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

2022

[1] 

Sarah L Sturgill, Lorien G Salyer, Vikram Shettigar, Elizabeth A Brundage, Brandon J Biesiadecki, and Mark T Ziolo
"Troponin I phosphorylation is essential for cardiac reserve."
J Gen Physiol 154, e2021ecc31 (2022).

[2] 

Enrique Lin-Shiao, Wolfgang G Pfeifer, Brian R Shy, Mohammad Saffari Doost, Evelyn Chen, Vivasvan S Vykunta, Jennifer R Hamilton, Elizabeth C Stahl, Diana M Lopez, Cindy R Sandoval Espinoza, Alexander E Deyanov, Rachel J Lew, Michael G Poirer, Alexander Marson, Carlos E Castro, and Jennifer A Doudna
"CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells."
Nucleic Acids Res 50, 1256-1268 (2022).

[3] 

Guillermo Dominguez-Huerta, Ahmed A Zayed, James M Wainaina, Jiarong Guo, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Mohamed Mohssen, Olivier Zablocki, Eric Pelletier, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, , Chris Bowler, Damien Eveillard, Lionel Guidi, Eric Karsenti, Jens H Kuhn, Hiroyuki Ogata, Patrick Wincker, Alexander Culley, Samuel Chaffron, and Matthew B Sullivan
"Diversity and ecological footprint of Global Ocean RNA viruses."
Science 376, 1202-1208 (2022).

[4] 

Ahmed A Zayed, James M Wainaina, Guillermo Dominguez-Huerta, Eric Pelletier, Jiarong Guo, Mohamed Mohssen, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Olivier Zablocki, Dylan Cronin, Lindsey Solden, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Hans-Joachim Ruscheweyh, Guillem Salazar, Elan Shatoff, , Ralf Bundschuh, Kurt Fredrick, Laura S Kubatko, Samuel Chaffron, Alexander I Culley, Shinichi Sunagawa, Jens H Kuhn, Patrick Wincker, Matthew B Sullivan, Silvia G Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stéphane Pesant, Christian Sardet, Sabrinia Speich, Lars Stemmann, Matthew B Sullivan, Shinichi Sungawa, and Patrick Wincker
"Cryptic and abundant marine viruses at the evolutionary origins of Earths RNA virome."
Science 376, 156-162 (2022).

[5] 

Tung T Nguyen, Daniel R Marzolf, Justin T Seffernick, Sten Heinze, and Steffen Lindert
"Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR."
Structure 30, 313-320.e3 (2022).

[6] 

Sunny Kwok, Manqi Pan, Nicholas Hazen, Xueliang Pan, and Jun Liu
"Mechanical Deformation of Peripapillary Retina in Response to Acute Intraocular Pressure Elevation."
J Biomech Eng 144, 061001 (2022).

 

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).

[9] 

Sunny Kwok, Nicholas Hazen, Keyton Clayson, Xueliang Pan, and Jun Liu
"Regional variation of corneal stromal deformation measured by high-frequency ultrasound elastography."
Exp Biol Med Maywood 246, 2184-2191 (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).

 

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