Publications

Paraskevaidi M, Baker MJ, Butler HJ, Byrne HJ, Chakkumpulakkal TPV, Christie L, Crean S, Gardner P, Gassner C, Kazarian SG, Kochan K, Kyrgiou M, Lima KMG, Martin-Hirsch PL, Paraskevaidis E, Pebotuwa S, Adegoke JA, Sala A, Santos , Sulé-Suso J, Tyagi G, Walsh MJ & Wood B. Applied Spectroscopy Reviews. Clinical applications of infrared and Raman spectroscopy in the fields of cancer and infectious diseases. 2021 (In Press). Link.

Mohiuddin S, Sreedhar S, Sreedhar H, Martinez D, Nazzal O, Gaba RC, Walsh MJ. Journal of Vascular and Interventional Radiology. Infrared Spectral Microscopy: A Primer for the Interventional Radiologist. 2021 (In Press) Link.

Sun MG, Luo Y, Teng T, Guaiquil V, Zhou Q, McGinn L, Nazzal O, Walsh MJ, Lee J, and Rosenblatt MI. Macromolecular Chemistry and Physics. "Silk Film Stiffness Modulates Corneal Epithelial Cell Mechanosignaling" 2021. Link.

Shachi Mittal, Tomasz P. Wrobel, Michael J Walsh, Andre Kajdacsy-Balla and Rohit Bhargava. Clinical Spectroscopy. Breast cancer histopathology using infrared spectroscopic imaging: The impact of instrumental configurations. 2021. In press. Link.

Songyun Liu, Deborah J. Hall, Craig J. Della Valle, Michael J. Walsh, Joshua J. Jacobs, and Robin Pourzal. Biotribology. Simultaneous Characterization of Implant Wear and Tribocorrosion Debris within its Corresponding Tissue Response Using Infrared Chemical Imaging. 2021. In Press. Link

Sreedhar H, Carns M, Aren K, Nazeer S, Walsh MJ* and Varga J*. *Joint corresponding authors. Vibrational Spectroscopy. Label-Free spectroscopic imaging of the skin characterizes biochemical changes associated with systemic sclerosis. *Joint senior authors. 2020 109:103102. Link.

Suryadevara V, Nazeer S, Sreedhar H, Adelaja O, Kajdacsy-Balla A, Natarajan V and Walsh MJ. Biomedical Optics Express. Infrared spectral microscopy as a tool to monitor lung fibrosis development in a model system. 2020 11:3996-4007.. Link. OPEN ACCESS!

Camilo LM Morais, Maria Paraskevaidi, Li Cui, Nigel J Fullwood, Martin Isabelle, Kássio MG Lima, Pierre L Martin-Hirsch, Hari Sreedhar, Júlio Trevisan, Michael J Walsh, Dayi Zhang, Yong-Guan Zhu, Francis L Martin. Nature Protocols. 2019 14(5):1546-1577.

Berisha S, Lotfollahi M, Jahanipour J, Gurcan I, Walsh MJ, Bhargava R, Nguyen H, and Mayerich D. Deep learning for FTIR histology: leveraging spatial and spectral features with convolutional neural networks. Analyst 2019. Link.

Kumar N., Uppala P., Duddu K., Sreedhar H., Varma V., Guzman G., Walsh MJ., and Sethi A. IEEE Transactions in Medical Imaging. Hyperspectral Tissue Image Segmentation using Semi-Supervised NMF and Hierarchical Clustering. 2019. Link.

Imran Uraizee*, Vishal K Varma*, Hari Sreedhar, Francesca Gambacorta, Shaiju Nazeer, Aliya Husain^#, Michael J Walsh^#. "Label-free identification of antibody-mediated rejection in cardiac allograft biopsies using infrared spectroscopic imaging." Transplantation 2019. Link.

Rupali Mankar, Michael J Walsh, Rohit Bhargava, Saurabh Prasad and David Mayerich " "Selecting optimal features from Fourier transform infrared spectroscopy for discrete-frequency imaging" Analyst 2019. Link.

Vishal Varma, Andre Kajdacsy-Balla, Sanjeev Akkina, Suman Setty, Michael J Walsh. "Predicting Fibrosis Progression in Renal Transplant Recipients Using Laser-Based Infrared Spectroscopic Imaging". Scientific Reports. Link. (2018).

Shaiju S Nazeer*, Hari Sreedhar*, Vishal K. Varma, David Martinez-Marin, Christine Massie, Michael J. Walsh. * Joint first. “"Infrared Spectroscopic Imaging: Label-Free Biochemical Analysis of Stroma and Tissue Fibrosis". Invited Imaging in Focus review article in the International Journal of Biochemistry and Cell Biology. (2017) 92:14-17. Link.

Hari Sreedhar, Vishal Varma, Benjamin Bird, Grace Guzman, and Michael J Walsh. 'Applications of QCL Imaging to the Advancement of Pathology'. Proc. SPIE, Medical Imaging (2017) 1014004. Link.

David Martinez-Marin, Hari Sreedhar, Vishal Varma, Catarina Eloy, Manuel Sobrinho-Simoes, Andre Kajdacsy-Balla and Michael J Walsh. "Accounting for tissue heterogeneity in infrared spectroscopic imaging for accurate diagnosis of thyroid carcinoma subtypes". Prominent Young Spectroscopist Edition of Vibrational Spectroscopy (2016) 91:77-82. Link.

Hari Sreedhar, Vishal Varma, Francesca Gambacorta, Grace Guzman, and Michael J. Walsh. "Infrared Spectroscopic Imaging Detects Chemical Modifications in Liver Fibrosis due to Diabetes and Disease". Biomedical Optics Express (2016) 7:2419-2424.link.

Varma V, Kajdacsy-Balla A, Akkina S, Setty S, Walsh MJ. Response to Letter to Editor: Infrared spectroscopic imaging for interrogating the carbohydrate biochemistry of diabetic nephropathy progression. Kidney International (2016) 90:226. Link.

Varma VK, Kajdacsy-Balla A, Akkina SK, Setty S and Walsh MJ. A label-free approach by infrared spectroscopic imaging for interrogating the biochemistry of diabetic nephropathy progression. Kidney International (2016) 89:1153-1159. Link.

Holly J Butler, Lorna Ashton, Benjamin Bird, Gianfelice Cinque, Kelly Curtis, Jennifer Dorney, Karen Esmonde-White, Nigel J Fullwood, Benjamin Gardner, Pierre L Martin-Hirsch, Michael J Walsh, Martin R McAinsh, Nicholas Stone & Francis L Martin. Using Raman spectroscopy to characterize biological materials. Nature Protocols (2016) 11:664-687. Link.

Using QCLs for MIR-Based Spectral Imaging — Applications in Tissue Pathology". Biophotonics (2015). Link. Next generation laser-based IR imaging of tissue!

Mayerich D, Walsh MJ, Kajdacsy-Balla A, Ray PS, Hewitt SM, Bhargava R. Stain-less staining for computed histopathology'. Technology 03 27 (2015). Link.

Hari Sreedhar*, Vishal K. Varma*, Peter L. Nguyen, Bennett Davidson, Sanjeev Akkina, Grace Guzman, Suman Setty, Andre Kajdacsy-Balla, Michael J. Walsh. High-definition Fourier Transform Infrared (FT-IR) Spectroscopic Imaging of Human Tissue Sections towards Improving Pathology. Journal of Visualized Experiments. Jan 2015. Link. Video instructions of high-definition IR imaging of kidney and liver tissues!

Kwak J, Kajdacsy-Balla A, Macias V, Walsh MJ, Sinha S, Bhargava R. 'Improving Prediction of Prostate Cancer Recurrence using Chemical Imaging' Scientific Reports 5 (2015). Link

Matthew J Baker, Julio trevisan, Paul Bassan, Rohit Bhargava, Holly J Butler, Konrad M Dorling, Peter R Fielden, Simon W Fogarty, Nigel J Fullwood, Kelly A Heys, Caryn Hughes,Peter Lasch, Pierre L Martin-Hirsch, Blessing Obinaju, Ganesh D Sockalingum, Josep Sulé-Suso, Rebecca J Strong, Michael J Walsh, Bayden R Wood, Peter Gardner & Francis L Martin. Using Fourier transform IR spectroscopy to analyze biological materials. Nature Protocols 9, 1771–1791 (2014).Link

Mayerich D, Van Dijk T, Walsh MJ, Schulmerich M, and Bhargava R. On the importance of image formation optics in the design of infrared spectroscopic imaging systems. Analyst (In Press).

Biswas S, Walsh MJ, Bhargava R. Fourier Transform Infrared (FT-IR) Spectroscopic Imaging for Solid Tumor Histopathology. Optical Spectroscopy and Computational Methods in Biology and Medicine. Challenges and Advances in Computational Chemistry and Physics (2014) 14:475-504

Mayerich DM, Walsh MJ; Kajdacsy-Balla A, Mittal S, Bhargava R. Breast histopathology using random decision forests-based classification of infrared spectroscopic imaging data. Proc. SPIE 9041, Medical Imaging 2014. Link.

Sreedhar H, Panta M, Ronquillo NR, Davidson B, Nguyen P, Chennuri R, Choi J, Herrara JA, Hinojosa AC, Jin M, Kajdacsy-Balla A, Guzman G, Walsh MJ. Investigating the Biochemical Progression of Liver Disease Through Fibrosis, Cirrhosis, Dysplasia and Hepatocellular Carcinoma using Fourier Transform Infrared Spectroscopic Imaging. Proc. SPIE 8939, Biomedical Vibrational Spectroscopy VI: Advances in Research and Industry 89390J. Link.

Varma VK, Ohlander S, Nguyen P, Vendryes C, Parthiban S, Hamilton B, Wallis MC, Kajdacsy-Balla A, Hannaford B, Lendvay T, Hotaling JM, Walsh MJ. "Fourier Transform Infrared Spectroscopic Imaging Identifies Early Biochemical Markers of Tissue Damage". Proc. SPIE 8939, Biomedical Vibrational Spectroscopy VI: Advances in Research and Industry 89390T. Link.

Mayerich D, Walsh MJ, Schulmerich MV, Bhargava R, “Real-Time Interactive Data Mining for Chemical Imaging Information: Application to Automated Histopathology.” BMC Bioinformatics (accepted) 2013. Series on Cancer Bioinformatics: Bioinformatic Methods, Network Biomarkers and Precision Medicine. Link.

Reddy RK, Walsh MJ, Schulmerich MV, Scott Carney P, Bhargava R. High-definition Infrared Spectroscopic Imaging. Applied Spectroscopy, 2013 67(1):93-105. Link. HD FT-IR Imaging in your own lab!

Ambekar R, Lau TY, Walsh MJ, Bhargava R, Toussaint K. Quantifying collagen structure in breast biopsies using second-harmonic generation imaging. Biomedical Optics Express. 2012 3(9):2021-2035 - Link.

Schulmerich MV, Walsh MJ, Gelber M, Kong R, Kole M,Harrison S, McKinney J, Thompson D, Kull L, Bhargava R. Journal of Agricultural and Food Chemistry, Computational Analysis of Soybean Seed by Transmission Raman Spectroscopy, 2012 (In Press).

Walsh MJ, Kajdacsy-Balla A, Holton S, Bhargava R. Attenuated Total Reflectance Fourier Transform Infrared Spectroscopic Imaging for Breast Histopathology. Vibrational Spectroscopy, 2012 60:23-28. Link.

Walsh MJ, Reddy RK, Bhargava R. Label-free Biomedical Imaging with Mid-Infrared Microspectroscopy. IEEE Journal of Selected Topics in Quantum Electronics, 2012 18(4):1502-1513. Link. Good review of the current state of the field of IR spectroscopy for biomedical applications if interested!

Reddy R, Mayerich D, Walsh MJ, Bhargava R. Optimizing the design of FT-IR spectroscopic imaging instruments to obtain increased spatial resolution of chemical species. IEEE International Symposium on Biomedical Imaging, 2012 354-357. Link.

Walsh MJ, Mayerich D, Kajdacsy-Balla, Bhargava R. High Resolution Mid-Infrared Imaging for Disease Diagnosis. Proc SPIE, 2012 82190R. Link.

Nguyen TH, Reddy RK, Walsh MJ, Schulmerich M, Popescu G, Do MN, Bhargava R. Denoising and Deblurring of Fourier Transform Infrared Spectroscopic Imaging Data. Proc SPIE, 2012. Link.

Reddy RK, Mayerich D, Walsh MJ, Carney PS, Bhargava R. Rigorous electromagnetic model of Fourier Transform Infrared (FT-IR) spectroscopic imaging applied to automated histology of prostate tissue specimens. International Journal of Engineering and Natural Sciences, special issue on Advances in Optics, Lasers and Spectroscopy (In Press). Links.

Holton S, Walsh MJ, Kajdacsy-Balla A, Bhargava R. Label-free characterization of cancer-activated fibroblasts using infrared spectroscopic imaging. Biophysical Journal, 2011 101:1513-1521. Link.

Mayerich D, Walsh MJ and Bhargava R. Designing Transfer Functions for Exploring Hyperspectral Images. Proceedings of the IEEE Conference on Visualization, Oct 2011. Link.

Nasse MJ, Walsh MJ, Mattson EC, Reininger R, Kajdacsy-Balla A, Macias V, Bhargava R and Hirschmugl CJ. High-resolution Fourier-transform infrared chemical imaging with multiple synchrotron beams. Nature Methods, 2011 8:413-416. Link. Nature Methods paper demonstrating the first ever high-resolution IR imaging of tissues!

Holton S, Walsh MJ, Bhargava R. Subcellular localization of early biochemical transformations in cancer-activated fibroblasts using infrared spectroscopic imaging. Analyst, 2011, 136:2953-2958. Link.

Martin FL, Kelly JG, Llabjani V, Martin-Hirsch PL, Patel II, Trevisan J, Fullwood NJ, Walsh MJ. Application of infrared spectroscopy to distinguish cell types or populations based on the derivation and computation analyses of a biochemical-cell fingerprint. Nature Protocols. 2010 5:1748-1760. Link. Nature Protocols paper on using IR spectroscopy for cell typing!

Walsh MJ and Bhargava R. Chapter 10; Infrared spectroscopic imaging: an integrative approach to pathology. Nanobiophotonics 2010 McGrawHill ISBN10: 0071737014. Link. Now available on the Kindle! Link. Also now available online - Link. Book Chapter describing the field and recent advances in biospectroscopy!

Walsh MJ, Nasse MN, Pounder FN, Macias V, Kajdacsy-Balla, Hirschmugl C and Bhargava R. AIP Conference Proceedings Volume 1214 WIRMS 5^th International workshop on infrared microscopy and spectroscopy with accelerator based sources. 2009; 105-107. Link.

Pounder FN, Reddy RJ, Walsh MJ and Bhargava R. Validating the cancer diagnosis potential of mid-infrared spectroscopic imaging. Proc SPIE, 2009; 71860F. Link.

Walsh MJ, Hammiche A, Fellous TG, Nicholson JM, Cotte M, Susini J, Fullwood NJ, Martin-Hirsch PM, Alison MR and Martin FL. Tracking the cell hierarchy in the human intestine using biochemical signatures derived by mid-infrared microspectroscopy. Stem Cell Research. 2009 3(1)15-27. Link.

Walsh MJ, Bruce SW, Pant K, Carmichael PL, Scott AD and Martin FL. Discrimination of a transformation phenotype in Syrian golden hamster embryo (SHE) cells using ATR-FTIR spectroscopy. Toxicology. 2009 258(1):33-38. Link.

Kelly JG, Singh MN, Stringfellow HF, Walsh MJ, Nicholson JM, Bahrami F, Ashton KM, Pitt MA, Martin-Hirsch PL and Martin FL. Derivation of a subtype-specific biochemical signature of endometrial carcinoma using synchrotron based Fourier-transform infrared microspectroscopy. Cancer Letters. 2009 274(2):208-217. Link.

Ahmad MS, Mirza B, Hussain M, Hanif M, Ali S, Walsh MJ, Martin FL. ATR-FTIR spectroscopy detects alterations induced by organotin(IV) carboxylates in MCF-7 cells at sub-cytotoxic concentrations. PMC Biophys. 2008 5(1).Link.

Kelly JG, Angelov PP, Walsh MJ, Pollock HM, Pitt MA, Martin-Hirsch PL, Martin FL. Intelligent interrogation of mid-IR spectroscopy data from exfoliative cervical cytology using self-learning classifier eClass. Int. Journ. Comp. Intell. Res. 2008 4(4) 392-401. Link.

Walsh MJ, Singh MN, Stringfellow HF, Pollock HM, Hammiche A, Grude O, Fullwood NJ, Pitt MA, Martin-Hirsch PL and Martin FL. FTIR microspectroscopy coupled with two class discrimination segregates markers responsible for inter and intra-category variance in exfoliative cytology. Biomarker Insights. 2008; 3:179-189. Link.

Singh MN, Stringfellow HF, Walsh MJ, Ashton KM, Paraskevaidis E, Abdo KR, Martin-Hirsch PL, Phillips DH and Martin FL. Quantifiable mRNA transcripts for tamoxifen-metabolising enzymes in human endometrium. Toxicology. 2008 249(1):85-90. Link.

Noel EE, Ragavan N, Walsh MJ, James SY, Matanhelia SS, Nicholson CM, Lu YJ, Martin FL. Differential gene expression in the peripheral zone compared to the transition zone of the human prostate gland. Prostate Cancer Prostatic Dis. 2007 11(2):173-180. Link.

Walsh MJ, Fellous TG, Hammiche A, Lin WR, Fullwood NJ, Grude O, Bahrami F, Nicholson JM, Cotte M, Susini J, Pollock HM, Brittan M, Martin-Hirsch PL, Alison MR, Martin FL. FTIR Micro-spectroscopy Identifies Symmetric PO2- Modifications as a Marker of the Putative Stem Cell Region of Human Intestinal Crypts. Stem Cells. 2007; 26(1):108-18. Link. Stem Cells paper - first demonstration of label-free identification of stem cells in the gastrointestinal tract!

Grude O, Hammiche A, Pollock H, Bentley AJ, Walsh MJ, Martin FL, Fullwood NJ. Near-field photothermal microspectroscopy for adult stem-cell identification and characterization. Journal of microscopy. 2007; 3(228): 366-372. Link.

Bi X, Walsh MJ, Wei X, Sheng G, Fu J, Martin-Hirsch PL, Thomas GO, Jones KC, Martin FL. Infrared spectral analysis of MCF-7 cells treated with serum-lipid extracts segregates predominantly brominated flame retardant-exposed subjects from those with mainly organochlorine exposures. Environ Sci Technol. 2007; 41(16):5915-22.Link.

Hammiche A, Walsh MJ, Pollock HM, Martin-Hirsch PL, Martin FL. Non-contact micro-cantilevers detect photothermally induced vibrations that can segregate different categories of exfoliative cervical cytology. J Biochem Biophys Methods. 2007; 70(4):675-7. Link.

Jiao H, Allinson SL, Walsh MJ, Hewitt R, Cole KJ, Phillips DH, Martin FL. Growth kinetics in MCF-7 cells modulate benzo[a]pyrene-induced CYP1A1 up-regulation. Mutagenesis. 2007; 22(2):111-6. Link.

Walsh MJ, Singh MN, Pollock HM, Cooper LJ, German MJ, Stringfellow HF, Fullwood NJ, Paraskevaidis E, Martin-Hirsch PL, Martin FL. ATR microspectroscopy with multivariate analysis segregates grades of exfoliative cervical cytology. Biochem Biophys Res Commun. 2007; 352(1):213-9. Link.

Barber JL, Walsh MJ, Hewitt R, Jones KC, Martin FL. Low-dose treatment with polybrominated diphenyl ethers (PBDEs) induce altered characteristics in MCF-7 cells. Mutagenesis. 2006;21(5):351-60. Link.

Walsh MJ, German MJ, Singh M, Pollock HM, Hammiche A, Kyrgiou M, Stringfellow HF, Paraskevaidis E, Martin-Hirsch PL, Martin FL. IR microspectroscopy: potential applications in cervical cancer screening. Cancer Lett. 2007; 246(1-2):1-11. Link.