L. Collado-Torres

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.

Interests

  • Genomics
  • R programming
  • Biostatistics
  • Teaching
  • Diversity

Education

  • PhD in Biostatistics, 2016

    Johns Hopkins Bloomberg School of Public Health

  • Bachelor in Genomic Sciences (LCG), 2009

    National Autonomous University of Mexico (UNAM)

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

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex

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

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

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

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

Background: RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable …
Carrie Wright *, Anandita Rajpurohit *, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger †, Joo Heon Shin †
Preprint PDF Code DOI

Recounting the FANTOM Cage Associated Transcriptome

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

Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia

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

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

From learning to using to teaching to developing R

Keynote to kickoff the CDSB Mexico 2018 R/Bioconductor workshop

Project Project Slides
Sat, May 12, 2018 11:40 AM — 12:00 PM Cold Spring Harbor Laboratory

BrainSeq Phase II: schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex

BrainSeq Phase II at Biology of Genomes 2018

Project Slides Video
Mon, Jun 20, 2016 12:00 AM — 12:00 AM Baltimore, Maryland, US

Annotation-agnostic differential expression and binding analyses

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

Project Project Slides

Recent & Upcoming Talks

Analyzing BrainSeq Phase II and generating the recount-brain resource

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

Reproducible RNA-seq analysis with recount2

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

Reproducible RNA-seq analysis with recount2 and recount-brain

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

Reproducible RNA-seq analysis with recount2 and recount-brain

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

Unique Molecular Correlates of Schizophrenia and Its Genetic Risk in the Hippocampus Compared to Frontal Cortex

BrainSeq Phase II at SOBP 2018
Sat, 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 Wed, Feb 12, 2020 12 min read rstats, Ideas

Learning from our search history

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.

Last updated on Tue, Feb 4, 2020 7 min read Conference, rstats

Conference feelings: from newbie to sponsor

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.

Last updated on Wed, Feb 12, 2020 11 min read rstats

Windows user space issues with installing R packages

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 Wed, Feb 12, 2020 8 min read Web, rstats

The evolution of my academic career as seen through posters and talks thanks to hugo academic 4.1

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 Wed, Feb 12, 2020 11 min read Science

How to write academic documents with GoogleDocs

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.

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

Ashkaun Razmara

MPH 2017-2018

Neuroscience, Reproducibility

Avatar

Amy Peterson

MPH 2017-2018

R programming, Biostatistics, Clinical Research

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.