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

2024

[1] 

Eleanor T Rimmerman and Mitchel R Stacy
"Applications of SPECT and PET Imaging for the Physiological Evaluation of Lower Extremity Peripheral Artery Disease."
Int J Mol Sci 25, 7474 (2024).

[2] 

Golbarg M Roozbahani, P L Colosi, Attila Oravecz, Elena M Sorokina, Wolfgang Pfeifer, Siamak Shokri, Yin Wei, Pascal Didier, Marcello DeLuca, Gaurav Arya, László Tora, Melike Lakadamyali, Michael G Poirier, and Carlos E Castro
"Piggybacking functionalized DNA nanostructures into live-cell nuclei."
Sci Adv 10, eadn9423 (2024).

[3] 

Mehmet H Kural, Umidahan Djakbarova, Bilal Cakir, Yoshiaki Tanaka, Emily T Chan, Valeria I Arteaga Muniz, Yasaman Madraki, Hong Qian, Jinkyu Park, Lorenzo R Sewanan, In-Hyun Park, Laura E Niklason, and Comert Kural
"Mechano-inhibition of endocytosis sensitizes cancer cells to Fas-induced Apoptosis."
Cell Death Dis 15, 440 (2024).

[4] 

Azariyas A Challa, Pablo Vidal, Santosh K Maurya, Chandan K Maurya, Lisa A Baer, Yang Wang, Natasha Maria James, Parth J Pardeshi, Matthew Fasano, Andrew N Carley, Kristin I Stanford, and E Douglas Lewandowski
"UCP1-dependent brown adipose activation accelerates cardiac metabolic remodeling and reduces initial hypertrophic and fibrotic responses to pathological stress."
FASEB J 38, e23709 (2024).

[5] 

Paige E Bowling, Saswata Dasgupta, and John M Herbert
"Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites."
J Chem Inf Model 64, 3912-3922 (2024).

[6] 

Shirley N Tang, Ana I Salazar-Puerta, Mary K Heimann, Kyle Kuchynsky, María A Rincon-Benavides, Mia Kordowski, Gilian Gunsch, Lucy Bodine, Khady Diop, Connor Gantt, Safdar Khan, Anna Bratasz, Olga Kokiko-Cochran, Julie Fitzgerald, Damien M Laudier, Judith A Hoyland, Benjamin A Walter, Natalia Higuita-Castro, and Devina Purmessur
"Engineered extracellular vesicle-based gene therapy for the treatment of discogenic back pain."
Biomaterials 308, 122562 (2024).

[7] 

Prerna Kabtiyal, Ariel Robbins, Elizabeth Jergens, Carlos E Castro, Jessica O Winter, Michael G Poirier, and Ezekiel Johnston-Halperin
"Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers."
Nano Lett 24, 3097-3103 (2024).

[8] 

Ting-Heng Chou, Mahboubeh Nabavinia, Nguyen K Tram, Eleanor T Rimmerman, Surina Patel, Kumudha Narayana Musini, Susan Natalie Eisert, Tatiana Wolfe, Molly K Wynveen, Yuichi Matsuzaki, Takahiro Kitsuka, Ryuma Iwaki, Sarah A Janse, Adam J Bobbey, Christopher K Breuer, Laurie Goodchild, Raphael Malbrue, Toshiharu Shinoka, Said A Atway, Michael R Go, and Mitchel R Stacy
"Quantification of Skeletal Muscle Perfusion in Peripheral Artery Disease Using "
J Am Heart Assoc 13, e031823 (2024).

[9] 

Ariel Robbins, Hazen Hildebolt, Michael Neuhoff, Peter Beshay, Jessica O Winter, Carlos E Castro, Ralf Bundschuh, and Michael G Poirier
"Cooperative control of a DNA origami force sensor."
Sci Rep 14, 4132 (2024).

[10] 

Fawwaz M Naeem, Bryan T Gemler, Zakkary A McNutt, Ralf Bundschuh, and Kurt Fredrick
"Analysis of programmed frameshifting during translation of "
RNA 30, 136-148 (2024).

[11] 

Lorien G Salyer, Hussam E Salhi, Elizabeth A Brundage, Vikram Shettigar, Sarah L Sturgill, Helena Zanella, Benjamin Templeton, Eaman Abay, Kathryn M Emmer, Jeovanna Lowe, Jill A Rafael-Fortney, Narasimham Parinandi, D Brian Foster, Timothy A McKinsey, Kathleen C Woulfe, Mark T Ziolo, and Brandon J Biesiadecki
"Troponin I Tyrosine Phosphorylation Beneficially Accelerates Diastolic Function."
Circ Res 134, 33-45 (2024).

[12] 

Christopher A Ayoub, Khadijah I Moore, and Jeff Kuret
"Quantification of Methylation and Phosphorylation Stoichiometry."
Methods Mol Biol 2754, 221-235 (2024).

[13] 

Ege Kacira, Mitchell Pittman, Dandan Yang, Sarah L Sturgill, Mark T Ziolo, Yuchi Han, Isabelle Deschênes, and Ji-Dong Fu
"Long-Axis Biplane Echocardiography Sensitively Detects the Progressing Functional Deterioration of Mouse Heart."
Circ Heart Fail 17, e011046 (2024).

 

2023

[1] 

Xin Li, Kai Jin, Tzu-Chun Cheng, You-Cheng Liao, Wen-Jui Lee, Abhjeet S Bhullar, Li-Ching Chen, Piotr Rychahou, Mitch A Phelps, Yuan Soon Ho, and Peixuan Guo
"RNA four-way junction 4WJ for spontaneous cancer-targeting, effective tumor-regression, metastasis suppression, fast renal excretion and undetectable toxicity."
Biomaterials 305, 122432 (2023).

[2] 

Xuan Fang, Vladimir Bogdanov, Jonathan P Davis, and Peter M Kekenes-Huskey
"Molecular Insights into the MLCK Activation by CaM."
J Chem Inf Model 63, 7487-7498 (2023).

[3] 

Eleanor T Rimmerman, Kumudha Narayana Musini, Ting-Heng Chou, Molly K Wynveen, Surina A Patel, Maren Beall, Adam J Bobbey, Said A Atway, Michael R Go, and Mitchel R Stacy
"Vessel-by-Vessel Computed Tomography Calcium Scoring of the Foot in Peripheral Artery Disease: Association with Patient-Level Factors."
Adv Wound Care New Rochelle 12, 603-610 (2023).

[4] 

Wang Zheng, Shaun Rawson, Zhangfei Shen, Elakkiya Tamilselvan, Harper E Smith, Julia Halford, Chen Shen, Swetha E Murthy, Maximilian H Ulbrich, Marcos Sotomayor, Tian-Min Fu, and Jeffrey R Holt
"TMEM63 proteins function as monomeric high-threshold mechanosensitive ion channels."
Neuron 111, 3195-3210.e7 (2023).

[5] 

Silvia Duarte-Sanmiguel, Ana I Salazar-Puerta, Ana Panic, Daniel Dodd, Carlie Francis, Diego Alzate-Correa, Lilibeth Ortega-Pineda, Luke Lemmerman, Maria A Rincon-Benavides, Kavya Dathathreya, William Lawrence, Neil Ott, Jingjing Zhang, Binbin Deng, Shipeng Wang, Sandra P Santander, David W McComb, Eduardo Reategui, Andre F Palmer, William E Carson, Natalia Higuita-Castro, and Daniel Gallego-Perez
"ICAM-1-decorated extracellular vesicles loaded with miR-146a and "
Biomater Sci 11, 6834-6847 (2023).

[6] 

Lilibeth Ortega-Pineda, Elizabeth Guilfoyle, Maria Angelica Rincon-Benavides, Amrita Lakshmi Anaparthi, Luke R Lemmerman, Tatiana Z Cuellar-Gaviria, William Lawrence, Jill L Buss, Binbin Deng, Britani N Blackstone, Ana Salazar-Puerta, David W McComb, Heather Powell, Daniel Gallego-Perez, and Natalia Higuita-Castro
"Engineered extracellular vesicles from human skin cells induce pro-β-cell conversions in pancreatic ductal cells."
Adv Nanobiomed Res 3, 2200173 (2023).

[7] 

Svetlana B Tikunova, Jenna Thuma, and Jonathan P Davis
"Mouse Models of Cardiomyopathies Caused by Mutations in Troponin C."
Int J Mol Sci 24, 12349 (2023).

[8] 

Ana I Salazar-Puerta, Mia Kordowski, Tatiana Z Cuellar-Gaviria, Maria A Rincon-Benavides, Jad Hussein, Dorma Flemister, Gabriel Mayoral-Andrade, Grant Barringer, Elizabeth Guilfoyle, Britani N Blackstone, Binbin Deng, Diana Zepeda-Orozco, David W McComb, Heather Powell, Lakshmi P Dasi, Daniel Gallego-Perez, and Natalia Higuita-Castro
"Engineered Extracellular Vesicle-Based Therapies for Valvular Heart Disease."
Cell Mol Bioeng 16, 309-324 (2023).

[9] 

Daniel P Veghte, Christian M ONeil, Sean Smrt, Giovanna Grandinetti, and Christopher Jaroniec
"Mass-per-Length Measurements Using STEM in SEM."
Microsc Microanal 29, 1010-1011 (2023).

[10] 

Ana I Salazar-Puerta, María A Rincon-Benavides, Tatiana Z Cuellar-Gaviria, Julian Aldana, Gabriela Vasquez Martinez, Lilibeth Ortega-Pineda, Devleena Das, Daniel Dodd, Charles A Spencer, Binbin Deng, David W McComb, Joshua A Englert, Samir Ghadiali, Diana Zepeda-Orozco, Loren E Wold, Daniel Gallego-Perez, and Natalia Higuita-Castro
"Engineered Extracellular Vesicles Derived from Dermal Fibroblasts Attenuate Inflammation in a Murine Model of Acute Lung Injury."
Adv Mater 35, e2210579 (2023).

[11] 

Margaret Bohmer, Abhjeet S Bhullar, Tao Weitao, Long Zhang, Jing-Huei Lee, and Peixuan Guo
"Revolving hexameric ATPases as asymmetric motors to translocate double-stranded DNA genome along one strand."
iScience 26, 106922 (2023).

[12] 

Austin M Cool and Steffen Lindert
"Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations."
J Chem Inf Model 63, 3534-3543 (2023).

[13] 

Eric R Hantz, Svetlana B Tikunova, Natalya Belevych, Jonathan P Davis, Peter J Reiser, and Steffen Lindert
"Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship."
J Chem Inf Model 63, 3462-3473 (2023).

[14] 

Jamie D Costabile, Kaarthik A Balakrishnan, Sina Schwinn, and Martin Haesemeyer
"Model discovery to link neural activity to behavioral tasks."
Elife 12, e83289 (2023).

[15] 

Elizabeth Jergens, Silvio de Araujo Fernandes-Junior, Yixiao Cui, Ariel Robbins, Carlos E Castro, Michael G Poirier, Metin N Gurcan, Jose J Otero, and Jessica O Winter
"DNA-caged nanoparticles "
Nanoscale 15, 9390-9402 (2023).

[16] 

Ting-Heng Chou, Molly K Wynveen, Eleanor T Rimmerman, Surina Patel, Michael R Go, and Mitchel R Stacy
"Detection of multivessel calcific disease progression in a patient with chronic limb-threatening ischemia using fluorine-18 sodium fluoride positron emission tomography imaging."
J Vasc Surg Cases Innov Tech 9, 101137 (2023).

[17] 

Puyi Ma, Da-Wei Li, and Rafael Brüschweiler
"Predicting protein flexibility with AlphaFold."
Proteins 91, 847-855 (2023).

[18] 

Ingrid M Bonilla, Stephen Baine, Anastasia Pokrass, Juan Ignacio Elio Mariángelo, Anuradha Kalyanasundaram, Vladimir Bogdanov, Louisa Mezache, Galina Sakuta, Casey M Beard, Andriy Belevych, Svetlana Tikunova, Radmila Terentyeva, Dmitry Terentyev, Jonathan Davis, Rengasayee Veeraraghavan, Cynthia A Carnes, and Sandor Györke
"STIM1 ablation impairs exercise-induced physiological cardiac hypertrophy and dysregulates autophagy in mouse hearts."
J Appl Physiol 1985 134, 1287-1299 (2023).

[19] 

Paige E Bowling, Dustin R Broderick, and John M Herbert
"Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions."
J Phys Chem Lett 14, 3826-3834 (2023).

[20] 

Benjamin T Donovan, Hengye Chen, Priit Eek, Zhiyuan Meng, Caroline Jipa, Song Tan, Lu Bai, and Michael G Poirier
"Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions."
Mol Cell 83, 1251-1263.e6 (2023).

[21] 

Mikhail Tarasov, Heather L Struckman, Yusuf Olgar, Alec Miller, Mustafa Demirtas, Vladimir Bogdanov, Radmila Terentyeva, Andrew M Soltisz, Xiaolei Meng, Dennison Min, Galina Sakuta, Izabella Dunlap, Antonia D Duran, Mark P Foster, Jonathan P Davis, Dmitry Terentyev, Sándor Györke, Rengasayee Veeraraghavan, and Przemysław B Radwański
"NaV1.6 dysregulation within myocardial T-tubules by D96V calmodulin enhances proarrhythmic sodium and calcium mishandling."
J Clin Invest 133, e152071 (2023).

[22] 

Hesham Kelani, Kara Corps, Sarah Mikula, Lesley C Fisher, Mahmoud T Shalaan, Sarah Sturgill, Mark T Ziolo, Mahmoud Abdel-Rasoul, D Michele Basso, and Hamdy Awad
"Mouse Model of Spinal Cord Hypoperfusion with Immediate Paralysis Caused by Endovascular Repair of Thoracic Aortic Aneurysm."
Anesthesiology 138, 403-419 (2023).

[23] 

Arden B Piepho, Jeovanna Lowe, Laurel R Cumby, Lisa E Dorn, Dana M Lake, Neha Rastogi, Megan D Gertzen, Sarah L Sturgill, Guy L Odom, Mark T Ziolo, Federica Accornero, Jeffrey S Chamberlain, and Jill A Rafael-Fortney
"Micro-dystrophin gene therapy demonstrates long-term cardiac efficacy in a severe Duchenne muscular dystrophy model."
Mol Ther Methods Clin Dev 28, 344-354 (2023).

[24] 

Hussam E Salhi, Vikram Shettigar, Lorien Salyer, Sarah Sturgill, Elizabeth A Brundage, Joel Robinett, Zhaobin Xu, Eaman Abay, Jeovanna Lowe, Paul M L Janssen, Jill A Rafael-Fortney, Noah Weisleder, Mark T Ziolo, and Brandon J Biesiadecki
"The lack of Troponin I Ser-23/24 phosphorylation is detrimental to in vivo cardiac function and exacerbates cardiac disease."
J Mol Cell Cardiol 176, 84-96 (2023).

[25] 

Maria A Rincon-Benavides, Natalia Claire Mendonca, Tatiana Z Cuellar-Gaviria, Ana I Salazar-Puerta, Lilibeth Ortega-Pineda, Britani N Blackstone, Binbin Deng, David W McComb, Daniel Gallego-Perez, Heather M Powell, and Natalia Higuita-Castro
"Engineered Vasculogenic Extracellular Vesicles Drive Nonviral Direct Conversions of Human Dermal Fibroblasts into Induced Endothelial Cells and Improve Wound Closure."
Adv Ther Weinh 6, 2200197 (2023).

[26] 

Zakkary A McNutt, Bappaditya Roy, Bryan T Gemler, Elan A Shatoff, Kyung-Mee Moon, Leonard J Foster, Ralf Bundschuh, and Kurt Fredrick
"Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae."
Nucleic Acids Res 51, 1927-1942 (2023).

[27] 

Benjamin T Donovan, Yi Luo, Zhiyuan Meng, and Michael G Poirier
"The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics."
Nucleic Acids Res 51, 1139-1153 (2023).

[28] 

Yu-Chieh Chung, Madhoolika Bisht, Jenna Thuma, and Li-Chun Tu
"Single-chromosome dynamics reveals locus-dependent dynamics and chromosome territory orientation."
J Cell Sci 136, jcs260137 (2023).

[29] 

Ting-Heng Chou, Eleanor T Rimmerman, Surina Patel, Molly K Wynveen, Susan N Eisert, Kumudha Narayana Musini, Sarah A Janse, Adam J Bobbey, Timur P Sarac, Said A Atway, Michael R Go, and Mitchel R Stacy
"Vessel-by-vessel analysis of lower extremity "
EJNMMI Res 13, 3 (2023).

[30] 

Jenna Thuma, Yu-Chieh Chung, and Li-Chun Tu
"Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization."
Front Mol Biosci 10, 1173545 (2023).

 

2022

[1] 

Carmem Peres Valgas Da Silva, Vikram K Shettigar, Lisa A Baer, Eaman Abay, Kelsey M Pinckard, Jorge Vinales, Sarah L Sturgill, Pablo Vidal, Mark T Ziolo, and Kristin I Stanford
"Exercise training after myocardial infarction increases survival but does not prevent adverse left ventricle remodeling and dysfunction in high-fat diet fed mice."
Life Sci 311, 121181 (2022).

[2] 

Eric R Hantz and Steffen Lindert
"Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C."
J Chem Inf Model 62, 6201-6208 (2022).

[3] 

Ruiqi Wu, Xiankun Li, Lijuan Wang, and Dongping Zhong
"Ultrafast Dynamics and Catalytic Mechanism of Fatty Acid Photodecarboxylase."
Angew Chem Int Ed Engl 61, e202209180 (2022).

[4] 

Megan M Allyn, Maria A Rincon-Benavides, Heather L Chandler, Natalia Higuita-Castro, Andre F Palmer, and Katelyn E Swindle-Reilly
"Sustained release of heme-albumin as a potential novel therapeutic approach for age-related macular degeneration."
Biomater Sci 10, 7004-7014 (2022).

[5] 

Kaveh Rayani, Eric R Hantz, Omid Haji-Ghassemi, Alison Y Li, Anne M Spuches, Filip Van Petegem, R John Solaro, Steffen Lindert, and Glen F Tibbits
"The effect of Mg"
FEBS J 289, 7446-7465 (2022).

[6] 

Abhjeet S Bhullar, Long Zhang, Nicolas Burns, Xiaolin Cheng, and Peixuan Guo
"Voltage controlled shutter regulates channel size and motion direction of protein aperture as durable nano-electric rectifier-----An opinion in biomimetic nanoaperture."
Biomaterials 291, 121863 (2022).

[7] 

Eric R Hantz and Steffen Lindert
"Actives-Based Receptor Selection Strongly Increases the Success Rate in Structure-Based Drug Design and Leads to Identification of 22 Potent Cancer Inhibitors."
J Chem Inf Model 62, 5675-5687 (2022).

[8] 

Austin M Cool and Steffen Lindert
"Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin."
J Chem Inf Model 62, 5666-5674 (2022).

[9] 

Ehsan Akbari, Melika Shahhosseini, Ariel Robbins, Michael G Poirier, Jonathan W Song, and Carlos E Castro
"Low cost and massively parallel force spectroscopy with fluid loading on a chip."
Nat Commun 13, 6800 (2022).

[10] 

Gregory Jameson, Xinyao Xiang, and Rafael Brüschweiler
"Quantitative Multistate Binding Model of Silica Nanoparticle-Protein Interactions Obtained from Multinuclear Spin Relaxation."
J Phys Chem B 126, 9089-9094 (2022).

[11] 

Montgomery Gray, Paige E Bowling, and John M Herbert
"Systematic Evaluation of Counterpoise Correction in Density Functional Theory."
J Chem Theory Comput 18, 6742-6756 (2022).

[12] 

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).

[13] 

Xin Li, Abhjeet S Bhullar, Daniel W Binzel, and Peixuan Guo
"The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development."
Adv Drug Deliv Rev 186, 114316 (2022).

[14] 

Nathaniel L Burge, Jenna L Thuma, Ziyong Z Hong, Kevin B Jamison, Jennifer J Ottesen, and Michael G Poirier
"H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes."
Biochemistry 61, 625-638 (2022).

[15] 

Shanna Hamilton, Radmila Terentyeva, Vladimir Bogdanov, Tae Yun Kim, Fruzsina Perger, Jiajie Yan, Xun Ai, Cynthia A Carnes, Andriy E Belevych, Christopher H George, Jonathan P Davis, Sandor Gyorke, Bum-Rak Choi, and Dmitry Terentyev
"Ero1α-Dependent ERp44 Dissociation From RyR2 Contributes to Cardiac Arrhythmia."
Circ Res 130, 711-724 (2022).

[16] 

Lilibeth Ortega-Pineda, Alec Sunyecz, Ana I Salazar-Puerta, Maria Angelica Rincon-Benavides, Diego Alzate-Correa, Amrita Lakshmi Anaparthi, Elizabeth Guilfoyle, Louisa Mezache, Heather L Struckman, Silvia Duarte-Sanmiguel, Binbin Deng, David W McComb, Daniel J Dodd, William R Lawrence, Jordan Moore, Jingjing Zhang, Eduardo Reátegui, Rengasayee Veeraraghavan, M Tyler Nelson, Daniel Gallego-Perez, and Natalia Higuita-Castro
"Designer Extracellular Vesicles Modulate Pro-Neuronal Cell Responses and Improve Intracranial Retention."
Adv Healthc Mater 11, e2100805 (2022).

[17] 

Luke R Lemmerman, Hallie N Harris, Maria H H Balch, Maria A Rincon-Benavides, Natalia Higuita-Castro, David W Arnold, and Daniel Gallego-Perez
"Transient Middle Cerebral Artery Occlusion with an Intraluminal Suture Enables Reproducible Induction of Ischemic Stroke in Mice."
Bio Protoc 12, e4305 (2022).

[18] 

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).

[19] 

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).

[20] 

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).

[21] 

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).

[22] 

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).

[23] 

Sarah L Sturgill, Vikram Shettigar, and Mark T Ziolo
"Antiquated ejection fraction: Basic research applications for speckle tracking echocardiography."
Front Physiol 13, 969314 (2022).

[24] 

Sm Bargeen Alam Turzo, Eric R Hantz, and Steffen Lindert
"Applications of machine learning in computer-aided drug discovery."
QRB Discov 3, e14 (2022).

[25] 

Lewis Rolband, Damian Beasock, Yang Wang, Yao-Gen Shu, Jonathan D Dinman, Tamar Schlick, Yaoqi Zhou, Jeffrey S Kieft, Shi-Jie Chen, Giovanni Bussi, Abdelghani Oukhaled, Xingfa Gao, Petr Šulc, Daniel Binzel, Abhjeet S Bhullar, Chenxi Liang, Peixuan Guo, and Kirill A Afonin
"Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions."
Comput Struct Biotechnol J 20, 6120-6137 (2022).

 

2021

[1] 

Ahmed A Zayed, Dominik Lücking, Mohamed Mohssen, Dylan Cronin, Ben Bolduc, Ann C Gregory, Katherine R Hargreaves, Paul D Piehowski, Richard A White Iii, Eric L Huang, Joshua N Adkins, Simon Roux, Cristina Moraru, and Matthew B Sullivan
"efam: an expanded, metaproteome-supported HMM profile database of viral protein families."
Bioinformatics 37, 4202-4208 (2021).

[2] 

Elan A Shatoff, Bryan T Gemler, Ralf Bundschuh, and Kurt Fredrick
"Maturation of 23S rRNA includes removal of helix H1 in many bacteria."
RNA Biol 18, 856-865 (2021).

[3] 

Vladimir Bogdanov, Andrew M Soltisz, Nicolae Moise, Galina Sakuta, Benjamin Hernandez Orengo, Paul M L Janssen, Seth H Weinberg, Jonathan P Davis, Rengasayee Veeraraghavan, and Sandor Györke
"Distributed synthesis of sarcolemmal and sarcoplasmic reticulum membrane proteins in cardiac myocytes."
Basic Res Cardiol 116, 63 (2021).

[4] 

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).

[5] 

Umidahan Djakbarova, Yasaman Madraki, Emily T Chan, and Cömert Kural
"Dynamic interplay between cell membrane tension and clathrin-mediated endocytosis."
Biol Cell 113, 344-373 (2021).

[6] 

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).

[7] 

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).

[8] 

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).

[9] 

Luke R Lemmerman, Maria H H Balch, Jordan T Moore, Diego Alzate-Correa, Maria A Rincon-Benavides, Ana Salazar-Puerta, Surya Gnyawali, Hallie N Harris, William Lawrence, Lilibeth Ortega-Pineda, Lauren Wilch, Ian B Risser, Aidan J Maxwell, Silvia Duarte-Sanmiguel, Daniel Dodd, Gina P Guio-Vega, Dana M McTigue, W David Arnold, Shahid M Nimjee, Chandan K Sen, Savita Khanna, Cameron Rink, Natalia Higuita-Castro, and Daniel Gallego-Perez
"Nanotransfection-based vasculogenic cell reprogramming drives functional recovery in a mouse model of ischemic stroke."
Sci Adv 7, eabd4735 (2021).

[10] 

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).

[11] 

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).

[12] 

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).

[13] 

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).

[14] 

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).

[15] 

Andriy E Belevych, Vladimir Bogdanov, Dmitry A Terentyev, and Sandor Gyorke
"Acute Detubulation of Ventricular Myocytes Amplifies the Inhibitory Effect of Cholinergic Agonist on Intracellular Ca"
Front Physiol 12, 725798 (2021).

 

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