HR job title
- Associate Professor
- Contact Info
- Websites
- ORCiD
- 0000-0003-3832-8207
Walsh, Alex Assistant Professor
Positions
- Assistant Professor, Biomedical Engineering, College of Engineering
Research Areas
- Overview
- Publications
- Teaching
- Background
- Contact
- Other
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Overview
Publications
selected publications
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academic article
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Benavides, O. R., White, B. P., Gibbs, H. C., Kaunas, R., Gregory, C. A., Maitland, K. C., & Walsh, A. J.
(2024).
Comparison of polystyrene and hydrogel microcarriers for optical imaging of adherent cells. Journal of Biomedical Optics.
29(Suppl 2), S22708.
-
Hu, L., De Hoyos, D., Lei, Y., West, A. P., & Walsh, A. J.
(2024).
3D convolutional neural networks predict cellular metabolic pathway use from fluorescence lifetime decay data. APL Bioengineering.
8(1), 016112.
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Sharma, D., Sharma, A., Hu, L., Chen, T., Voon, S., Bayless, K. J., ... Zhao, F.
(2023).
Perfusability and immunogenicity of implantable pre-vascularized tissues recapitulating features of native capillary network. Bioactive Materials.
30, 184-199.
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Yu, W., Chen, Y., Putluri, N., Osman, A., Coarfa, C., Putluri, V., ... Sandulache, V. C.
(2023).
Evolution of cisplatin resistance through coordinated metabolic reprogramming of the cellular reductive state. British Journal of Cancer.
128(11), 2013-2024.
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Hu, L., Morganti, S., Nguyen, U., Benavides, O. R., & Walsh, A. J.
(2023).
Label-free optical imaging of cell function and collagen structure for cell-based therapies. Current Opinion in Biomedical Engineering.
25, 100433-100433.
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Hu, L., Ter Hofstede, B., Sharma, D., Zhao, F., & Walsh, A. J.
(2023).
Comparison of phasor analysis and biexponential decay curve fitting of autofluorescence lifetime imaging data for machine learning prediction of cellular phenotypes. 3, 1210157.
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Hu, L., Wang, N., Bryant, J. D., Liu, L., Xie, L., West, A. P., & Walsh, A. J.
(2023).
Label-free spatially maintained measurements of metabolic phenotypes in cells. Frontiers in Bioengineering and Biotechnology.
11, 1293268.
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Liu, L., Zhou, Y. i., Liu, Z., Li, J., Hu, L., He, L., ... Xie, L.
(2023).
Osr1 Regulates Macrophage-mediated Liver Inflammation in Nonalcoholic Fatty Liver Disease Progression. CMGH Cellular and Molecular Gastroenterology and Hepatology.
15(5), 1117-1133.
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Wang, N., Hu, L., & Walsh, A. J.
(2023).
POSEA: A novel algorithm to evaluate the performance of multi-object instance image segmentation. PLoS ONE.
18(3), e0283692-e0283692.
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Benavides, O. R., Gibbs, H. C., White, B. P., Kaunas, R., Gregory, C. A., Walsh, A. J., & Maitland, K. C.
(2023).
Volumetric imaging of human mesenchymal stem cells (hMSCs) for non-destructive quantification of 3D cell culture growth. PLoS ONE.
18(3), e0282298-e0282298.
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VandenHeuvel, S. N., Farris, H. A., Noltensmeyer, D. A., Roy, S., Donehoo, D. A., Kopetz, S., ... Raghavan, S.
(2022).
Decellularized organ biomatrices facilitate quantifiable in vitro 3D cancer metastasis models. SOFT MATTER.
18(31), 5791-5806.
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Cardona, E. N., & Walsh, A. J.
(2022).
Identification of rare cell populations in autofluorescence lifetime image data. Cytometry Part A.
101(6), 497-506.
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Miskolci, V., Tweed, K. E., Lasarev, M. R., Britt, E. C., Walsh, A. J., Zimmerman, L. J., ... Huttenlocher, A.
(2022).
In vivo fluorescence lifetime imaging of macrophage intracellular metabolism during wound responses in zebrafish. eLife.
11, e66080.
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Theodossiou, A., Hu, L., Wang, N., Nguyen, U., & Walsh, A. J.
(2021).
Autofluorescence Imaging to Evaluate Cellular Metabolism. Journal of Visualized Experiments.
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Schmitz, R., Tweed, K., Walsh, C., Walsh, A. J., & Skala, M. C.
(2021).
Extracellular pH affects the fluorescence lifetimes of metabolic co-factors. 26(5), 056502-056502.
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Lee, W., Kingstad-Bakke, B., Paulson, B., Larsen, A., Overmyer, K., Marinaik, C. B., ... Suresh, M.
(2021).
Carbomer-based adjuvant elicits CD8 T-cell immunity by inducing a distinct metabolic state in cross-presenting dendritic cells. PLOS Pathogens.
17(1), e1009168-e1009168.
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Walsh, A. J., Mueller, K. P., Tweed, K., Jones, I., Walsh, C. M., Piscopo, N. J., ... Skala, M. C.
(2021).
Classification of T-cell activation via autofluorescence lifetime imaging. Nature Biomedical Engineering.
5(1), 77-88.
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Hu, L., Wang, N., Cardona, E., & Walsh, A. J.
(2020).
Fluorescence intensity and lifetime redox ratios detect metabolic perturbations in T cells. Biomedical Optics Express.
11(10), 5674-5688.
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Wang, Z. J., Walsh, A. J., Skala, M. C., & Gitter, A.
(2020).
Classifying T cell activity in autofluorescence intensity images with convolutional neural networks. Journal of Biophotonics.
13(3), e201960050.
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Heaster, T. M., Walsh, A. J., Zhao, Y., Hiebert, S. W., & Skala, M. C.
(2018).
Autofluorescence imaging identifies tumor cell-cycle status on a single-cell level. Journal of Biophotonics.
11(1),
-
Zhang, Q., Jeppesen, D. K., Higginbotham, J. N., Demory Beckler, M., Poulin, E. J., Walsh, A. J., ... Coffey, R. J.
(2018).
Mutant KRAS Exosomes Alter the Metabolic StateofRecipient ColonicEpithelial Cells. CMGH Cellular and Molecular Gastroenterology and Hepatology.
5(4), 627-629.e6.
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Walsh, A. J., Cook, R. S., & Skala, M. C.
(2017).
Functional Optical Imaging of Primary Human Tumor Organoids: Development of a Personalized Drug Screen. JOURNAL OF NUCLEAR MEDICINE.
58(9), 1367-1372.
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Walsh, A. J., Tolstykh, G. P., Martens, S., Ibey, B. L., & Beier, H. T.
(2016).
Action potential block in neurons by infrared light. Neurophotonics.
3(4), 040501-040501.
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Walsh, A. J., Castellanos, J. A., Nagathihalli, N. S., Merchant, N. B., & Skala, M. C.
(2016).
Optical Imaging of Drug-Induced Metabolism Changes in Murine and Human Pancreatic Cancer Organoids Reveals Heterogeneous Drug Response. Pancreas.
45(6), 863-869.
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Walsh, A. J., Sharick, J. T., Skala, M. C., & Beier, H. T.
(2016).
Temporal binning of time-correlated single photon counting data improves exponential decay fits and imaging speed. Biomedical Optics Express.
7(4), 1385-1399.
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Walsh, A. J., Cook, R. S., Sanders, M. E., Arteaga, C. L., & Skala, M. C.
(2016).
Drug response in organoids generated from frozen primary tumor tissues. Scientific Reports.
6(1), 18889.
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Nagathihalli, N. S., Castellanos, J. A., Shi, C., Beesetty, Y., Reyzer, M. L., Caprioli, R., ... Merchant, N. B.
(2015).
Signal Transducer and Activator of Transcription 3, Mediated Remodeling of the Tumor Microenvironment Results in Enhanced Tumor Drug Delivery in a Mouse Model of Pancreatic Cancer. Gastroenterology.
149(7), 1932-1943.e9.
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Shah, A. T., Diggins, K. E., Walsh, A. J., Irish, J. M., & Skala, M. C.
(2015).
In Vivo Autofluorescence Imaging of Tumor Heterogeneity in Response to Treatment. Neoplasia.
17(12), 862-870.
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Campos-Delgado, D. U., Navarro, O. G., Arce-Santana, E. R., Walsh, A. J., Skala, M. C., & Jo, J. A.
(2015).
Deconvolution of fluorescence lifetime imaging microscopy by a library of exponentials. Optics Express.
23(18), 23748-23767.
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Campos-Delgado, D. U., Gutierrez-Navarro, O., Arce-Santana, E. R., Skala, M. C., Walsh, A. J., & Jo, J. A.
(2015).
Blind deconvolution estimation of fluorescence measurements through quadratic programming. Journal of Biomedical Optics.
20(7), 075010-075010.
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Walsh, A. J., Cook, R. S., Lee, J. H., Arteaga, C. L., & Skala, M. C.
(2015).
Collagen density and alignment in responsive and resistant trastuzumab-treated breast cancer xenografts. Journal of Biomedical Optics.
20(2), 26004-026004.
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Walsh, A. J., & Skala, M. C.
(2015).
Optical metabolic imaging quantifies heterogeneous cell populations. Biomedical Optics Express.
6(2), 559-573.
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Cannon, T. M., Shah, A. T., Walsh, A. J., & Skala, M. C.
(2015).
High-throughput measurements of the optical redox ratio using a commercial microplate reader. Journal of Biomedical Optics.
20(1), 010503-010503.
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Walsh, A. J., Cook, R. S., Sanders, M. E., Aurisicchio, L., Ciliberto, G., Arteaga, C. L., & Skala, M. C.
(2014).
Quantitative optical imaging of primary tumor organoid metabolism predicts drug response in breast cancer. 74(18), 5184-5194.
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McCormack, D. R., Walsh, A. J., Sit, W., Arteaga, C. L., Chen, J., Cook, R. S., & Skala, M. C.
(2014).
In vivo hyperspectral imaging of microvessel response to trastuzumab treatment in breast cancer xenografts. Biomedical Optics Express.
5(7), 2247-2261.
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Shah, A. T., Demory Beckler, M., Walsh, A. J., Jones, W. P., Pohlmann, P. R., & Skala, M. C.
(2014).
Optical metabolic imaging of treatment response in human head and neck squamous cell carcinoma. 9(3), e90746-e90746.
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Venkateswaran, A., Sekhar, K. R., Levic, D. S., Melville, D. B., Clark, T. A., Rybski, W. M., ... Freeman, M. L.
(2014).
The NADH oxidase ENOX1, a critical mediator of endothelial cell radiosensitization, is crucial for vascular development. Cancer Research.
74(1), 38-43.
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Walsh, A. J., Cook, R. S., Manning, H. C., Hicks, D. J., Lafontant, A., Arteaga, C. L., & Skala, M. C.
(2013).
Optical metabolic imaging identifies glycolytic levels, subtypes, and early-treatment response in breast cancer. 73(20), 6164-6174.
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Poole, K. M., Tucker-Schwartz, J. M., Sit, W. W., Walsh, A. J., Duvall, C. L., & Skala, M. C.
(2013).
Quantitative optical imaging of vascular response in vivo in a model of peripheral arterial disease. American Journal of Physiology. Heart and Circulatory Physiology.
305(8), H1168-H1180.
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Venkateswaran, A., Friedman, D. B., Walsh, A. J., Skala, M. C., Sasi, S., Rachakonda, G., ... Sekhar, K. R.
(2013).
The novel antiangiogenic VJ115 inhibits the NADH oxidase ENOX1 and cytoskeleton-remodeling proteins. Investigational New Drugs.
31(3), 535-544.
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Givens, R., Walsh, A. J., & Skala, M. C.
(2013).
The effects of varying glucose concentrations on cellular glycolytic rates. 3, 62-64.
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Walsh, A. J., Masters, D. B., Jansen, E. D., Welch, A. J., & Mahadevan-Jansen, A.
(2012).
The effect of temperature on the autofluorescence of scattering and non-scattering tissue. LASERS IN SURGERY AND MEDICINE.
44(9), 712-718.
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Walsh, A. J., Poole, K. M., Duvall, C. L., & Skala, M. C.
(2012).
Ex vivo optical metabolic measurements from cultured tissue reflect in vivo tissue status. Journal of Biomedical Optics.
17(11), 116015-116015.
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Walsh, A., Cook, R. S., Rexer, B., Arteaga, C. L., & Skala, M. C.
(2012).
Optical imaging of metabolism in HER2 overexpressing breast cancer cells. Biomedical Optics Express.
3(1), 75-85.
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Bi, X., Walsh, A., Mahadevan-Jansen, A., & Herline, A.
(2011).
Development of spectral markers for the discrimination of ulcerative colitis and Crohn's disease using Raman spectroscopy. Diseases of the Colon and Rectum.
54(1), 48-53.
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Zaman, R. T., Rajaram, N., Walsh, A., Oliver, J., Rylander, H. G., Tunnell, J. W., Welch, A. J., & Mahadevan-Jansen, A.
(2011).
Variation of fluorescence in tissue with temperature. LASERS IN SURGERY AND MEDICINE.
43(1), 36-42.
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Wang, N., Hu, L., & Walsh, A. J.
Evaluation of Cellpose segmentation with sequential thresholding for instance segmentation of cytoplasms within autofluorescence images. Computers in Biology and Medicine.
179, 108846-108846.
-
Benavides, O. R., White, B. P., Gibbs, H. C., Kaunas, R., Gregory, C. A., Maitland, K. C., & Walsh, A. J.
(2024).
Comparison of polystyrene and hydrogel microcarriers for optical imaging of adherent cells. Journal of Biomedical Optics.
29(Suppl 2), S22708.
-
chapter
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Martinez, J., Wang, N., Hu, L., Cardona Benitez, E., Nguyen, U., Martinez, R., & Walsh, A. J.
(2022).
Imaging in Scaffolds. Winter, J. O., & Rao, S. (Eds.),
Biomaterial Based Approaches to Study the Tumour Microenvironment.
0.
The Royal Society of Chemistry.
-
Walsh, A. J., Shah, A. T., Sharick, J. T., & Skala, M. C.
(2015).
Fluorescence Lifetime Measurements of NAD(P)H in Live Cells and Tissue. Springer Series in Chemical Physics.
Becker, W. (Eds.),
Advanced Time-Correlated Single Photon Counting Applications.
(pp. 435-456).
Springer Nature.
-
Martinez, J., Wang, N., Hu, L., Cardona Benitez, E., Nguyen, U., Martinez, R., & Walsh, A. J.
(2022).
Imaging in Scaffolds. Winter, J. O., & Rao, S. (Eds.),
Biomaterial Based Approaches to Study the Tumour Microenvironment.
0.
The Royal Society of Chemistry.
-
conference paper
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Hu, L., & Walsh, A. J.
(2023).
Identifying cancer cell metabolic states in autofluorescence lifetime images with machine learning. Progress in Biomedical Optics and Imaging - Proceedings of SPIE.
1239104-1239104-5.
-
Walsh, A. J., Hu, L., Wang, N., & Threet, A.
(2023).
Quantitative analysis of label-free fluorescence lifetime images for single cell measurements of metabolism (Conference Presentation). 10.
-
Hu, L., Sharma, D., Zhao, F., & Walsh, A. J.
(2023).
Metabolic perturbations of macrophages on engineered collagen scaffolds with label-free fluorescence lifetime imaging (Conference Presentation). 15.
-
Martinez, J., Theodossiou, A., & Walsh, A. J.
(2023).
Infrared light effects on coenzyme binding and cellular metabolism. 11.
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Hu, L., & Walsh, A. J.
(2022).
Modeling key metabolic pathways of cancer cells using label-free fluorescence lifetime imaging. Proceedings of SPIE.
1197206-1197206-7.
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Sharma, D., Hu, L., Chen, T., Sharma, A., He, W., Goldman, J., Walsh, A. J., & Zhao, F.
(2022).
Perfusable Human Mesenchymal Stem Cell Patch Ameliorates Innate Immune Response. Tissue Engineering Part A.
208-209.
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Walsh, A. J., Sedelnikova, A., Tolstykh, G. P., Ibey, B. L., & Beier, H. T.
(2017).
Fluorescence Lifetime Imaging of Calcium Flux in Neurons in Response to Pulsed Infrared Light. Proceedings of SPIE.
100691b-100691b-8.
-
Walsh, A. J., Tolstykh, G. P., Martens, S. L., Ibey, B. L., & Beier, H. T.
(2017).
Short Infrared Laser Pulses Block Action Potentials in Neurons. Proceedings of SPIE.
100520j-100520j-7.
-
Walsh, A. J., Cantu, J. C., Ibey, B. L., & Beier, H. T.
(2017).
Short Infrared Laser Pulses Increase Cell Membrane Fluidity. Proceedings of SPIE.
100620d-100620d-6.
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Walsh, A. J., Tolstykh, G., Martens, S., Sedelnikova, A., Ibey, B. L., & Beier, H. T.
(2016).
All Optical Experimental Design for Neuron Excitation, Inhibition, and Action Potential Detection. Proceedings of SPIE.
96901p-96901p-6.
-
Walsh, A. J., & Beier, H. T.
(2016).
Temporal and spatial binning of TCSPC data to improve signal-to-noise ratio and imaging speed. Proceedings of SPIE.
97120r-97120r-7.
-
Walsh, A. J., & Skala, M. C.
(2014).
An automated image processing routine for segmentation of cell cytoplasms in high-resolution autofluorescence images. Proceedings of SPIE.
89481m-89481m-6.
-
Walsh, A. J., Cook, R. S., Arteaga, C. L., & Skala, M. C.
(2013).
Optical metabolic imaging of live tissue cultures. Proceedings of SPIE.
858820-858820-6.
-
Walsh, A., Masters, B., Jansen, D., Welch, A. J., & Mahadevan-Jansen, A.
(2010).
The effect of temperature of fluorescence: an animal study. Proceedings of SPIE.
75620w-75620w-5.
-
Hu, L., & Walsh, A. J.
(2023).
Identifying cancer cell metabolic states in autofluorescence lifetime images with machine learning. Progress in Biomedical Optics and Imaging - Proceedings of SPIE.
1239104-1239104-5.
-
institutional repository document
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Benavides, O. R., White, B. P., Gibbs, H. C., Kaunas, R., Gregory, C. A., Maitland, K. C., & Walsh, A. J.
(2023).
Comparison of polystyrene and hydrogel microcarriers for optical imaging of adherent cells
-
Schmitz, R. L., Tweed, K. E., Rehani, P., Samimi, K., Riendeau, J., Jones, I., ... Skala, M. C.
(2023).
Autofluorescence lifetime imaging classifies human lymphocyte activation and subtype
-
Wang, Z. J., Walsh, A. J., Skala, M. C., & Gitter, A.
(2019).
Classifying T cell activity in autofluorescence intensity images with convolutional neural networks
-
Benavides, O. R., White, B. P., Gibbs, H. C., Kaunas, R., Gregory, C. A., Maitland, K. C., & Walsh, A. J.
(2023).
Comparison of polystyrene and hydrogel microcarriers for optical imaging of adherent cells
-
patent
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Skala, M. C., Gitter, A., Wang, Z., & Walsh, A. J.
(2020).
Systems and methods for classifying activated T cells
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Skala, E. C., & Walsh, A. J.
(2019).
Systems and methods for sorting T cells by activation state
-
Skala, M. C., Gitter, A., Wang, Z., & Walsh, A. J.
(2020).
Systems and methods for classifying activated T cells
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software
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Walsh, A.
(2023).
CancerCellMetabolism
-
Walsh, A.
(2023).
POSEA
-
Walsh, A.
(2023).
PhasorML
-
Walsh, A.
(2022).
Simulation and Analysis of Fluorescence Lifetime Image (FLIM) Data to Identify Rare Cells
-
Walsh, A.
(2021).
Fluorescence lifetime image analysis code and example data of NADH and FAD images
-
Walsh, A.
(2023).
CancerCellMetabolism
Teaching
teaching activities
- BMEN291 Hnr-research Instructor
- BMEN291 Hnr-research Instructor
- BMEN322 Biosignal Analysis Instructor
- BMEN422 Bioelectromagnetism Instructor
- BMEN491 Hnr-research Instructor
- BMEN608 Biophotonics Ii Instructor
- BMEN622 Bioelectromagnetism Instructor
- BMEN685 Directed Studies Instructor
- BMEN691 Research Instructor
Background
education and training
- Ph.D. in Biomedical Engineering, Vanderbilt University - (Nashville, Tennessee, United States) 2015
- M.S. in Biomedical Engineering, Vanderbilt University - (Nashville, Tennessee, United States) 2012
- B.E. in Biomedical Engineering, Vanderbilt University - (Nashville, Tennessee, United States) 2010
awards and honors
Contact
first name
- Alex
has last name
- Walsh
Other
- walshaj@tamu.edu