Most GWAS associations have been found outside protein-coding genes, leading to growing interest in studying non-coding DNA to understand biology and treat disease. In this talk, I'll present my group's recent work on methods development for analysis of genomic intervals. Through algorithmic advances and novel machine learning applications, we have developed several approaches to study non-coding genomic intervals in new ways. I'll also present applications and results of these approaches to recent questions in cancer biology.

Presentation of several recent developments for the UNC Human Functional Genomics Group. The PEPATAC ATAC-seq pipeline, Sequence Collections, and RegionSet2Vec.

An overview of several Sheffield lab projects for new algorithms, machine learning approaches, and databases to handle the growing corpus of genomic interval data (BED files).

Introduction to 3 tools for standardizing sample metadata, computing environments, and reference genome resources.

An introduction to epigenomics and discussion of standardizing project metadata with Portable Encapsulated Projects, followed by two region-based analysis approaches, LOLA and AIList.

An introduction to PEP, and brief overview of PEPATAC, LOLA, and MIRA.

A discussion of standardizing project metadata with Portable Encapsulated Projects and a presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.

Introduction to Portable Encapsulated Projects and the pepkit system

A presentation of tools we have developed: LOLA, MIRA, and the PEP ecosystem.

A quick overview of the basic and advanced features of our python-based pipeline workflow system. Pypiper is a user-friendly large-data informatics pipeline framework. Looper is a project manager that distributes jobs across a cluster for you. Updated to reflect the PEP division.

Intro and literature review of challenges and approaches to single-cell epigenomics analysis. Presentation for the 2017 American Foundation for AIDS Research Think Tank Meeting.

Brief introduction to research in the group

Exploring DNA methylation data in a rare pediatric cancer.

2015 European Bioconductor Developers Meeting, Cambridge, UK. A guide to building, using, modifying, and sharing R environments based on Bioconductor Docker containers

A presentation of seqcol, a GA4GH standard for unique identifiers of reference genomes.

Collected introductions to a variety of lab projects: LOLA, MIRA, COCOA, Refgenie, PEP, bulker, etc.

Introduction to looper to scatter CWL workflows across tabular data, and how bulker can create portable interactive computing environments from CWL workflows.

Lightning talk introducing refgenie and using it from within R

Introduction to refgenie

Description of the BiocProject bioconductor package, which provides an integration between PEP and Bioconductor

Short talk introducing the COCOA bioconductor package.

A presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.

Short talk introducing the MIRA bioconductor package.

Short talk introducing the LOLA bioconductor package.

Discussion of the layers of collaboration in software development and introduction to git and GitHub.

Introductions to several methods in computational epigenetics developed in the Sheffield lab: LOLA, MIRA, and COCOA.

A talk about pipeline development and introduction to the Sheffield Lab modular ecosystem supporting bioinformatics pipeline development.

Introductions to epigenomics and interval analysis projects in the lab. Lecture for CS undergraduate course in Computational Biology.

A presentation of seqcol, a GA4GH standard for unique identifiers of reference genomes.

Philosophy of how to read a paper

Overview of open chromatin and ATAC sequencing

Introduction to pipelines in general, and PEPATAC, an ATAC-seq pipeline.

Overview of tools and methods for downstream ATAC-seq analysis

Overview of DNA methylation and bisulfite sequencing

A historical and philosophical introduction to epigenetics and epigenomics.

Overview of epigenomics; basics and applications of ATAC-seq and Bisulfite-seq.

Discussion of the layers of collaboration in software development and introduction to git and GitHub.

A presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.

Presentation highlighting common issues with scientific writing and how to solve them.