Departmental Affiliations
Contact Info
Research Interests
At the Lieber Institute for Brain Development (), 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 open to any LIBD staff member and we organize the , among other initiatives. Our 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:
- discuss papers and software in our team meetings:
Join the team
If you are interested in joining the R/Bioconductor-powered Team Data Science group, please check our open positions at the . You might be interested in checking our , 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.
Additional Links
Experiences & Accomplishments
At the Lieber Institute for Brain Development (), I lead the group. I am also an Assistant Professor in the Department of Biostastics at the Johns ÎÚÑ»´«Ã½. Additionally, I am interested in outreach activities as a board member of the .
As a quick background, I graduated from the from the National Autonomous University of Mexico () in 2009 and worked for two years at Winter Genomics analyzing high-throughput sequencing data. I then got a PhD in 2016 from the at thanks to a . There I worked with and in developing and . 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 and , and on some days I . Occasionally I write about them and other tools. I’m a co-founder of the and the of R and Bioconductor developers in Mexico and Latin America, that we described at the . In the past, I also served on the and the advisory board for .
Honors & Awards
See for Leo's honors.
Select Publications
Check , , or 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. 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. 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. 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. 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. BMC Genomics. 2022 Jun 10;23(1):434. doi: 10.1186/s12864-022-08601-w. PubMed PMID: 35689177; PubMed Central PMCID: PMC9188087.