Computational Biophysics
@ USF Physics
Home
Research
Publications
Software
People


Google Scholar Citations

Refereed Journal Articles

  1. Akter S, Ullah G, and Ullah A. Investigating the Role of Inositol 1,4,5-Trisphosphate Receptors in the Pathogenesis of Alzheimer's Disease Through Computational Modeling, Submitted.

  2. Passlick S, Ullah G, and Henneberger C. Bidirectional dysregulation of synaptic glutamate signaling after transient metabolic failure, Submitted (bioRxiv link).

  3. Adeoye T, Shah S I, and Ullah G. Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer's Disease, Submitted (bioRxiv link).

  4. Ullah G*, Nosyreva E D*, Thompson D, Cuello V, Cuello L G, Syeda R. Analysis of pressure activated Piezo1 open and sub conductance states at a single channel level, Journal of Biological Chemistry 2024.
    * Shared first authorship.

  5. Everaerts K*, Thapaliya P*, Pape N, Durry S, Eitelmann S, Roussa E, Ullah G, and Rose C R. Inward Operation of NBCe1 Promotes Astrocytic Na+ loading and Loss of ATP in Mouse Neocortex during Brief Chemical Ischemia, Cells 2023, 12(23) 2675.
    * Shared first authorship.

  6. Shah S I, Parker I, Ullah G, and Demuro A. Aβ42 and Aβ40 form transient and persistent pores with different time evolutions and toxicities, Submitted.

  7. Kolen B, Kortzak D, Borghans B, Hannack C, Guzman R, Ullah G, and Fahlke C. Vesicular glutamate transporters are H+-anion exchangers that operate at variable stoichiometry, Nature Communications 2023, 14:2723.

  8. Thapaliya P, Pape N, Rose C R, and Ullah G. Modeling the heterogeneity of sodium and calcium homeostasis between cortical and hippocampal astrocytes and its impact on bioenergetics, Frontiers in Cellular Neuroscience 2023, 17:1035553

  9. Shah S I, Demuro A, and Ullah G. Modeling the kinetics of amyloid beta pores and long-term evolution of their Ca2+ toxicity, bioRxiv 2022.05.02.490365.

  10. Pensalfini A, Umar A R, Glabe C, Parker I, Ullah G, and Demuro A. Intracellular injection of brain extracts from Alzheimer’s disease patients trigger unregulated Ca2+ release from intracellular stores that hinders cellular bioenergetics, Cells 2022, 11(22), 3630.

  11. Adeoye T, Shah S I, Demuro A, Rabson D A, and Ullah G. Upregulated Ca2+ release from the endoplasmic reticulum leads to impaired presynaptic function in Alzheimer’s disease, Cells (2022) 11(14), 2167.
    Code and instructions for this paper can be found Here

  12. Kanithi M, Junapudi S, Shah S I, Alavala M R, Ullah G, and Chidipi B. Alterations of mitochondrial network by cigarette and e-cigarette vaping, Cells (2022) 11(10) 1688.

  13. Andrew R D, Farkas E, Hartings J A, Brennan K C, Herreras O, Müller M, Kirov S A, Ayata C, Ollen-Bittle N, Reiffurth C, Revah O, Robertson R M, Dawson-Scully K D, Ullah G, Shuttleworth C W, and Dreier J P. Questioning glutamate excitotoxicity in acute brain damage: the importance of spreading depolarization, Neurocritical Care, (2022) 37, 11–30.

  14. Andrew R D, Hartings J A, Ayata C, Brennan K C, Dawson-Scully K D, Farkas E, Herreras O, Kirov S A, Müller M, Ollen-Bittle N, Reiffurth C, Revah O, Robertson R M, Shuttleworth C W, Ullah G, and Dreier J P. The critical role of spreading depolarizations in early brain injury: consensus and contention, Neurocritical Care, (2022) 37, 83–101.

  15. Chidipi B, Mariana B A, Shah S I, Rieser M, Ullah G, McDonald T V, and Noujaim S F. The mitochondrial network is altered in friedreich’s ataxia cardiomyopathy, The International Journal of Biochemistry and Cell Biology (2022) 143, 106137 .

  16. Chidipi B, Shah S I, Reiser M, Kanithi M, Garces A, Cha B J, Ullah G, and Noujaim S F. All-trans retinoic acid increases DRP1 levels and promotes mitochondrial fission, Cells (2021) 10(5) 1202.

  17. Jansen N A, Perez C, Schenke N, Van Beurden A W, Dehghani A, Voskuyl R A, Thijs R D, Ullah G, Van Den Maagdenberg A M J M, Tolner E A. Impaired theta-gamma coupling indicates inhibitory dysfunction and seizure risk in a Dravet syndrome mouse model, Journal of Neuroscience (2021) 41(3) 524-537.

  18. Perez C, Felix L, Rose C R, and Ullah G. On the Origin of Ultraslow Spontaneous Na+ Fluctuations in Neurons of the Neonatal Forebrain, Journal of Neurophysiology (2021) 125(2) 408-425.

  19. Shah S I and Ullah G. The Function of Mitochondrial Calcium Uniporter at the Whole-Cell and Single Mitochondrion Levels in WT, MICU1 KO, and MICU2 KO Cells, Cells (2020) 9, 1520.

  20. Ullah G and Miti T. The role of transporters and synaptic cleft morphology in glutamate and GABA homeostasis and their effect on neuronal function, (2020) in review.

  21. Shah S I, Ong H L, Demuro A, and Ullah G. PunctaSpecks: A Tool for Automated Detection, Tracking, and Analysis of Multiple Types of Fluorescently Labeled Biomolecules, Cell Calcium (2020) 102224.
    The software, user manual, and sample data for this paper can be found Here

  22. Shah S I, Paine J, Perez C, and Ullah G. Mitochondrial fragmentation and network architecture in degenerative diseases, PLoS One (2019) 14(9) e0223014.

  23. Shafiq-ul-Hassan M, Zhang G G, Latifi K, Ullah G, Gillies R J, and Moros E G. Computed Tomography Texture Phantom Dataset for evaluating the impact of CT imaging parameters on Radiomics Features, The Cancer Imaging Archive (2019) (DOI: http://doi.org/10.7937/TCIA.2019.4l24tz5g).

  24. Perez C, Miti T, Hasecke F, Meisl G, Hoyer W, Muschol M, and Ullah G. Mechanism of fibril and soluble oligomer formation in amyloid beta and hen egg white lysozyme proteins, Journal of Physical Chemistry B (2019) 123(27) 5678-5689.

  25. Toglia P and Ullah G. Mitochondrial dysfunction and role in spreading depolarization and seizure, Journal of Computational Neuroscience (2019) 47(2-3) 91-108.

  26. Shafiq-ul-Hassan M, Zhang G G, Latifi K, Ullah G, Gillies R J, and Moros E G. Credence Cartridge Radiomics Phantom CT Scans with Controlled Scanning Approach, The Cancer Imaging Archive (2018) (DOI: http://doi.org/10.7937/TCIA.2019.4l24tz5g).

  27. Shah S I, Smith M, Swaminathan D, Parker I, Ullah G, Demuro A. CellSpecks: A Software for Automated Detection and Analysis of Calcium Channels in Live Cells, Biophysical Journal (2018) 115(11) 2141-2151.
    The software, code, and user manual are archieved with the paper in the Supporting Material on the Biophysical Journal website.

  28. Toglia P, Demuro A, Mak DOD, and Ullah G. Data-driven modeling of mitochondrial dysfunction in Alzheimer's disease, Cell Calcium (2018) 76, 23-35.

  29. Shah S I, Demuro A, Mak DOD, Parker I, Pearson JE, and Ullah G. TraceSpecks: a software for automated idealization of noisy patch-clamp and imaging data, Biophysical Journal, (2018) 115(1) 9-21.
    The software, code, and user manual are archieved with the paper in the Supporting Material on the Biophysical Journal website.

  30. Shafiq-ul-Hassan M, Latifi K, Zhang G G, Ullah G, Gillies R J, and Moros E G. Voxel-size and gray level normalization of CT radiomic features in lung cancer tumors, Scientific Reports (2018) 8(1) 10545.

  31. Hasecke F, Miti T, Perez C, Schölzel D, Gremer L, Grüning C S R, Matthews G, Meisl G, Knowles T P J, Willbold D, Neudecker P, Heise H, Ullah G, Hoyer W, Muschol M. Origin of metastable oligomers and their effects on amyloid fibril self-assembly, Chemical Science (2018) 9, 5937-5948.

  32. Perez C and Ullah G. Reduced cooperativity of voltage-gated sodium channels in the hippocampal interneurons of aged mouse model of Alzheimer's disease, European Biophysics Journal (2018) 47(5) 539-547.

  33. Shafiq‐ul‐Hassan M, Zhang G G, Hunt D C, Latifi K, Ullah G, Gillies R J, Moros E G. Accounting for reconstruction kernel-induced variability in CT radiomic features using noise power spectra, Journal of Medical Imaging (2017) 5(1): 011013.

  34. Hübel N, Mahshid S Hosseini-Zare, Ziburkus J, and Ullah G. The role of glutamate in neuronal ion homeostasis: a case study of spreading depolarization, PLoS Computational Biology (2017) 13(10): e1005804
    Code reproducing key results is archieved with the paper in Supporting Information Text 2.

  35. Toglia P, Ullah G, and Pearson J E. Analyzing optical imaging of Ca2+ signals via TIRF microscopy: the limits on resolution due to chemical rates and depth of the channels, Cell Calcium (2017) 67:65-73.

  36. Shafiq‐ul‐Hassan M, Zhang G G, Latifi K, Ullah G, Hunt D C, Balagurunathan Y, Abdullah M A, Schabath M B, Goldgof D G, Mackin D, Court L E, Gillies R J, Moros E G. Intrinsic dependencies of CT Radiomics features on voxel size and number of gray levels, Medical Physics (2017) 44(3): 1050-1062.

  37. Perez C, Ziburkus J, and Ullah G. Analyzing and modeling the dysfunction of inhibitory neurons in Alzheimer's disease, PLoS One, (2016) 11(12): e0168800.

  38. Toglia P and Ullah G. The Gain-of-Function Enhancement of IP3-Receptor Channel Gating by Familial Alzheimer's Disease-Linked Presenilin Mutants Increases the Open Probability of Mitochondrial Permeability Transition Pore, Cell Calcium, (2016) 60(2) 13-24.

  39. Ullah G and Ullah A. Mode switching of inositol 1,4,5-trisphosphate receptor channel shapes the spatiotemporal scales of Ca2+ signals, Journal of Biological Physics, (2016) DOI:10.1007/s10867-016-9419-2

  40. Toglia P, Cheung KH, Mak DOD, and Ullah G. Impaired mitochondrial function due to familial Alzheimers disease-causing presenilins mutants via Ca2+ disruptions, Cell Calcium, (2016) 59(5) 240-250.

  41. Hübel N and Ullah G. Astrocytes swell more than neurons during prolonged depolarizations in anions-dependent manner, PLoS One, (2016) 11(3):e0147060
    Code for this paper can be found Here

  42. Hübel N, Andrew DR, and Ullah G. Large extracellular space leads to neuronal susceptibility to ischemic injury in Na+/K+ pumps-dependent manner, Journal of Computational Neuroscience, (2016) 40(2) 177-192
    Code for this paper can be found Here

  43. Mak DOD, Cheung KH, Toglia P, Foskett JK, and Ullah G. Analyzing and quantifying the gain-of-function enhancement of IP3 receptor gating by Familial Alzheimer’s disease-causing mutant presenilins, PLoS Computational Biology, 11(10) (2015) e1004529.

  44. Ullah G, Demuro A, Parker I, and Pearson JE. Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer’s disease pathology, PLoS ONE 10(9) (2015) e0137357.
    Code for this paper can be found Here

  45. Ullah G, Wei Y, Dahlem MA, Wechselberger M, Schiff SJ. The role of cell volume in the dynamics of seizure, spreading depression, and anoxic depolarization, PLoS Computational Biology, 11(8) (2015) e1004414.
    Code for this paper can be found here

  46. Wei Y, Ullah G, Schiff SJ, Unification of neuronal spikes, seizures, and spreading depression, Journal of Neuroscience, 34(35) (2014) 11733.
    Code for this paper can be found here

  47. Ullah A, Jung P, Ullah G, and Machaca K. The role of IP3 receptor channel clustering in Ca2 + wave propagation during oocyte maturation, Progress in Molecular Biology and Translational Science, 123 (2014) 83.

  48. Wei Y, Ullah G, Ingram J, and Schiff SJ. Oxygen and seizure dynamics: II. Computational modeling, Journal of Neurophysiology, 112(2) (2014) 213.

  49. Bruno W, Ullah G, Mak DOD, and Pearson JE. Automated maximum likelihood separation of signal from baseline in noisy quantal data, Biophysical Journal, 105 (2013) 68..
    Code for this paper can be found here

  50. Vais H, Foskett KJ, Ullah G, Pearson JE, and Mak DOD. Permeant calcium ion feedback regulation of single inositol 1,4,5-trisphosphate receptor channel gating, Journal of General Physiology, 140 (2012) 697. Evaluated as "Very Good" by Faculty of 1000 View.


  51. Ullah G, Mak DOD, and Pearson JE. A data-driven model of a modal gated ion channel: the inositol 1,4,5-trisphosphate receptor in insect Sf9 cell, Journal of General Physiology, 140 (2012) 159.

  52. Ullah G, Bruno W, and Pearson JE. Simplification of reversible Markov chains by removal of states with low equilibrium occupancy, Journal of Theoretical Biology, 311 (2012) 117.
    Code for this paper can be found Here

  53. Ullah G, Parker I, Mak DOD, and Pearson JE. Multi-scale data-driven modeling and observation of calcium puffs, Cell Calcium, 52, (2012) 152.

  54. Ahmad F, Ullah G, and Kim SH. A neighborhood method for statistical analysis of fMRI data, Open Journal of Biophysics, 2(1) (2012) 15.

  55. Wei Y, Ullah G, Parekh R, Ziburkus J, and Schiff SJ, Kalman filter tracking of intracellular neuronal voltage and current, 50th IEEE Conference on Decision and Control and European Control Conference, (2011) 12-15.

  56. Ullah G and Schiff SJ. Assimilating seizure dynamics, PLoS Computational Biology, 6 (2010), e1000776.
    Code for this paper can be found Here

  57. Swaminathan D, Ullah G, and Jung P. A simple sequential-binding model for Calcium puffs, Chaos, 19 (2009) 037109.

  58. Ghanim Ullah and Steven J. Schiff, Models of epilepsy, Scholarpedia, 4(7) (2009) 1409.

  59. Ullah G and Schiff SJ. Tracking and control of neuronal Hodgkin-Huxley dynamics, Physical Review E, 79, 040901(R) (2009).
    Code for this paper can be found Here

  60. Ullah G, Cressman JR, Barreto E, and Schiff SJ. The influence of sodium and potassium dynamics on excitability, seizures, and the stability of persistent states: II. Network and glial dynamics, Journal of Computational Neuroscience, 26 (2009) 171.
    Code for this paper can be found here

  61. Cressman JR, Ullah G, Ziburkus J, Schiff SJ, and Barreto E. The influence of sodium and potassium dynamics on excitability, seizures, and the stability of persistent states: I. Single neuron dynamics, Journal of Computational Neuroscience, 26 (2009) 159.
    Code for this paper can be found here

  62. Ullah G, Jung P, and Machaca K. Modelling Ca signaling differentiation during oocyte maturation", Cell Calcium, 42 (2007) 556

  63. Ullah G and Jung P. Modeling the statistics of elementary calcium release events, Biophysical Journal, 90 (2006) 3485.

  64. Ullah G, Jung P, and Cornell-Bell AH. Anti-phase calcium oscillations in Astrocytes via inositol 1,4,5-trisphosphate regeneration. ", Cell Calcium, 39 (2006) 197.

  65. Jung P, Neiman AB, Afghan MKN, Nadkarni S, and Ullah G. Thermal activation by power-limited coloured noise, New Journal of Physics, 7 (2005) 17.