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Research talks

2022 July
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.
2021 November
Presentation of several recent developments for the UNC Human Functional Genomics Group. The PEPATAC ATAC-seq pipeline, Sequence Collections, and RegionSet2Vec.
2021 September
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).
2019 September
Introduction to 3 tools for standardizing sample metadata, computing environments, and reference genome resources.
2019 March
An introduction to epigenomics and discussion of standardizing project metadata with Portable Encapsulated Projects, followed by two region-based analysis approaches, LOLA and AIList.
2019 January
An introduction to PEP, and brief overview of PEPATAC, LOLA, and MIRA.
2018 September
A discussion of standardizing project metadata with Portable Encapsulated Projects and a presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.
2018 March
Introduction to Portable Encapsulated Projects and the pepkit system
2017 November
A presentation of tools we have developed: LOLA, MIRA, and the PEP ecosystem.
2017 November
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.
2017 April
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.
2017 February
Brief introduction to research in the group
2017 February
Exploring DNA methylation data in a rare pediatric cancer.
2015 December
2015 European Bioconductor Developers Meeting, Cambridge, UK. A guide to building, using, modifying, and sharing R environments based on Bioconductor Docker containers

Short talks

2021 November
A presentation of seqcol, a GA4GH standard for unique identifiers of reference genomes.
2021 March
Collected introductions to a variety of lab projects: LOLA, MIRA, COCOA, Refgenie, PEP, bulker, etc.
2021 January
Introduction to looper to scatter CWL workflows across tabular data, and how bulker can create portable interactive computing environments from CWL workflows.
2020 July
Lightning talk introducing refgenie and using it from within R
2019 August
Introduction to refgenie
2019 June
Description of the BiocProject bioconductor package, which provides an integration between PEP and Bioconductor
2019 June
Short talk introducing the COCOA bioconductor package.
2018 September
A presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.
2018 July
Short talk introducing the MIRA bioconductor package.
2018 July
Short talk introducing the LOLA bioconductor package.

Educational lectures

2023 October
Introductions to several methods in computational epigenetics developed in the Sheffield lab: LOLA, MIRA, and COCOA.
2023 October
A talk about pipeline development and introduction to the Sheffield Lab modular ecosystem supporting bioinformatics pipeline development.
2022 April
Introductions to epigenomics and interval analysis projects in the lab. Lecture for CS undergraduate course in Computational Biology.
2021 November
A presentation of seqcol, a GA4GH standard for unique identifiers of reference genomes.
2021 September
Philosophy of how to read a paper
2020 April
Overview of open chromatin and ATAC sequencing
2020 April
Introduction to pipelines in general, and PEPATAC, an ATAC-seq pipeline.
2020 April
Overview of tools and methods for downstream ATAC-seq analysis
2019 June
Overview of DNA methylation and bisulfite sequencing
2019 June
A historical and philosophical introduction to epigenetics and epigenomics.
2019 March
Overview of epigenomics; basics and applications of ATAC-seq and Bisulfite-seq.
2019 March
Discussion of the layers of collaboration in software development and introduction to git and GitHub.
2018 September
A presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.
2017 July
Presentation highlighting common issues with scientific writing and how to solve them.