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

2021

[1] 

Xinyao Xiang, Alexandar L Hansen, Lei Yu, Gregory Jameson, Lei Bruschweiler-Li, Chunhua Yuan, and Rafael Brüschweiler
"Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation."
J Am Chem Soc 143, 13593-13604 (2021).

[2] 

Daniel R Marzolf, Justin T Seffernick, and Steffen Lindert
"Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data."
J Chem Theory Comput 17, 2619-2629 (2021).

[3] 

Gregory Jameson and Rafael Brüschweiler
"NMR Spin Relaxation Theory of Biomolecules Undergoing Highly Asymmetric Exchange with Large Interaction Partners."
J Chem Theory Comput 17, 2374-2382 (2021).

[4] 

Kevin J Walsh, Stavan V Shah, Ping Wei, Samuel D Oberdick, Nicole M Karn, Dana M McTigue, and Gunjan Agarwal
"Effects of fixatives on histomagnetic evaluation of iron in rodent spleen."
J Magn Magn Mater 521, 167531 (2021).

[5] 

Eric R Hantz and Steffen Lindert
"Adaptative Steered Molecular Dynamics Study of Mutagenesis Effects on Calcium Affinity in the Regulatory Domain of Cardiac Troponin C."
J Chem Inf Model 61, 3052-3057 (2021).

[6] 

Austin M Cool and Steffen Lindert
"Computational Methods Elucidate Consequences of Mutations and Post-translational Modifications on Troponin I Effective Concentration to Troponin C."
J Phys Chem B 125, 7388-7396 (2021).

[7] 

Harper Smith, Nick Pinkerton, David B Heisler, Elena Kudryashova, Aaron R Hall, Kelly R Karch, Andrew Norris, Vicki Wysocki, Marcos Sotomayor, Emil Reisler, Dimitrios Vavylonis, and Dmitri S Kudryashov
"iRounding Out/i the Understanding of ACD Toxicity with the Discovery of Cyclic Forms of Actin Oligomers."
Int J Mol Sci 22, E718 (2021).

[8] 

Stephanie S Kim, Michele J Alves, Patrick Gygli, Jose Otero, and Steffen Lindert
"Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex."
Curr Comput Aided Drug Des 17, 57-68 (2021).

 

2020

[1] 

Aparna Unnikrishnan, Carlos Amero, Deepak Kumar Yadav, Kye Stachowski, Devante Potter, and Mark P Foster
"DNA binding induces a icis/i-to-itrans/i switch in Cre recombinase to enable intasome assembly."
Proc Natl Acad Sci U S A 117, 24849-24858 (2020).

[2] 

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).

[3] 

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).

[4] 

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).

[5] 

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).

[6] 

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).

[7] 

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).

[8] 

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).

[9] 

Patrick G Dougherty, Jack H Wellmerling, Amritendu Koley, Jessica K Lukowski, Amanda B Hummon, Estelle Cormet-Boyaka, and Dehua Pei
"Cyclic Peptidyl Inhibitors against CAL/CFTR Interaction for Treatment of Cystic Fibrosis."
J Med Chem 63, 15773-15784 (2020).

[10] 

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).

[11] 

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).

[12] 

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).

[13] 

Blain Jones, Jeffrey R Tonniges, Anna Debski, Benjamin Albert, David A Yeung, Nikhit Gadde, Advitiya Mahajan, Neekun Sharma, Edward P Calomeni, Michael R Go, Chetan P Hans, and Gunjan Agarwal
"Collagen fibril abnormalities in human and mice abdominal aortic aneurysm."
Acta Biomater 110, S1742-70612030219-1 (2020).

[14] 

William C L Stewart, Komla M Gnona, Peter White, Ben Kelly, Mark Klebanoff, Irina A Buhimschi, and Leif D Nelin
"Prediction of short-term neonatal complications in preterm infants using exome-wide genetic variation and gestational age: a pilot study."
Pediatr Res 88, 653-660 (2020).

[15] 

Sunny Kwok, Keyton Clayson, Nicholas Hazen, Xueliang Pan, Yanhui Ma, Andrew J Hendershot, and Jun Liu
"Heartbeat-Induced Corneal Axial Displacement and Strain Measured by High Frequency Ultrasound Elastography in Human Volunteers."
Transl Vis Sci Technol 9, 33 (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).

 

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