At the Lieber Institute for Brain Development, I lead the R/Bioconductor-powered Team Data Science team. My team 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, for which I’m part of its Community Advisory Board. From my position at LIBD, I’m able to interact with and collaborate with fantastic biologists, data scientists, researchers at Johns Hopkins University and beyond. Furthermore, I officially help mentor LIBD employees in data science and R tools.
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. I worked with Jeff Leek and Andrew Jaffe in developing derfinder and recount. I then worked ~ 3.5 years as a Staff Scientist in Andrew Jaffe’s lab on a variety of data analysis projects.
Every day I use R and Bioconductor, and on some days I write R packages. Occasionally I blog 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, just like we described at the R Consortium website.
If you want to join my team, please get in touch! ^_^ 💪🏽🇲🇽
PhD in Biostatistics, 2016
Johns Hopkins Bloomberg School of Public Health
Bachelor in Genomic Sciences (LCG), 2009
National Autonomous University of Mexico (UNAM)
that drive me
BrainSeq Consortium lead by LIBD to understand the genetics and gene expression variability in schizophrenia disorder
Uniform processing of human RNA-seq data to improve usability and power methods development
† indicates corresponding author, * indicates equal contribution
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.
Webinar for The Scientist sponsored by 10x Genomics. Approximately 600 individuals registered for the webinar and you can watch it on demand. I presented this talk at LIIGH-UNAM 2020 for LCG-EJ-UNAM students and during the CDSB2020 workshop.
BrainSeq Phase II at Biology of Genomes 2018
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 1.
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.
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.
Yesterday was an extremely exciting day for me and my colleagues. We finished a project we had been working on and shared it with the world. Meaning, it’s done and we can relax for a little bit while we wait for feedback from our peers.
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: