Publications

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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

  1. Seekins, Tyler, Ph.D. Chemical Engineering 2023. ‘Computer vision for paper fiber quantification’. (Co-chair with Dr. Douglas Bousfield).
  2. Batchelder, Kendra, I.Ph.D. Computational Biomedicine 2023. ‘Longitudinal analysis of mammographic microenvironment tissue disruption accompanying tumorigenesis’.
  3. Toner, Brian, Ph.D. Computer Science 2019. ‘A Longitudinal Study of Mammograms Utilizing the Automated Wavelet Transform Modulus Maxima Method’.
  4. 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).
  5. 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).
  1.  McCarthy, Margaret, M.S. Biomedical Engineering 2023. ‘Quantitative visualization of mammographic tissue microenvironment disruption’.
  2. Raza, Madison, M.S. Biomedical Engineering 2023. ‘Mammographic tissue microenvironment assessment using the Metric Space Technique’.
  3. White, Basel, M.S. Biomedical Engineering 2023. ‘Hybrid power spectral and wavelet image roughness analysis’.
  4. 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)
  5. Jarvis, Katherine, M.S. Biochemistry 2021. ‘Mathematical modeling of signaling pathways in yeast’. (Co-chair with Dr. Josh Kelley)
  6. Varney, Hannah, M.S. Biomedical Engineering 2021. ‘Segmentation and Statistical Analysis of Imaged and Simulated 3D Chromosome Territories’.
  7. Liu, Julia, M.S. Earth Sciences 2020. ‘Automated Terminus Detection For Greenland’s Peripheral Marine-Terminating Glaciers’. (Co-chair with Dr. Ellyn Enderlin)
  8. Juybari, Jeremy, M.A. Mathematics 2020. ‘A Method to Reclaim Multifractal Statistics from Saturated Images’. (Co-chair with Dr. David Bradley)
  9. Connerty-Marin, Zachary, M.A. Mathematics 2017. ‘Automated tracking of marine extremophiles from 3D digital holographic microscopy’.
  10. Toner, Brian, M.A. Mathematics 2015. ‘The Geometric Properties of Cells Exhibiting Huntington’s Disease’.
  11. Cox, Derrick, M.A. Mathematics 2014. ‘Computational Analysis of Mammographic Breast Tissue Using the Metric Space Technique’.
  12. Mooers, Kendra, M.A. Mathematics 2013. ‘Characterization of Mammographic Breast Lesions and Their Microenvironment: An Application of a Wavelet-Based Multifractal Formalism’.
  13. Potter, Matthew, M.A. Mathematics 2010. ‘Prime Modulo and Pascal’s Triangle as Seen With Fractal Geometry’.
  14. Grant, Jeremy, M.A. Mathematics 2008. ‘Wavelet-Based Segmentation of Fluorescence Microscopy Images in Two and Three Dimensions’.
  15. 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).
  16. 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).
  1. White, Basel, B.S. Biomedical Engineering 2021. ‘Automated segmentation of breast tissue from mammograms.’
  2. 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.
  3. Canning, Dexter, B.A. Honors Mathematics 2019. ‘Wavelet-Based Mammographic Analysis of Normal and Tumorous Tissue Microenvironment’.
  4. Plourde, Shayne, B.A. Honors Mathematics 2015. ‘Modeling the Growth of Breast Microcalcifications in Mathematically-Generated Breast Tissue Environments Using an Agent-Based Model’.
  5. Ossanna, Elliot, B.A. Honors Mathematics 2015. ‘Fractal Dimension of Residues Sets Within Pascal’s Triangle Under Square-Free Moduli’.
  6. 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).