Graduate Student Researcher

University of Pennsylvania, Philadelphia, PA | Aug 2015 – Feb 2022 (6 years)
IGV browser screenshot showing greenscreen and blacklist tracks above bedgraph signals for IgG, H3, and H3K27me3 in Arabidopsis. Greenscreen and blacklist regions align with ultrahigh peaks from mapped reads, indicating shared artifacts across experiments.
From my graduate work on artifact detection in ChIP-seq and Cut & Run datasets, this IGV screenshot shows greenscreen and blacklist tracks (top), and bedgraph signals for IgG, H3, and H3K27me3 (bottom) from fixed and non-fixed Arabidopsis tissues (Zheng & Gehring, 2019). Ultrahigh peaks from mapped reads overlap with greenscreen regions, revealing shared artifacts across experiments(Klasfeld et al 2022).

Summary

  • Developed Greenscreen method to accurately identify and mask false-positive ChIP-seq peaks with efficacy in Arabidopsis, Drosophila, and Oryza sativa resulting in 1st author publication

  • Designed and orchestrated Next Generation Sequencing (NGS) data analysis (eg. ChIP-Seq, RNA-seq, MNase-seq) to measure the activity and outcomes of mobile and DNA binding proteins functional in cellular reprogramming, resulting in three 2nd author publications

Selected Awards

  • Honorable Mention of the 2016 National Science Foundation (NSF) Graduate Research Fellowship
Publications

Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data

Klasfeld, S., Roulé, T., & Wagner, D.

The Plant Cell • 2022

Molecular regulation of plant developmental transitions and plant architecture via PEPB family proteins–an update on mechanism of action

Zhu, Y., Klasfeld, S., & Wagner, D.

Journal of Experimental Botany • 2021

LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

Jin, R., Klasfeld, S., et al., & Wagner, D.

Nature Communications • 2021

TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T

Zhu, Y., Klasfeld, S., et al., & Wagner, D.

Nature Communications • 2020

Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis

Xiao, J., .., Klasfeld, S., ..., & Wagner, D.

Nature Genetics • 2017

Presentations

Improving resolution of protein binding sites by filtering conserved ultra-high signal in Arabidopsis

Klasfeld, S., & Wagner, D.

Poster University of Pennsylvania Genomics and Computational Biology Graduate Group Retreat • The College of Physicians of Philadelphia, Philadelphia, PA • June 12, 2019

Resolving the mechanism of PRC2 during plant stress

Klasfeld, S., & Wagner, D.

Poster University of Pennsylvania Epigenetics Retreat • Independence Seaport Museum, Philadelphia, PA • November 15, 2018

The characterization and discovery of novel Polycomb and Trithorax Recruitment Elements in plants

Klasfeld, S., & Wagner, D.

Poster University of Pennsylvania Epigenetics Retreat • Citizens Bank Park, Philadelphia, PA • October 13, 2017
References
Wagner Lab Greenscreen Graduate Research Fellowship Program (GRFP) Integrative Genomics Viewer (IGV) Comparative Genomics Platform (CoGe)

More Work Experiences

Postdoctoral Fellow

Pfizer, Cambridge, MA | Feb 2022 – Feb 2025 (3 years)
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Postbaccalaureate Fellow

National Institutes of Health, Bethesda, MD | Aug 2014 – June 2015 (1 year)
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