Fields

that drive me

R

Genomics

Education

Community

Projects

*
All BrainSeq Consortium recount2 derfinder

BrainSEQ™ Consortium

BrainSeq Consortium lead by LIBD to understand the genetics and gene expression variability in schizophrenia disorder

recount2

Uniform processing of human RNA-seq data to improve usability and power methods development

derfinder

Annotation-agnostic methods for gene expression data

Recent Publications

and posters

Quickly discover relevant content by filtering publications.

† indicates corresponding author, * indicates equal contribution

DNA methylation (DNAm) is a key epigenetic regulator of gene expression across development. The developing prenatal brain is a highly …
Preprint PDF DOI

Background: DNA methylation (DNAm) is a critical regulator of both development and cellular identity and shows unique patterns in …
Preprint PDF Code DOI

Background: RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable …
Preprint PDF Code DOI

Long non-coding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression …
Preprint PDF Code Dataset Project DOI

The hippocampus formation, although prominently implicated in schizophrenia pathogenesis, has been overlooked in large-scale genomics …
Preprint PDF Code Dataset Project DOI
See all publications

Favorite talks

Jul 30, 2018 10:00 AM — 10:30 AM Cuernavaca, MEX

Keynote to kickoff the CDSB Mexico 2018 R/Bioconductor workshop
Project Project Slides
May 12, 2018 11:40 AM — 12:00 PM Cold Spring Harbor Laboratory

BrainSeq Phase II at Biology of Genomes 2018
Project Slides Video
Jun 20, 2016 12:00 AM — 12:00 AM Baltimore, Maryland, US

L. Collado-Torres’s Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics Ph.D. defense talk
Project Project Slides

Recent & Upcoming Talks

Update on BrainSeq Phase II and recount-brain for the LIBD 2019 staff seminar series
Feb 25, 2019 1:00 PM — 2:10 PM Baltimore, Maryland, US
Project Project Slides

Junior Research Symbiont Award Presentation for Excellence in Data Sharing at PSB2019
Jan 5, 2019 4:24 PM — 4:24 PM Hawaii, US
Project Slides

Work in progress presentation on recount-brain for the Joint Genomics Meeting
Nov 29, 2018 4:24 PM — 4:24 PM JHU Biostats, Baltimore, US
Project Slides

Guest lecture for LCG-UNAM spanning some recent research
May 30, 2018 1:00 PM — 3:00 PM Remote
Project Slides

BrainSeq Phase II at SOBP 2018
May 12, 2018 3:00 PM — 3:30 PM New York, USA
Project Slides
See all talks

Recent Posts

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

Last updated on 11 min read rstats

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.
Last updated on 8 min read Web, rstats

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.
Last updated on 11 min read Science

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.
Last updated on 7 min read rstats, Conference, UNAM

This blog post was first published at the CDSBMexico website. #CDSBMexico: remember to apply for BioC2019 travel scholarships!! Due date is March 15thhttps://t.co/iegG0qQzwu Let us help you! Here we give you some ideas 💡We can also give you feedback via Slack ✅#rstats #bioconductor @Bioconductor #bioc2019 #diversity #LatAm #rstatsES pic.twitter.com/EORg8d2Qxj — ComunidadBioInfo (@CDSBMexico) March 1, 2019 About 10 months ago we announced our plans to start a new community of R/Bioconductor developers in Mexico and Latin America.
Last updated on 9 min read Misc

In the past months I’ve had a recurrent conversation with many people. This conversation is typically started with the question: why do you like living where you live? Some of them might be considering moving to the city I live in for work, some of them are thinking about leaving, some are happy here. Ultimately, everyone is different and what makes some happy might not be for the rest. Some friends want to live in larger cities, others want different climates, others want to move in with their long distance relationship partners, etc.
See all posts

Curriculum vitae

Download my cv or view it at GitHub.

Mentoring

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

Alumni

Avatar

Amy Peterson

MPH 2017-2018

R programming, Biostatistics, Clinical Research

Avatar

Ashkaun Razmara

MPH 2017-2018

Neuroscience, Reproducibility

Teaching

LIBD

2019

  1. Instructor and member of the Organizing Committee for the CDSB Workshop 2019: How to Build and Create Tidy Tools

2018

  1. Keynote speaker and member of the Organizing Committee for the Latin American R/BioConductor Developers Workshop 2018

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.