What do we publish?
While we routinely help our customers in conducting and publishing original research, our bioinformaticians have authored quite a long list of papers on their own as well. Here we summarize our team's papers in a few graphs.
Sense of tumor, above all
As of May 2022, our publication list in Google Scholar has almost 400 items with over of 21,000 citations combined. Most are normal publications in academic journals, but the list includes manuals, theses, patent applications and other less typical items as well.
The word cloud below shows the 120 most frequent words in the titles of our papers. The frequency ranges from six to 106 occurrences (for "cancer"). The types of word ranges from uninformative ("during", "between") to jargony ("landscape", "characterization") to slightly specific ("cancer", "gene") and even more specific ("hydroxylase", "androgen").
(The markedly pronounced "prostate" is just a benign telltale of our Chief Scientific Officer's research focus.)
The most frequent words reveal a strong cancer bias. Although our bioinformaticians come from a wide range of backgrounds — from computer science to evolutionary biology —, cancer research is clearly the most common major topic. Of our team's most cited papers, 44% are directly related to cancer (14 out of the 32 papers with more than 100 citations). More specifically, prostate cancer, leukemia, glioblastoma and breast cancer appear to be the most studied malignancies in our team.
Overall, the terms suggest a strong leaning towards biology as opposed to algorithms — stronger than one may have assumed from a bioinformatics team. This shows that our bioinformaticians, out of choice or necessity, have been collaborating more with biologists rather than developing computational tools on their own. The most cited paper, however, is an exception. Published in the journal Bioinformatics, it presents a tool called BUSCO, which is widely used to assess genome assemblies.
Where do we publish?
On below left, we have plotted the average number of citations our papers have in each journal against the total number of papers we have published in it. The top five journals by citations are Bioinformatics, Nature, Cell, Science and Molecular Biology and Evolution. While the number of citations is high in these journals, (from several hundreds to thousands), we do not publish in them very often: apart from Molecular Biology and Evolution, our team has one or two papers in each of these journals. Papers with no citations (most of the very recent ones) were excluded.
The top five journals by the number of papers our team members have authored are PLoS One, Nucleic Acids Research, Journal of Biological Chemistry, Nature Communications and Genome Biology and Evolution. We have nine articles in PloS One and seven in the other four journals each.
While we only show the actual citations of our papers and not the journal impact factors, there seems to be a connection between the two. (Just how much the number of citations is due to the prestige of the journal is a separate question...)
The plot above on the right shows the citations of individual papers across time. We see that the number of citations tends to grow strongly for the first few years, and rarely reaches several hundred or more.
Enough graphs! To browse the actual papers, see our scientific references.
You will find papers resulting from our customer projects under our genomic, transcriptomic and epigenomic analysis pages. (See the "Selected publications from our customers" sections — these are papers which our customers have published with our help.)
And finally, dear reader(s?), I must ask you to leave us a message if you are interested in our 'omics analysis service. Just a 30-minute discussion about your data analysis needs with one of our bioinformaticians may go a long way to speed up your projects!