Publications by authors named "AR Bishop"

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Contribution of DNA breathing to physical interactions with transcription factors.
Waqaas Butt, Ben Lai, Tsu-Pei Chiu, Manish Bhattarai, Sheng Qian, Alan R Bishop

bioRxiv· January 2025

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DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.
Anowarul Kabir, Manish Bhattarai, Selma Peterson, Yonatan Najman-Licht, Kim Ø Rasmussen, Alan R Bishop

Nucleic Acids Res· October 2024

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A nonlinear journey from structural phase transitions to quantum annealing.
Mithun Thudiyangal, Panayotis G Kevrekidis, Avadh Saxena, Alan R Bishop

Chaos· May 2024

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Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention.
Anowarul Kabir, Manish Bhattarai, Kim Ø Rasmussen, Amarda Shehu, Alan R Bishop

bioRxiv· February 2024

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Examining DNA breathing with pyDNA-EPBD.
Anowarul Kabir, Manish Bhattarai, Kim Ø Rasmussen, Amarda Shehu, Anny Usheva, Alan R Bishop

Bioinformatics· November 2023

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Examining DNA Breathing with pyDNA-EPBD.
Anowarul Kabir, Manish Bhattarai, Kim Ø Rasmussen, Amarda Shehu, Anny Usheva, Alan R Bishop

bioRxiv· September 2023

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Patterns and Stability of Coupled Multi-Stable Nonlinear Oscillators.
G Bel, B S Alexandrov, A R Bishop, K Ø Rasmussen

Chaos Solitons Fractals· January 2023

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Bubble Relaxation Dynamics in Homopolymer DNA Sequences.
Malcolm Hillebrand, George Kalosakas, Alan R Bishop, Charalampos Skokos

Molecules· January 2023

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Measurement and memory in the periodically driven complex Ginzburg-Landau equation.
T Mithun, P G Kevrekidis, A Saxena, A R Bishop

Phys Rev E· March 2022

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Bubble lifetimes in DNA gene promoters and their mutations affecting transcription.
M Hillebrand, G Kalosakas, A R Bishop, Ch Skokos

J Chem Phys· September 2021

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Distributions of bubble lifetimes and bubble lengths in DNA.
M Hillebrand, G Kalosakas, Ch Skokos, A R Bishop

Phys Rev E· December 2020

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Mechanical, elution, and antibacterial properties of simplex bone cement loaded with vancomycin.
Sunjung Kim, Aaron R Bishop, Matthew W Squire, Warren E Rose, Heidi-Lynn Ploeg

J Mech Behav Biomed Mater· March 2020

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Metabolomics and the pig model reveal aberrant cardiac energy metabolism in metabolic syndrome.
Maryam Karimi, Victoria Petkova, John M Asara, Michael J Griffin, Frank W Sellke, Alan R Bishop

Sci Rep· February 2020

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Publisher Correction: Electrosynthesis of high-entropy metallic glass nanoparticles for designer, multi-functional electrocatalysis.
Matthew W Glasscott, Andrew D Pendergast, Sondrica Goines, Anthony R Bishop, Andy T Hoang

Nat Commun· July 2019

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Electrosynthesis of high-entropy metallic glass nanoparticles for designer, multi-functional electrocatalysis.
Matthew W Glasscott, Andrew D Pendergast, Sondrica Goines, Anthony R Bishop, Andy T Hoang

Nat Commun· June 2019

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Vancomycin elution, activity and impact on mechanical properties when added to orthopedic bone cement.
Aaron R Bishop, Sunjung Kim, Matthew W Squire, Warren E Rose, Heidi-Lynn Ploeg

J Mech Behav Biomed Mater· November 2018

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Data for vancomycin elution, activity and impact on mechanical properties when incorporated into orthopedic bone cement.
Aaron R Bishop, Sunjung Kim, Matthew Squire, Warren E Rose, Heidi-Lynn Ploeg

Data Brief· October 2018

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Control of zeolite framework flexibility and pore topology for separation of ethane and ethylene.
Pablo J Bereciartua, Ángel Cantín, Avelino Corma, José L Jordá, Miguel Palomino, Adeana R Bishop

Science· November 2017

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Speed-of-light pulses in the massless nonlinear Dirac equation with a potential.
Niurka R Quintero, Franz G Mertens, Fred Cooper, Avadh Saxena, A R Bishop

Phys Rev E· November 2017

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Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.
Ludmil B Alexandrov, Kim Ø Rasmussen, Alan R Bishop, Boian S Alexandrov

Sci Rep· August 2017

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Variational approach to studying solitary waves in the nonlinear Schrödinger equation with complex potentials.
Franz G Mertens, Fred Cooper, Edward Arévalo, Avinash Khare, Avadh Saxena, A R Bishop

Phys Rev E· September 2016

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Dynamical playground of a higher-order cubic Ginzburg-Landau equation: From orbital connections and limit cycles to invariant tori and the onset of chaos.
V Achilleos, A R Bishop, S Diamantidis, D J Frantzeskakis, T P Horikis

Phys Rev E· July 2016

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Soliton dynamics in optical fibers using the generalized traveling-wave method.
Niurka R Quintero, Franz G Mertens, Anatoly Efimov, A R Bishop

Phys Rev E· April 2016

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The role of structural parameters in DNA cyclization.
Ludmil B Alexandrov, Alan R Bishop, Kim Ø Rasmussen, Boian S Alexandrov

BMC Bioinformatics· February 2016

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Possible Demonstration of a Polaronic Bose-Einstein(-Mott) Condensate in UO2(+x) by Ultrafast THz Spectroscopy and Microwave Dissipation.
Steven D Conradson, Steven M Gilbertson, Stephanie L Daifuku, Jeffrey A Kehl, Tomasz Durakiewicz, Alan R Bishop

Sci Rep· October 2015

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