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Faculty Detail    
Name HASSAN FATHALLAH-SHAYKH
  
Campus Address FOT 1020 Zip 3401
Phone  (205) 934-1813
E-mail  hfshaykh@uabmc.edu
Other websites
     

Education
Medical School  American University of Beirut    1985  M.D. 
Undergraduate  American University of Beirut    1985  BS Mathematics 
Residency  American University of Beirut    1986  Internship 
Residency  The University of Chicago    1989  Neurology Residency 
Residency  Duke University    1990  PGY2 Internal Medicine 
Fellowship  Memorial Sloan Kettering Cancer Center    1992  Molecular Immunology 
Fellowship  Memorial Sloan Kettering Cancer Center    1993  Neuro-Oncology Fellowship 
Graduate  University of Illinois at Chicago    2007  Ph.D. in Pure Mathematics 
Graduate  University of Alabama at Birmingham    2021  MBA with concentrations in Finance, Marketing, and Entrepreneurship 

Certifications
American Board of Psychiatry and Neurology  1994 
United Council of Neurologic Subspecialties: Neuro-Oncology  2011 


Faculty Appointment(s)
Appointment Type Department Division Rank
Primary  Neurology Chair Office  Neurology Chair Office Professor
Secondary  Mechanical Engineering (Org Ret)  Mechanical Engineering (Org Ret) Associate Professor
Secondary  Mathematics (Org Ret)  Mathematics (Org Ret) Associate Professor
Secondary  Electrical & Computer Engineering  Electrical & Computer Engineering Associate Professor
Center  Ctr for Clinical & Translational Sci  Ctr for Clinical & Translational Sci Professor
Center  Comprehensive Neuroscience Center  Comprehensive Neuroscience Center Professor
Center  Comprehensive Cancer Center  Comprehensive Cancer Center Professor
Secondary  Cell, Developmntl, & Integrative Biology  Cell, Developmntl, & Integrative Biology Associate Professor
Secondary  Biomedical Engineering  Biomedical Engineering Associate Professor

Graduate Biomedical Sciences Affiliations
Cell, Molecular, & Developmental Biology 
Comprehensive Neuroscience Center 
Engineering 

Biographical Sketch 
2016: Our Team was a winner of the 2016 BRATS Challenge (http://braintumorsegmentation.org) 2015: Runner-up Best Paper Award at the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015) 2014: President, Society of Industrial and Applied Mathematics, Southeastern Section (SIAM-SEAS) 2013: Treasurer, SIAM-SEAS



Research/Clinical Interest
Title
Computational Personalized Medicine and Mathematics
Description
My goals are (i) to apply mathematical tools to advance our understanding of basic medical sciences, (ii) to build computational tools that foster personalized medicine, and (iii) to advance mathematics. I have a multidisciplinary background in medicine, neurology, neuro-oncology, basic medical sciences, and pure and applied mathematics. I take care of patients with brain tumors and neurological diseases. Accurate and timely image segmentation can assist radiologists by transforming medical images into numerical schemes amenable to statistical analysis. I have also developed equations to model molecular networks and gliomas; the equations are built with the goal of approaching the simplest representation of current biological understanding. Simulations have uncovered novel ideas on the long-run behavior of circadian clocks and on fundamental properties of tumors like natural evolution, transformation, migration, recurrence patterns, and response to clinical trials (computational trials). These computational tools can advance medical practice by personalizing medical decisions and by optimizing the timing of delivery of care; examples include cancer, multiple sclerosis, and degenerative disorders of the brain. The models consist of new ordinary and partial differential equations; they pose problems that generate new computational and theoretical mathematics.

Selected Publications 
Publication PUBMEDID
Inception Modules Enhance Brain Tumor Segmentation. Cahall, DE, Ghulam Rasool, G, Bouaynaya, NC , Fathallah-Shaykh, HM. Front.
Comput. Neurosci. 2019, In Press, DOI: 10.3389/fncom.2019.00044. 		  
Diagnosing growth in low-grade gliomas with and without longitudinal volume measurements: A retrospective observational study
Fathallah-Shaykh, HM, DeAtkine, A, Coffee, E, Khayat, E, Bag, AK, Han, X, Warren, PP, Bredel, M, Fiveash, J, Markert, J, Bouaynaya, N, Nabors, LN. 2019, PLoS Med 16 (5): e1002810. https://doi.org/10.1371/journal. 		 1002810 
Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS Challenge. Spyridon Bakas, Mauricio Reyes, Andras Jakab, Stefan Bauer, Markus Rempfler, Alessandro Crimi, Russell Takeshi Shinohara, Christoph Berger, Sung Min Ha, Martin Rozycki, Marcel Prastawa, Esther Alberts, Jana Lipkova, John Freymann, Justin Kirby, Michel Bilello, Hassan Fathallah-Shaykh, Roland Wiest, Jan Kirschke, Benedikt Wiestler, Rivka Colen, Aikaterini Kotrotsou, Pamela Lamontagne, Daniel Marcus, Mikhail Milchenko, Arash Nazeri, Marc-Andre Weber, Abhishek Mahajan, Ujjwal Baid, Elizabeth Gerstner, Dongjin Kwon, Gagan Acharya, Manu Agarwal, Mahbubul Alam, Alberto Albiol, Antonio Albiol, Francisco J. Albiol, Varghese Alex, Nigel Allinson, Pedro H. A. Amorim, Abhijit Amrutkar, Ganesh Anand, Simon Andermatt, Tal Arbel, Pablo Arbelaez, Aaron Avery, Muneeza Azmat, Pranjal B., W Bai, Subhashis Banerjee, Bill Barth, Thomas Batchelder, Kayhan Batmanghelich, Enzo Battistella, Andrew Beers, Mikhail Belyaev, Martin Bendszus, Eze Benson, Jose Bernal, Halandur Nagaraja Bharath, George Biros, Sotirios Bisdas, James Brown, Mariano Cabezas, Shilei Cao, Jorge M. Cardoso, Eric N Carver, Adrià Casamitjana, Laura Silvana Castillo, Marcel Catà, Philippe Cattin, Albert Cerigues, Vinicius S. Chagas, Siddhartha Chandra, Yi-Ju Chang, Shiyu Chang, Ken Chang, Joseph Chazalon, Shengcong Chen, Wei Chen, Jefferson W Chen, Zhaolin Chen, Kun Cheng, Ahana Roy Choudhury, Roger Chylla, Albert Clérigues, Steven Colleman, Ramiro German Rodriguez Colmeiro, Marc Combalia, Anthony Costa, Xiaomeng Cui, Zhenzhen Dai, Lutao Dai, Laura Alexandra Daza, Eric Deutsch, Changxing Ding, Chao Dong, Shidu Dong, Wojciech Dudzik, Zach Eaton-Rosen, Gary Egan et al. arXiv:1811.02629v2. 2019 Mar 19.   
Approximate Kernel Reconstruction for Time-Varying Networks. Ditzler G, Bouaynaya N, Shterenberg R, Fathallah-Shaykh HM. BioData Min. 2019 Feb 6;12:5. doi: 10.1186/s13040-019-0192-1. eCollection 2019.  30774716  
Global Asymptotic Stability in a Model of Networks
Fathallah-Shaykh HM, Freiji A.
Dynamical Systems, 2017, 2018, 1:159-183, DOI: 10.1080/14689367.2017.1326464. 		  
Key rates for the grades and transformation ability of glioma: model simulations and clinical cases.
Scribner E, Hackney JR, Machemehl HC, Afiouni R, Patel KR, Fathallah-Shaykh HM.
J Neurooncol. 2017 Apr 27. doi: 10.1007/s11060-017-2444-6. http://rdcu.be/rEum 		 28451993 
Interactive Semi-automated Method Using Non-negative Matrix Factorization and Level Set Segmentation for the BRATS Challenge.
Dera, D, Raman, R, Bouaynaya, N and Fathallah-Shaykh, HM.
Crimi A,Menze B, Maier O, Reyes M, and Handels H (Eds.).
Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries, 2017.
Springer International Publishing AG. 		  
Single Cell Mathematical Model Successfully Replicates Key Features of GBM: Go-Or-Grow Is Not Necessary.
Scribner E, Fathallah-Shaykh HM.
PloS one. 2017; 12(1):e0169434. 		 28046101  
The Case for Neurological Network Diseases.
Machemehl H, Eloubeidi D, Fathallah-Shaykh H.
JAMA neurology. 2016; 73(3):261-2. 		 26783994 
Computational Trials: Unraveling Motility Phenotypes, Progression Patterns, and Treatment Options for Glioblastoma Multiforme.
Raman F, Scribner E, Saut O, Wenger C, Colin T, Fathallah-Shaykh HM.
PloS one. 2016; 11(1):e0146617. 		 26756205 
Automated Robust Image Segmentation: Level Set Method Using Nonnegative Matrix Factorization with Application to Brain MRI.
Dera D, Bouaynaya N, Fathallah-Shaykh HM.
Bulletin of mathematical biology. 2016; 78(7):1450-76. 		 27417984 
Phase I dose-escalation study of the PI3K/mTOR inhibitor voxtalisib (SAR245409, XL765) plus temozolomide with or without radiotherapy in patients with high-grade glioma.
Wen PY, Omuro A, Ahluwalia MS, Fathallah-Shaykh HM, Mohile N, Lager JJ, Laird AD, Tang J, Jiang J, Egile C, Cloughesy TF.
Neuro-oncology. 2015; 17(9):1275-83. 		 26019185  
Effects of anti-angiogenesis on glioblastoma growth and migration: model to clinical predictions.
Scribner E, Saut O, Province P, Bag A, Colin T, Fathallah-Shaykh HM.
PloS one. 2014; 9(12):e115018. 		 25506702  
A multilayer grow-or-go model for GBM: effects of invasive cells and anti-angiogenesis on growth.
Saut O, Lagaert JB, Colin T, Fathallah-Shaykh HM.
Bulletin of mathematical biology. 2014; 76(9):2306-33. 		 25149139 
Tracking of time-varying genomic regulatory networks with a LASSO-Kalman smoother.
Khan J, Bouaynaya N, Fathallah-Shaykh HM.
EURASIP journal on bioinformatics & systems biology. 2014; 2014(1):3. 		 24517200 
Proper orthogonal decomposition for parameter estimation in oscillating biological networks.
Rehm A, Scribner E, Fathallah-Shaykh HM.
Journal of computational and applied mathematics. 2014 March 01; 258:135-150. 		  
c-Src and neural Wiskott-Aldrich syndrome protein (N-WASP) promote low oxygen-induced accelerated brain invasion by gliomas.
Tang Z, Araysi LM, Fathallah-Shaykh HM.
PloS one. 2013; 8(9):e75436. 		 24069415 
Fractal dimension of the Drosophila circadian clock.
Fathallah-Shaykh HM.
Fractals. 2011 December; 19(4):423-430. 		  
Dynamics of the Drosophila circadian clock: theoretical anti-jitter network and controlled chaos.
Fathallah-Shaykh HM.
PloS one. 2010; 5(10):e11207. 		 20967246 
Mathematical model of the Drosophila circadian clock: loop regulation and transcriptional integration.
Fathallah-Shaykh HM, Bona JL, Kadener S.
Biophysical journal. 2009; 97(9):2399-408. 		 19883582 
Noise and rank-dependent geometrical filter improves sensitivity of highly specific discovery by microarrays.
Fathallah-Shaykh HM.
Bioinformatics (Oxford, England). 2005; 21(23):4255-62. 		 16179359 
Logical networks inferred from highly specific discovery of transcriptionally regulated genes predict protein states in cultured gliomas.
Fathallah-Shaykh HM.
Biochemical and biophysical research communications. 2005; 336(4):1278-84. 		 16169516 
Genomic discovery reveals a molecular system for resistance to oxidative and endoplasmic reticulum stress in cultured glioma.
Fathallah-Shaykh HM.
Archives of neurology. 2005; 62(2):233-6. 		 15710851 
Mathematical algorithm for discovering states of expression from direct genetic comparison by microarrays.
Fathallah-Shaykh HM, He B, Zhao LJ, Badruddin A.
Nucleic acids research. 2004; 32(13):3807-14. 		 15266007 
Genomic expression discovery predicts pathways and opposing functions behind phenotypes.
Fathallah-Shaykh HM, He B, Zhao LJ, Engelhard HH, Cerullo L, Lichtor T, Byrne R, Munoz L, Von Roenn K, Rosseau GL, Glick R, Sherman C, Farooq K.
The Journal of biological chemistry. 2003; 278(26):23830-3. 		 12700229 
Mathematical modeling of noise and discovery of genetic expression classes in gliomas.
Fathallah-Shaykh HM, Rigen M, Zhao LJ, Bansal K, He B, Engelhard HH, Cerullo L, Roenn KV, Byrne R, Munoz L, Rosseau GL, Glick R, Lichtor T, DiSavino E.
Oncogene. 2002; 21(47):7164-74. 		 12370806 
Gene transfer into brain parenchyma elicits antitumor effects.
Fathallah-Shaykh HM, Kafrouni AI, Zhao LJ, Smith GM, Forman J.
Cancer research. 2000; 60(7):1797-9. 		 10766160 
Gene transfer of IFN-gamma into established brain tumors represses growth by antiangiogenesis.
Fathallah-Shaykh HM, Zhao LJ, Kafrouni AI, Smith GM, Forman J.
Journal of immunology (Baltimore, Md. : 1950). 2000; 164(1):217-22. 		 10605014 
Priming in the brain, an immunologically privileged organ, elicits anti-tumor immunity.
Fathallah-Shaykh HM, Gao W, Cho M, Herrera MA.
International journal of cancer. 1998; 75(2):266-76. 		 9462718 
Cloning of a leucine-zipper protein recognized by the sera of patients with antibody-associated paraneoplastic cerebellar degeneration.
Fathallah-Shaykh H, Wolf S, Wong E, Posner JB, Furneaux HM.
Proceedings of the National Academy of Sciences of the United States of America. 1991; 88(8):3451-4. 		 2014264 
 

Keywords
Glioma, Cancer, Clinical Trials, Multiple Sclerosis, Image Segmentation, Motility, Modeling, Dynamical Systems, Chaos, Networks, Circadian Clocks, Ordinary Differential Equations, Partial Differential Equations