Publications (co-)authored by students in the Biophysics program

2020

[1] 

Rachael E Rayner, Jack Wellmerling, Wissam Osman, Sean Honesty, Maria Alfaro, Mark E Peeples, and Estelle Cormet-Boyaka
"In vitro 3D culture lung model from expanded primary cystic fibrosis human airway cells."
J. Cyst. Fibros. 19, S1569-19932030151-X (2020).

[2] 

Joel R Palko, Yanhui Ma, Xueliang Pan, James Liu, Catherine Reppa, Maxwell W Dixon, Keyton Clayson, Anthony Lubniewski, and Jun Liu
"Mechanical Stability of Cryopreserved Split-Thickness Tectonic Corneal Grafts."
Cornea 39, 1151-1156 (2020).

[3] 

Yanhui Ma, Sunny Kwok, Jiajun Sun, Xueliang Pan, Elias Pavlatos, Keyton Clayson, Nicholas Hazen, and Jun Liu
"IOP-induced regional displacements in the optic nerve head and correlation with peripapillary sclera thickness."
Exp. Eye Res. 200, S0014-48352030460-7 (2020).

[4] 

Stephen A Pearson, Christine Wachnowsky, and J A Cowan
"Defining the mechanism of the mitochondrial Atm1p 2Fe-2S cluster exporter."
Metallomics 12, 902-915 (2020).

[5] 

Bin Liu, Qing Lou, Heather Smith, Florencia Velez-Cortes, Wolfgang H Dillmann, Björn C Knollmann, Antonis A Armoundas, and Sándor Györke
"Conditional Up-Regulation of SERCA2a Exacerbates RyR2-Dependent Ventricular and Atrial Arrhythmias."
Int J Mol Sci 21, E2535 (2020).

[6] 

Patrick Houston, Nicolas Macro, Minhee Kang, Long Chen, Jin Yang, Lijuan Wang, Zhengrong Wu, and Dongping Zhong
"Ultrafast Dynamics of Water-Protein Coupled Motions around the Surface of Eye Crystallin."
J. Am. Chem. Soc. 142, 3997-4007 (2020).

[7] 

Keyton Clayson, Thomas Sandwisch, Yanhui Ma, Elias Pavlatos, Xueliang Pan, and Jun Liu
"Corneal Hydration Control during Ex Vivo Experimentation Using Poloxamers."
Curr. Eye Res. 45, 111-117 (2020).

[8] 

Abhilasha Dehankar, Thomas Porter, Joshua A Johnson, Carlos E Castro, and Jessica O Winter
"Erratum: Compact quantum dot surface modification to enable emergent behaviors in quantum dot-DNA composites J. Chem. Phys. 151, 144706 2019."
J Chem Phys 152, 059901 (2020).

[9] 

Keyton Clayson, Elias Pavlatos, Xueliang Pan, Thomas Sandwisch, Yanhui Ma, and Jun Liu
"Ocular Pulse Elastography: Imaging Corneal Biomechanical Responses to Simulated Ocular Pulse Using Ultrasound."
Transl Vis Sci Technol 9, 5 (2020).

[10] 

Weili Zheng, Matthew Orchard, Harper Smith, Lucas A Runyan, Edward H Egelman, and Dmitri S Kudryashov
"Osteogenesis imperfecta mutations in plastin 3 lead to impaired calcium regulation of actin bundling."
Bone Res 8, 21 (2020).

 

2019

[1] 

Maximillian Westphal, David Frankhouser, Carmine Sonzone, Peter G Shields, Pearlly Yan, and Ralf Bundschuh
"SMaSH: Sample matching using SNPs in humans."
BMC Genomics 20, 1001 (2019).

[2] 

Dengke Zhao, Jenny V Le, Michael A Darcy, Kyle Crocker, Michael G Poirier, Carlos Castro, and Ralf Bundschuh
"Quantitative Modeling of Nucleosome Unwrapping from Both Ends."
Biophys. J. 117, S0006-34951930880-X (2019).

[3] 

Gregory Jameson, Alexandar L Hansen, Dawei Li, Lei Bruschweiler-Li, and Rafael Brüschweiler
"Extreme Nonuniform Sampling for Protein NMR Dynamics Studies in Minimal Time."
J. Am. Chem. Soc. 141, 16829-16838 (2019).

[4] 

Abhilasha Dehankar, Thomas Porter, Joshua A Johnson, Carlos E Castro, and Jessica O Winter
"Compact quantum dot surface modification to enable emergent behaviors in quantum dot-DNA composites."
J Chem Phys 151, 144706 (2019).

[5] 

Jack H Wellmerling, Sheng-Wei Chang, Eunsoo Kim, Wissam H Osman, Prosper N Boyaka, Michael T Borchers, and Estelle Cormet-Boyaka
"Reduced expression of the Ion channel CFTR contributes to airspace enlargement as a consequence of aging and in response to cigarette smoke in mice."
Respir. Res. 20, 200 (2019).

[6] 

Kaivon Assani, Chandra L Shrestha, Hannah Rinehardt, Shuzhong Zhang, Frank Robledo-Avila, Jack Wellmerling, Santiago Partida-Sanchez, Estelle Cormet-Boyaka, Susan D Reynolds, Larry S Schlesinger, and Benjamin T Kopp
"AR-13 reduces antibiotic-resistant bacterial burden in cystic fibrosis phagocytes and improves cystic fibrosis transmembrane conductance regulator function."
J. Cyst. Fibros. 18, S1569-19931830869-5 (2019).

[7] 

Justin T Seffernick, He Ren, Stephanie S Kim, and Steffen Lindert
"Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder."
J Phys Chem B 123, 7103-7112 (2019).

[8] 

Matthew Brehove, Elan Shatoff, Benjamin T Donovan, Caroline M Jipa, Ralf Bundschuh, and Michael G Poirier
"DNA sequence influences hexasome orientation to regulate DNA accessibility."
Nucleic Acids Res. 47, 5617-5633 (2019).

[9] 

Benjamin T Donovan, Anh Huynh, David A Ball, Heta P Patel, Michael G Poirier, Daniel R Larson, Matthew L Ferguson, and Tineke L Lenstra
"Live-cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting."
EMBO J. 38, e100809 (2019).

[10] 

Stephanie S Kim, Melanie L Aprahamian, and Steffen Lindert
"Improving inverse docking target identification with Z-score selection."
Chem Biol Drug Des 93, 1105-1116 (2019).

[11] 

Joshua Sifford, Kevin J Walsh, Sheng Tong, Gang Bao, and Gunjan Agarwal
"Indirect magnetic force microscopy."
Nanoscale Adv 1, 2348-2355 (2019).

[12] 

Dengke Zhao, William D Baez, Kurt Fredrick, and Ralf Bundschuh
"RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling."
Bioinformatics 35, 1486-1493 (2019).

[13] 

Carol J Huseby, Ralf Bundschuh, and Jeff Kuret
"The role of annealing and fragmentation in human tau aggregation dynamics."
J. Biol. Chem. 294, 4728-4737 (2019).

[14] 

Benjamin T Donovan, Hengye Chen, Caroline Jipa, Lu Bai, and Michael G Poirier
"Dissociation rate compensation mechanism for budding yeast pioneer transcription factors."
Elife 8, e43008 (2019).

[15] 

Yanhui Ma, Elias Pavlatos, Keyton Clayson, Xueliang Pan, Sunny Kwok, Thomas Sandwisch, and Jun Liu
"Mechanical Deformation of Human Optic Nerve Head and Peripapillary Tissue in Response to Acute IOP Elevation."
Invest. Ophthalmol. Vis. Sci. 60, 913-920 (2019).

[16] 

Chao-Min Huang, Anjelica Kucinic, Jenny V Le, Carlos E Castro, and Hai-Jun Su
"Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis."
Nanoscale 11, 1647-1660 (2019).

[17] 

David A Yeung, Nirvan Shanker, Anjum Sohail, Brent A Weiss, Carolyn Wang, Jack Wellmerling, Subhadip Das, Ramesh K Ganju, Jeanette L C Miller, Andrew B Herr, Rafael Fridman, and Gunjan Agarwal
"Clustering, Spatial Distribution, and Phosphorylation of Discoidin Domain Receptors 1 and 2 in Response to Soluble Collagen I."
J. Mol. Biol. 431, 368-390 (2019).

[18] 

Carol J Huseby, Claire N Hoffman, Grace L Cooper, Jean-Christophe Cocuron, Ana P Alonso, Stefani N Thomas, Austin J Yang, and Jeff Kuret
"Quantification of Tau Protein Lysine Methylation in Aging and Alzheimers Disease."
J. Alzheimers Dis. 71, 979-991 (2019).

 

2018

[1] 

A R Blissett, B Deng, P Wei, K J Walsh, B Ollander, J Sifford, A D Sauerbeck, D W McComb, D M McTigue, and G Agarwal
"Sub-cellular In-situ Characterization of Ferritiniron in a Rodent Model of Spinal Cord Injury."
Sci Rep 8, 3567 (2018).

[2] 

Grace L Cooper, Carol J Huseby, Claire N Chandler, Jean-Christophe Cocuron, Ana P Alonso, and Jeff Kuret
"A liquid chromatography tandem mass spectroscopy approach for quantification of protein methylation stoichiometry."
Anal. Biochem. 545, 72-77 (2018).

[3] 

Pearson T Maugeri, Julia J Griese, Rui M Branca, Effie K Miller, Zachary R Smith, Jürgen Eirich, Martin Högbom, and Hannah S Shafaat
"Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in a Heterobimetallic Oxidase."
J. Am. Chem. Soc. 140, 1471-1480 (2018).

[4] 

Stephanie S Kim, Justin T Seffernick, and Steffen Lindert
"Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application."
J Phys Chem B 122, 3920-3930 (2018).

[5] 

Elias Pavlatos, Yanhui Ma, Keyton Clayson, Xueliang Pan, and Jun Liu
"Regional Deformation of the Optic Nerve Head and Peripapillary Sclera During IOP Elevation."
Invest. Ophthalmol. Vis. Sci. 59, 3779-3788 (2018).

[6] 

Sheng-Wei Chang, Jack Wellmerling, Xiaoli Zhang, Rachael E Rayner, Wissam Osman, Sara Mertz, Amal O Amer, Mark E Peeples, Prosper N Boyaka, and Estelle Cormet-Boyaka
"The psychoactive substance of cannabis Δ9-tetrahydrocannabinol THC negatively regulates CFTR in airway cells."
Biochim Biophys Acta Gen Subj 1862, 1988-1994 (2018).

 

2017

[1] 

Nathaniel A Wesley, Christine Wachnowsky, Insiya Fidai, and J A Cowan
"Understanding the molecular basis for multiple mitochondrial dysfunctions syndrome 1 MMDS1: impact of a disease-causing Gly189Arg substitution on NFU1."
FEBS J. 284, 3838-3848 (2017).

[2] 

Nathaniel A Wesley, Christine Wachnowsky, Insiya Fidai, and J A Cowan
"Analysis of NFU-1 metallocofactor binding-site substitutions-impacts on iron-sulfur cluster coordination and protein structure and function."
FEBS J. 284, 3817-3837 (2017).

[3] 

Keyton Clayson, Elias Pavlatos, Yanhui Ma, and Jun Liu
"3D Characterization of corneal deformation using ultrasound speckle tracking."
J Innov Opt Health Sci 10, 1742005 (2017).

[4] 

Meng Zhang, Lijuan Wang, and Dongping Zhong
"Photolyase: Dynamics and electron-transfer mechanisms of DNA repair."
Arch. Biochem. Biophys. 632, 158-174 (2017).

[5] 

Martin James Ross, Insiya Fidai, and James A Cowan
"Analysis of Structure-Activity Relationships Based on the Hepatitis C Virus SLIIb Internal Ribosomal Entry Sequence RNA-Targeting GGHYRFK⋅Cu Complex."
Chembiochem 18, 1743-1754 (2017).

[6] 

Maximillian S Westphal, Sara N Lim, Sultana N Nahar, Enam Chowdhury, and Anil K Pradhan
"Broadband, monochromatic and quasi-monochromatic x-ray propagation in multi-Z media for imaging and diagnostics."
Phys Med Biol 62, 6361-6378 (2017).

[7] 

Bobo Shi, Yun Kyung Shin, Ali A Hassanali, and Sherwin J Singer
"Biomolecules at the amorphous silica/water interface: Binding and fluorescence anisotropy of peptides."
Colloids Surf B Biointerfaces 157, 83-92 (2017).

[8] 

Elihu C Ihms, Ian R Kleckner, Paul Gollnick, and Mark P Foster
"Mechanistic Models Fit to Variable Temperature Calorimetric Data Provide Insights into Cooperativity."
Biophys. J. 112, 1328-1338 (2017).

[9] 

Jeffrey W Slater, Sean C Marguet, Sabrina L Cirino, Pearson T Maugeri, and Hannah S Shafaat
"Experimental and DFT Investigations Reveal the Influence of the Outer Coordination Sphere on the Vibrational Spectra of Nickel-Substituted Rubredoxin, a Model Hydrogenase Enzyme."
Inorg Chem 56, 3926-3938 (2017).

[10] 

Christine Wachnowsky, Nathaniel A Wesley, Insiya Fidai, and J A Cowan
"Understanding the Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 1 MMDS1-Impact of a Disease-Causing Gly208Cys Substitution on Structure and Activity of NFU1 in the Fe/S Cluster Biosynthetic Pathway."
J. Mol. Biol. 429, 790-807 (2017).

[11] 

E John Tokarsky, Petra C Wallenmeyer, Kenneth K Phi, and Zucai Suo
"Significant impact of divalent metal ions on the fidelity, sugar selectivity, and drug incorporation efficiency of human PrimPol."
DNA Repair Amst. 49, 51-59 (2017).

[12] 

Meng Zhang, Lijuan Wang, and Dongping Zhong
"Photolyase: Dynamics and Mechanisms of Repair of Sun-Induced DNA Damage."
Photochem. Photobiol. 93, 78-92 (2017).

[13] 

Shane D Walton, Harshini Chakravarthy, Vikram Shettigar, Andrew J ONeil, Jalal K Siddiqui, Benjamin R Jones, Svetlana B Tikunova, and Jonathan P Davis
"Divergent Soybean Calmodulins Respond Similarly to Calcium Transients: Insight into Differential Target Regulation."
Front Plant Sci 8, 208 (2017).

[14] 

Keyton Clayson, Xueliang Pan, Elias Pavlatos, Ryan Short, Hugh Morris, Richard T Hart, and Jun Liu
"Corneoscleral stiffening increases IOP spike magnitudes during rapid microvolumetric change in the eye."
Exp. Eye Res. 165, 29-34 (2017).

[15] 

Jon delEtoile and Hojjat Adeli
"Graph Theory and Brain Connectivity in Alzheimers Disease."
Neuroscientist 23, 616-626 (2017).

 

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