Leonardo Collado-Torres
Investigator @ LIBD, Assistant Professor, Department of Biostatistics @ JHBSPH
Lieber Institute for Brain Development
Johns Hopkins Blomberg School of Public Health
At the Lieber Institute for Brain Development (LIBD), I lead the R/Bioconductor-powered Team Data Science group. I am also an Assistant Professor in the Department of Biostastics at the Johns Hopkins Bloomberg School of Public Health. Additionally, I am interested in outreach activities as a board member of the Community of Bioinformatics Software Developers.
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 2016 from the Department of Biostatistics at Johns Hopkins Bloomberg School of Public Health thanks to a CONACyT scholarship. There I worked with Jeff Leek and Andrew Jaffe in developing derfinder and recount. I then worked ~ 4 years as a Staff Scientist and Research Scientist in Andrew Jaffe’s lab on a variety of data analysis projects. I became a principal investigator in September 2020.
Every day I use R and Bioconductor, and on some days I write R packages. Occasionally I write blog posts about them and other tools. I’m a co-founder of the LIBD rstats club and the CDSB community of R and Bioconductor developers in Mexico and Latin America, that we described at the R Consortium website. In the past, I also served on the Bioconductor Community Advisory Board and the advisory board for rOpenSci’s Statistical Software Peer Review.
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)
Latest
- Integrating gene expression and imaging data across Visium capture areas with visiumStitched
- Molecular impact of nicotine and smoking exposure on the developing and adult mouse brain
- Benchmarking cell type deconvolution methods with human brain data
- Network nature of ligand-receptor interactions underlies disease comorbidity in the brain
- Lessons from spatially-resolved transcriptomics of postmortem human brain data projects
- Systems biology dissection of PTSD and MDD across brain regions, cell types, and blood
- HumanPilot: first spatially-resolved transcriptomics study using Visium
- Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry.
- Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus
- How to reduce the size of a large GitHub repo
- lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression
- Transcriptomic analysis of the human habenula in schizophrenia
- 2024 Current Topics in Biostatistics guest seminar
- Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex
- The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics
- TrkB-dependent regulation of molecular signaling across septal cell types
- Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
- escheR: Unified multi-dimensional visualizations with Gestalt principles
- Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation
- VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data
- Comparison of gene expression in living and postmortem human brain
- Lessons from spatially-resolved transcriptomics of postmortem human brain data projects
- BiocMAP: A Bioconductor-friendly, GPU-Accelerated Pipeline for Bisulfite-Sequencing Data
- Studying the human prefrontal cortex transcriptome at different resolutions
- BioC2023 Package Demo: analyzing spatially-resolved transcriptomics data from Visium using spatialLIBD
- Lessons from working on the edge of human brain transcriptomics with spatially-resolved transcriptomics and deconvolution
- Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
- Harnessing the power of spatially-resolved transcriptomics one step at a time
- Harnessing the power of spatially-resolved transcriptomics one step at a time
- Activity-regulated gene expression across cell types of the mouse hippocampus
- Lessons from working on the edge of human brain transcriptomics with spatially-resolved transcriptomics and deconvolution
- Navigating human brain gene expression measurements at different resolutions to study psychiatric disorders
- Applying Visium Spatial Proteogenomics (Visium-SPG) to study Alzheimer’s Disease
- Splicing accuracy varies across human introns, tissues and age
- IntroVerse: a comprehensive database of introns across human tissues
- Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes
- Spatially-resolved Transcriptomics Analysis with R/Bioconductor and Beyond
- Comment on: What genes are differentially expressed in individuals with schizophrenia? A systematic review
- Spatially-resolved Transcriptomics Analysis with R/Bioconductor and Beyond
- Applications, limitations, and future directions of spatial transcriptomics technology in the human brain
- spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
- Applications, limitations, and future directions of spatial transcriptomics technology in the human brain
- Spatial Transcriptomics Analysis of Aβ-tau Synergy in the Inferior Temporal Cortex of the Human Brain in Alzheimer’s Disease
- SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
- R/Bioconductor-powered Team Data Science (TLDR 2022)
- Deconvolution of RNA-seq data in the postmortem human brain: the present and preparing the future
- Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways
- Genetics and Brain Transcriptomics of Completed Suicide
- recount3: summaries and queries for large-scale RNA-seq expression and splicing
- Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain
- Extending Spatial Analysis with R/Bioconductor and beyond
- Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk
- Launch of CDSB2021
- NIH DS bootcamp: finding data panel
- Studying the Topography of Spatial Gene Expression in the Human Brain
- Getting started with scRNA-seq analyses with Bioconductor
- SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/Bioconductor-powered RNA-seq analyses
- BioTuring webinar
- Detection of pathogenic splicing events from RNA-sequencing data using dasper
- Developmental Profile of Psychiatric Risk Associated With Voltage-Gated Cation Channel Activity
- Megadepth: efficient coverage quantification for BigWigs and BAMs
- CDC/ATSDR R User Group
- ConectaR2021
- Bioconductor Technical Advisory Board
- Ryten lab
- Promoting the next wave of R/Bioconductor developers in Latin America starting in Mexico
- Launch of CDSB2020
- Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
- BioC2020 Birds of a Feather on the CDSB community
- BioC2020 recount workshop
- Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex
- SynGAP isoforms differentially regulate synaptic plasticity and dendritic development
- Latin American Communities and Organizations
- Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders
- Transcriptome-Scale Spatial Gene Expression in the Human Dorsolateral Prefrontal Cortex
- Profiling gene expression in the human dentate gyrus granule cell layer reveals insights into schizophrenia and its genetic risk
- Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information
- Recounting the FANTOM CAGE–Associated Transcriptome
- Jaffelab: learn from our search history
- Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs
- Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia
- Analyzing BrainSeq Phase II and generating the recount-brain resource
- Launch of CDSB2019
- BioC2019 recount workshop
- BioC2019: CDSB updates
- Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods
- Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia
- recount-brain: a curated repository of human brain RNA-seq datasets metadata
- Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells
- Analyzing BrainSeq Phase II and generating the recount-brain resource
- Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer's disease
- Reproducible RNA-seq analysis with recount2
- Reproducible RNA-seq analysis with recount2 and recount-brain
- Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses
- Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia
- Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome
- From learning to using to teaching to developing R
- Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis
- BrainSeq Phase II: schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex
- Reproducible RNA-seq analysis with recount2 and recount-brain
- Unique Molecular Correlates of Schizophrenia and Its Genetic Risk in the Hippocampus Compared to Frontal Cortex
- BrainSeq Phase II: schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex
- recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
- Improving the value of public RNA-seq expression data by phenotype prediction
- RNA-seq transcript quantification from reduced-representation data in recount2
- Getting started with recount2 and accessing it via R
- Guiding Principles for Interactive Graphics Based on LIBD Data Science Projects
- recount workshop: Learn to leverage 70,000 human RNA-seq samples for your projects
- Reproducible RNA-seq analysis with recount2
- Reproducible Research and Bioinformatics
- RNA-seq samples beyond the known transcriptome with derfinder available via recount2
- Introduction at Kandahar University MPH training event
- recount: facilitando el análisis de miles de muestras de RNA-seq
- Using Data Science to Study Human Brain Genomic Measurements
- Annotation-agnostic differential expression and binding analyses
- Annotation-agnostic differential expression analysis
- dbFinder
- Annotation-agnostic differential expression analysis
- Annotation-agnostic RNA-seq differential expression analysis software
- Easy parallel computing with BiocParallel and HTML reports with knitrBootstrap
- Dissecting human brain development at high resolution using RNA-seq
- Does mapping simulated RNA-seq reads provide information?
- Developmental regulation of human cortex transcription and its clinical relevance at single base resolution
- derfinder tutorial
- Developmental regulation of human cortex transcription at base-pair resolution
- Git for research
- Fast Annotation-Agnostic Differential Expression Analysis
- Fast differential expression analysis annotation-agnostic across groups with biological replicates
- Fast Annotation-Agnostic Differential Expression Analysis
- Introduction to ggbio
- Fast differential expression analysis annotation-agnostic across groups with biological replicates
- Fast differential expression analysis annotation-agnostic across groups with biological replicates
- Differential expression analysis of RNA-seq data at base-pair resolution in multiple biological replicates
- Differential expression RNA-seq analysis with a large data set from brain samples
- Introduction to knitr
- Introduction to High-Throughput Sequencing and RNA-seq
- DEXSeq paper discussion
- Introduction to R and Biostatistics (2012 version)
- Introducing Git while making your academic webpage
- Introduction to R and Biostatistics
- Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus
- RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
- Bacterial Transcription
- Global Analysis of Transcription Start Sites and Transcription Units in Bacterial Genomes
- Introduction to using Bioconductor for High Throughput Sequencing Analysis
- Global Analysis of Transcription Start Sites and Transcription Units in Bacterial Genomes
- Bacteriófagos: analizando su diversidad