Publications
Published Refereed Journal Articles & Published Conference Proceedings
2025
- Hamilton, J, Attaya-Harris, A, Lary, C, Batchelder, K, Khalil, A 2025 Image-based breast cancer risk assessment based on dense mammographic tissue subtypes. Cancer Research, In press.
- Juybari, J, Hamilton, J, Chen, C, Khalil, A, Zhu, Y 2025 Context-guided segmentation for histopathological cancer segmentation. Scientific Reports, 15 (1), 5404.
2024
- Johnson, CP, Hart, A, Jarvis, KF, Latario, SG, Shrestha, S, Leclerc, N, Khalil, A, Kelley, JB 2024 The G-alpha Gpa1 directs septin localization in the mating projection of Saccharomyces cerevisiae through its Ubiquitination Domain and Endocytic Machinery. Journal of Biological Chemistry, 300 (3), 106773.
- Ellis, CPS, Tero, BW, Potts, CM, Malka, KT, Yang, X, Hamilton, J, Vary, C, Khalil, A, Liaw, L 2024 Cellular Characteristics and Protein Signatures of Human Adipose Tissues from Donors With or Without Advanced Coronary Artery Disease. Biomedicines, 12 (11), 2453.
- Hamilton, J, Olzinski, M, Batchelder, K, Brooks, P, Tilbury, K, Khalil, A 2024 Multiscale Computational Analysis of Patient-Matched Multi-Modal Imaging of Breast Tissue Microenvironment. Cancer Research, 84, 9, P03-07-01
2022
- Hamilton, J, Breggia, A, Fitzgerald, TL, Jones, MA, Brooks, PC, Tilbury, KB, Khalil, A 2022 Multiscale anisotropy analysis of second-harmonic generation collagen imaging of human pancreatic cancer. Frontiers in Oncology, 12:991850. doi: 10.3389/fonc.2022.991850
- Liu, J, Enderlin, E, Marshall, HP, Khalil, A 2022 Synchronous retreat of southeast Greenland’s peripheral glaciers. Geophysical Research Letters 49 (13), e2022GL097756. doi: 10.1029/2022GL097756.
- Juybari, J, Khalil, A 2022 Elimination of image saturation effects on multifractal statistics using the 2D WTMM method. Frontiers in Physiology. 13:921869. doi: 10.3389/fphys.2022.921869.
2021
- Willows, JW, Blaszkiewicz, M, Lamore, A, Borer, S, Dubois, AL, Garner, E, Breeding, WP, Tilbury, KB, Khalil, A, Townsend, K 2021 Visualization and analysis of whole depot adipose tissue neural innervation. iScience. 24(10), 103127. doi: 10.1016/j.isci.2021.103127
- Castro, IJ, Toner, BC, Xie, SQ, Swingland, J, Hodges, A, Tabrizi, SJ, Turkheimer, F, Pombo, A, Khalil, A 2021 Altered nuclear architecture in blood cells from Huntington’s disease patients. Neurological Sciences. 43 (1) 379-385. doi: 10.1007/s10072-021-05289-w
- Tilbury, K, Han, X, Brooks, P, Khalil, A 2021. Multiscale Anisotropy Analysis of Second-Harmonic Generation Collagen Imaging of Mouse Skin. Journal of Biomedical Optics. 26(6), 065002. doi: 10.1117/1.JBO.26.6.065022
- Gerasimova-Chechkina, E, Toner, BC, Batchelder, KA, White, B, Freynd, G, Antipev, I, Arneodo, A, Khalil, A 2021. Loss of mammographic tissue homeostasis in invasive lobular and ductal breast carcinomas vs. benign lesions. Frontiers in Physiology – Fractal Physiology. 12, 660883. doi: 10.3389/fphys.2021.660883
- Liu, J, Enderlin, EM, Marshall, HP, Khalil, A 2021. Automated detection of marine glacier calving fronts using the 2D Wavelet Transform Modulus Maxima (WTMM) segmentation method. IEEE Transactions on Geoscience and Remote Sensing. 59(11), 9047-9057. DOI: 10.1109/TGRS.2021.3053235
2020
- Toner, B, Khalil, A 2020. Exploratory computational longitudinal analysis of mammographic microenvironment disruption preceding breast tumorigenesis. Cancer Research, 80 (4 supplement), P6-06-04.
- Robitaille, JF, Abdeldayem, A, Joncour, I, Moraux, E, Motte, F, Lesaffre, P, Khalil, A 2020. Statistical model for filamentary structures of molecular clouds. The modified multiplicative random cascade model and its multifractal nature. Astronomy & Astrophysics. 641, A138 (11 pages).
- Harling, M, Juybari, J, Johnson, J, Townsend, K, Khalil, A, Tilbury, K. 2020. Wavelet-based characterization of the spatial relationship of nerve and collagen in neuropathic adipose tissue. In Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVII. 112450R (10 pages).
Abstracts
- 2025
- Morse, S, Khalil, A 2025. Wavelet-based Segmentation Method for Glioblastoma in MRI Scans. University of Maine Student Symposium, Orono, ME. Abstract #510.
- Puccio, I, Hamilton, J, Khalil, A 2025. Color Normalization and Deconvolution Effects on the Anisotropy Analysis of Breast Tissue. University of Maine Student Symposium, Orono, ME. Abstract #537.
- Lally, D, Wisell, M, Adnee, M, Hamilton, J, Khalil, A, Juybari, J 2025. A Novel Classification Integration for AI Segmentation Models in Digital Pathology. University of Maine Student Symposium, Orono, ME. Abstract #538.
- Miner, J, Raite, J, Brooks, P, Khalil, A, Tilbury, K 2025. A Prospective Therapeutic Reduces Migration in Metastatic Breast Cancer Driven by Integrin α2β1. University of Maine Student Symposium, Orono, ME. Abstract #540.
- Hamilton, J, Khalil, A 2025. Breast Cancer Risk Prediction Using Dense Tissue Stratification and Complementary Texture-Based Approaches. University of Maine Student Symposium, Orono, ME. Abstract #588.
- 2024
- Miner, J, Raite, J, Khalil, A, Tilbury, K 2024. Developing Integrin α2β1 Knockdown Cell Lines for 3D Breast Cancer Spheroid Migration Models. University of Maine Student Symposium, Orono, ME. Abstract #501.
- Hamilton, J, Khalil, A 2024. Enhancing Tumor Microenvironment Analysis Through Combination of Multiscale Anisotropy and Principal Component Analysis. University of Maine Student Symposium, Orono, ME. Abstract #502.
- Morse, S, Hamilton, J, Khalil, A 2024. Comparing Anisotropy of H&E Stained Breast Tissue Histology Slides Across Differing Color Spaces. University of Maine Student Symposium, Orono, ME. Abstract #518.
- Claudio, S, Juybari, J, Khalil, A 2024. Investigation of Loss Functions for Medical Dataset Imbalance. University of Maine Student Symposium, Orono, ME. Abstract #553.
- 2023
- Johnson, CP, Hart, A, Jarvis, KF, Latario, SG, Shrestha, S, Leclerc, N, Khalil, A, Kelley, JB, 2023. The G-alpha Gpa1 directs septin localization in the mating projection of Saccharomyces cerevisiae through its Ubiquitination Domain and endocytic machinery. Cell Bio 2023 – An ASCB|EMBO Meeting, Boston, MA. Abstract #P1477.
- Batchelder, KA, Khalil A 2023. Longitudinal Assessment of Active and Passive Dense Mammographic Tissue. 10th International Breast Density & Cancer Risk Assessment Workshop, Kailua-Kona, HI. Abstract #25.
- Hamilton, J, Batchelder, KA, Olzinski, M, Brooks, P, Tilbury, K, Khalil A 2023. Multiscale Anisotropy Analysis of Second-Harmonic Generation Images of Breast Tissue Microenvironment. 10th International Breast Density & Cancer Risk Assessment Workshop, Kailua-Kona, HI. Abstract #38.
- McCarthy, M, Batchelder, KA, Khalil, A 2023. Quantitative Visualization Tool for the Assessment of Risky Dense Mammographic Tissue. 49th Annual Northeast Bioengineering Conference (NEBEC 2023) Philadelphia, PA.
- Raza, M, Batchelder, KA, Khalil, A 2023. Assessment of Classification Algorithms for Determination of Cancerous Mammography Images. 49th Annual Northeast Bioengineering Conference (NEBEC 2023) Philadelphia, PA.
- Miner, JN, Vittum, Z, Brooks, P, Khalil, A, Tilbury, K 2023. Development of a 3D Breast Cancer Spheroid Migration Model Targeting the Integrin α10β1 Collagen Binding Site. 49th Annual Northeast Bioengineering Conference (NEBEC 2023) Philadelphia, PA.
- Hamilton, J, Juybari, J, Zhu, Y, Khalil, A 2023. Using Deep Learning for Artificial Intelligence Pathology. University of Maine 2023 Student Symposium, Orono, ME. Abstract #522.
- Ham, M, Khalil, A 2023. A numerical Exploration in Estimating the Hurst Exponent Using Fractal Box Counting. University of Maine 2023 Student Symposium, Orono, ME. Abstract #535.
- Boos, M, Olzinski, M, Khalil, A 2023. Analysis of Information from Susan G. Komen Database Including Mammograms and H&E-Stained Histology Images. University of Maine 2023 Student Symposium, Orono, ME. Abstract #543.
- Miner, J, Vittum, Khalil, A, Tilbury, K 2023. Development of a 3D Breast Cancer Spheroid Migration Model Targeting the Integrin α10β1 Collagen Binding Site. University of Maine 2023 Student Symposium, Orono, ME. Abstract #562.
theses
- Seekins, Tyler, Ph.D. Chemical Engineering 2023. ‘Computer vision for paper fiber quantification’. (Co-chair with Dr. Douglas Bousfield).
- Batchelder, Kendra, I.Ph.D. Computational Biomedicine 2023. ‘Longitudinal analysis of mammographic microenvironment tissue disruption accompanying tumorigenesis’.
- Toner, Brian, Ph.D. Computer Science 2019. ‘A Longitudinal Study of Mammograms Utilizing the Automated Wavelet Transform Modulus Maxima Method’.
- Richard, Christian, Ph.D. Functional Genomics 2014. ‘A Wavelet-Based Phenotyping Algorithm Characterizing Seizure Morphology And Frequency Variation In Genetic Models Of Absence Epilepsy’ (Co-chair with Dr. Wayne Frankel).
- Wu, Yongfeng, Ph.D. Astrophysics 2010. ‘Multi-Scale Three-Dimensional Analysis of Galaxy Distributions Using the Metric Space Technique’ (Co-chair with Dr. David Batuski).
- McCarthy, Margaret, M.S. Biomedical Engineering 2023. ‘Quantitative visualization of mammographic tissue microenvironment disruption’.
- Raza, Madison, M.S. Biomedical Engineering 2023. ‘Mammographic tissue microenvironment assessment using the Metric Space Technique’.
- White, Basel, M.S. Biomedical Engineering 2023. ‘Hybrid power spectral and wavelet image roughness analysis’.
- Hamilton, Josh, M.S. Biomedical Engineering 2022. ‘Anisotropy analysis of collagen architecture in pancreatic and breast tumor tissue slides.’ (Co-chair with Dr. Karissa Tilbury)
- Jarvis, Katherine, M.S. Biochemistry 2021. ‘Mathematical modeling of signaling pathways in yeast’. (Co-chair with Dr. Josh Kelley)
- Varney, Hannah, M.S. Biomedical Engineering 2021. ‘Segmentation and Statistical Analysis of Imaged and Simulated 3D Chromosome Territories’.
- Liu, Julia, M.S. Earth Sciences 2020. ‘Automated Terminus Detection For Greenland’s Peripheral Marine-Terminating Glaciers’. (Co-chair with Dr. Ellyn Enderlin)
- Juybari, Jeremy, M.A. Mathematics 2020. ‘A Method to Reclaim Multifractal Statistics from Saturated Images’. (Co-chair with Dr. David Bradley)
- Connerty-Marin, Zachary, M.A. Mathematics 2017. ‘Automated tracking of marine extremophiles from 3D digital holographic microscopy’.
- Toner, Brian, M.A. Mathematics 2015. ‘The Geometric Properties of Cells Exhibiting Huntington’s Disease’.
- Cox, Derrick, M.A. Mathematics 2014. ‘Computational Analysis of Mammographic Breast Tissue Using the Metric Space Technique’.
- Mooers, Kendra, M.A. Mathematics 2013. ‘Characterization of Mammographic Breast Lesions and Their Microenvironment: An Application of a Wavelet-Based Multifractal Formalism’.
- Potter, Matthew, M.A. Mathematics 2010. ‘Prime Modulo and Pascal’s Triangle as Seen With Fractal Geometry’.
- Grant, Jeremy, M.A. Mathematics 2008. ‘Wavelet-Based Segmentation of Fluorescence Microscopy Images in Two and Three Dimensions’.
- Robitaille, Jean-François, M.S. Astrophysics 2008. ‘Analyse Métrique de Structure HI dans le Plan Galactique’ (Co-Chair with Dr. Gilles Joncas, Université Laval, Canada).
- Wu, Yongfeng, M.S. Astrophysics 2007. ‘New Statistical Methods to Get the Fractal Dimension of Bright Galaxies Distributions from the Sloan Digital Sky Survey Data’ (Co-Chair with Dr. David Batuski).
- White, Basel, B.S. Biomedical Engineering 2021. ‘Automated segmentation of breast tissue from mammograms.’
- Abay, Betelhem, B.S. Biomedical Engineering 2020. ‘Exploration of The Relationship Between The Fractal Dimension Of Microcalcification Clusters And The Hurst Exponent Of Background Tissue Disruption In Mammograms.
- Canning, Dexter, B.A. Honors Mathematics 2019. ‘Wavelet-Based Mammographic Analysis of Normal and Tumorous Tissue Microenvironment’.
- Plourde, Shayne, B.A. Honors Mathematics 2015. ‘Modeling the Growth of Breast Microcalcifications in Mathematically-Generated Breast Tissue Environments Using an Agent-Based Model’.
- Ossanna, Elliot, B.A. Honors Mathematics 2015. ‘Fractal Dimension of Residues Sets Within Pascal’s Triangle Under Square-Free Moduli’.
- Dewey, Hannah, B.A. Honors Mathematics 2014. ‘Wavelet-Based Multifractal Analysis of Brain Images’.
Books & industrial reports
- Books
- Wu, Y and Khalil, A 2009. The Evolution of the Universe. VDM Verlag, (76 pages).
- Wu, Y, Batuski, D, and Khalil, A 2008. The Fractal Structure of the Universe. VDM Verlag, (80 pages).
- Industrial Reports
- Khalil, A, Mason, MD 2008. Image Analysis of Soft-Tissue In-Growth into Artificial Bone Implants: Part II: PSF and SLM Implants, Stryker Orthopaedics, (4 pages).
- Khalil, A, Mason, MD 2006. Image Analysis of Soft-Tissue In-Growth into and Attachment to Alumina Ceramic Foam for Canines, Stryker Orthopaedics, (14 pages).