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.
We constantly create new content to share what we are learning or working on, which you might be interested in. In particular, we:
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.
that drive us
Genomics, R programming, Biostatistics, Teaching, Diversity
bulk RNA-seq, workflows, machine learning methodologies
bulk and single cell RNA-seq, building computational pipelines
bulk and single cell RNA-seq, spatial transcriptomics, RNA scope data, DEGs, data visualization
bulk and single cell RNA-seq, spatial transcriptomics, building computational pipelines
Pharmaceutics, Drug discovery, Pharmacogenomics
Developmental biology, Transcriptomics - Epigenetics, ML
R programming, Biostatistics, Clinical Research
transcriptomics, human evolutionary genomics
R programming, Regeneration, Stem cells
RNA-seq, gene-networks, data processing/pipeline building
R programming, Human diseases, Science communication
Invited seminar by Mina Ryten
For an overview of our recent work, check this video and companion slides.
Presentation about our work at CDSB for the JSM 2020 session organized by Stephanie Hicks; Show Me the Data: Making Statistics and Data Science More Diverse and Inclusive in 2020.
† indicates corresponding author, * indicates equal contribution
I’m excited for the opportunity to participate at the #CZILatAmMtg in 2023 organized by CZI Science. I’m also thankful to those who nominated me, and in particular to Alejandra Medina Rivera.
Yesterday there was a controversy because the Mexican Women’s softball team at the Tokyo 2020 Olympics (Wikipedia, Instagram) threw several uniforms and equipment to the trash (source: ESPN). Right now I’m really disappointed with the negative reaction and personal attacks against the members of said team.
Today was an unusual day at work given the US Elections. This meant that I had fewer meetings than what I’ve had lately. Earlier in the day I noticed an email announcing that the Bioconductor 3.
Today I have accepted a new role at the Lieber Institute for Brain Development (LIBD) as an Investigator. Since LIBD is affiliated with Johns Hopkins University (JHU), LIBD will support me on becoming a JHU faculty member ^[The rules are Department and School specific at JHU, which is something that I have yet to explore in detail.
Oh ohh! 😱 What do you do now? The data me and my colleagues work with is typically too big for our personal computers, so we use a high performance computing environment (cluster) and mostly interact with it through the command line terminal.
While working at Winter Genomics I taught two courses for students of the Biomedical Sciences PhD Program (PDCB) from the National Autonomous University of Mexico (UNAM).
While I was at the Institute of Biotechnology (UNAM) working with the Winter Genomics crew I organized two courses. One was a series of various bioinformatics and biology mini-courses and another one involved members of different academic institutions.
I taught three courses during my undergrad stage at the Undergraduate Program on Genomic Sciences (LCG). Each of these courses has its own website organizing the material. These are: