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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-Th茅r猫se 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 M眉hlhausen, 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, .

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), .
The software and sample data for this paper can be found

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, .

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, .

Passlick S, Ullah G, and Henneberger C. Bidirectional dysregulation of synaptic glutamate signaling after transient metabolic failure, .

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, .
* Shared first authorship.
.

 

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, .
* Shared first authorship.

Shah S I, Parker I, Ullah G, and Demuro A. A尾42 and A尾40 form transient and persistent pores with different time evolutions and toxicities, .

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, .

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,

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

Pensalfini A, Umar A R, Glabe C, Parker I, Ullah G, and Demuro A. Intracellular injection of brain extracts from Alzheimer鈥檚 disease patients trigger unregulated Ca2+ release from intracellular stores that hinders cellular bioenergetics, .

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鈥檚 disease, .
Code and instructions for this paper can be found

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, .

Andrew R D, Farkas E, Hartings J A, Brennan K C, Herreras O, Mu虉ller 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, .

Andrew R D, Hartings J A, Ayata C, Brennan K C, Dawson-Scully K D, Farkas E, Herreras O, Kirov S A, Mu虉ller 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, .

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鈥檚 ataxia cardiomyopathy, .

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, .

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, .

Perez C, Felix L, Rose C R, and Ullah G. On the Origin of Ultraslow Spontaneous Na+ Fluctuations in Neurons of the Neonatal Forebrain, .

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, .

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, .
The software, user manual, and sample data for this paper can be found

Shah S I, Paine J, Perez C, and Ullah G. Mitochondrial fragmentation and network architecture in degenerative diseases, .

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, .

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, .

Toglia P and Ullah G. Mitochondrial dysfunction and role in spreading depolarization and seizure, .

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, .

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, .
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, .

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, .
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, .

Hasecke F, Miti T, Perez C, Sch枚lzel D, Gremer L, Gr眉ning 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, .

Perez C and Ullah G. Reduced cooperativity of voltage-gated sodium channels in the hippocampal interneurons of aged mouse model of Alzheimer's disease, .

Shafiq鈥恥l鈥怘assan 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, .

H眉bel N, Mahshid S Hosseini-Zare, Ziburkus J, and Ullah G. The role of glutamate in neuronal ion homeostasis: a case study of spreading depolarization,
Code reproducing key results is archieved with the paper in .

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, .

Shafiq鈥恥l鈥怘assan 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, .

Perez C, Ziburkus J, and Ullah G. Analyzing and modeling the dysfunction of inhibitory neurons in Alzheimer's disease, .

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, .

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, .

H眉bel N and Ullah G. Astrocytes swell more than neurons during prolonged depolarizations in anions-dependent manner,

H眉bel N, Andrew DR, and Ullah G. Large extracellular space leads to neuronal susceptibility to ischemic injury in Na+/K+ pumps-dependent manner,

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鈥檚 disease-causing mutant presenilins, .

Ullah G, Demuro A, Parker I, and Pearson JE. Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer鈥檚 disease pathology, .

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, .
Code for this paper can be found

Wei Y, Ullah G, Schiff SJ, Unification of neuronal spikes, seizures, and spreading depression, .

Ullah A, Jung P, Ullah G, and Machaca K. The role of IP3 receptor channel clustering in Ca2 + wave propagation during oocyte maturation, .

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, .
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, . Evaluated as "Very Good" by Faculty of 1000 .

 

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, .

Ullah G, Bruno W, and Pearson JE. Simplification of reversible Markov chains by removal of states with low equilibrium occupancy, .
Code for this paper can be found

Ullah G, Parker I, Mak DOD, and Pearson JE. Multi-scale data-driven modeling and observation of calcium puffs, .

Ahmad F, Ullah G, and Kim SH. A neighborhood method for statistical analysis of fMRI data, .

Wei Y, Ullah G, Parekh R, Ziburkus J, and Schiff SJ, Kalman filter tracking of intracellular neuronal voltage and current, .

Ullah G and Schiff SJ. Assimilating seizure dynamics, .
Code for this paper can be found

Swaminathan D, Ullah G, and Jung P. A simple sequential-binding model for Calcium puffs, .

Ghanim Ullah and Steven J. Schiff, Models of epilepsy, .

Ullah G and Schiff SJ. Tracking and control of neuronal Hodgkin-Huxley dynamics, .
Code for this paper can be found

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.