Kevin Chen, Kivilcim Ozturk, Ted Liefeld, Michael Reich, Jill P Mesirov, Hannah Carter, Stephanie I Fraley. A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells. STAR Protoc. (2021)

Kiersten Elizabeth Scott, Stephanie I Fraley, Padmini Rangamani. A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes. Proceedings of the National Academy of Sciences of the United States of America. (2021).


Kevin Chen, Kivilcim Ozturk, Ryne L Contreras, Jessica Simon, Sean McCann, Wei Ji Chen, Hannah Carter, Stephanie I Fraley. Phenotypically supervised single-cell sequencing parses within-cell-type heterogeneity. iScience. (2021).

Lennart Langouche, April Aralar, Mridu Sinha, Shelley M Lawrence, Stephanie I Fraley, Todd P Coleman. Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power. Bioinformatics, (2020).

April Aralar, Yixu Yuan, Kevin Chen, Yunshu Geng, Daniel Ortiz Velez, Mridu Sinha, Shelley Lawrence, and Stephanie I. Fraley. Improving Quantitative Power in Digital PCR Through Digital High Resolution Melting. Journal of Clinical Microbiology, (2020).

Pranjali Beri, Anna Popravko, Benjamin Yeoman, Aditya Kumar, Kevin Chen, Enio Hodzic, Alyssa Chiang, Afsheen Banisadr, Jesse K. Placone, Hannah Carter, Stephanie I. Fraley, Parag Katira, and Adam J. Engler. Cell Adhesiveness Serves as a Biophysical Marker for Metastatic Potential. Cancer Research, (2020).

Kevin Chen, Ryne L. Contreras, and Stephanie I. Fraley. Phenotypically Supervised Single Cell Sequencing Reveals Coordination Between Migration, Proliferation, and Immunity in Breast Cancer. (in review)

Augustine C. Obirieze, Mridu Sinha, Hannah Mack, William Leineweber, April Aralar, Todd P. Coleman, and Stephanie I. Fraley. A Probabilistic Approach to Melt Cure-Based DNA Profiling Enables Novelty Detection. (in review)


Kiersten E. Scott, Kevin Rychel, Sural Ranamukhaarachchi, Padmini Rangamani, Stephanie I. Fraley. Emerging Themes and Unifying Concepts Underlying Cell Behavior Regulation by the Pericellular Space. Acta Biomaterialia, (2019).

Daniel O. Velez, Sural K. Ranamukhaarachchi, Rishi N. Modi, Aditya Kumar, Esther Lim, Adam J. Engler, Christian M. Metallo, and Stephanie I. Fraley. 3D collagen architecture regulates cell adhesion through degradability, thereby controlling metabolic and oxidative stress. Integrative Biology, (2019).

Sural K. Ranamukhaarachchi, Rishi N. Modi, Anthony Han, Daniel O. Velez, Aditya Kumar, Adam J. Engler, and Stephanie I. Fraley. Crowding tunes 3D collagen fibers and reveals matrix regulation of cancer cell morphogenesis. Biomaterials Science, (2019).


Mridu Sinha, Julietta Jupe, Hannah Mack, Todd P. Coleman, Shelley M. Lawrence, and Stephanie I. Fraley. Emerging Technologies for Molecular Diagnosis of Sepsis. Clinical Microbiology Reviews, 31(2) (2018). *Cover *IF 17.046.

Mridu Sinha, Hannah Mack, Todd P. Coleman, and Stephanie I. Fraley. A high resolution digital DNA melting platform for robust sequence profiling and enhanced genotype discrimination. SLAS Technology (2018).

Wei Zhang, Ana Bojorquez-Gomez, Daniel Ortiz Velez, Guorong Xu, Kyle Sanchez, John Paul Shen, Kevin Chen, Katherine Licon, Collin Melton, Katrina Olson, Michael Ku Yu, Justin K. Huang, Hannah Carter, Emma Farley, Michael Snyder, Stephanie Fraley, Jason F. Kreisberg, Trey Ideker. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nature Genetics (2018). *IF 27.959.


D. Ortiz, B. Tsui, T. Goshia, C.L Chute, A. Han, H. Carter, S.I. Fraley. 3D collagen architecture induces a conserved migratory and transcriptional response linked to Vasculogenic Mimicry. Nature Communications (2017). *IF 12.124.

D. Ortiz, H. Mack, J. Jupe, S. Hawker, N. Kulkarni, B. Hedayatnia, Y. Zhang, S. Lawrence, S. I. Fraley. Massively parallel digital high resolution melt for rapid and absolutely quantitative sequence profiling. Scientific Reports (2017).


S.I. Fraley, P. Athamanolap, B.J. Masek, J. Hardick, K.C. Carroll, Y.-H. Hsieh, R.E. Rothman, C. Gaydos, T.-H. Wang, S. Yang. Nested machine learning algorithm facilitates increased sequence content for large-scale automated High Resolution Melt genotyping. Scientific Reports (2016).


S.I. Fraley, P.-H. Wu, L. He, Y. Feng, R. Krishnamurthy, G.D. Longmore, D. Wirtz. Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions. Scientific Reports.


P. Athamanolap, V. Agarwal, V. Parekh, D.J. Shin, S.I. Fraley, M.A. Jacobs, T.-H. Wang, S. Yang. Trainable High Resolution Melt curve classifier for accurate large-scale genotyping of sequence variants. PLoS ONE.


S.I. Fraley, J. Hardick, B. Masek, P. Athamanolap, R. Rothman, C. Gaydos, K. C. Carroll, T. Wakefield, T.-H. Wang, S. Yang. Universal Digital High Resolution Melt: A novel approach to broad-based profiling of heterogeneous biological samples. Nucleic Acids Research.

The Physical Sciences Oncology Network. A physical sciences network characterization of non-tumorigenic and metastatic cells. Scientific Reports.


K. Yap, S.I. Fraley, M.M. Thiaville, N. Jinawath, K. Nakayama, J.-L. Wang, T.-L. Want, D. Wirtz, and I.-M. Shih. NAC1 is an actin-binding protein that is essential for effective cytokinesis is cancer cells. Cancer Research.

S.I. Fraley, Y. Feng, G.D. Longmore, & D. Wirtz. Dimensional and temporal controls of three-dimensional cell migration by zyxin and binding partners. Nature Communications.


C.C. L. Wong, D. Gilkes, H. Zhang, J. Chen, H. Wei, P. Chaturvedi, S.I. Fraley, C. M. Wong, U.-S. Khoo, I.O.L. Ng, D. Wirtz, and G.L. Semenza. Hypoxia-inducible factor 1 is a master regulator of breast cancer metastatic niche formation. Proceedings of the National Academy of Sciences.

S.I. Fraley, C.M. Hale, R.J. Bloom, A. Celedon, J.S.H. Lee, and D. Wirtz.

Intra- and extracellular microrheology of endothelial cells in a 3D matrix. Biophysical Regulation of Vascular Differentiation and Assembly.

S.I. Fraley, Y. Feng, D. Wirtz, & G. D. Longmore. Reply: reducing background fluorescence reveals adhesions in 3D matrices. Nature Cell Biology.


S.I. Fraley, Y. Feng, R. Krishnamurthy, D.-H. Kim, A. Celedon, G. Longmore, and D. Wirtz. A Distinctive Role for Focal Adhesion Proteins in 3-Dimensional Cell Motility. Nature Cell Biology.


R. Bailey, F. Jones, S.I. Wilson (Fraley), and J. Hiestand. Effects of Packing and Aspect Ratio on Mixing and Heterogeneous Catalysis in Microchannels. 5th Joint ASME/JSME Fluids Engineering Conference.

F. Jones, R. Bailey, Stephanie Wilson, and J. Hiestand. The Effects of Engineering Design on Heterogeneous Biocatalysis in Microchannels. Applied Biochemistry and Biotechnology.