Summary
Initially trained as a bench scientist studying the role of cell-cell contacts on the Notch signalling pathway, I have since transitioned into studying transcription factor binding mechanics. My interest lie in developing model-based solutions to quantitative problems, currently applied to detection of tumor signatures in circulating DNA.
Education
The Johns Hopkins University
Ph.D. Biological Sciences, 2014-2020
Taylor Lab
Program in Cell, Molecular, and Developmental Biology, and Biophysics
Boise State University
B.S. Cell and Molecular Biology, 2010-2014
Albig Lab
Minor in Chemistry, Honors Scholar, Cum Laude
Research Experience
Computational Biologist
RUO Assay Development, Invitae
2020-Present
- As part of the RUO Assay Development team, worked on improving the performance of the personalized cancer monitoring product.
Bioinformatics Analyst
Center for Genes, Environment & Health, National Jewish Health
Max Seibold Lab – 2020-2021
- Analyze high throughput sequencing data to develop insights into disease, particularly asthma.
- Develop pipelines for analytical methods such as response-eQTL analysis and qPCR.
- Establish protocols for managing production, backup, and compilation of large volume datasets from diverse instrumentation.
Graduate Research
Department of Biological Sciences, Johns Hopkins University
James Taylor Lab – 2015-2020
- Use machine learning methods on genomic data
- Develop a model for representating shape features of transcription factor binding sites
- Study gene regulation
Student Research Initiative
Department of Biology, Boise State University
Allan R. Albig Lab – 2014
- Investigated initiation events of angiogenesis.
- Analyzed the relative strengths of pro-and anti-angiogenic signals contributing to the angiogenic switch.
Undergraduate Honors Research
Department of Biology, Boise State University
Allan R. Albig Lab – 2012-2014
- Investigated integrin and Notch signaling pathway interactions.
- Investigated extracellular matrix molecule mediated control of angiogenesis.
Analytical Chemistry Technician
TestAmerica, Inc.
Richland, WA – 2011-2012
- Radioanalysis of Carbon-14, Tritium, and Radon-222 levels in soil and water samples.
- Used standards and quality controls to ensure integrity of all data obtained.
Teaching Experience
Cold Spring Harbor Laboratory
Cold Spring Harbor, New York
- Teaching Assistant, Computational and Comparative Genomics, 2016-2019.
Johns Hopkins University
Baltimore, Maryland
- Certificate of Completion, Teaching Academy, 2019.
- Guest Lecturer, Introduction to Scientific Computing in BME using Python, Matlab, and R, 2018.
- Teaching Assistant, Genomes and Development lab (graduate), 2015-2019.
- Teaching Assistant, Quantitative Biology Bootcamp (graduate), 2015-2019.
- Teaching Assistant, Biochemistry (undergraduate), 2015.
- Teaching Assistant, Cell Biology (undergraduate), 2016.
Boise State University
Boise, Idaho
- Teaching Assistant, Applied Statistics with Computers (undergraduate), 2012-2014.
- Tutor, Calculus, Physics, Chemistry, Statistics, 2011-2014.
Awards and Honors
- Victor Corces Teaching Award
Department of Biology, Johns Hopkins University, 2016 - Owens Fellow
Johns Hopkins University, 2014-2017 - GEM scholarship recipient
Boise State University, 2010-2014 - Student Research Initiative Fellow
Boise State University, 2014 - Idaho INBRE Fellow
2013
Publications
Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium.
Sajuthi, S.P., DeFord, P.M., Jackson, N.D., Montgomery, M.T., Everman,
J.L., Rios, C.L., Pruesse, E., Nolin, J.D., Plender, E.G., Wechsler, M.E., Mak,
A.C., Eng, C., Salazar, S., Medina, V., Wohlford, E.M., Huntsman, S., Nickerson,
D.A., Germer, S., Zody, M.C., Abecasis, G., Kang, H.M., Rice, K.M., Kumar, R.,
Oh, S., Rodriguez-Santana, J., Burchard, E.G., and Seibold, M.A.
(2020) bioRxiv [preprint], doi: 10.1101/2020.04.09.034454
COVID-19-related Genes in Sputum Cells in Asthma. Relationship to Demographic Features and Corticosteroids.
Peters, M.C., Sajuthi, S., DeFord, P.M., Christenson, S., Rios, C.,
Montgomery, M.T., Woodruff, P.G., Mauger, D.T., Erzurum, S.C., Johansson, M.W.,
Denlinger, L.C., Jarjour, N.N., Castro, M., Hastier, A.T., Moore, W., Ortega,
V.E., Bleecker, E.R., Wenzel, S.E., Israel, E., Levy, B.D., Seibold, M.A.,
and Fahy, J.V.
(2020) Am J Respir Crit Care Med. , doi: 10.1164/rccm.202003-0821OC
DNA shape complements sequence-based representations of transcription factor binding sites.
DeFord, P.M. and Taylor, J.
(2019) bioRxiv [preprint], doi: 10.1101/666735
Natural variation in stochastic photoreceptor specification and color
preference in Drosophila.
Anderson, C., Reiss, I., Zhou, C., Cho, A., Siddiqi, H., Mormann, B., Avelis, C.M.,
DeFord, P.M., Bergland, A., Roberts, E., Taylor, J., Vasiliauskas, D.,
Johnston, R.J.
(2017) eLIFE, doi:10.7554/eLife.29593
A cloud-based learning environment for comparing RNA-seq aligners.
Baskin, E., DeFord, P.M., Dennis, A., Misner, I., Tan, F.J., Busby, B.
(2016) F1000R, doi:10.12688/f1000research.8684.1
The insulator protein BEAF-32 is required for Hippo pathway activity in the terminal differentiation of neuronal subtypes.
Jukam, D., Viets, K., Anderson, C., Zhou C., DeFord, P.M., Yan, J., Cau, J., Johnston, R.J. (2016) Development, doi:10.1242/dev.134700
MAGP2 controls Notch via interactions with RGD binding integrins: Identification of a novel ECM-integrin-Notch signaling axis.
DeFord, P.M., Brown, K., Richards, R.L., King, A., Newburn, K., Westover, K., Albig, A.R.
(2016) Exp. Cell Res. doi:10.1016/j.yexcr.2016.01.011
Select Presentations
StruMs—A flexible and information-rich representation of DNA motifs.
DeFord, P.M., Taylor, J. (2016) Invited talk at the 2016 Biological Data Sciences Meeting, Cold Spring Harbor Laboratory, NY.
Invited talk at the Waksman Student Scholars event
DeFord, P.M. (May 22, 2016) Johns Hopkins University. Invited by Dr. Forrest Spencer.
The Influence of Integrin Binding RGD domains on Notch Signaling and Angiogenesis
DeFord, P.M., Westover, K., Albig, A.
(2014) Poster presented at the National Conference on Undergraduate Research, Lexington, KY.
The Influence of Integrin Binding RGD domains on Notch Signaling and Angiogenesis.
DeFord, P.M., Westover, K., and Albig, A.R.
(2013) Poster presented at the Idaho INBRE Summer Research Conference, Moscow, ID.