Image credit: NAR

derfinder

Image credit: NAR

derfinder

The goal of my Ph.D. with Jeff Leek and Andrew Jaffe at JHBSPH was to develop statistical methods and software that enable researchers to differentiate the sources of variation observed in RNA-seq while minimizing the dependance on known annotation. This allows researchers to correct for technological variation and study the biological variation driving their phenotype of interest. This work lead to the development of the derfinder and regionReport Bioconductor packages. We then applied these methods to further our understanding of neuropsychiatric disorders using the Lieber Institute for Brain Development human brains collection.

Publications

derfinder analysis using expressed region-level and single base-level approaches provides a compromise between full transcript …

We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across …

regionReport is an R package for generating detailed interactive reports from region-level genomic analyses as well as feature-level …

Transcriptome analysis of human brain provides fundamental insight into development and disease, but it largely relies on existing …

There has been a major shift from microarrays to RNA-sequencing (RNA-seq) for measuring gene expression as the price per measurement …

Talks

Keynote to kickoff the CDSB Mexico 2018 R/Bioconductor workshop

recount2 overview for the ICSA 2017 conference

Showcasing how derfinder and recount2 can be used together to perform annotation-agnostic RNA-seq analyses at SOBP2017

Introduction of my work to kick off the epidemiology and biostatistics training for Kandahar University MPH faculty.

Desde que es derfinder hasta como se puede usar con recount2

Motivating SACNAS2016 attendees to pursue a career in STEM by showcasing my research

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

derfinder overview for ENAR2016

Adapting derfinder to find differentially bound peaks using ChIP-seq data

derfinder overview for the JHU Genomics Symposium 2015

derfinder overview for ENAR2015

derfinder tutorial for Leek’s group lab meeting

In depth overview of derfinder and it’s applications to the human brain for the IS3B-INMEGEN conference

derfinder overview for the LCG 10 year anniversary symposium

Work in progress presentation on derfinder for the Joint Genomics Meeting

Introduction to high throughput sequencing and derfinder for the JHU Biostat Journal Club