard, Himber) the allegations should be taken seriously:
    “Transitivity-dependent and -independent cell-to-cell movement of RNA silencing”
    Christophe Himber, Patrice Dunoyer, Guillaume Moissiard, Christophe Ritzenthaler, Olivier Voinnet, EMBO J., 22 (2003)
    https://pubpeer.com/publications/449061EBFBD6BD82B2AFF7CF0AA417

  • A fact January 29, 2015 at 5:55 pm

    Dr. Olivier Voinnet is on the European Commission’s European Research Council Grant Panel, Genetics, Genomics, Bioinformatics and Systems Biology (LS2):
    http://erc.europa.eu/sites/default/files/content/selection_panel/erc_2014_stg_panel_members.pdf

  • Not Academie des Sciences January 29, 2015 at 6:29 pm

    The French Academie des Sciences elected Olivier Voinnet to membership in November last year, so a few months *after* the first posts on PubPeer.

    http://www.academie-sciences.fr/academie/membre/Voinnet_Olivier.htm

  • Virasol January 30, 2015 at 10:32 pm

    Does anyone know if Prof. Olivier Voinnet attended the SWISSPLANT 2015 Symposium, 28–30 January 2015?
    https://swissplantscienceweb.ch/research/swissplant-2015-symposium/
    Given the circumstances, maybe a SWISSPLANT representative could provide some feed-back or commentary at Retraction Watch.

  • reli February 3, 2015 at 6:10 am

    Does anyone know if Prof. Olivier Voinnet will attende the keystone symposia RNA Silencing in Plants, 17–22 February 2015?
    http://www.keystonesymposia.org/15G1
    Some of the of Voinnet co-authors, like Thierry Lagrange, involved in the pubpeer papers will be present. As suggested by Virasol, given the circumstances, maybe a keystone representative could provide some feed-back or commentary at Retraction Watch.

    • Andikoerper February 12, 2015 at 2:12 pm

      A brief look on the conference schedule revealed that he is one of the speakers.

    • Did Voinnet appear? February 25, 2015 at 1:53 pm

      Does anyone know if he made it to this meeting last weekend and said anything else about the growing controversy?

  • Leonid Schneider February 10, 2015 at 6:12 am

    We at Laborjournal were informed by the organiser that Olivier Voinnet did not participate in the SWISSPLANT 2015 Symposium.

  • Correction February 18, 2015 at 7:22 am

    The first correction has appeared in the 2004 Genes & Development paper:
    Genes & Dev. 2015. 29: 465
    http://genesdev.cshlp.org/content/29/4/465.full
    The original:
    http://genesdev.cshlp.org/content/18/18/2237.short

    Unfortunately, a 20 US$ paywall. Anyone with access, please post the full text here, for the public record. Perhaps someone could convince Cold Spring Harbor Laboratory Press that there is more value in public visibility than 20$/one day download.

    Apparently, Voinnet did not attend SWISS PLANT 2015.

  • Leonid Schneider February 18, 2015 at 9:46 am

    Genes and Development publishes an Erratum for one of the criticised Voinnet-papers (Parizotto et al, 2004):
    http://genesdev.cshlp.org/content/29/4/465.full
    http://imgur.com/p8zPJuk
    This Erratum utterly ignores the concerns raised on Pubpeer , but corrects an hitherto unnoticed case of image aberration. Why is this and why is this bizarre erratum behind paywall?

  • Voinnet appeared February 25, 2015 at 11:18 pm

    Voinnet appeared. However, it is unclear what was discussed behind closed doors or between partners. Perhaps the Keystone Symposium organizers, Voinnet or some of his partners might like to provide some feedback?

  • Secondhand Tweet about Voinnet Keystone appearance February 26, 2015 at 8:34 pm

    This Tweet is not from a direct observer at the Keystone meeting, so it will be interesting to learn any details of what Voinnet “acknowledged + claimed responsibility for” and what exactly “figure shenanigans” entail:

    David Baltrus ‏@surt_lab Feb 21
    Just heard (secondhand) that Voinnet acknowledged + claimed responsibility for figure shenanigans while speaking at Keystone meeting.

  • Voinnet queries March 12, 2015 at 2:47 pm

    2 months have passed. Can Voinnet and authors please indicate when we can get an update or some public accountability for the queries into the approx. 30-35 papers questioned at PubPeer?

  • Update March 27, 2015 at 2:26 pm

    The English version of the LabJournal editorial, written by Leonid Schneider, and focusing on Olivier Voinnet, is available:
    http://www.labtimes.org/editorial/e_594.lasso

  • Prizes March 29, 2015 at 5:14 pm

    A web search reveals that Olivier Voinnet has obtained a lot more than the Roessler prize mentioned in Leonid’s article, if my understanding of these links is correct.

    http://www.lemonde.fr/disparitions/article/2009/06/11/nominations-le-monde-date-vendredi-12-juin_1205674_3382.html

    http://www2.cnrs.fr/presse/communique/1242.htm

    The first was a prize of 750k that was presumably shared, while the second was worth 250k. So he has obtained more than 800k in prizes. Nice work if you can get it.

    Amusingly, the EMBO Gold Medal is only worth 10k in money terms.

    • PS March 29, 2015 at 11:19 pm

      The second link is fascinating. It states (my translation): “At only 35 years of age, he has authored 36 publications, 9 of which are in Nature or Science, with a very high citation index.” The article then lists the following prizes and distinctions:
      “2007 Membre permanent de l’EMBO (European Molecular Biology Organization)
      2007 Médaille d’argent du CNRS
      2006 Médaille d’Or de l’Académie d’Agriculture de France
      2005 Grand Prix de la Fondation Schlumberger pour l’Education et la Recherche
      2005 Prix Victor Noury, Thorlet, Henri Becquerel, Jules et Augusta Lazare de l’Académie des Sciences
      2004 Médaille de bronze du CNRS
      2002 Science Magazine Prize for Young Scientist of the year”

      Does anyone have a detailed list of the prizes from 2008-2015?

  • Fizz April 1, 2015 at 1:47 pm

    Le Monde, one of France’s premier newspapers, is covering the Olivier story:
    http://www.lemonde.fr/sciences/article/2015/03/31/une-star-de-la-biologie-dans-la-tourmente_4606643_1650684.html
    The introductory line (my translation):
    “Major scientific fraud or a series of misaligned benign negligences?”

  • D April 2, 2015 at 8:43 am

    Why does the Lab Times article claim in the abstract that “more than 30 of his publications” contain suspicious figures, although it is clear from the discussion here and elsewhere, that for many of them it is not entirely clear whether these are e.g. compression effects. Although I clearly see and condemn the scientific misconduct that had happened in some papers, I would like to ask all people that write articles like this one to stick to the facts! Not doing it looks for me like a campaign and after reading this article, I don’t actually see a huge difference between Lab Times and other newspapers such as ‘The Sun’ or the german ‘Bild’.

    • Leonid Schneider April 24, 2015 at 5:33 pm

      Aplogies for delayed reply. It far from being clear to me that anything at all was a compression artefact, actually, by now some new papers or new aspects came under criticism. Sticking to the facts, 30-35 publications have been questioned on PubPeer. Meanwhile there have been new developments I have reported recently: http://www.labtimes.org/editorial/e_600.lasso

      • JH April 28, 2015 at 12:25 pm

        Guilty until proven innocent, or innocent until proven guilty. The way you write the article strongly implies that everything is proven already, that is not true. Yes, proven to be guilty in one case (-> retraction). 34 other publications -> please wait for the official statements and corrections/retractions. So we really have to be careful! If I would have gotten information from a website, where people can anonymously post that someone punched or killed 35 people, although it is not entirely (!!) clear what had happened, would it be ok to write an article entitled: “Too much to be nothing”, which implies that the person indeed punched or killed 35 people (or at least 10-15)?

  • relij April 24, 2015 at 9:59 am

    Institut de France posted a film about the work of Prof Voinnet just 2 hours ago while the CNRS sets up a scientific commission of inquiry.
    https://www.youtube.com/watch?v=ANntLsH8tGI

    • JATdS April 24, 2015 at 12:42 pm

      The film simply reports on the importance of the Vaucheret/Voinnet work, not on its accuracy. IT would be very important to have independent scientists involved with RNA silencing-mediated antiviral defense in plants come forward with their opinions and analysis. An institutional video contributes almost nothing to clarity, only to defending their image.

  • Corrigendum issued April 29, 2015 at 11:25 am

    James C. Carrington issues a correction:
    http://www.plantcell.org/content/27/3/944.full.pdf+html
    “An incorrect immunoblot panel for samples from inoculated leaves was mistakenly included in Figure 3A. The data for coat protein (CP) accumulation in inoculated leaves in the original panel A were incorrectly based on the samples from systemically infected inflorescence tissues shown in panel B (7 DAI time point). This was an inadvertent mistake, as the blots were very similar in appearance. A corrected version of Figure 3A using the intended inoculated leaf samples and corresponding recalculated values for relative levels of CP/infection focus (shown in panel A) is given here.” “The figure legend is unchanged from the original version. This correction does not affect any of the conclusions of the article. We regret that this error was not detected prior to publication.”

    Original paper:
    Hernan Garcia-Ruiz, Atsushi Takeda, Elisabeth J. Chapman, Christopher M. Sullivan, Noah Fahlgren, Katherine J. Brempelis, James C. Carrington (2010) Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip mosaic virus infection. Plant Cell 22: 481–496.
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845422/
    http://www.plantcell.org/content/22/2/481.abstract
    http://www.plantcell.org/content/22/2/481.full.pdf+html?with-ds=yes

    https://pubpeer.com/publications/7850A6E12550CB11D8E88A65D37546

  • Another correction May 14, 2015 at 3:10 pm

    Correction appears for the 2013 PLoS Genetics paper:
    http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003791
    14 May 2015: Ciaudo C, Jay F, Okamoto I, Chen CJ, Sarazin A, et al. (2015) Correction: RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells. PLoS Genet 11(5): e1005247. doi: 10.1371/journal.pgen.1005247
    http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005247
    Note also: http://imgur.com/OD2Xpsv

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