At the Lieber Institute for Brain Development, I am part of the Data Science team whose goals include better understanding and characterizing genomics signatures in the human brain. We use high-throughput technologies such as DNA methylation and RNA sequencing. I help mentor other team members, provide support for LIBD projects and I am advancing my academic career as part of Andrew Jaffe‘s lab.
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 the Department of Biostatistics at Johns Hopkins Bloomberg School of Public Health thanks to a CONACyT scholarship awarded in 2011. I worked with Jeff Leek and Andrew Jaffe in developing derfinder, regionReport, recount as well as other applied projects.
Every day I use R and Bioconductor. Occasionally I blog about them and other tools. I’m a co-founder of the LIBD rstats club and the CDSBMexico community of R and Bioconductor developers in Latin America.
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
Keynote to kickoff the CDSB Mexico 2018 R/Bioconductor workshop
BrainSeq Phase II at Biology of Genomes 2018
L. Collado-Torres’s Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics Ph.D. defense talk
Origin of the idea Recently the team I work with has had a few new members and I’ve been thinking lately of ways we could try to help them. The team leader was traveling this week, which gave me the opportunity to come up with a new type of session and test it out. That’s the origin of this learning from our search history idea. We tested it today and I’m quite happy with the results so far, so I thought it would be useful to document what we did and share it with others.
In the summer of 2008, nearly 12 years ago, I attended my first R/Bioconductor conference: BioC2008. Just last week I went to my second rstudio::conf(2020) which I greatly enjoyed. After some tweets exchanges today, I started reflecting on my journey and wanted to share my thoughts. Why I like going to conferences I typically enjoy going to conferences, though I also end up exhausted. via GIPHY Part of it could be the traveling and all that goes with it, but I think that conferences are mostly mentally taxing.
Are you a Microsoft Windows R user? Does your Windows username include a space? Like Firstname Lastname. Then you might occassionally run into issues installing packages due to spaces. Solutions You could either re-install Windows with a username that has no spaces such as Lastname 1, but that’s probably not an easy option. Or you can: Edit your TMP and TEMP environment variables to a location with no spaces, like C:\TEMP following instructions like these ones.
The hugo-academic theme which powers my website is active and frequently updated. I don’t update my website that frequently anymore, but I recently found about many of their changes when I made the CDSB website. We are delighted to share with you our new webpage at https://t.co/rNuiRlNixV with both English and Spanish support Estamos encantados de compartirles nuestra nueva página web que viene en español e inglés It'll replace/remplazará a https://t.
These past months I’ve been mostly working on one huge project which might be close to an end, hopefully! This project involves a massive manuscript with many supplementary figures and tables. Today we sent it out to other members in our team, and to celebrate, I’m now writing more 😅: though this is a blog post. I’m allowing myself to do so before I dive into the pile of tasks I haven’t completed1.
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 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: