Rebecca J. Whelan

Dr. Rebecca Whelan
  • Associate Professor

Contact Info

220E MRB
2030 Becker Dr
Lawrence, KS 66047-1620


B.A. in Chemistry and English, Lawrence University, 1996
Ph.D. in Chemistry, Stanford University, 2003
Postdoctoral Research Fellow, Bioanalytical Chemistry, University of Michigan, 2003–2004


  • Bioanalytical chemistry
  • Capillary separations
  • Biosensors
  • Mass spectrometry
  • Cancer biomarkers
  • Affinity assays and reagents


Whelan Group Research Poster

Achieving improved clinical outcomes for cancer patients will require discovery of new biological markers and improved understanding of biomarkers already in use. To this end, the Whelan lab employs diverse analytical methods including proteomics, microscale separations, bioinformatics, and affinity reagent development. Areas of ongoing research focus include:


Characterization of ovarian cancer biomarker CA125 using bioanalytical methods. CA125 is the gold standard biomarker for managing ovarian cancer. Despite its clinical importance, little is known about its structure and function. We are interested in identifying the binding site(s) of CA125-specific antibodies as part of a long-term effort to intelligently develop alternative affinity recognition approaches. This effort uses solid-phase peptide synthesis or bacterial protein expression to prepare individual subdomains of CA125. We then characterize the interactions between these subdomains and CA125-specific antibodies using Western blotting, enzyme-linked immunoassay, surface plasmon resonance spectroscopy, and affinity-probe capillary electrophoresis. In parallel efforts, CA125 is isolated from patient-derived samples, enzymatically digested into peptides, and analyzed using nano-liquid chromatography/tandem mass spectrometry. Novel analytical methods—including preparative capillary electrophoresis fractionation and solid-phase supported deglycosylation—have been developed in our lab to improve peptide and protein identification of CA125 and other targets. These proteomics-based studies are complemented by ongoing efforts to determine the cDNA sequence of CA125 in cell lines and patient samples using nanopore sequencing. Such sequence data may reveal differences in the composition of this important biomarker across individuals and during cancer treatment.


Development and application of nucleic-acid affinity reagents. Ovarian cancer is most often diagnosed as advanced, metastatic disease. Analytical methods to reliably detect biomarkers of ovarian cancer at earlier stage would improve long-term survival. Motivated by the idea that a biomarker is only as good as the tools available to detect it, we have developed aptamers: single-stranded oligonucleotides that function as “artificial antibodies” and could be the basis of new affinity-based detection methods that complement the existing immunoassay. We selected aptamers for CA-125 using a novel “one-pot” method, and for a complementary cancer marker (HE4) using capillary electrophoresis. We were early adopters of high-throughput DNA sequencing as the penultimate step in aptamer selection, an approach that yields orders of magnitude more data than conventional DNA cloning and sequencing. Exploiting this rich sequence data requires developing and adapting aptamer-specific bioinformatics tools. Ongoing aptamer selection efforts go beyond isolated protein biomarker targets to focus on whole-cell targets. Once cancer-specific aptamers are developed, they will be used as payload-directing agents for targeted therapies, and as the basis of instrument-free detection devices, in a platform similar to a home pregnancy test.

Selected Publications

Wang, C-W., Weaver, S.D., Boonpattrawong, N., Schuster-Little, N., Patankar, M., and Whelan, R.J. A Revised Molecular Model of Ovarian Cancer Biomarker CA125 (MUC16) Enabled by Long-read Sequencing. Cancer Res. Commun. 2024 Jan 31;4(1):253-263. DOI: 10.1158/2767-9764.CRC-23-0327

Hanson, E.K., Wang, C-W., Minkoff, L., and Whelan, R.J. Strategies for Mitigating Commercial Sensor Chip Variability with Experimental Design Controls. Sensors 2023, 23, 6703.

Wang, C., Hanson, E.K., Minkoff, L., and Whelan, R.J.* Individual recombinant repeats of MUC16 display variable binding to CA125 antibodies. Cancer Biomarkers, 2023, 37, 85–94. doi: 10.3233/CBM-220191

Hanson, E.K. and Whelan, R.J.* Application of the Nicoya OpenSPR to studies of biomolecular binding: a review of the literature from 2016 to 2022. Sensors, 2023, 23, 4831 (22 pages). doi: 10.3390/s23104831

Claus, M.J., Gionfriddo, E., Monahan, J., Whelan, R.J., and Vitha, M.F.* Threshold concepts in analytical chemistry. J. Chem. Educ.2023, 100, 427–431.

DeRosa, C.M., Weaver, S.D., Wang, C., Schuster-Little, N., and Whelan, R.J.* Simultaneous N-deglycosylation and digestion of complex samples on S-Traps enables efficient glycosite hypothesis generation. ACS Omega, 2023, 8, 4410–4418. doi: 10.1021/acsomega.2c08071

Weaver, S.D., Ambrose, G.A., and Whelan, R.J.* Activity: Teaching coding in R through discipline-focused problem-solving in an analytical chemistry course. J. Chem. Educ., 2022, 99, 3068–3073. doi: 10.1021/acs.jchemed.2c00395

Weaver, S.D., Schuster-Little, N., and Whelan, R.J.* Preparative capillary electrophoresis (CE) fractionation of protein digests improves protein and peptide identification in bottom-up proteomics. Anal. Meth., 2022, 14, 1103–1110. doi: 10.1039/D1AY02145A

Sherman, L.M., Findley, M.D., Borsari, R.K., Schuster-Little, N., Strausser, S.L., Whelan, R.J.*, Jenkins, D.M.*, and Camden, J.P*. N-Heterocyclic carbene ligand stability on gold nanoparticles in biological media. ACS Omega, 2022, 7, 1444–1451. doi: 10.1021/acsomega.1c06168

Mace, C., Morrin, A., and Whelan, R.J. Introduction to bioanalytical sensors for real-world applications. Anal. Meth., 2021, 13, 1776. doi: 10.1039/D1AY90015C

Weaver, S.D. and Whelan, R.J.* Characterization of DNA aptamer-protein binding using fluorescence anisotropy assays in low-volume, high-efficiency plates. Anal. Meth., 2021, 13, 1302–1307. doi: 10.1039/D0AY02256J

Schuster-Little, N., Fritz-Klaus, R., Etzel, M., Patankar, N., Javeri, S., Patankar, M.S.*, and Whelan, R.J.* Affinity-free enrichment and mass spectrometry analysis of the ovarian cancer biomarker CA125 (MUC16) from patient-derived ascites. Analyst, 2021, 146, 85–94. doi: 10.1039/D0AN01701A

Awards & Honors

  • Vice Chair-Elect, Gordon Research Conference on Bioanalytical Sensors, 2022
  • Finalist for Professor Props Award for Favorite Instructor and Advisor, Oberlin College, 2013 and 2010
  • Henry Dreyfus Teacher-Scholar Award, 2011
  • Distinguished Alumni Scholar, Stanford University, 2010
  • W.M. Keck Foundation Fellowship, 2008
  • Research Corporation, Cottrell College Science Award, 2006
  • Walter J. Gores Award (Stanford University’s highest honor recognizing excellence in teaching), 1999