Departmental Affiliations
Leonardo Collado Torres, PhD '16, develops open-source tools for analyzing genomic data to understand gene expression in the human brain and its role in neuropsychiatric disorders.
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: LIBS 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.
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.
When I write code, 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.
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, 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.
Huuki-Myers LA, Spangler A, Eagles NJ, Montgomery KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, Hyde TM, Kleinman JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, Collado-Torres L, Maynard KR. A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science. 2024 May 24;384(6698):eadh1938. doi: 10.1126/science.adh1938. Epub 2024 May 24. PubMed PMID: 38781370; PubMed Central PMCID: PMC11398705.
Huuki-Myers LA, Montgomery KD, Kwon SH, Cinquemani S, Eagles NJ, Gonzalez-Padilla D, Maden SK, Kleinman JE, Hyde TM, Hicks SC, Maynard KR, Collado-Torres L. Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex. Genome Biol. 2025 Apr 7;26(1):88. doi: 10.1186/s13059-025-03552-3. PubMed PMID: 40197307; PubMed Central PMCID: PMC11978107.