Category Archives: Update

Update: The BuzzCloud for 2016

A new year has begun, so it is time for an update of the BuzzCloud.


Comparing it to the cloud from 2015 year, it is clear that not much has happened in terms of new scientific buzzwords. However, readers of this blog will likely be pleased to see that the terms “data analytics”, “data science”, “data technology”, and not least “citizen science” and “open science” are all trending.

Update: The BuzzCloud for 2015

Having just downloaded the new Medline baseline, it is time to update the BuzzCloud and see what has changed since last year:


Comparing the cloud to that of last year, one new notable term is medical proteomics, which I believe is indeed something we will see become reality over the next years. The term precision medicine keeps going strong and has spawned a related term, namely precision oncology. Also related to this topic, wearable electronics receive increasing attention in the biomedical literature.

Update: The BuzzCloud for 2014

It has been almost two years since the last BuzzCloud update. So this update is well overdue:

BuzzCloud 2014

As you can see two of the biggest buzzwords in the cloud are computational proteomics and precision medicine. I am obviously quite happy to see that, considering that I currently have an open postdoc position in proteome bioinformatics and is involved in work on data mining of electronic health records.

Update: The BuzzCloud for 2011

With the Oscars out of the way, it is time for the much more important scientific awards of of the year. It is with great pride that I can present to you the best of buzzwords 2011:

Click the image for an interactive version of the BuzzCloud. For an explanation of how to understand the visualization, please see the original BuzzCloud post.

The awards are:

  • Best upcoming buzzword. The word in the cloud that looks most to me as an actual upcoming buzzword is optogenetics. It appeared first as a strong newcomer on the 2010 cloud, and it has only strengthened since.
  • BuzzWord most ready for retirement. The award goes to synthetic biology, which first appeared on the cloud of 2004; despite being an exciting field, as buzzwords go it is becoming long in the tooth. Close runner up is omics, which first appeared on the cloud of 2005.
  • Worst single-journal buzzword of 2011. Again this year we see buzzwords that have made it onto the cloud thanks to a single journal. The award is split between theranostic nanomedicine, which is pushed by the journal Accounts of Chemical Research, and vaccinomics, which is pushed by the (unfortunately named) journal OMICS. The irony that two distinctly medical-sounding buzzwords are championed by two non-medical journal has not escaped me.
  • Worst buzzword to fail to disappear. In the BuzzCloud for 2010, I pointed out that astrology had to my horror popped up as a new buzzword in the biomedical literature. Sadly it has failed to disappear from the cloud in 2011!

Update: The BuzzCloud for 2010

With about one month delay relative to the release of the new baseline of PubMed, here is the updated BuzzCloud visualization for what was hot and up-coming 2010 (click image for larger interactive version):

Here is a quick overview of some of the trends that I found interesting:

  • Geoepidemiology. A bit of searching in PubMed reveals this to be a buzzword primarily due to the journal Autoimmunity Reviews, which for some reason decided to publish 19 papers with this word in the title in 2010.
  • Network pharmacology and systems pharmacology. Due to my personal interests, these buzzword caught my eye although they were mentioned in only 7 and 11 papers from 2010, respectively. I would have been more pleased of one of those had not been in a journal with a history of publishing pseudoscience.
  • Metatranscriptomics and viral metagenomics. With metagenomics becoming reality rather than mere buzz, related and derived terms are predictably following suit.
  • Orbitrap technology and iTRAQ proteomics. Like metagenomics, large-scale proteomics has become an established field. This is well reflected by two of the best-known proteomics technologies appearing in the 2010 BuzzCloud.
  • Astrology. Falling firmly in the “dislike” category, I can only hope that it will be gone in next year’s BuzzCloud.

Update: The BuzzCloud for 2009

It is that time of the year again: NCBI has rolled out the new PubMed baseline, and it is my pleasure to present you with the latest and greatest of biomedical buzzwords. I present to you the BuzzCloud 2009 (click for a larger interactive version):

In case you have no idea what a BuzzCloud is, it is a visualization of some of the most trendy words in PubMed. To make a long story short, the size of the word represents how many times it was mentioned in the past, whereas the brightness represents how much it was mentioned in the year compared to the previous ten years. For more details, please refer to the original blog post.

The three largest words on the BuzzCloud 2009 are all reruns from earlier years: metagenomics and synthetic biology were both first seen on the BuzzCloud 2004) and click chemistry appeared in 2006. One can only conclude that these research areas continue to grow.

At the other end of the scale we have the small and bright words. These are the words that are rising most rapidly but have not appeared that many times in PubMed yet. Below are three selected examples that I think may be of particular interest to the readership of this blog.

  • Personal genomics. No surprise here except that I expected this word would have turned up much earlier considering the broad publicity of the 1000 Genomes Project and the Personal Genome Project.
  • Proteogenomics. Why we need a separate word for referring to the combination of proteomics and genomics is beyond me. There is even a paper on comparative proteogenomics published in Genome Research. One can only wonder when someone will compare metabolomics, proteomics, transcriptomics, and genomics data across environmental samples and coin the term comparative metametaboproteotranscriptogenomics.
  • Translational bioinformatics. Where bioinformatics meets clinical medicine (see blog post by Russ Altman). I think that bioinformaticians are indeed increasingly working on medically relevant data, which in my view is a good thing. It just makes me wonder what happened to medical informatics?

On a closing note, I am again pleasantly surprised how well the words picked up by a completely automated procedure fit with the ongoing activities in my lab. It is almost eerie.

Update: The BuzzCloud for 2008

Yes, it is that time of the year again – we are now almost three weeks into 2009, most papers published in 2008 have hopefully made it into Medline, and it is time to reveal the words of 2008. In other words, I have updated the BuzzCloud resource and here is the result for 2008 (click on the image to go to the web resource):

BuzzCloud 2008

I am thrilled to see the outcome. Without any cheating or tweaking, several buzzwords related to proteomics make it on the list with “phosphoproteomics” and “quantitative phosphoproteomics” being the two most prominent of them. Nice for me to see considering that my new research group at the Novo Nordisk Foundation Center for Protein Research will focus heavily on improving and applying the NetworKIN and NetPhorest resources for analysis of phosphoproteomics data.

Update: Warda and Han, one month after the storm

As most readers of this blog are probably aware, Mohammad Warda and Jin Han published a paper in Proteomics that contained several pages of text copied from unreferenced sources. Exactly one month ago it was thus retracted “due to a substantial overlap of the content of this article with previously published articles in other journals”.

Plagiarism is, however, not the main issue. The paper by Warda and Han also claimed to disprove the endosymbiotic origin of mitochondria, mentioned fingerprints of a mighty creator, and proposed mitochondria to be the missing link between the body and the preserved wisdom of the soul!

It remains a mystery how a manuscript with such unsubstantiated claims was accepted for publication in a respectable, peer-reviewed journal. The retraction notice by Proteomics made no attempt to explain this, and their approved draft press release merely states that it was due to “human error”. I would have been really worried if it could happen without human error being involved. Although this draft was approved a month ago, the final version is nowhere to be found on the internet, also not on the Proteomics website. I thus wonder if an official press release was ever published.

Attila Csordas, PZ Myers, Steven Salzberg, and I have decided to mark the one month anniversary of the retraction by pointing out the important questions that still remain to be answered by the Editor in Chief of Proteomics, Prof. Michael J. Dunn.

The manuscript contains four parts with unsupported claims that should have been caught by any peer reviewer or editor:

  1. Title – “Mitochondria, the missing link between body and soul”.
  2. Abstract – “These data are presented with novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative”.
  3. Section 3.4 – “More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life”.
  4. Conclusions – “We realize so far that the mitochondria could be the link between the body and this preserved wisdom of the soul devoted to guaranteeing life”.

My questions to Michael J. Dunn are when in the publication process these parts first appeared:

  1. Were they already in the initial version that was submitted to Proteomics and sent out for peer review?
  2. Did they appear in a revised version that was sent to the peer reviewers?
  3. Were they introduced in a revised version that was accepted without sending it to the reviewers?
  4. Or were they added at the copy editing stage, that is after the manuscript had formally been accepted?

I want to make explicit that the aim with these questions is not to place the blame but to elucidate what went wrong in the publication process. To prevent similar incidents inthe future, it is important to know whether the editor and the peer reviewers overlooked glaring flaws of the manuscript or if the flawed parts were introduced after peer review. It is not important who the editor and the peer reviewers are. I sincerely hope that Prof. Dunn will help improve the procedures for peer reviewed publication by answering the questions in this post and in the related posts on PIMM, Pharyngula, and Genomics, Evolution, and Pseudoscience.

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Update: Not treasure but buried

There is good news regarding the Warda and Han scandal. After numerous researchers including myself emailed the Editor in Chief of Proteomics, Michael J. Dunn, the paper is now listed as retracted. I am pleased to see that the editorial team of Proteomics has acted swiftly against plagiarism.

Edit: The last author of the paper, Jin Han, has written a reply to PZ Myers. According to the email, he has himself contacted the editorial office and requested that the paper be retracted. I am still looking forward to hearing an official explanation from Proteomics of how this paper got accepted in the first place.

Edit: Michael J. Dunn has emailed me a copy of the approved press release from Proteomics that announces the retraction of the paper by Warda and Han. The only explanation offered is that the paper made it through peer review due to “human error” – or in other words “someone did something wrong”. I would have been truly worried if a paper like this had been accepted without human error being involved. I hope that Proteomics will provide the scientific community with more details when they have completed the internal investigation of the incident.

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