CV

Education

• B.A. in Biochemistry , Goshen College, 2018
• Ph.D. in Integrated Biomedical Sciences (Genomics and Proteomics), University of Notre Dame, 2025 (expected)

Work experience

• 2020-present: Graduate Research Assistant, Champion and Whelan Labs, University of Notre Dame, Notre Dame, IN
  • Small protein discovery in Mycobacteria with bottom-up proteomics
  • MUC16 proteomics research, aptamer binding research with CE and FA
  • Data analysis and informatics tool development
• 2018-2020: Associate Scientist, Pharmaceutical Product Development (PPD), Madison, WI
  • Biopharmaceutical method development and validation in a GMP laboratory environment
  • Experience with CE and HPLC
• 2017-2018: Research Assistant, Goshen College, Goshen, IN
  • Genomic editing of C. elgegans with CRISPR/Cas9 in the lab of Dr. Kristopher Schmidt
  • Tagging unc-53 with GFP for spatio-temporal expression analysis
• Summer 2017: Intern of Integrated Solutions and Engineering, Promega Corportation, Madison, WI
  • Integration of nucleic acid chemistries into liquid handling robots
  • Experience with DNA and RNA purificaion and analysis, along with debugging software
• Summer 2016: Laboratory Technician, Centro Medico Pedro P. Diaz, Arequipa, Peru
  • Laboratory analysis of patient blood and urine samples
  • Basic phlebotomy training

Skills

• Analytical method development: CE and HPLC
• Data processing, analysis, and visualization with R and Python
• Scientific writing

Publications

Characterization of DNA aptamer–protein binding using fluorescence anisotropy assays in low volume, high-efficiency plates

Weaver, SD., Whelan, RJ. (2021). "Characterization of DNA aptamer–protein binding using fluorescence anisotropy assays in low volume, high-efficiency plates" Analytical Methods. 13, 1302-1307. DOI: 10.1039/D0AY02256J.

Preparative capillary electrophoresis (CE) fractionation of protein digests improves protein and peptide identification in bottom-up proteomics

Weaver, SD., Schuster-Little, N. Whelan, RJ. (2022). "Preparative capillary electrophoresis (CE) fractionation of protein digests improves protein and peptide identification in bottom-up proteomics" Analytical Methods. 14, 1103-1110. DOI: 10.1039/D1AY02145A.

Activity: Teaching Coding in R through Discipline-Focused Problem-Solving in an Analytical Chemistry Course

Weaver, SD., Ambrose, GA. Whelan, RJ. (2022). "Activity: Teaching Coding in R through Discipline-Focused Problem-Solving in an Analytical Chemistry Course" Journal of Chemical Education. 99, 3068-3073. DOI:10.1021/acs.jchemed.2c00395

PrIntMap-R: an online application for intra-protein intensity and peptide visualization in bottom-up proteomics

Weaver, SD., DeRosa, CM., Schultz, SR., Champion, MM. (2023). "PrIntMap-R: an online application for intra-protein intensity and peptide visualization in bottom-up proteomics" Journal of Proteome Research. 22 (2), 432–441. DOI: 10.1021/acs.jproteome.2c00606

Simultaneous N-deglycosylation and digestion of complex samples on S-Traps enables efficient glycosite hypothesis generation

DeRosa, CM., Weaver, SD., Wang, CW., Schuster-Little, N., Whelan, RJ. (2022) "Simultaneous N-deglycosylation and digestion of complex samples on S-Traps enables efficient glycosite hypothesis generation". ACS Omega. 8 (4), 4410-4418. DOI: 10.1021/acsomega.2c08071

An N-acetyltransferase required for EsxA N-terminal protein acetylation and virulence in 2 Mycobacterium marinum

Collars, OA., Jones, BS., Hu, DD., Weaver, SD., Sherman, TA., Champion, MM., Champion, PA. (2023) "An N-acetyltransferase required for EsxA N-terminal protein acetylation and virulence in Mycobacterium marinum". mBio. 14(5). DOI: [https://doi.org/10.1101/2023.03.14.532585](https://doi.org/10.1128/mbio.00987-23)https://doi.org/10.1128/mbio.00987-23

A Revised Molecular Model of Ovarian Cancer Biomarker CA125 (MUC16) Enabled by Long-read Sequencing

Wang, CW., Weaver, SD., Boonpattrawong, N., Schuster-Little, N., Patankar, M., Whelan, RJ. (2024) "A revised molecular model of ovarian cancer biomarker CA125 (MUC16) enabled by long-read sequencing". Cancer Res Commun. 4(1). DOI: 10.1158/2767-9764.CRC-23-0327

Talks

Low-Volume Fluorescence Anisotropy Will Allow Efficient Characterization of Aptamer Binding to Deamidation Products

December 02, 2020

Presentation at Center for Bioanalytical Metrology Industry Advisory Board Meeting, Virtual

Introducing computational programming skills to an analytical chemistry class using discipline-focused problem solving in R

October 14, 2021

Poster at Midwest Universities Analytical Chemistry Conference, Ohio State University

Adapting bottom-up proteomics for detection of the ovarian cancer biomarker CA125/MUC16

November 17, 2021

Presentation at Goshen College Science Speaker Lecture Series, Goshen College

Capillary electrophoresis (CE) fractionation of complex samples in bottom-up proteomics for cancer biomarker characterization

March 14, 2022

Poster at 10th Annual Harper Cancer Research Day, University of Notre Dame - Harper Cancer Research Inst.

PrIntMap-R: an online application for intra-protein intensity and peptide visualization in bottom-up proteomics

February 02, 2023

Poster at UBUNTU Proteomics, Stellenbosch, South Africa

Using PrIntMap-R to visualize protein glycosylation sites in enzymatically deglycosylated samples

May 16, 2023

Oral at CBBI Symposium, University of Notre Dame, Notre Dame, IN

Teaching

Organic Chemistry Teaching Assistant

Biochemistry Teaching Assistant

Advanced Cell Biology Teaching Assistant

Guest Lecturer - Analytical Chemistry

Honors and Postitions

• President, IBMS Grad Student Organization - 2023
• Berry Family Foundation Fellowship, Berthiaume Institute for Precision Health - 2023-2024
• Lucy Family Institute for Data and Society Graduate Scholar - 2023-2025
• UND Center for Research Computing Graduate Award for Computational Sciences and Visualization - 2023
• CBBI Symposium 1st Place Oral Presentation Contest Winner - May 2023
• Harper Cancer Research Inst. 10th annual Cancer Research Day Poster Contest 1st Place Award - March 2022
• University of Notre Dame Chemistry, Biochemistry, and Biology Interface (CBBI) Fellowship - 2021-2023
• Employee of the Month (PPD) - May 2019
• Presidential Leadership Award Winner (Goshen College, top academic scholarship) - 2014

Test Scores

GRE (2019) - Verbal: 163 (93rd Percentile), Quantitative: 170 (96th Percentile), Analytical: 5.5 (98th Percentile)