Stephanie Fraley

Title(s)Associate Professor, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Digital High Resolution Melt and Machine Learning for Rapid and Specific Diagnosis in Neonatal Sepsis
    NIH R01AI134982May 1, 2018 - Apr 30, 2023
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A simple solid media assay for detection of synergy between bacteriophages and antibiotics. Microbiol Spectr. 2024 Mar 25; e0322123. 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. PMID: 38526142.
      View in: PubMed   Mentions:    Fields:    
    2. Universal Digital High-Resolution Melt Analysis for the Diagnosis of Bacteremia. J Mol Diagn. 2024 Feb 21. 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. PMID: 38395408.
      View in: PubMed   Mentions:    Fields:    
    3. Grand Challenges at the Interface of Engineering and Medicine. IEEE Open J Eng Med Biol. 2024; 5:1-13. Subramaniam S, Akay M, Anastasio MA, Bailey V, Boas D, Bonato P, Chilkoti A, Cochran JR, Colvin V, Desai TA, Duncan JS, Epstein FH, Fraley S, Giachelli C, Grande-Allen KJ, Green J, Guo XE, Hilton IB, Humphrey JD, Johnson CR, Karniadakis G, King MR, Kirsch RF, Kumar S, Laurencin CT, Li S, Lieber RL, Lovell N, Mali P, Margulies SS, Meaney DF, Ogle B, Palsson B, A Peppas N, Perreault EJ, Rabbitt R, Setton LA, Shea LD, Shroff SG, Shung K, Tolias AS, van der Meulen MCH, Varghese S, Vunjak-Novakovic G, White JA, Winslow R, Zhang J, Zhang K, Zukoski C, Miller MI. PMID: 38415197; PMCID: PMC10896418.
      View in: PubMed   Mentions:
    4. Divergent iron-regulatory states contribute to heterogeneity in breast cancer aggressiveness. bioRxiv. 2024 Feb 13. Leineweber WD, Rowell MZ, Ranamukhaarachchi S, Walker A, Li Y, Villazon J, Farrera AM, Hu Z, Yang J, Shi L, Fraley SI. PMID: 37425829; PMCID: PMC10327122.
      View in: PubMed   Mentions:
    5. Decoding human cytomegalovirus for the development of innovative diagnostics to detect congenital infection. Pediatr Res. 2024 Jan; 95(2):532-542. Lawrence SM, Goshia T, Sinha M, Fraley SI, Williams M. PMID: 38146009; PMCID: PMC10837078.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. 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. Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR. PMID: 37801397; PMCID: PMC10842420.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    7. Universal Digital High Resolution Melt for the detection of pulmonary mold infections. bioRxiv. 2023 Nov 09. Goshia T, Aralar A, Wiederhold N, Jenks JD, Mehta SR, Sinha M, Karmakar A, Sharma A, Shrivastava R, Sun H, White PL, Hoenigl M, Fraley SI. PMID: 37986859; PMCID: PMC10659414.
      View in: PubMed   Mentions:
    8. A broad-based probe-free qPCR assay for detection and discrimination of three human herpes viruses. J Virol Methods. 2023 Dec; 322:114824. Gupta A, Lawrence SM, Fraley SI. PMID: 37778538.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    9. Universal digital high resolution melt analysis for the diagnosis of bacteremia. medRxiv. 2023 Sep 08. Aralar A, Goshia T, Ramchandar N, Lawrence SM, Karmakar A, Sharma A, Sinha M, Pride DT, Kuo P, Lecrone K, Chiu M, Mestan K, Sajti E, Vanderpool M, Lazar S, Crabtree M, Tesfai Y, Fraley SI. PMID: 37732245; PMCID: PMC10508820.
      View in: PubMed   Mentions:
    10. A simple solid media assay for detection of synergy between bacteriophages and antibiotics. bioRxiv. 2023 Aug 24. Khong E, Oh J, 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. PMID: 37662290; PMCID: PMC10473724.
      View in: PubMed   Mentions:
    11. Adhesion tunes speed and persistence by coordinating protrusions and extracellular matrix remodeling. Dev Cell. 2023 08 07; 58(15):1414-1428.e4. Leineweber WD, Fraley SI. PMID: 37321214; PMCID: PMC10527808.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    12. Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signalling. J Physiol. 2023 02; 601(3):483-515. Khalilimeybodi A, Fraley SI, Rangamani P. PMID: 36463416.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    13. Can rubrics combat gender bias in faculty hiring? Science. 2022 07; 377(6601):35-37. Blair-Loy M, Mayorova OV, Cosman PC, Fraley SI. PMID: 35771928.
      View in: PubMed   Mentions: 1     Fields:    
    14. Interpretation of cancer mutations using a multiscale map of protein systems. Science. 2021 Oct; 374(6563):eabf3067. Zheng F, Kelly MR, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ, Ideker T. PMID: 34591613; PMCID: PMC9126298.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    15. A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells. STAR Protoc. 2021 06 18; 2(2):100561. Chen K, Ozturk K, Liefeld T, Reich M, Mesirov JP, Carter H, Fraley SI. PMID: 34095869; PMCID: PMC8165572.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    16. A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes. Proc Natl Acad Sci U S A. 2021 05 18; 118(20). Scott KE, Fraley SI, Rangamani P. PMID: 33990464; PMCID: PMC8157940.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    17. Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power. Bioinformatics. 2021 Apr 01; 36(22-23):5337-5343. Langouche L, Aralar A, Sinha M, Lawrence SM, Fraley SI, Coleman TP. PMID: 33355665; PMCID: PMC8016452.
      View in: PubMed   Mentions: 4     Fields:    
    18. Phenotypically supervised single-cell sequencing parses within-cell-type heterogeneity. iScience. 2021 Jan 22; 24(1):101991. Chen K, Ozturk K, Contreras RL, Simon J, McCann S, Chen WJ, Carter H, Fraley SI. PMID: 33490901; PMCID: PMC7808958.
      View in: PubMed   Mentions: 7  
    19. Improving Quantitative Power in Digital PCR through Digital High-Resolution Melting. J Clin Microbiol. 2020 05 26; 58(6). Aralar A, Yuan Y, Chen K, Geng Y, Ortiz Velez D, Sinha M, Lawrence SM, Fraley SI. PMID: 32295887; PMCID: PMC7269394.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    20. Cell Adhesiveness Serves as a Biophysical Marker for Metastatic Potential. Cancer Res. 2020 02 15; 80(4):901-911. Beri P, Popravko A, Yeoman B, Kumar A, Chen K, Hodzic E, Chiang A, Banisadr A, Placone JK, Carter H, Fraley SI, Katira P, Engler AJ. PMID: 31857292; PMCID: PMC7024658.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    21. Emerging themes and unifying concepts underlying cell behavior regulation by the pericellular space. Acta Biomater. 2019 09 15; 96:81-98. Scott KE, Rychel K, Ranamukhaarachchi S, Rangamani P, Fraley SI. PMID: 31176842.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    22. 3D collagen architecture regulates cell adhesion through degradability, thereby controlling metabolic and oxidative stress. Integr Biol (Camb). 2019 05 01; 11(5):221-234. Velez DO, Ranamukhaarachchi SK, Kumar A, Modi RN, Lim EW, Engler AJ, Metallo CM, Fraley SI. PMID: 31251330; PMCID: PMC6657753.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    23. Macromolecular crowding tunes 3D collagen architecture and cell morphogenesis. Biomater Sci. 2019 Jan 29; 7(2):618-633. Ranamukhaarachchi SK, Modi RN, Han A, Velez DO, Kumar A, Engler AJ, Fraley SI. PMID: 30515503; PMCID: PMC6375559.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    24. A High-Resolution Digital DNA Melting Platform for Robust Sequence Profiling and Enhanced Genotype Discrimination. SLAS Technol. 2018 12; 23(6):580-591. Sinha M, Mack H, Coleman TP, Fraley SI. PMID: 29652558.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    25. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 04; 50(4):613-620. Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. PMID: 29610481; PMCID: PMC5893414.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    26. Emerging Technologies for Molecular Diagnosis of Sepsis. Clin Microbiol Rev. 2018 04; 31(2). Sinha M, Jupe J, Mack H, Coleman TP, Lawrence SM, Fraley SI. PMID: 29490932; PMCID: PMC5967692.
      View in: PubMed   Mentions: 106     Fields:    Translation:Humans
    27. 3D collagen architecture induces a conserved migratory and transcriptional response linked to vasculogenic mimicry. Nat Commun. 2017 11 21; 8(1):1651. Velez DO, Tsui B, Goshia T, Chute CL, Han A, Carter H, Fraley SI. PMID: 29162797; PMCID: PMC5698427.
      View in: PubMed   Mentions: 67     Fields:    Translation:Humans
    28. Massively parallel digital high resolution melt for rapid and absolutely quantitative sequence profiling. Sci Rep. 2017 02 08; 7:42326. Velez DO, Mack H, Jupe J, Hawker S, Kulkarni N, Hedayatnia B, Zhang Y, Lawrence S, Fraley SI. PMID: 28176860; PMCID: PMC5296755.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    29. Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping. Sci Rep. 2016 Jan 18; 6:19218. Fraley SI, Athamanolap P, Masek BJ, Hardick J, Carroll KC, Hsieh YH, Rothman RE, Gaydos CA, Wang TH, Yang S. PMID: 26778280; PMCID: PMC4726007.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    30. Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples. Nucleic Acids Res. 2016 Jan 08; 44(1):508. Fraley SI, Hardick J, Masek BJ, Athamanolap P, Rothman RE, Gaydos CA, Carroll KC, Wakefield T, Wang TH, Yang S. PMID: 26476457; PMCID: PMC4705649.
      View in: PubMed   Mentions: 2     Fields:    
    31. Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions. Sci Rep. 2015 Oct 01; 5:14580. Fraley SI, Wu PH, He L, Feng Y, Krisnamurthy R, Longmore GD, Wirtz D. PMID: 26423227; PMCID: PMC4589685.
      View in: PubMed   Mentions: 99     Fields:    Translation:HumansCells
    32. Trainable high resolution melt curve machine learning classifier for large-scale reliable genotyping of sequence variants. PLoS One. 2014; 9(9):e109094. Athamanolap P, Parekh V, Fraley SI, Agarwal V, Shin DJ, Jacobs MA, Wang TH, Yang S. PMID: 25275518; PMCID: PMC4183555.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    33. Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples. Nucleic Acids Res. 2013 Oct; 41(18):e175. Fraley SI, Hardick J, Masek BJ, Jo Masek B, Athamanolap P, Rothman RE, Gaydos CA, Carroll KC, Wakefield T, Wang TH, Yang S. PMID: 23935121; PMCID: PMC3794612.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    34. A physical sciences network characterization of non-tumorigenic and metastatic cells. Sci Rep. 2013; 3:1449. Physical Sciences - Oncology Centers Network, Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, Damania D, Davies PC, Decuzzi P, Dickinson L, Estevez-Salmeron L, Estrella V, Ferrari M, Fischbach C, Foo J, Fraley SI, Frantz C, Fuhrmann A, Gascard P, Gatenby RA, Geng Y, Gerecht S, Gillies RJ, Godin B, Grady WM, Greenfield A, Hemphill C, Hempstead BL, Hielscher A, Hillis WD, Holland EC, Ibrahim-Hashim A, Jacks T, Johnson RH, Joo A, Katz JE, Kelbauskas L, Kesselman C, King MR, Konstantopoulos K, Kraning-Rush CM, Kuhn P, Kung K, Kwee B, Lakins JN, Lambert G, Liao D, Licht JD, Liphardt JT, Liu L, Lloyd MC, Lyubimova A, Mallick P, Marko J, McCarty OJ, Meldrum DR, Michor F, Mumenthaler SM, Nandakumar V, O'Halloran TV, Oh S, Pasqualini R, Paszek MJ, Philips KG, Poultney CS, Rana K, Reinhart-King CA, Ros R, Semenza GL, Senechal P, Shuler ML, Srinivasan S, Staunton JR, Stypula Y, Subramanian H, Tlsty TD, Tormoen GW, Tseng Y, van Oudenaarden A, Verbridge SS, Wan JC, Weaver VM, Widom J, Will C, Wirtz D, Wojtkowiak J, Wu PH. PMID: 23618955; PMCID: PMC3636513.
      View in: PubMed   Mentions: 83     Fields:    Translation:HumansCells
    35. NAC1 is an actin-binding protein that is essential for effective cytokinesis in cancer cells. Cancer Res. 2012 Aug 15; 72(16):4085-96. Yap KL, Fraley SI, Thiaville MM, Jinawath N, Nakayama K, Wang J, Wang TL, Wirtz D, Shih IeM. PMID: 22761335; PMCID: PMC3421062.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    36. Dimensional and temporal controls of three-dimensional cell migration by zyxin and binding partners. Nat Commun. 2012 Mar 06; 3:719. Fraley SI, Feng Y, Giri A, Longmore GD, Wirtz D. PMID: 22395610; PMCID: PMC4380184.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansCells
    37. Hypoxia-inducible factor 1 is a master regulator of breast cancer metastatic niche formation. Proc Natl Acad Sci U S A. 2011 Sep 27; 108(39):16369-74. Wong CC, Gilkes DM, Zhang H, Chen J, Wei H, Chaturvedi P, Fraley SI, Wong CM, Khoo US, Ng IO, Wirtz D, Semenza GL. PMID: 21911388; PMCID: PMC3182724.
      View in: PubMed   Mentions: 222     Fields:    Translation:HumansCells
    38. A distinctive role for focal adhesion proteins in three-dimensional cell motility. Nat Cell Biol. 2010 Jun; 12(6):598-604. Fraley SI, Feng Y, Krishnamurthy R, Kim DH, Celedon A, Longmore GD, Wirtz D. PMID: 20473295; PMCID: PMC3116660.
      View in: PubMed   Mentions: 272     Fields:    Translation:Cells
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