Departmental Affiliations
Contact Info
Research Interests
At the Lieber Institute for Brain Development (LIBD), our group works on understanding the roots and signatures of disease (particularly psychiatric disorders) by zooming in across dimensions of gene activity. We achieve this by studying gene expression at all expression feature levels (genes, exons, exon-exon junctions, and un-annotated regions) and by using different gene expression measurement technologies (bulk RNA-seq, single cell/nucleus RNA-seq, and spatial transcriptomics) that provide finer biological resolution and localization of gene expression. We work closely with collaborators from LIBD as well as from Johns Hopkins University (JHU) and other institutions, which reflects the cross-disciplinary approach and diversity in expertise needed to further advance our understanding of high throughput biology.
In order to provide a supportive and stimulating research environment at LIBD, our group provides Data Science guidance sessions open to any LIBD staff member and we organize the LIBD rstats club, among other initiatives. Our documentation book website contains more details for on boarding, how to ask for help, bootcamps, writing papers, authorship, configuration files, and much more.
Check out the content we share
We constantly create new content to share what we are learning or working on, which you might be interested in. In particular, we:
- run the LIBD rstats club: rstats club schedule
- discuss papers and software in our team meetings: team meeting schedule
Join the team
If you are interested in joining the R/Bioconductor-powered Team Data Science group, please check our open positions at the LIBD career opportunities website. You might be interested in checking our anonymous team survey results, which highlights some strengths but also some weaknesses and areas we can improve.
If we don’t have any open positions, please reach out to Leonardo with your CV, GitHub/GitLab/etc profile with open-source software, and a short description of why you are interested in our team.
Experiences & Accomplishments
At the Lieber Institute for Brain Development (LIBD), I lead the R/Bioconductor-powered Team Data Science group. I am also an Assistant Professor in the Department of Biostastics at the Johns Hopkins Bloomberg School of Public Health. Additionally, I am interested in outreach activities as a board member of the Community of Bioinformatics Software Developers.
As a quick background, I graduated from the Undergraduate Program on Genomic Sciences from the National Autonomous University of Mexico (UNAM) in 2009 and worked for two years at Winter Genomics analyzing high-throughput sequencing data. I then got a PhD in 2016 from the Department of Biostatistics at Johns Hopkins Bloomberg School of Public Health thanks to a CONACyT scholarship. There I worked with Jeff Leek and Andrew Jaffe in developing derfinder and recount. I then worked ~ 4 years as a Staff Scientist and Research Scientist in Andrew Jaffe’s lab on a variety of data analysis projects. I became a principal investigator in September 2020.
Every day I use R and Bioconductor, and on some days I write R packages. Occasionally I write blog posts about them and other tools. I’m a co-founder of the LIBD rstats club and the CDSB community of R and Bioconductor developers in Mexico and Latin America, that we described at the R Consortium website. In the past, I also served on the Bioconductor Community Advisory Board and the advisory board for rOpenSci’s Statistical Software Peer Review.
Honors & Awards
See https://lcolladotor.github.io/cv/#honors for Leo's honors.
Select Publications
Check https://lcolladotor.github.io/#publications, ORCiD, or Google Scholar for all of Leo's publications including pre-prints.
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29. PubMed PMID: 27694310; PubMed Central PMCID: PMC5314792.
Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Reproducible RNA-seq analysis using recount2. Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. PubMed PMID: 28398307; PubMed Central PMCID: PMC6742427.
Collado-Torres L, Burke EE, Peterson A, Shin J, Straub RE, Rajpurohit A, Semick SA, Ulrich WS, Price AJ, Valencia C, Tao R, Deep-Soboslay A, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE. Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia. Neuron. 2019 Jul 17;103(2):203-216.e8. doi: 10.1016/j.neuron.2019.05.013. Epub 2019 Jun 4. PubMed PMID: 31174959; PubMed Central PMCID: PMC7000204.
Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams SR, Catallini JL 2nd, Tran MN, Besich Z, Tippani M, Chew J, Yin Y, Kleinman JE, Hyde TM, Rao N, Hicks SC, Martinowich K, Jaffe AE. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nat Neurosci. 2021 Mar;24(3):425-436. doi: 10.1038/s41593-020-00787-0. Epub 2021 Feb 8. PubMed PMID: 33558695; PubMed Central PMCID: PMC8095368.
Pardo B, Spangler A, Weber LM, Page SC, Hicks SC, Jaffe AE, Martinowich K, Maynard KR, Collado-Torres L. spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data. BMC Genomics. 2022 Jun 10;23(1):434. doi: 10.1186/s12864-022-08601-w. PubMed PMID: 35689177; PubMed Central PMCID: PMC9188087.