A. Refereed Archival Journal Publications

A-[001] M.V. Boland, M.K. Markey, R.F. Murphy, “Automated recognition of patterns characteristic of subcellular structures in fluorescence microscopy images,” Cytometry 33:366-375 (November 1998). PMID: 9822349

A-[002] M.K. Markey, M.V. Boland, R.F. Murphy, “Toward objective selection of representative microscopy images,” Biophysical Journal 76:2230-2237 (April 1999). PMCID: PMC1300196

A-[003] G.D. Tourassi, M.K. Markey, J.Y. Lo, C.E. Floyd, Jr., “A neural network approach to breast cancer diagnosis as a constraint satisfaction problem,” Medical Physics 28:804-811 (May 2001). PMID: 11393476

A-[004] G.D. Tourassi, E.D. Frederick, M.K. Markey, C.E. Floyd, Jr., “Application of the mutual information criterion for feature selection in computer-aided diagnosis,” Medical Physics 28:2394-2402 (December 2001). PMID: 11797941

A-[005] J.Y. Lo, M.K. Markey, J.A. Baker, C.E. Floyd, Jr., “Cross-institutional evaluation of BI-RADS predictive model for mammographic diagnosis of breast cancer,” American Journal of Roentgenology 178:457-463 (February 2002). PMID: 11804918

A-[006] M.K. Markey, J.Y. Lo, R. Vargas-Voracek, G.D. Tourassi, C.E. Floyd, Jr., “Perceptron error surface analysis: a case study in breast cancer diagnosis,” Computers in Biology and Medicine 32:99-109 (March 2002). PMID: 11879823

A-[007] M.K. Markey, J.Y. Lo, C.E. Floyd, Jr., “Differences between the computer-aided diagnosis of breast masses and that of calcifications,” Radiology 223:489-493 (May 2002). (The Radiological Society of North America highlighted this study in a press release, April 30, 2002). PMID: 11997558

A-[008] M.K. Markey, J.Y. Lo, G.D. Tourassi, C.E. Floyd, Jr., “Self-organizing map for cluster analysis of a breast cancer database,” Artificial Intelligence in Medicine 27:113-127 (February 2003). PMID: 12636975

A-[009] M.K. Markey, G.D. Tourassi, C.E. Floyd, Jr., “Decision tree classification of proteins identified by mass spectrometry of blood serum samples from people with and without lung cancer,” Proteomics 3:1678-1679 (September 2003). (short communication) PMID: 12636975

A-[010] S.Y. Park, T. Collier, J. Aaron, M.K. Markey, R. Richards-Kortum, K. Sokolov, N. Mackinnon, C. MacAulay, L. Coghlan, A. Milbourne, M. Follen, “Multispectral digital microscopy for in vivo monitoring of oral neoplasia in the hamster cheek pouch model of carcinogenesis,” Optics Express 13:749-762 (February 2005). PMID: 19494935

A-[011] S. Gupta, M.K. Markey, “Correspondence in texture features between two mammographic views,” Medical Physics 32:1598-1606 (June 2005). PMID: 16013719

A-[012] M.K. Markey, G.D. Tourassi, M. Margolis*, and D.M. DeLong, “Impact of missing data in evaluating artificial neural networks trained on complete data,” Computers in Biology and Medicine 36:516-525 (May 2006). PMID: 15893745

A-[013] S. Gupta, P.F. Chyn*, M.K. Markey, “Breast cancer CADx based on BI-RADS™ descriptors from two mammographic views,” Medical Physics 33:1810-1817 (June 2006). PMID: 16872088

A-[014] M.P. Sampat, G.J. Whitman, T.W. Stephens, L.D. Broemeling, N.A. Heger, A.C. Bovik, M.K. Markey, “The reliability of measuring physical characteristics of spiculated masses on mammography,” British Journal of Radiology 79:S134-S140 (December 2006). PMID: 17209119

A-[015] M.S. Kim, G.P. Reece, E.K. Beahm, M.J. Miller, E.N. Atkinson, M.K. Markey, “Objective assessment of aesthetic outcomes of breast cancer treatment: measuring ptosis from clinical photographs,” Computers in Biology and Medicine 37:49-59 (January 2007). PMID: 16438948

A-[016] E.A. Fischer, M.A. Friedman*, M.K. Markey, “Empirical comparison of tests for differential expression on time-series microarray experiments,” Genomics 89:460-470 (April 2007). PMID: 17188839

A-[017] M.P. Sampat, G.J. Whitman, A.C. Bovik, M.K. Markey, “Comparison of algorithms to enhance spicules of spiculated masses on mammography,” Journal of Digital Imaging 21:9-17 (March 2008). PMCID: PMC3043831

A-[018] H. Shin, B. Sheu*, M. Joseph*, M.K. Markey, “Guilt-by-association feature selection: identifying biomarkers from proteomic profiles,” Journal of Biomedical Informatics 41:124-136 (February 2008). PMID: 17544868

A-[019] H. Shin, M. Mutlu*, J.M. Koomen, M.K. Markey, “Parametric power spectral density analysis of noise from instrumentation in MALDI TOF mass spectrometry,” Cancer Informatics 3:317-328 (September 2007). PMCID: PMC2675828

A-[020] M.S. Kim, W.N. Rodney*, T. Cooper, C. Kite, G.P. Reece, M.K. Markey, “Toward quantifying the aesthetic outcomes of breast cancer treatment: comparison of clinical photography and colorimetry,” Journal of Evaluation in Clinical Practice 15:20-31 (February 2009). PMCID: PMC3072466

A-[021] S.Y. Park, M. Follen, A. Milbourne, H. Rhodes, A. Malpica, N. MacKinnon, C. MacAulay, M.K. Markey, R. Richards-Kortum, “Automated image analysis of digital colposcopy for the detection of cervical neoplasia,” Journal of Biomedical Optics 13:014029 (January 2008). PMID: 18315387

A-[022] L.T. Nieman, C.W. Kan, A. Gillenwater, M.K. Markey, K. Sokolov, “Probing local tissue changes in the oral cavity for the early detection of cancer using oblique polarized reflectance spectroscopy: a pilot clinical trial,” Journal of Biomedical Optics 13:024011 (March 2008). PMID: 18465974

A-[023] M.P. Sampat, A.C. Bovik, G.J. Whitman, M.K. Markey, “A model-based framework for the detection of spiculated lesions on mammography,” Medical Physics 35:0094-2405 (May 2008). PMID: 18561687

A-[024] M.P. Sampat, A.C. Patel*, Y. Wang*, S. Gupta, C.W. Kan, A.C. Bovik, M. K. Markey, “Indices for three-class classification performance assessment – an empirical comparison,” IEEE Transactions on Information Technology in Biomedicine 13:300-312 (May 2009). PMID: 19171528

A-[025] M.P. Sampat, Z. Wang, S. Gupta, A.C. Bovik, and M.K. Markey, “Complex Wavelet Structural Similarity: a new image similarity index,” IEEE Transactions on Image Processing 18:2385-2401 (November 2009). PMID: 19556195

A-[026] G. M. Pocock, R. G. Aranibar, N. J. Kemp, C. S. Specht, M. K. Markey, H. G. Rylander III, “The relationship between retinal ganglion cell axon constituents and fiber layer birefringence in the primate retinal nerve,” Investigative Ophthalmology and Visual Sciences 50:5238-5246 (November 2009). PMCID: PMC2783205

A-[027] S.P. Borgaonkar, H. Hocker*, H. Shin, M.K. Markey, “Comparison of normalization methods for the identification of biomarkers using MALDI-TOF and SELDI-TOF mass spectra,” OMICS 14:115-126 (February 2010). PMID: 20141334

A-[028] S. Gupta, C.W. Kan, M.K. Markey, “Reducing variability in the output of pattern classifiers using histogram shaping,” Medical Physics 37:1850-1862 (April 2010). PMID: 20443507

A-[029] H. Shin, M.P. Sampat, J.M. Koomen, M.K. Markey, “Wavelet-based adaptive denoising and baseline correction for MALDI TOF MS,” OMICS 14:283-295 (June 2010). PMID: 20455751

A-[030] C.W. Kan, A.Y. Lee*, L.T. Nieman, K. Sokolov, M.K. Markey, “Adaptive spectral window sizes for extraction of diagnostic features from optical spectra,” Journal of Biomedical Optics 15: 047012 (July/August 2010). PMCID: PMC3188638

A-[031] G.S. Muralidhar, A.C. Bovik, J.D. Giese*, M.P. Sampat, G.J. Whitman, T.M. Haygood, T.W. Stephens, M.K. Markey, “Snakules: a model-based active contour algorithm for the annotation of spicules on mammography,” IEEE Transactions on Medical Imaging 29:1768-1780 (October 2010). PMID: 20529728

A-[032] S. Gupta, M.K. Markey, A.C. Bovik, “3D anthropometric face recognition,” International Journal of Computer Vision 90:331-349 (October 2010).

A-[033] G.S. Muralidhar, G.J. Whitman, T.M. Haygood, T.W. Stephens, A.C. Bovik, M.K. Markey, “Evaluation of stylus for radiographic image annotation,” Journal of Digital Imaging 23:701-705 (December 2010). PMCID: PMC3046686

A-[034] J. Lee, M. Kawale, F.A. Merchant, J. Weston, M.C. Fingeret, D. Ladewig, G.P. Reece, M.A. Crosby, E.K. Beahm, M.K. Markey, “Validation of stereophotogrammetry of the human torso,” Breast Cancer: Basic and Clinical Research 5:15–25 (February 2011). PMCID: PMC3076012

A-[035] M. Kawale, J. Lee, S.Y. Leung*, M.C. Fingeret, G.P. Reece, M.A. Crosby, E.K. Beahm, M.K. Markey, F.A. Merchant, “3D symmetry measure invariant to subject pose during image acquisition,” Breast Cancer: Basic and Clinical Research 5:131-142 (June 2011). PMCID: PMC3140267

A-[036] M.S. Kim, A. Burgess, A.J. Waters, G.P. Reece, E.K. Beahm, M.A. Crosby, K.M. Basen-Engquist, M.K. Markey, “A pilot study on using eye-tracking to understand assessment of surgical outcomes from clinical photography,” Journal of Digital Imaging 24: 778-786 (October 2011). PMCID: PMC3180533

A-[037] M. Dabeer, E. Kim*, G.P. Reece, F. Merchant, M.A. Crosby, E.K. Beahm, M.K. Markey, “Automatic calculation of symmetry measure on clinical photographs,” Journal of Evaluation in Clinical Practice 17:1129-1136 (December 2011). PMCID: PMC2958233

A-[038] M.S. Kim, W.N. Rodney*, G.P. Reece, E.K. Beahm, M.A. Crosby, M.K. Markey, “Quantifying the aesthetic outcomes of breast cancer treatment: assessment of surgical scars from clinical photographs,” Journal of Evaluation in Clinical Practice 17:1075-1082 (December 2011). PMID: 20630016

A-[039] D. Wang, A. Arapostathis, C.O. Wilke, M.K. Markey, “Principal-Oscillation-Pattern analysis of gene expression,” PLoS ONE 7(1): e28805. doi:10.1371/journal.pone.0028805 (January 2012). PMCID: PMC3254616

A-[040] D. Wang, M.K. Markey, C.O. Wilke, A. Arapostathis, “Eigen-genomic System Dynamic-pattern Analysis (ESDA): Modeling mRNA degradation and self-regulation,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(2):430-437 (March 2012). PMID: 22084146

A-[041] J. Lee, S. Chen*, G.P. Reece, M.A. Crosby, E.K. Beahm, M.K. Markey, “A novel quantitative measure of breast curvature based on catenary,” IEEE Transactions on Biomedical Engineering, 59(4):1115-1124 (April 2012). PMCID: PMC3334380

A-[042] J.C. Dwelle, S. Liu, B. Wang, A. McElroy, D. Ho*, M.K. Markey, T.E. Milner, H.G. Rylander III, “Thickness, birefringence, and reflectance of the retinal nerve fiber layer in normal and glaucomatous non-human primates,” Investigative Ophthalmology & Visual Science 53:4380-95 (July 2012). (journal cover artwork) PMCID: PMC3394663

A-[043] G.S. Muralidhar, A.C. Bovik, M.K. Markey, “A steerable, multiscale singularity index,” IEEE Signal Processing Letters 20:7-10 (January 2013).

A-[044] R. Hennessy, S.L. Lim, M.K. Markey, and J.W. Tunnell, “Monte Carlo lookup table-based inverse model for extracting optical properties from tissue-simulating phantoms using diffuse reflectance spectroscopy,” Journal of Biomedical Optics, 18(3), 037003 (March 2013). PMCID: PMC3584151.

A-[045] M. Kawale, G.P. Reece, M.A. Crosby, E.K. Beahm, M.C. Fingeret, M.K. Markey, F. Merchant, “Automated identification of fiducial points on 3D torso images,” Biomedical Engineering and Computational Biology 5:57-68 (July 2013). PMCID: PMC4147764.

A-[046] B. Wang, B. Yin, J. Dwelle, H.G. Rylander, M.K. Markey, T.E. Milner, “Path-length-multiplexed scattering-angle-diverse optical coherence tomography for retinal imaging,” Optical Letters 38(21), pp. 4374-4377 (November 2013). PMCID: PMC3903005.

A-[047] C.S. Sun, G.P. Reece, M.A. Crosby, M.C. Fingeret, R.J. Skoracki, M.T. Villa, M.M. Hanasono, D.P. Baumann, D.W. Chang, S.B. Cantor, M.K. Markey, “Plastic surgeon expertise in predicting breast reconstruction outcomes for patient decision analysis,” Journal of Plastic and Reconstructive Surgery Global Open 1:e78 (November 2013). PMCID: PMC4044723.

A-[048] G.S. Muralidhar, A.C. Bovik, M.K. Markey, “Noise analysis of a new singularity index,” IEEE Transactions on Signal Processing 61: 6150-6163  (December 2013).

A-[049] M. Sharma, R. Hennessy, M.K. Markey, J.W. Tunnell, “Verification of a two-layer inverse Monte Carlo absorption model using multiple source-detector separation diffuse reflectance spectroscopy,” Biomedical Optics Express 5(1):40-53 (January 2014). PMCID: PMC3891344.

A-[050] S. Liu, B. Wang, B. Yin, T.E. Milner, M.K. Markey, S.J. McKinnon, H.G. Rylander III, “Retinal nerve fiber layer reflectance for early glaucoma diagnosis,” Journal of Glaucoma 23:e45-e52 (January 2014). PMCID: PMC3844555.

A-[051] C.S. Sun, S.B. Cantor, G.P. Reece, M.C. Fingeret, M.A. Crosby, M.K. Markey, “Assessing women’s preferences and preference modeling for breast reconstruction decision-making,” Journal of Plastic and Reconstructive Surgery Global Open 2:e125 (March 2014). PMCID: PMC4120963.

A-[052] G.S. Muralidhar, M.K. Markey, A.C. Bovik, T.M. Haygood, T.W. Stephens, W.R. Geiser, N. Garg, B.E. Adrada, B.E. Dogan, S. Carkaci, R. Khisty, G.J. Whitman, “Stereoscopic interpretation of low dose breast tomosynthesis projection images,” Journal of Digital Imaging 27:248-254 (April 2014). PMCID: PMC3948934.

A-[053] C.S. Sun, S.B. Cantor, G.P. Reece, M.C. Fingeret, M.A. Crosby, M.K. Markey, “Helping patients make choices about breast reconstruction: A decision analysis approach,” Plastic & Reconstructive surgery 134:597-608 (October 2014). PMCID: PMC4217136.

A-[054] N. Verma, G.S. Muralidhar, A.C. Bovik, M.C. Cowperthwaite, M.G. Burnett, M.K. Markey, “3D brain MRI segmentation via knowledge-driven decision theory”, Journal of Medical Imaging 1(3):034001 (October 2014). doi:10.1117/1.JMI.1.3.034001.

A-[055] R. Hennessy, W. Goth, M. Sharma, M.K. Markey, J.W. Tunnell, “Effect of probe geometry and optical properties on the sampling depth for diffuse reflectance spectroscopy,” Journal of Biomedical Optics 19(10), 107002 (October 2014). doi:10.1117/1.JBO.19.10.107002.

A-[056] L. Lim, B. Nichols, M. Migden, N. Rajaram, J. Reichenberg, M.K. Markey, M. Ross, J.W. Tunnell, “Clinical study of noninvasive in vivo melanoma and nonmelanoma skin cancer using multi-modal spectral diagnosis,” Journal of Biomedical Optics 19(11), 117003 (November 2014). doi:10.1117/1.JBO.19.11.117003

A-[057] H. Khatam, G.P. Reece, M.C. Fingeret, M.K Markey, K. Ravi-Chandar, “In-vivo quantification of human breast deformation associated with the position change from supine to upright,” Medical Engineering & Physics 37:13-22 (January 2015). NIHMS646879.

A-[058] R. Hennessy, M.K. Markey, J.W. Tunnell, “Impact of one-layer assumption on diffuse reflectance spectroscopy of skin,” Journal of Biomedical Optics 20(2), 027001 (February 2015). doi:10.1117/1.JBO.20.2.027001.

A-[059] S. Liu, A. Datta*, D. Ho*, J. Dwelle, D. Wang, T.E. Milner, H.G. Rylander, M.K. Markey, “Effect of image registration on longitudinal analysis of retinal nerve fiber layer thickness of non-human primates using Optical Coherence Tomography (OCT),” Eye and Vision 2:3 (February 2015).

A-[060] J. Slater, P. Boyce, M. Jancaitis, H. Gaubert, A. Chang, M.K. Markey, W. Frey, “Modulation of endothelial cell migration via manipulation of adhesion site growth using nanopatterned surfaces,” ACS Applied Materials & Interfaces 7: 4390–4400 (February 2015).

A-[061] G.P. Reece, F. Merchant, J. Andon, H. Khatam, K. Ravi-Chandar, J. Weston, M.C. Fingeret, C. Lane, K. Duncan, M.K. Markey, “3D surface imaging of the human female torso in upright to supine positions”, Medical Engineering & Physics 37:375–383 (April 2015).

A-[062] G.P. Reece, F. Merchant, J. Andon, H. Khatam, K. Ravi-Chandar, J. Weston, M.C. Fingeret, C. Lane, K. Duncan, M.K. Markey, “3D surface imaging of the human female torso in upright to supine positions”, Medical Engineering & Physics 37:375–383 (April 2015). PMID: 25703742. PMCID: PMC4380553.

A-[063] J. Lee, I. Teo, M. Guindani, G.P. Reece, M.K. Markey, M.C. Fingeret, “Associations between psychosocial functioning and smiling intensity in patients with head and neck cancer,” Psychology, Health & Medicine 20:469-76 (June 2015). PMID: 25159529. [PubMed – in process]

A-[064] G.S. Muralidhar, A.C. Bovik, M.K. Markey, “Disparity estimation on stereo mammograms,” IEEE Transactions on Image Processing 24:2851-2863 (September 2015). PMID: 25974940 [PubMed – indexed for MEDLINE]

A-[065] J. Lee, E. Kim, G.P. Reece, M.A. Crosby, E.K. Beahm, M.K. Markey, “Automated calculation of ptosis on lateral clinical photographs,” Journal of Evaluation in Clinical Practice 21:900-910 (October 2015). doi: 10.1111/jep.12397. PMID: 26083280 [PubMed – in process]

A-[066] N. Verma, S.N. Beretvas, B. Pascual, J.C. Masdeu, M.K. Markey, The Alzheimer’s Disease Neuroimaging Initiative, “New scoring methodology improves the sensitivity of the Alzheimer’s Disease Assessment Scale-Cognitive subscale (ADAS-Cog) in clinical trials,” Alzheimer’s Research & Therapy 7:64 (November 2015). PMID: 26560146. PMCID: PMC4642693.

A-[067] G. Wen, A. Aizenman, T. Drew, J.M. Wolfe, T.M. Haygood, M.K. Markey, “Computational assessment of visual search strategies in volumetric medical images,” Journal of Medical Imaging 3:015501 (January 2016). PMID: 26759815. PMCID: PMC4702525.

A-[068] M.S. Kim, M.R. Aro, K.J. Lage, K.L. Ingalls, V. Sindhwani, M.K. Markey, “Exploring the usability of mobile apps supporting radiologists’ training in diagnostic decision making,” The Journal of the American College of Radiology 13:335-43 (March 2016). doi: 10.1016/j.jacr.2015.07.021. PMID: 26482814

A-[069] A. Raina*, R. Hennessy, M. Rains, J. Allred, J.M. Hirshburg, D. Diven, M.K. Markey, “Objective measurement of erythema in psoriasis using digital color photography with color calibration,” Skin Research and Technology 22:375-80 (August 2016). doi: 10.1111/srt.12276 PMID: 26517973.

* J. Lee, I. Teo, M. Guindani, G.P. Reece, M.K. Markey, M.C. Fingeret, “Associations between psychosocial functioning and smiling intensity in patients with head and neck cancer,” Psychology, Health & Medicine (in press).

* J. Lee, M.C. Fingeret, A.C. Bovik, G.P. Reece, R.J. Skoracki, M. M. Hanasono, M.K. Markey, “Eigen-disfigurement model for simulating plausible facial disfigurement after reconstructive surgery,” BMC Medical Imaging (in press).