2024
Narasimhan BN, Fraley SI. Degradability tunes ECM stress relaxation and cellular mechanics. bioRxiv [Preprint], 2024.
Debnath B, Narasimhan BN, Fraley SI, Rangamani P. Modeling collagen fibril degradation as a function of matrix microarchitecture. Soft Matter [in press], 2024.
Ranamukhaarachchi S, Walker A, Tang M-H, Leineweber WD, Lam S, Rappel W-J, Fraley SI, Distinct Matrix Remodeling Programs Drive Divergent Cell Polarization and Collective Migration Modes. Dev Cell [Preprint], 2024.
Gleerup D, Trypsteen W, Fraley SI, De Spiegelaere W. Digital PCR in virology: current applications and future perspectives. Molecular Diagnosis & Therapy [Accepted], 2024.
Jafarinia H, Khalilimeybodi A, Barrasa-Fano J, Fraley SI, Rangamani P, Carlier A. Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction. NPJ Syst Biol Appl. 2024 Aug 15;10(1):90.
Leineweber WD, Rowell MZ, Ranamukhaarachchi SK, Walker A, Li Y, Villazon J, Mestre-Farrera A, Hu Z, Yang J, Shi L, Fraley SI. Divergent iron regulatory states contribute to heterogeneity in breast cancer aggressiveness. iScience, 2024 Aug 3;27(9):110661.
Goshia T, Aralar A, Wiederhold N, Jenks JD, Mehta SR, Karmakar A, E S M, Sharma A, Sun H, Kebadireng R, White PL, Sinha M, Hoenigl M, Fraley SI. Universal digital high-resolution melting for the detection of pulmonary mold infections. J Clin Microbiol. 2024 Jun 12;62(6):e0147623.
Khong E, Oh JJ, Jimenez JM, Liu R, Dunham S, Monsibais A, Rhoads A, Ghatbale P, Garcia A, Cobián Güemes AG, Blanc AN, Chiu M, Kuo P, Proost M, Kline A, Aslam S, Schooley RT, Whiteson K, Fraley SI, Pride DT. A simple solid media assay for detection of synergy between bacteriophages and antibiotics. Microbiol Spectr. 2024 May 2;12(5):e0322123.
Aralar A, Goshia T, Ramchandar N, Lawrence SM, Karmakar A, Sharma A, Sinha M, Pride DT, Kuo P, Lecrone K, Chiu M, Mestan KK, Sajti E, Vanderpool M, Lazar S, Crabtree M, Tesfai Y, Fraley SI. Universal Digital High-Resolution Melt Analysis for the Diagnosis of Bacteremia. J Mol Diagn. 2024 May;26(5):349-363.
Boussina A, Langouche L, Obirieze AC, Sinha M, Mack H, Leineweber W, Aralar A, Pride DT, Coleman TP, Fraley SI. Machine learning based DNA melt curve profiling enables automated novel genotype detection. BMC Bioinformatics. 2024 May 10;25(1):185.
Lawrence SM, Goshia T, Sinha M, Fraley SI, Williams M. Decoding human cytomegalovirus for the development of innovative diagnostics to detect congenital infection. Pediatr Res. 2024 Jan;95(2):532-542.
2023
Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR 3rd. An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections. Expert Rev Mol Diagn. 2023 Jul-Dec;23(12):1135-1152.
Gupta A, Lawrence SM, Fraley SI. A broad-based probe-free qPCR assay for detection and discrimination of three human herpes viruses. J Virol Methods. 2023 Dec;322:114824.
Leineweber WD, Fraley SI. Adhesion tunes speed and persistence by coordinating protrusions and extracellular matrix remodeling. Dev Cell. 2023 Aug 7;58(15):1414-1428.e4.
2022
Khalilimeybodi A, Fraley SI, Rangamani P. Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signalling. J Physiol. 2023 Feb;601(3):483-515. doi: 10.1113/JP283966.
Mary Blair-Loy, Olga V. Mayorova, Pamela C. Cosman, and Stephanie I. Fraley. Can rubrics combat gender bias in faculty hiring?. Science, (2022), Vol 377, Issue 6601
2021
Fan Zheng, Marcus R. Kelly, Dana J. Ramms, Marissa L. Heintschel, Stephanie i. Fraley et al. Interpretation of cancer mutations using a multiscale map of protein systems. Science, (2021), Vol 374, Issue 6563.
Kevin Chen, Kivilcim Ozturk, Ted Liefeld, Michael Reich, Jill P Mesirov, Hannah Carter, and 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, and 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).
2020
Kevin Chen, Kivilcim Ozturk, Ryne L Contreras, Jessica Simon, Sean McCann, Wei Ji Chen, Hannah Carter, and 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, and 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)
2019
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).
2018
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.
2017
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).
2016
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).
2015
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.
2014
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.
2013
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.
2012
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.
2011
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.
2010
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.
2007
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.