Selected Publications

† indicates corresponding author, * indicates equal contribution

Reproducible RNA-seq analysis using recount2

PDF Code Project Bioconductor Pre-print

Flexible expressed region analysis for RNA-seq with derfinder

PDF Code Project Bioconductor Pre-print

Recent Publications

More Publications

† indicates corresponding author, * indicates equal contribution

RNA-seq transcript quantification from reduced-representation data in recount2

PDF Pre-print

Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome

PDF Pre-print

Altered expression of histamine signaling genes in autism spectrum disorder

PDF Code

Recent Posts

More Posts

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.

I have recently been getting reminder emails from the Science & SciLifeLab Prize for Young Scientists. The application deadline is July 15th, 2018! Last year I submitted an entry to this competition and I enjoyed the experience, even if it was a bit rushed. The process of joining the competition is relatively straight forward: Write an essay about your Ph.D. thesis work. Get a recommendation letter from your Ph.

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This is a joint blog post between Stephanie Hicks and Leonardo Collado-Torres. We want to share with you our experience using Slack and why you should join us. This post is in an interview style. What is Slack? [SH] Slack is a communication tool for teams. The main idea is you have individual chat rooms (referred to as channels that always begin with the # symbol), which are organized by topics.

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I recently participated for the first time in a silent retreat (6 hrs) as part of a Mindfulness-Based Stress Reduction course. I’ve really been enjoying this course and the experience of learning new ways (for me) to live better and enjoy life more. If you haven’t heard of mindfulness before (like me a few months ago), Wikipedia defines it as: Mindfulness is the psychological process of bringing one's attention to experiences occurring in the present moment, which can be developed through the practice of meditation and other training.

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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.