Computational Biophysics
Publications
Refereed Journal Articles
Nelson JSE, Meyer J, Gerkau NJ, Kafitz KW, Ullah G, Santamaria F, and Rose CR. Spatio-temporal dynamics of lateral Na+ diffusion in apical dendrites of mouse CA1 pyramidal neurons, Submitted.
Jurynec MJ, Nosyreva E, Thompson D, Munoz C, Novak KA, Matheson DJ, Veerabhadraiah
SR,Smith MC, Kazmers NH, Feier S, Ullah, G, and Ruhma Syeda. PIEZO1 variants that
reduce open channel probability are associated with familial osteoarthritis, Submitted.
Annika Zink, Dao-Fu Dai, Annika Wittich, Marie-Thérèse Henke, Giulia Pedrotti, Sonja
Heiduschka, Guillem S. Aguilar, Tancredi Massimo Pentimalli, Christian Brueser, Sofia
Notopoulou, Aleksandra Zhaivoron, Abdul Rahim Umar, Laura Petersilie, Caleb Jerred,
Jesper Bergmans, Fabian Schumacher, Jan Keller-Findeisen, Agnieszka Rybak-Wolf, Daniel
Stach, Jeanette Reinshagen, Andrea Zaliani, Undine Haferkamp, Liliya Euro, Alessia
Di Donfrancesco, Chiara Santanatoglia, Enrica Cappellozza, Marta Suarez Cubero, Mario
Pavez-Giani, Oleh Bakumenko, David Meierhofer, Alan Foley, Susanne Morales-Gonzalez,
Isabella Tolle, Diran Herebian, Daniele Bonesso, Ildiko Szabo, Giulia Cecchetto, Sakurako
Wong, Monica Moresco, Alessandra Maresca, Ilaria Decimo, Merel J.W. Adjobo-Hermans,
Burkhard Kleuser, Lukas Cyganek, Chris Mühlhausen, Lars Schlotawa, Valeria Tiranti,
Andrea Rossi, Ertan Mayatepek, Chiara La Morgia, Valerio Carelli, Thomas Klopstock,
Felix Distelmaier, Ghanim Ullah, Stefan Jakobs, Christine R. Rose, Nikolaus Rajewsky,
Spyros Petrakis, Frank Edenhofer, Werner Koopmann, Dario Brunetti, Pawel Lisowski,
Anu Suomalainen, Antonio del Sol, Emanuela Bottani, Ole Pless, Markus Schuelke, Alessandro
Prigione. Sildenafil as a drug candidate for the mitochondrial disease Leigh syndrome,
Submitted.
Adeoye T and Ullah G. Pathological calcium influx through amyloid beta pores disrupts
synaptic function, Submitted.
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.
Bhattarai A, Meyer J, Petersilie L, Shah S I, Leu L, Rose C R, Ullah G. A Deep Learning-Based
Segmentation of Cells and Analysis (DL-SCAN), Biomolecules, 2024, 14(11) 1348.
The software and sample data for this paper can be found Here
Fajemisin J A, Gonzalez G, Rosenberg S A, Ullah G, Redler G, Latifi K, Moros E G,
El Naqa I. Magnetic Resonance-guided Cancer Therapy Radiomics and Machine Learning
Models for Response Prediction, Tomography, 2024, 10(9) 1439-1454.
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, Aging and Disease 2024.
Passlick S, Ullah G, and Henneberger C. Bidirectional dysregulation of synaptic glutamate
signaling after transient metabolic failure, eLife 2024.
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, 300 (4), 107156.
* Shared first authorship.
Spotlight on the paper: Subconductance states add complexity to Piezo1 gating model.
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.
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.
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.
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
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.
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.
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
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.
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.
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.
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 .
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.
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.
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.
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.
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.
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
Shah S I, Paine J, Perez C, and Ullah G. Mitochondrial fragmentation and network architecture
in degenerative diseases, PLoS One (2019) 14(9) e0223014.
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).
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.
Toglia P and Ullah G. Mitochondrial dysfunction and role in spreading depolarization
and seizure, Journal of Computational Neuroscience (2019) 47(2-3) 91-108.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
Hübel N and Ullah G. Astrocytes swell more than neurons during prolonged depolarizations
in anions-dependent manner, PLoS One, (2016) 11(3):e0147060
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
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.
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.
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
Wei Y, Ullah G, Schiff SJ, Unification of neuronal spikes, seizures, and spreading
depression, Journal of Neuroscience, 34(35) (2014) 11733.
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.
Wei Y, Ullah G, Ingram J, and Schiff SJ. Oxygen and seizure dynamics: II. Computational
modeling, Journal of Neurophysiology, 112(2) (2014) 213.
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
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.
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.
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
Ullah G, Parker I, Mak DOD, and Pearson JE. Multi-scale data-driven modeling and observation
of calcium puffs, Cell Calcium, 52, (2012) 152.
Ahmad F, Ullah G, and Kim SH. A neighborhood method for statistical analysis of fMRI
data, Open Journal of Biophysics, 2(1) (2012) 15.
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.
Ullah G and Schiff SJ. Assimilating seizure dynamics, PLoS Computational Biology, 6 (2010), e1000776.
Code for this paper can be found Here
Swaminathan D, Ullah G, and Jung P. A simple sequential-binding model for Calcium
puffs, Chaos, 19 (2009) 037109.
Ghanim Ullah and Steven J. Schiff, Models of epilepsy, Scholarpedia, 4(7) (2009) 1409.
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
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
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
Ullah G, Jung P, and Machaca K. Modelling Ca signaling differentiation during oocyte
maturation", Cell Calcium, 42 (2007) 556
Ullah G and Jung P. Modeling the statistics of elementary calcium release events,
Biophysical Journal, 90 (2006) 3485.
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.
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.