Publications

Published Refereed Journal Articles

  1. 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. https://doi.org/10.1016/j.isci.2021.103127
  2. 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. 7 pages.  https://doi.org/10.1007/s10072-021-05289-w
  3. 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. https://doi.org/10.1117/1.JBO.26.6.065002
  4. 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 https://doi.org/10.3389/fphys.2021.660883
  5. 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 https://doi.org/10.1109/TGRS.2021.3053235
  6. 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). https://doi.org/10.1051/0004-6361/201937085
  7. Marquis, K, Chasse, B, Regan, DP, Boutiette, A, Khalil, A, Howell, C 2019, Vascularized Polymers Spatially Control Bacterial Cells on Surfaces. Advanced Biosystems, 4 (10), 1900216. https://doi.org/10.1002/adbi.201900216
  8. Bailey, EC, Alrowaished, SS, Kilroy, EA, Crooks, ES, Drinkert, DM, Karunasiri, CM, Belanger, JJ, Khalil, A, Kelley, JB, & Henry, CA 2019, NAD+ improves neuromuscular development in a zebrafish model of FKRP-associated dystroglycanopathy. Skeletal Muscle, 9 (1), 1-23. http://dx.doi.org/10.1186/s13395-019-0206-1
  9. Bradley, DM, D’Alessio, D, Khalil, A, Niemeyer, RG, Ossanna, E, Tanenbaum, A, Toner, B 2019, On the relative frequency of residue classes in Pascal’s Triangle modulo a prime. Fractals, 27 (06) 1950098. https://doi.org/10.1142/S0218348X19500981
  10. Garrett, AM, Khalil, A, Walton, D, Burgess, RW 2018, DSCAM promotes self-avoidance in the developing mouse retina by masking the functions of cadherin superfamily members. PNAS, 115 (43), E10216-E10224. https://doi.org/10.1073/pnas.1809430115
  11. Bradley, DM, Khalil, A, Niemeyer, RG, Ossanna, E 2018 The Box-Counting Dimension of Pascal’s Triangle r mod p. Fractals, 26, 05, 1850071. https://doi.org/10.1142/S0218348X18500718
  12. Bradley, DM, Khalil, A, Niemeyer, RG, Ossanna, E 2018 The box-counting dimension of Pascal’s triangle r mod p. Fractals. Accepted for publication https://doi.org/10.1142/S0218348X18500718
  13. Marin, Z, Wallace, JK, Nadeau, J and Khalil, A 2017 Wavelet-based tracking of bacteria in unreconstructed off-axis holograms. Methods. https://doi.org/10.1016/j.ymeth.2017.09.003
  14. Marin, Z, Batchelder, KA, Toner, BC, Guimond, L, Gerasimova-Chechkina, E, Harrow, AR, Arneodo, A and Khalil, A 2017 Mammographic evidence of microenvironment changes in tumorous breasts. Medical Physics, 44, 1324-1336. https://doi.org/10.1002/mp.12120
  15. Gerasimova-Chechkina, E, Toner, B, Marin, Z, Audit, B, Roux, SG, Argoul, F, Khalil, A, Gileva, O, Naimark, O, Arneodo, A 2016 Comparative multifractal analysis of dynamic infrared thermograms and X-ray mammograms enlightens changes in the environment of malignant tumors, Frontiers in Physiology, 7, 336 (15 pages). https://doi.org/10.3389/fphys.2016.00336
  16. Plourde, SM, Marin, Z, Smith, ZR, Toner, BC, Batchelder, KA, Khalil, A 2016. Computational growth model of breast microcalcification clusters in simulated mammographic environments. Computers in Biology and Medicine, 76, 7-13. http://dx.doi.org/10.1016/j.compbiomed.2016.06.020
  17. Richard, CD, Tanenbaum, AB, Audit, B, Arneodo, A, Khalil, A, Frankel, WN 2015. SWDreader: A Wavelet-Based Algorithm Using Spectral Phase to Detect and Characterize Spike-Wave Discharges in Three Genetic Mouse Models of Absence Epilepsy, Journal of Neuroscience Methods, 242, 127. https://doi.org/10.1016/j.jneumeth.2014.12.016
  18. Batchelder, KA, Tanenbaum, AB, Albert, S, Guimond, L, Kestener, P, Arneodo, A, Khalil, A 2014. Wavelet-based 3D reconstruction of microcalcification clusters from two mammographic views: New Evidence that fractal tumors are malignant and Euclidean tumors are benign, PLoS One. http://dx.doi.org/10.1371/journal.pone.0107580
  19. Gerasimova, E, Audit, B, Roux, SG, Khalil, A, Argoul, F, Naimark, O, Gileva, O, Arneodo, A 2014. Interdisciplinary approach for estimating and differentiating healthy and cancerous breast tissues with a multifractal analysis of skin temperature dynamics, Russian Journal of Biomechanics, 18(1), 90.
  20. Gerasimova, E, Audit, B, Roux, SG, Khalil, A, Gileva, O, Argoul, F, Naimark, O, Arneodo, A 2014 Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis, Frontiers in Physiology, 5, 176. https://doi.org/10.3389/fphys.2014.00176
  21. Gerasimova, E, Audit, B, Roux, SG, Khalil, A, Argoul, F, Naimark, O, Arneodo, A, 2013. Multifractal Analysis of Dynamic Infrared Imaging of Breast Cancer, Europhysics Letters, 104 (6), 68001.
  22. Wu, Y, Batuski, D, Khalil, A, 2013. Nearest Neighbor Vector Analysis of SDSS DR5 Galaxy Distribution, Natural Science, 5 (1), 26619. http://dx.doi.org/10.4236/ns.2013.51008
  23. Goody, MF, Kelly, MW, Reynolds, CJ, Khalil, A, Crawford, BD, Henry, CA 2012. NAD+ Biosynthesis Ameliorates a Zebrafish Model of Muscular Dystrophy, PLoS Biology, 10 (10), e1001409. https://doi.org/10.1371/journal.pbio.1001409
  24. Wu, Y, Batuski, D, Khalil, A, 2012. Three-Dimensional Filamentation Analysis of SDSS DR5 Survey, IRSN Astronomy & Astrophysics, 171829. https://doi.org/10.5402/2012/171829
  25. McAteer, RT, Kestener, P, Arneodo, A, Khalil, A 2010. Automated Coronal Loop Detection using a Wavelet Transform Modulus Maxima Method, Solar Physics, Solar Image Processing and Analysis, 262,387-397. https://doi.org/10.1007/s11207-010-9530-7
  26. Robitaille, JF, Joncas, G, Khalil, A 2010. Morphological Analysis of HI Features. III. Metric Space Technique Revisited, Monthly Notices of the Royal Astronomical Society, 405, 636-656. https://doi.org/10.1111/j.1365-2966.2010.16489.x
  27. Kestener, P, Conlon, PA, Khalil, A, Fennell, L, McAteer, RTJ, Gallagher, PT, Arneodo, A 2010. Characterising Complexity in Compound Systems: Segmentation in Wavelet-Space, Astrophysical Journal, 717, 995-1005. http://dx.doi.org/10.1088/0004-637X/717/2/995
  28. Goody, MF, Kelly, MW, Lessard, KN, Khalil, A, Henry, CA 2010. Nrk2b-mediated NAD+ production regulates cell adhesion and is required for muscle morphogenesis in vivo: Nrk2b and NAD+ in muscle morphogenesis, Developmental Biology, 344, 809-826. https://doi.org/10.1016/j.ydbio.2010.05.513
  29. Grant, J, Verrill, C, Coustham, V, Arneodo, A, Paladino, F, Monier, K, Khalil, A 2010. Perinuclear distribution of heterochromatin in developing C. elegans embryos, Chromosome Research, 18, 873-885. http://dx.doi.org/10.1007/s10577-010-9175-2
  30. Khalil A, Aponte, C, Zhang R, Davisson, TH, Dickey, I, Engelman D, Hawkins M, Mason, M 2009. Image analysis of soft-tissue in-growth and attachment into highly porous alumina ceramic foam metals, Medical Engineering and Physics, 31, 775-783. https://doi.org/10.1016/j.medengphy.2009.02.007
  31. Wu, Y, Batuski, D, Khalil, A 2009. Multi-Scale Morphological Analysis of SDSS DR5 Survey Using the Metric Space Technique, Astrophysical Journal, 707, 1160-1167. http://dx.doi.org/10.1088/0004-637X/707/2/1160
  32. Roland, T, Khalil, A, Tanenbaum, A, Berguiga, L, Delicheree, P, Bonneviot, L, Elezgaray, J, Arneodo, A, Argoul, F 2009. Revisiting the physical processes of vapodeposited thin gold films on chemically modified glass by atomic force and surface plasmon microscopies, Surface Science, 603, 3307-3320. https://doi.org/10.1016/j.susc.2009.09.021
  33. Snow, CJ, Goody, M, Kelly, MW, Oster, EC, Jones, R, Khalil, A, and Henry, CA 2008, Time-lapse analysis and mathematical characterization elucidate novel mechanisms underlying muscle morphogenesis. PLoS Genetics, 4(10):e1000219 (18pp). https://doi.org/10.1371/journal.pgen.1000219
  34. Snow CJ, Peterson, M, Khalil, A, Henry C 2008. Muscle development is disrupted in zebrafish embryos deficient for Fibronectin, Developmental Dynamics, 237, 2542-2553. https://doi.org/10.1002/dvdy.21670
  35. Khalil, A, Grant, JL, Caddle, LB, Atzema, E, Mills, KD, Arneodo, A 2007. Chromosome territories have a highly non-spherical morphology and non-random positioning. Chromosome Research, 15, 899-916. https://doi.org/10.1007/s10577-007-1172-8
  36. Caddle, LB, Grant, JL, van Hase, J, Denegre, J, Shirley, BJ, Bewersdorf, J, Cremer, C, Arneodo, A, Khalil, A, & Mills, KD 2007 Heterologous chromosome territory neighborhoods promote translocation susceptibility in primary lymphocytes. Chromosome Research, 15, 1061-1073.
  37. Khalil, A, Joncas, G, Nekka, F, Kestener, P, & Arneodo, A 2006, Morphological Analysis of HI Features II: Wavelet-Based Multifractal Formalism, Astrophysical Journal Supplement Series, 165, 512-550. 10.1086/505144
  38. Khalil, A, Joncas, G, & Nekka, F 2004, Morphological Analysis of HI Features I: Metric Space Technique, Astrophysical Journal, Vol. 601, 352-364

Refereed Conference Articles

  1. Harling, M, Blaszkiewicz, M, Willows, J, Johnson, J, Townsend, K, Khalil, A, Tilbury, K. 2020. 3D analysis of the spatial relationships of collagen and nerves in adipose tissue using the Metric Space Technique. In Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVII. 112450R (10 pages). https://doi.org/10.1117/12.2546918
  2. Liu, J, Enderlin, EM, Khalil, A, 2019. Unsupervised glacier terminus detection in satellite imagery using the 2D Wavelet Transform Modulus Maxima (WTMM) segmentation method. GeoComputation 2019, Queenstown, New Zealand (8 pages). https://doi.org/10.17608/k6.auckland.9869606.v1
  3. Breeding, PW, M Blaszkiewicz, K Townsend, A Khalil, and KB Tilbury 2019 Exploratory investigation of the spatial relationships of collagen and nerves in subcutaneous white adipose tissue (scWAT) using 2-photon microscopy. In Multiphoton Microscopy in the Biomedical Sciences XIX (Vol. 10882, p. 1088218). International Society for Optics and Photonics. (8 pages). https://doi.org/10.1117/12.2510753
  4. Gerasimova, E, Toner, B, Marin, Z, Audit, B, Roux, SG, Argoul, F, Khalil, A, Gileva, O, Naimark, O, Arneodo, A 2016 Combining multifractal analyses of digital mammograms and infrared thermograms to assist in early breast cancer diagnosis, in AIP Conference Proceedings, 1760, 020018 (11 pages). https://doi.org/10.1063/1.4960237
  5. Gerasimova, E, Audit, B, Roux, SG, Khalil, A, Gileva, O, Argoul, F, Naimark, O, Arneodo, A 2014 A wavelet-based method for multifractal analysis of medical signals: Application to dynamic infrared thermograms of breast cancer, in Nonlinear Dynamics of Electronic Systems: Communications in Computer and Information Science, 438, p. 288-300. http://dx.doi.org/10.1007/978-3-319-08672-9_34
  6. Dickey, ID, Donahue, DW, Peshlov, B, Nohe, A, Khalil, A, Mason, M, Zhang, R, Aponte, C, Davisson, TH, Engelman, D, Hawkins, M 2009. Pore size modulates strength of soft-tissue in-growth and growth factor expression into novel porous titanium implants, Transactions of the Orthopaedic Research Society, 34, 2213.
  7. Khalil, A, Mason, M, Dickey, ID, Zhang, R, Aponte, C, Davisson, TH, Engelman, D, Hawkins, M 2009. Pore size and morphology modulate patterning of soft-tissue in-growth into porous titanium implants based on novel imaging tools, Transactions of the Orthopaedic Research Society, 34, 478.
  8. Khalil, A, Mason, M, Dickey, I, Zhang, R, Aponte, C, Davisson, T, Engelman, D, Hawkins, M 2008, Pattern of Soft Tissue In-Growth into Porous Implants Based on Novel Imaging Tools, Transactions of the Orthopaedic Research Society, 33, 1877.
  9. Mills, KD, Caddle, LB, Khalil, A, Bewersdorf, J. 2006. Imaging the Cancer Genome: High Resolution Microscopy and Quantitative Analyses, Optical Society of America, paper WB5, 3pp. https://doi.org/10.1364/BIO.2006.WB5
  10. Khalil A, Joncas G, Nekka F 2002. Exotic Tools for the Morphological Analysis of HI Clouds, ASP Conference Proceedings, Vol. 276, Edited by A. R. Taylor, T.L. Landecker, and A.G. Willis, San Francisco, Astronomical Society of the Pacific, p. 194-197.

Published Conference Proceedings/Abstracts

  1. Enderlin, EM, Liu, J, Bollen, K, Muhlheim, R, Khalil, A 2020. Exploring Stability of Greenland’s Peripheral Marine-Terminating Glaciers through Analysis of Automated Terminus Position Time Series. American Geophysical Union Fall Meeting, Online.
  2. Liu, J, Enderlin, EM, Khalil, A, Marshall, HP. 2020. Southeast Greenland’s marine-terminating peripheral glaciers underwent synchronous retreat in 2016 in respond to ocean-forcing. American Geophysical Union Fall Meeting, Online.
  3. Toner, B, Khalil, A 2020. Exploratory computational longitudinal analysis of mammographic microenvironment disruption preceding breast tumorigenesis. Cancer Research, 80 (4 supplement), P6-06-04.
  4. Khalil, A 2020. Wavelet based multifractal analysis of loss of tissue homeostasis in mammographic breast tissue. AMS Special Session on Fractal Geometry, Dynamical Systems, and Applications, I. Joint Mathematics Meetings (American Mathematical Society and Mathematical Association of America), Denver, CO. Abstract #1154-92-1315.
  5.  Liu, J, Enderlin, EM, Khalil, A 2020. Investigating spatiotemporal patterns in Greenland glacier terminus changes using automated edge detection in satellite images. IASC-NAG Workshop on the Dynamics and Mass Budget of Arctic Glaciers & cross-cutting activity, Obergugl, Austria.
  6. Liu, J, Enderlin, EM, Khalil, A 2019. Greenland Marine Glacier Terminus Mapping in Satellite Imagery using the Automated 2D Wavelet Transform Modulus Maxima (WTMM) Segmentation Method. American Geophysical Union Fall Meeting, San Francisco, CA.
  7. Liu, J, Enderlin, EM, Khalil, A 2019. Investigating Changes to Greenland’s Peripheral Marine-Terminating Glaciers Through Automated Analysis of Satellite Imagery. University of Maine Climate Change Institute 2019 Annual Meeting.
  8. Mills, KD, Cyr, A, Maclay, T, Day, M, Hasham, MG, Khalil, A 2017. A small molecule RAD51 inhibitor preferentially affects cells expressing high cytidine deaminase activity. American Society of Hematology 59th Annual Meeting & Exposition, Atlanta, GA.
  9. Garrett, AM, Tadenev, ALD, Khalil, A, Fuerst, PG, Burgess, RW 2016. Dscam promotes self-avoidance in neurodevelopment by masking diverse cell adhesion molecules. Annual Meeting of the Society for Neuroscience: San Diego, CA.
  10. Garrett, AM, Tadenev, ALD, Khalil, A, Fuerst, PG, Burgess, RW 2015. Dscams promote selfavoidance by masking adhesion through both PDZ-dependent and –independent mechanisms. Annual Meeting of the Society for Neuroscience: Chicago, IL.
  11. Burgess, RW, Garrett, AM, Tadenev, ALD, Khalil, A, Fuerst, PG 2014. Dscams promote self-avoidance by masking adhesion through both MAGI-dependent and –independent mechanisms. Annual Meeting of the Society for Neuroscience: Washington, DC.
  12. Richard, CD, Khalil, A, Frankel, W 2013. Novel computational approach to detect absence seizures in mutant mouse strains. Annual Meeting of the Society for Neuroscience: San Diego, CA.
  13. Kestener, P, Khalil, A, Arneodo, A 2010. A continuous wavelet-based segmentation tool to analyze multifractal properties of quiet and active regions from solar magnetogram data. In ADA6, Astronomical Data Analysis Conference, Monastir, Tunisia.
  14. Wu, Y, Batuski, D, Khalil, A 2010. Properties of Density Field Clusters from the SDSS, Bulletin of the American Astronomical Society, 42, 385.
  15. Wu, Y, Batuski, D, Khalil, A 2009. Application of the Metric Space Technique in 2D and 3D to SDSS DR5, Bulletin of the American Astronomical Society, 41, 449.
  16. Wu, Y, Batuski, D, Khalil, A 2007. New statistical methods to analyze the Sloan Digital Sky Survey Data, Joint New England Sections of the American Physics Society and AAPT Spring Meeting.
  17. Wu, Y, Batuski, D, Khalil, A 2007. New Statistical Methods to Determine the Fractal Dimension of Structures Evident in the SDSS, WMAP, and 2MASS Surveys, Bulletin of the American Astronomical Society, 39, 804.
  18. Wu, Y, Batuski, D, & Khalil, A 2006. New statistical methods to analyze the SDSS DR5 galaxy distribution, Bulletin of the American Astronomical Society, 38, 1000.

Theses

  1.  Juybari, Jeremy 2020. A Method to Reclaim Multifractal Statistics from Saturated Images. MA Thesis. Mathematics. University of Maine. https://digitalcommons.library.umaine.edu/etd/3176/
  2. Marin, Zach 2017. Wavelet-Based Particle Tracking in Unreconstructed, Off-axis Holograms. MA Thesis. Mathematics. University of Maine. https://digitalcommons.library.umaine.edu/etd/2670/
  3. Toner, Brian 2015. The Geometric Properties of Cells Exhibiting Huntington’s Disease. MA Thesis. Mathematics. University of Maine. https://digitalcommons.library.umaine.edu/etd/2304/
  4. Ossana, Elliot 2015. Fractal Dimension of Residues Sets Within Pascal’s Triangle Under Square-Free Moduli. Honors Thesis. Mathematics. University of Maine.
  5. Plourde, Shayne 2015. Modeling the Growth of Breast Microcalcifications in Mathematically-Generated Breast Tissue Environments Using an AgentBased Model. Honors Thesis. Mathematics. University of Maine.
  6. Richard, Christian 2014. Novel Computational Approaches to Detect and Characterize Absence Seizures in Seizure-Prone Mutant Mouse Strains. PhD Thesis. Functional Genomics. University of Maine.
  7. Dewey, Hannah 2014. Wavelet-Based Multifractal Analysis of Brain Images. Honors Thesis. Mathematics. University of Maine.
  8. Cox, Derrick 2014. Computational Analysis of Mammographic Breast Tissue Using the Metric Space Technique. MA Thesis. Mathematics. University of Maine. https://digitalcommons.library.umaine.edu/etd/2182/
  9. Mooers, Kendra 2013. Characterization of Mammographic Breast Lesions And Their Microenvironment: An Application of a Wavelet-Based Multifractal Formalism. MA Thesis. Mathematics. University of Maine. https://digitalcommons.library.umaine.edu/etd/1910/
  10. Wu, Yongfeng 2010. Multi-Scale Three-Dimensional Analysis of Galaxy Distributions Using the Metric Space Technique. PhD Thesis. Astrophysics. University of Maine.
  11. Potter, Matthew 2010. Prime Modulo and Pascal’s Triangle As Seen With Fractal Geometry. MA Thesis. Mathematics. University of Maine. https://digitalcommons.library.umaine.edu/etd/1011/
  12. Grant, Jeremy 2008. Wavelet-Based Segmentation of Fluorescence Microscopy Images in Two and Three Dimensions. MA Thesis. Mathematics. University of Maine. https://digitalcommons.library.umaine.edu/etd/1022/
  13. Robitaille, Jean-Francois 2008. Analyse Metrique de Structure HI dans le Plan Galactique. MS Thesis. Astrophysics. Université Laval, QC, Canada.
  14. Wu, Yongfeng, 2007. New Statistical Methods to Get the Fractal Dimension of Bright Galaxies Distributions from the Sloan Digital Sky Survey Data. MS Thesis. Astrophysics. University of Maine.
  15. Khalil, Andre 2004. Structural Analysis of the Atomic Hydrogen in the Galactic Plane. PhD Thesis. Mathematics and Astrophysics. Universite Laval Quebec. 218pp.
  16. Khalil, Andre 1998. Exploration of the Fractal Dimension. MS Thesis. Mathematics. Concordia University Montreal. 68pp.

Books

  1. Wu, Y and Khalil, A 2009. The Evolution of the Universe. VDM Verlag, 76pp.
  2. Wu, Y, Batuski, D, and Khalil, A 2008. The Fractal Structure of the Universe. VDM Verlag, 80pp.

Industry Reports

  1. Khalil, A, Mason, MD 2008. Image Analysis of Soft-Tissue In-Growth into Artificial Bone Implants: Part II: PSF and SLM Implants, Stryker Orthopaedics, 4pp.
  2. Khalil, A, Mason, MD 2006. Image Analysis of Soft-Tissue In-Growth into and Attachment to Alumina Ceramic Foam for Canines, Stryker Orthopaedics, 14pp.