Research Scientist: an academic career launch pad

After a long start to 2020 including the past four very busy weeks, I’m happy to announce that today March 16th 2020 I accepted a position as Research Scientist at the Lieber Institute for Brain Development in Baltimore, MD, USA.


What will I do as a Research Scientist at LIBD?

At LIBD we currently have the following scientific ranks:

  • Research Technician
  • Research Assistant
  • Research Associate
  • Staff Scientist I, II and III
  • Research Scientist (+ Lead and Senior)
  • Investigator (+ Lead and Senior)

Research Scientists carry out research, do so scholarly, are tasked with being creative, are encouraged to seek funding, and can have supervisory and mentor roles.

In my agreement with LIBD, I will remain affiliated with the Data Science Team I led by Andrew E Jaffe while also having the opportunity to interact with and collaborate with fantastic biologists, data scientists, and researchers at LIBD, Johns Hopkins University, and beyond. Furthermore, I will officially help mentor LIBD scientists in data science and R tools. LIBD will support me while I build a small team around my research interests and prepare my first set of grant submissions. There will be a transition period and many things I need to learn: from requesting a budget to writing a job ad, as well as many details about grant requests. But ultimately, LIBD offered me a launch pad for an academic career.



One of my first tasks will be to refine the details of my role. For example, right now on the teaching side of things I’m imagining doing the following:

  • Lead a weekly LIBD rstats club meeting where I can go over topics common to several users.
  • Hold one-on-one data science guidance sessions, similar to the MPH capstone sessions I did during my teaching assistant years at JHBSPH.
  • Occasionally lead internal workshops, which could benefit from workshops I prepare for CDSB and elsewhere.
  • Get certified by RStudio and attend more R conferences & workshops.

From the scientific side, I will also learn more about the biological questions my LIBD colleagues are working on. These hypothesis-driven projects will provide me a new set of challenges and I will perform what me and my LCG-UNAM classmates were trained to do: to function as a bridge between multiple fields. I will also keep learning from my JHU colleagues and working with them as I refine my ideas. Currently, this is how I have framed my research interests:

My research aims to better understand the roots and signatures of disease (particularly psychiatric disorders) by zooming in across dimensions of gene activity: from studying gene expression at all feature levels (genes to exons to exon-exon junctions and un-annotated regions of expression), to using different gene expression measurement technologies (bulk RNA-seq, single cell/nuclei RNA-seq to spatial transcriptomics) that provide finer biological resolution and localization of gene expression. I’m interested in both hypothesis-driven projects as well as building general resources such as recount2 that enable us to contextualize our findings across all of the public human gene expression landscape. I use the R programming language for nearly all my work and like to organize my code in R packages that I share mostly through the Bioconductor project.


unsplash-logoMarvin Meyer

As for building my team, I know that overall one of the challenges everyone faces is recruiting talent. I’ll give this complicated process a shot by tapping into my network which includes many immigrants. I will also expand my network online and through conferences. Furthermore, I am committed to my outreach projects such as CDSB but will synergize them even more: re-use training materials, potentially recruit team members, and help me expand my network. In the meantime, if you are interested in working with me or my colleagues, please let me know!

Final decision

The decision I had to make was challenging, but in the end, I decided to stay at LIBD because they offered me a path to become a principal investigator in academia which it’s something I want to explore and see where it leads me. I will also formally be someone’s boss and gain managerial experience, work much closer with biologists in hypothesis-driven projects, and overall gain more experience and skills. My brother’s job tasks changed last week, to which I told him: “welcome to the real world”. Well, I guess that’s how it’ll be for me too.


I want to thank everyone that helped me through this decision-making process, provided me with information, asked me questions, answered questions, expanded my universe, advocated for me, advised me, cheered for me, and supported me. Thank you! I look forward to working with you!


This blog post was made possible thanks to:


[1] C. Boettiger. knitcitations: Citations for 'Knitr' Markdown Files. R package version 1.0.12. 2021. URL:

[2] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.28.0. 2023. DOI: 10.18129/B9.bioc.BiocStyle. URL:

[3] H. Wickham, W. Chang, R. Flight, K. Müller, et al. sessioninfo: R Session Information. R package version 1.2.2. 2021. URL:

[4] Y. Xie, A. P. Hill, and A. Thomas. blogdown: Creating Websites with R Markdown. Boca Raton, Florida: Chapman and Hall/CRC, 2017. ISBN: 978-0815363729. URL:


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Leonardo Collado-Torres
Leonardo Collado-Torres
Investigator @ LIBD, Assistant Professor, Department of Biostatistics @ JHBSPH

#rstats @Bioconductor/🧠 genomics @LieberInstitute/@lcgunam @jhubiostat @jtleek @andrewejaffe alumni/@LIBDrstats @CDSBMexico co-founder

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