DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors
Kabir, Anowarul, Bhattarai, Manish, Peterson, Selma, Najman-Licht, Yonatan, Rasmussen, Kim Ø, Shehu, Amarda, Bishop, Alan R, Alexandrov, Boian, Usheva, Anny
Published in Nucleic acids research (13.09.2024)
Published in Nucleic acids research (13.09.2024)
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Journal Article
Bubble Relaxation Dynamics in Homopolymer DNA Sequences
Hillebrand, Malcolm, Kalosakas, George, Bishop, Alan R, Skokos, Charalampos
Published in Molecules (Basel, Switzerland) (20.01.2023)
Published in Molecules (Basel, Switzerland) (20.01.2023)
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Journal Article
Metabolomics and the pig model reveal aberrant cardiac energy metabolism in metabolic syndrome
Karimi, Maryam, Petkova, Victoria, Asara, John M., Griffin, Michael J., Sellke, Frank W., Bishop, Alan R., Alexandrov, Boian S., Usheva, Anny
Published in Scientific reports (26.02.2020)
Published in Scientific reports (26.02.2020)
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Journal Article
Mammalian stem cells reprogramming in response to terahertz radiation
Bock, Jonathan, Fukuyo, Yayoi, Kang, Sona, Phipps, M Lisa, Alexandrov, Ludmil B, Rasmussen, Kim Ø, Bishop, Alan R, Rosen, Evan D, Martinez, Jennifer S, Chen, Hou-Tong, Rodriguez, George, Alexandrov, Boian S, Usheva, Anny
Published in PloS one (31.12.2010)
Published in PloS one (31.12.2010)
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Journal Article
Specificity and Heterogeneity of Terahertz Radiation Effect on Gene Expression in Mouse Mesenchymal Stem Cells
Alexandrov, Boian S., Phipps, M. Lisa, Alexandrov, Ludmil B., Booshehri, Layla G., Erat, Anna, Zabolotny, Janice, Mielke, Charles H., Chen, Hou-Tong, Rodriguez, George, Rasmussen, Kim Ø., Martinez, Jennifer S., Bishop, Alan R., Usheva, Anny
Published in Scientific reports (31.01.2013)
Published in Scientific reports (31.01.2013)
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Journal Article
Evolution of Charge-Lattice Dynamics across the Kuramoto Synchronization Phase Diagram of Quantum Tunneling Polarons in Cuprate Superconductors
Velasco, Victor, Silva Neto, Marcello B., Perali, Andrea, Wimberger, Sandro, Bishop, Alan R., Conradson, Steven D.
Published in Condensed matter (01.12.2021)
Published in Condensed matter (01.12.2021)
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Journal Article
Possible Demonstration of a Polaronic Bose-Einstein(-Mott) Condensate in UO2(+x) by Ultrafast THz Spectroscopy and Microwave Dissipation
Conradson, Steven D., Gilbertson, Steven M., Daifuku, Stephanie L., Kehl, Jeffrey A., Durakiewicz, Tomasz, Andersson, David A., Bishop, Alan R., Byler, Darrin D., Maldonado, Pablo, Oppeneer, Peter M., Valdez, James A., Neidig, Michael L., Rodriguez, George
Published in Scientific reports (16.10.2015)
Published in Scientific reports (16.10.2015)
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Journal Article
Non-thermal effects of terahertz radiation on gene expression in mouse stem cells
Alexandrov, Boian S, Rasmussen, Kim Ø, Bishop, Alan R, Usheva, Anny, Alexandrov, Ludmil B, Chong, Shou, Dagon, Yossi, Booshehri, Layla G, Mielke, Charles H, Phipps, M Lisa, Martinez, Jennifer S, Chen, Hou-Tong, Rodriguez, George
Published in Biomedical optics express (01.09.2011)
Published in Biomedical optics express (01.09.2011)
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Journal Article
Cross-polarized excitons in carbon nanotubes
Kilina, Svetlana, Tretiak, Sergei, Doorn, Stephen K, Luo, Zhengtang, Papadimitrakopoulos, Fotios, Piryatinski, Andrei, Saxena, Avadh, Bishop, Alan R
Published in Proceedings of the National Academy of Sciences - PNAS (13.05.2008)
Published in Proceedings of the National Academy of Sciences - PNAS (13.05.2008)
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Journal Article
Pre-melting dynamics of DNA and its relation to specific functions
Alexandrov, Boian, Voulgarakis, Nikolaos K, Rasmussen, Kim Ø, Usheva, Anny, Bishop, Alan R
Published in Journal of physics. Condensed matter (21.01.2009)
Published in Journal of physics. Condensed matter (21.01.2009)
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Journal Article
Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics
Nowak-Lovato, Kristy, Alexandrov, Ludmil B, Banisadr, Afsheen, Bauer, Amy L, Bishop, Alan R, Usheva, Anny, Mu, Fangping, Hong-Geller, Elizabeth, Rasmussen, Kim Ø, Hlavacek, William S, Alexandrov, Boian S
Published in PLoS computational biology (01.01.2013)
Published in PLoS computational biology (01.01.2013)
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Journal Article
Excitons and Peierls Distortion in Conjugated Carbon Nanotubes
Tretiak, Sergei, Kilina, Svetlana, Piryatinski, Andrei, Saxena, Avadh, Martin, Richard L, Bishop, Alan R
Published in Nano letters (01.01.2007)
Published in Nano letters (01.01.2007)
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Journal Article
Toward a detailed description of the thermally induced dynamics of the core promoter
Alexandrov, Boian S, Gelev, Vladimir, Yoo, Sang Wook, Bishop, Alan R, Rasmussen, Kim Ø, Usheva, Anny
Published in PLoS computational biology (01.03.2009)
Published in PLoS computational biology (01.03.2009)
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Journal Article
A nonlinear journey from structural phase transitions to quantum annealing
Thudiyangal, Mithun, Kevrekidis, Panayotis G, Saxena, Avadh, Bishop, Alan R
Published in Chaos (Woodbury, N.Y.) (01.05.2024)
Published in Chaos (Woodbury, N.Y.) (01.05.2024)
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Journal Article
Examining DNA breathing with pyDNA-EPBD
Kabir, Anowarul, Bhattarai, Manish, Rasmussen, Kim Ø, Shehu, Amarda, Usheva, Anny, Bishop, Alan R, Alexandrov, Boian
Published in Bioinformatics (Oxford, England) (01.11.2023)
Published in Bioinformatics (Oxford, England) (01.11.2023)
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Journal Article
DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases
Alexandrov, Boian S, Valtchinov, Vlad I, Alexandrov, Ludmil B, Gelev, Vladimir, Dagon, Yossi, Bock, Jonathan, Kohane, Isaac S, Rasmussen, Kim Ø, Bishop, Alan R, Usheva, Anny
Published in PloS one (20.05.2011)
Published in PloS one (20.05.2011)
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Journal Article
Correlation of strontium anharmonicity with charge-lattice dynamics of the apical oxygens and their coupling to cuprate superconductivity
Conradson, Steven D, Velasco, Victor, Silva Neto, Marcello B, Jin, Chang-Qing, Li, Wen-Min, Cao, Li-Peng, Gauzzi, Andrea, Karppinen, Maarit, Perali, Andrea, Wimberger, Sandro, Bishop, Alan R, Baldinozzi, Gianguido, Latimer, Matthew, Gilioli, Edmondo
Published in Superconductor science & technology (01.02.2024)
Published in Superconductor science & technology (01.02.2024)
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Journal Article
Numerical approaches to time evolution of complex quantum systems
Fehske, Holger, Schleede, Jens, Schubert, Gerald, Wellein, Gerhard, Filinov, Vladimir S., Bishop, Alan R.
Published in Physics letters. A (01.06.2009)
Published in Physics letters. A (01.06.2009)
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