Selected Publications

† indicates corresponding author, * indicates equal contribution

Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia

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Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

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Reproducible RNA-seq analysis using recount2

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Flexible expressed region analysis for RNA-seq with derfinder

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Recent Publications

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† indicates corresponding author, * indicates equal contribution

Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses

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Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

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Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation

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Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer's disease

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Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia

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Recent & Upcoming Talks

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Recent Posts

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Posts with the rstats category can also be found at RBloggers, R Weekly and DataCamp Community. Also check the LIBD rstats club where I am a contributor. You can also view posts grouped by category or tag.

Recently I’ve been thinking on the subject of asking for help. In short, it’s hard to ask for help. It involves admitting to yourself that you can’t solve the problem alone, opening yourself up, hoping that another person will understand you and guide you in the right direction. Thus it can be painful if your request for help is misunderstood, met with criticism or ignored. Regardless of these obstacles, I think that the potential rewards make it worth it.

CONTINUE READING

I can’t tell you how many times I’ve started to write this post in my mind since May 2018. Today I’m finally typing it on the computer. This will be a rather long post that ties in several threads. I’ll talk about Cold Spring Harbor’s Biology of Genomes conference and its relationship to my undergrad in Mexico. I’ll also introduce you to Aldo Barrientos (1987-2011) who was was my undergrad classmate.

CONTINUE READING

I recently wrote several blog posts with many tweets1 as a way of taking notes during the American Society of Human Genetics 2018 conference. A few friends asked me how I did this so fast. The process can be summarized into the following main steps. Save links of tweets you want to highlight in your post. Use a hugo-powered blog to obtain the code for embedding tweets easily2. Proofread, edit and post.

CONTINUE READING

Curriculum vitae

Download my cv or view it at GitHub.

Students

Here you can find the students that I've mentored as their advisor and/or are currently working with me.

LIBD

2017-2018

Teaching

LIBD

2016

  1. Biostatistics and Stata instructor at a workshop for Kandahar University Faculty, organized by Johns Hopkins University.
  2. Invited instructor for the Genomeeting 2016 course biostat INMEGEN, Mexico City, Mexico.

JHBSPH

2015-2016

  1. Teaching assistant and guest lecturer for Introduction to R for Public Health Researchers
  2. Teaching assistant for Statistical Methods in Public Health I (140.621)
  3. Lead teaching assistant for Statistical Methods in Public Health II (140.622).
  4. Teaching assistant for the MPH capstone project.

2014-2015

  1. Lead teaching assistant for Statistical Methods in Public Health I (140.621) and II (140.622).
  2. Teaching assistant for the MPH capstone project.

2013-2014

  1. Teaching assistant for Statistical Methods in Public Health I (140.621) and II (140.622).
  2. Teaching assistant for the MPH capstone project. Developed a shiny application that allows students to sign up for a TA session (code) and wrote a report of the number of TA sessions available here.

2012-2013

  1. Teaching assistant for Statistical Methods in Public Health I (140.621), II (140.622), III (140.623), and IV (140.624) courses.

UNAM

PDCB

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).

  1. Analysis of High-Throughput Sequencing data with Bioconductor Aug-Dec 2010.
  2. Introduction to R and Biostatistics (along with two other teachers).

IBT

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.

  1. Introduction to R for bench biologists Oct-Nov 2009. This mini-course has quite a bit of material on learning how to make plots with R.
  2. Métodos Estadísticos y Analíticos de Datos Genómicos (Statistical Methods and Analysis of Genomic Data) Jan 2010. This one week course had lectures about Perl, using a Cluster, high-throughput technologies, R and Bioconductor, C, and biology overviews.

LCG

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:

  1. Intensive course on R/Bioconductor Oct-Nov 2008 (backup)
  2. Principles of Statistics Feb-June 2009 (backup)
  3. Seminar III: R/Bioconductor Aug-Dec 2009 (backup)

Contact

If you have questions about the Bioconductor packages I maintain, please read this post. If you send me an email, I'll simply refer you to the same post.