B. Alexandrov

发表

Contaminant source identification using semi-supervised machine learning.

D. O'Malley, V. Vesselinov, B. Alexandrov, 2017, Journal of contaminant hydrology.

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Erik N. Bergstrom, Samuel W. Brady, M. Stratton, 2020, bioRxiv.

Nonnegative tensor factorization for contaminant source identification.

D. O'Malley, V. Vesselinov, B. Alexandrov, 2019, Journal of contaminant hydrology.

Blind source separation for groundwater pressure analysis based on nonnegative matrix factorization

Velimir V. Vesselinov, Boian S. Alexandrov, V. Vesselinov, 2014 .

Non-Negative Matrix Factorization for Selection of Near-Native Protein Tertiary Structures

Gopinath Chennupati, Hristo Djidjev, Nasrin Akhter, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Tucker-1 Boolean Tensor Factorization with Quantum Annealers

H. Djidjev, D. O'Malley, B. Alexandrov, 2020, 2020 International Conference on Rebooting Computing (ICRC).

Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization

Alan R Bishop, Boian S Alexandrov, L. Alexandrov, 2017, Scientific Reports.

Nonlinearity in DNA and its Relation to Specific Functions

A. Bishop, K. Rasmussen, B. Alexandrov, 2009, Journal of biological physics.

Pre-melting dynamics of DNA and its relation to specific functions

Boian Alexandrov, Alan R Bishop, A. Usheva, 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

The cardiac molecular setting of metabolic syndrome in pigs reveals disease susceptibility and suggests mechanisms that exacerbate COVID-19 outcomes in patients

F. Sellke, A. Usheva, M. Hiromura, 2021, Scientific Reports.

A nonlinear dynamic model of DNA with a sequence-dependent stacking term

L. Alexandrov, A. Usheva, A. Bishop, 2009, Nucleic acids research.

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

X. Hua, Jianxin Shi, K. Brown, 2018, Nature Communications.

From copy number alterations to structural variants: the evolutionary cascade of papillary renal cell carcinomas

X. Hua, Jianxin Shi, K. Brown, 2018, bioRxiv.

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

X. Hua, Jianxin Shi, K. Brown, 2018, Nature Communications.

DNA Dynamics Is Likely to Be a Factor in the Genomic Nucleotide Repeats Expansions Related to Diseases

Isaac S. Kohane, Alan R. Bishop, Ludmil B. Alexandrov, 2011, PloS one.

Profiling the thermodynamic softness of adenoviral promoters.

A. Smerzi, Jae suk Park, A. Usheva, 2008, Biophysical journal.

FedSPLIT: One-Shot Federated Recommendation System Based on Non-negative Joint Matrix Factorization and Knowledge Distillation

Luke E. Richards, Maksim E. Eren, Roberto Yus, 2022, ArXiv.

SeNMFk-SPLIT: Large Corpora Topic Modeling by Semantic Non-negative Matrix Factorization with Automatic Model Selection

Maksim E. Eren, B. Alexandrov, Charles Nicholas, 2022, ArXiv.

Patterns and Stability of Coupled Multi-Stable Nonlinear Oscillators

G. Bel, A. Bishop, B. Alexandrov, 2022, 2208.11748.

Process Modeling, Hidden Markov Models, and Non-negative Tensor Factorization with Model Selection

S. Eidenbenz, A. Hollis, B. Alexandrov, 2022, ArXiv.

Improved Protein Decoy Selection via Non-Negative Matrix Factorization

Kazi Lutful Kabir, H. Djidjev, Amarda Shehu, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Bubble statistics and dynamics in double-stranded DNA.

A. Bishop, K. Blagoev, L. Wille, 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions

M. Wall, N. Vesselinova, B. Alexandrov, 2016, bioRxiv.

Nonnegative/Binary matrix factorization with a D-Wave quantum annealer

Velimir V. Vesselinov, Ludmil B. Alexandrov, Boian S. Alexandrov, 2017, PloS one.

Determination of latent dimensionality in international trade flow

Duc P. Truong, B. Alexandrov, E. Skau, 2020, Mach. Learn. Sci. Technol..

Metabolomics and the pig model reveal aberrant cardiac energy metabolism in metabolic syndrome

J. Asara, F. Sellke, A. Usheva, 2020, Scientific Reports.

Distributed non-negative RESCAL with Automatic Model Selection for Exascale Data

James P. Smith, H. Djidjev, S. Rajopadhye, 2022, SSRN Electronic Journal.

Determination of the number of clusters by symmetric non-negative matrix factorization

Gopinath Chennupati, Raviteja Vangara, Boian S. Alexandrov, 2021, Defense + Commercial Sensing.

Automatic Model Determination for Quaternion NMF

Erik Skau, Boian Alexandrov, Giancarlo Sanchez, 2021, IEEE Access.

Finding the Number of Latent Topics With Semantic Non-Negative Matrix Factorization

Erik Skau, Gopinath Chennupati, Hristo Djidjev, 2021, IEEE Access.

Semantic Nonnegative Matrix Factorization with Automatic Model Determination for Topic Modeling

James P. Smith, H. Djidjev, B. Alexandrov, 2020, 2020 19th IEEE International Conference on Machine Learning and Applications (ICMLA).

Identification of Anomalous Diffusion Sources by Unsupervised Learning pdf

Raviteja Vangara, Boian S. Alexandrov, Dimiter N. Petsev, 2020, Physical Review Research.

Distributed non-negative matrix factorization with determination of the number of latent features

Erik Skau, Gopinath Chennupati, Boian Alexandrov, 2020, The Journal of Supercomputing.

Unsupervised Machine Learning for Analysis of Phase Separation in Ternary Lipid Mixture.

S. Gnanakaran, Cesar A. López, Cesar A. Löpez, 2019, Journal of chemical theory and computation.

Nonnegative tensor decomposition with custom clustering for microphase separation of block copolymers

Velimir V. Vesselinov, Boian S. Alexandrov, Valentin Stanev, 2019, Stat. Anal. Data Min..

Unsupervised Machine Learning for Analysis of Coexisting Lipid Phases and Domain Growth in Biological Membranes

Velimir V. Vesselinov, Sandrasegaram Gnanakaran, Boian S. Alexandrov, 2019, bioRxiv.

Unsupervised Machine Learning Based on Non-Negative Tensor Factorization for Analyzing Reactive-Mixing

Satish Karra, Maruti Kumar Mudunuru, Velimir V. Vesselinov, 2018, J. Comput. Phys..

Identification of release sources in advection–diffusion system by machine learning combined with Green’s function inverse method

Velimir V. Vesselinov, Boian S. Alexandrov, Valentin Stanev, 2018, Applied Mathematical Modelling.

Unsupervised phase mapping of X-ray diffraction data by nonnegative matrix factorization integrated with custom clustering

Ichiro Takeuchi, Velimir V. Vesselinov, Boian S. Alexandrov, 2018, npj Computational Materials.

Nonnegative Matrix Factorization for identification of unknown number of sources emitting delayed signals

Filip L Iliev, Valentin G Stanev, Velimir V Vesselinov, 2016, PloS one.

Machine learning approach for identification of release sources in advection-diffusion systems pdf

Velimir V. Vesselinov, Boian S. Alexandrov, Filip L. Iliev, 2016, ArXiv.

Sources identification using shifted non-negative matrix factorization combined with semi-supervised clustering

Filip L. Iliev, V. Vesselinov, B. Alexandrov, 2016, ArXiv.

DNA Breathing Dynamics in the Presence of a Terahertz Field.

A R Bishop, A. Usheva, A. Bishop, 2009, Physics letters. A.

Distributed out-of-memory NMF on CPU/GPU architectures

Maksim E. Eren, S. Eidenbenz, B. Alexandrov, 2022, The Journal of Supercomputing.

Robust effect of metabolic syndrome on major metabolic pathways in the myocardium

J. Asara, F. Sellke, A. Usheva, 2019, PloS one.

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells

A. Usheva, N. Horikoshi, Yayoi Fukuyo, 2012, Nucleic acids research.

Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing.

A. Bishop, K. Rasmussen, B. Alexandrov, 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics

Fangping Mu, William S. Hlavacek, Elizabeth Hong-Geller, 2013, PLoS Comput. Biol..

A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder.

Jianxin Shi, Pablo V Gejman, Jubao Duan, 2014, American journal of human genetics.

Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization

L. Alexandrov, A. Bishop, K. Rasmussen, 2017, Scientific Reports.

The role of structural parameters in DNA cyclization

Ludmil B. Alexandrov, Boian S. Alexandrov, Kim Ø. Rasmussen, 2016, BMC Bioinformatics.

Protein-DNA binding and breathing dynamics of DNA

A. Usheva, A. Bishop, K. Rasmussen, 2013 .

76 Protein–DNA binding and breathing dynamics of DNA

A. Usheva, A. Bishop, K. Rasmussen, 2013 .

Specificity and Heterogeneity of Terahertz Radiation Effect on Gene Expression in Mouse Mesenchymal Stem Cells

Alan R. Bishop, Ludmil B. Alexandrov, M. Lisa Phipps, 2013, Scientific Reports.

Non-thermal effects of terahertz radiation on gene expression in mouse stem cells

Alan R. Bishop, Ludmil B. Alexandrov, M. Lisa Phipps, 2011, Biomedical optics express.

Mammalian Stem Cells Reprogramming in Response to Terahertz Radiation

Alan R. Bishop, Ludmil B. Alexandrov, M. Lisa Phipps, 2010, PloS one.

One-Shot Federated Group Collaborative Filtering

Luke E. Richards, Roberto Yus, B. Alexandrov, 2022, 2022 21st IEEE International Conference on Machine Learning and Applications (ICMLA).

General-purpose Unsupervised Cyber Anomaly Detection via Non-negative Tensor Factorization

Juston S. Moore, B. Alexandrov, E. Skau, 2022, Digital Threats: Research and Practice.

Entropy–Driven Conformations Controlling DNA Functions

Alan R. Bishop, Boian S. Alexandrov, Kim Ø. Rasmussen, 2012 .

DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation

Alan R. Bishop, Ludmil B. Alexandrov, Sang Wook Yoo, 2009, Nucleic acids research.

Ultra-violet light induced changes in DNA dynamics may enhance TT-dimer recognition.

A. Bishop, K. Blagoev, B. Alexandrov, 2006, DNA repair.

Feigenbaum cascade of discrete breathers in a model of DNA.

A. Bishop, P. Maniadis, K. Rasmussen, 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

Nonnegative canonical tensor decomposition with linear constraints: nnCANDELINC

G. Manzini, B. Alexandrov, Derek DeSantis, 2019, Numer. Linear Algebra Appl..

Nonnegative Canonical Polyadic Decomposition with Rank Deficient Factors pdf

Erik Skau, Gianmarco Manzini, Boian Alexandrov, 2019, ArXiv.

Quantum annealing algorithms for Boolean tensor networks

H. Djidjev, Georg Hahn, B. Alexandrov, 2021, Scientific Reports.

Boolean Hierarchical Tucker Networks on Quantum Annealers pdf

Georg Hahn, Boian S. Alexandrov, Daniel O'Malley, 2021, LSSC.

Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter

Sang Wook Yoo, Boian S. Alexandrov, Kim Ø. Rasmussen, 2009, PLoS Comput. Biol..

Factorization of Binary Matrices: Rank Relations, Uniqueness and Model Selection of Boolean Decomposition

Duc P. Truong, B. Alexandrov, Derek DeSantis, 2020, ACM Trans. Knowl. Discov. Data.

Boolean Matrix Factorization via Nonnegative Auxiliary Optimization

Erik Skau, Boian Alexandrov, Duc P. Truong, 2021, IEEE Access.

Factorizations of Binary Matrices - Rank Relations and the Uniqueness of Boolean Decompositions pdf

Erik Skau, Boian Alexandrov, Derek DeSantis, 2020, ArXiv.

Increased irrigation water salinity enhances nitrate transport to deep unsaturated soil

G. Bel, U. Yermiyahu, O. Dahan, 2020, Vadose Zone Journal.

Metabolomics and the pig model reveal aberrant cardiac energy metabolism in metabolic syndrome

J. Asara, F. Sellke, A. Usheva, 2020, Scientific Reports.

Challenging the Curse of Dimensionality in Multidimensional Numerical Integration by Using a Low-Rank Tensor-Train Format

G. Manzini, B. Alexandrov, E. Skau, 2023, Mathematics.

Robust accidental nodes and zeros and critical quasiparticle scaling in iron-based multiband superconductors.

B. Alexandrov, V. Stanev, P. Nikolić, 2010, 1006.0447.

Distributed Non-Negative Tensor Train Decomposition

Erik Skau, Gopinath Chennupati, Boian Alexandrov, 2020, 2020 IEEE High Performance Extreme Computing Conference (HPEC).

Impaired cardiac glycolysis and glycogen depletion are linked to poor myocardial outcomes in juvenile male swine with metabolic syndrome and ischemia

A. Usheva, B. Alexandrov, F. Selke, 2023, Physiological reports.

Coarse-grain cluster analysis of tensors with application to climate biome identification pdf

Boian Alexandrov, Phillip J. Wolfram, Derek DeSantis, 2020, Mach. Learn. Sci. Technol..

Decoy Selection in Protein Structure Determination via Symmetric Non-negative Matrix Factorization

Gopinath Chennupati, Hristo Djidjev, Amarda Shehu, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia

A. McRae, M. Gill, A. Corvin, 2012, Molecular Psychiatry.

Examining DNA Breathing with pyDNA-EPBD

Amarda Shehu, B. Alexandrov, Anowarul Kabir, 2023, bioRxiv.

New Insights into Protein-DNA Binding from Simulations of DNA Breathing Dynamics

L. Alexandrov, A. Bauer, Fangping Mu, 2013 .

Interactive Distillation of Large Single-Topic Corpora of Scientific Papers

B. Alexandrov, Manish Bhattarai, N. Solovyev, 2023, ArXiv.

Nonnegative Matrix Factorization for identification of unknown number of sources emitting delayed signals

Filip L. Iliev, V. Vesselinov, B. Alexandrov, 2016, PloS one.

Non-negative Tensor Factorization for Robust Exploratory Big-Data Analytics

Hristo Djidjev, Velimir V. Vesselinov, Boian S. Alexandrov, 2018 .

Tensor Networks for Solving Realistic Time-independent Boltzmann Neutron Transport Equation

Duc P. Truong, G. Manzini, B. Alexandrov, 2023, ArXiv.

The tensor-train mimetic finite difference method for three-dimensional Maxwell's wave propagation equations

G. Manzini, B. Alexandrov, Radoslav G. Vuchkov, 2023, Math. Comput. Simul..

Double-period breathers in a driven and damped lattice

G. Bel, A. Bishop, K. Rasmussen, 2018, Physical Review E.

Robust Adversarial Defense by Tensor Factorization

B. Alexandrov, Manish Bhattarai, Ryan Barron, 2023, 2023 International Conference on Machine Learning and Applications (ICMLA).

A neural network for determination of latent dimensionality in non-negative matrix factorization pdf

Raviteja Vangara, Boian S. Alexandrov, Benjamin T. Nebgen, 2020, Machine Learning: Science and Technology.

Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention

Amarda Shehu, B. Alexandrov, Anowarul Kabir, 2024, bioRxiv.

Conotoxin Prediction: New Features to Increase Prediction Accuracy

Duc P. Truong, Hau B. Nguyen, P. Fenimore, 2023, Toxins.

Specificity and tunability of efflux pumps: a new role for the proton gradient?

D. Segal, B. Alexandrov, Duncan Kirby, 2024, bioRxiv.