Recently, Matthias Mann and colleagues published a preprint (doi: 10.1101/2020.12.22.423933v1) reporting a label-free mass spectrometry method for single-cell proteomics. Many colleagues asked me what I think about the preprint, and I summarized a few comments in the peer review below. I did not examine all aspects of the work, but I hope my comments are … Continue reading Label-free single-cell proteomics
My experience with elite journals
Over the last 15 years, my opinion about the significance of publishing in elite journals has evolved considerably. Below are some of main phases and the factors that have shaped my opinion: As a beginning PhD student, I took several classes based on discussing primary research papers. Many of these papers, especially in my biochemistry course, … Continue reading My experience with elite journals
Promoting (your) research
"I am a scientist focused on conducting research, not on promoting it." This thinking strongly resonated with me when I was a PhD student. If it resonates with you, read on to learn why and how you should promote (your) research. Common approaches to promoting your research include aiming to publish your papers in elite … Continue reading Promoting (your) research
Bibliography for NIH proposals
NIH requires adding PMCID to references cited in proposals, and PMCID may be difficult to add because many reference libraries and citation styles omit them. As a result, some colleagues add them manually, which is rather time consuming. To avoid this drudgery, I wrote a couple of scripts available from this GitHub repository that allow … Continue reading Bibliography for NIH proposals
The cost of omics
Next generation DNA sequencing is ubiquitously integrated in modern biomedical research while mass-spectrometry proteomics remains less ubiquitous. In fact, mass-spectrometry proteomics is conspicuously missing from projects that desperately need it. Why is DNA sequencing better integrated with biomedical research? This question comes up often in my conversations with colleagues. A commonly suggested answer is the … Continue reading The cost of omics
Research success
We -- the research community -- can be much more successful if we invest more time and effort in what matters: Coming up with original new leads and helping each other grow as scientists and people. Happy and successful year to everybody!
The bigger picture
Publishing a paper in a top journal may be relatively unimportant.
When do you need single-cell analysis?
At HUPO, I have been repeatedly asked: "Why analyze single cells when you can identify more peptides in bulk samples?"
Direct causal mechanisms
Understanding biological systems: In search of direct causal mechanisms The advent of DNA-microarrays spurred a vigorous effort to reverse engineer biological networks. Recently, these efforts have been reinvigorated by the availability of RNA-seq data from perturbed and unperturbed single cells. In the talk below, I discuss the opportunities and limitations of using such data for … Continue reading Direct causal mechanisms
Evaluating preprints
I am hugely enthusiastic for communicating research by preprints. So naturally, I am happy to see when the president and strategic advisers of one of the most elite funding institutes embraces preprints: https://twitter.com/slavovLab/status/1095734247384641541 For centuries, publishing a scientific article was just about sharing the results. More recently, publishing research articles in a journal has served … Continue reading Evaluating preprints
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