Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter. - Boian S. Alexandrov; Vladimir Gelev; Sang Wook Yoo; Alan R. Bishop; Kim Ø. Rasmussen; Anny Usheva (PLoS Comput. Biol., 2009)

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics. - Kristy Nowak-Lovato; Ludmil B. Alexandrov; Afsheen Banisadr; Amy L. Bauer; Alan R. Bishop; Anny Usheva; Fangping Mu; Elizabeth Hong-Geller; Kim Ø. Rasmussen; William S. Hlavacek; Boian S. Alexandrov (PLoS Comput. Biol., 2013)

The role of structural parameters in DNA cyclization. - Ludmil B. Alexandrov; Alan R. Bishop; Kim Ø. Rasmussen; Boian S. Alexandrov (BMC Bioinform., 2016)

Nonnegative tensor decomposition with custom clustering for microphase separation of block copolymers. - Boian S. Alexandrov; Valentin G. Stanev; Velimir V. Vesselinov; Kim Ø. Rasmussen (Stat. Anal. Data Min., 2019)

Identification of Anomalous Diffusion Sources by Unsupervised Learning. - Raviteja Vangara; Kim Ø. Rasmussen; Dimiter N. Petsev; Golan Bel; Boian S. Alexandrov (CoRR, 2020)

SeNMFk-SPLIT: large corpora topic modeling by semantic non-negative matrix factorization with automatic model selection. - Maksim Ekin Eren; Nick Solovyev 001; Manish Bhattarai; Kim Ø. Rasmussen; Charles Nicholas; Boian S. Alexandrov (DocEng, 2022)

Process Modeling, Hidden Markov Models, and Non-negative Tensor Factorization with Model Selection. - Erik Skau; Andrew Hollis; Stephan J. Eidenbenz; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2022)

Robust Adversarial Defense by Tensor Factorization. - Manish Bhattarai; Mehmet Cagri Kaymak; Ryan Barron; Ben Nebgen; Kim Ø. Rasmussen; Boian S. Alexandrov (ICMLA, 2023)

Interactive Distillation of Large Single-Topic Corpora of Scientific Papers. - Nicholas Solovyev 001; Ryan Barron; Manish Bhattarai; Maksim Ekin Eren; Kim Ø. Rasmussen; Boian S. Alexandrov (ICMLA, 2023)

MalwareDNA: Simultaneous Classification of Malware, Malware Families, and Novel Malware. - Maksim Ekin Eren; Manish Bhattarai; Kim Ø. Rasmussen; Boian S. Alexandrov; Charles Nicholas (ISI, 2023)

Tensor Networks for Solving Realistic Time-independent Boltzmann Neutron Transport Equation. - Duc P. Truong; Mario I. Ortega; Ismael Boureima; Gianmarco Manzini; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2023)

Examining DNA breathing with pyDNA-EPBD. - Anowarul Kabir; Manish Bhattarai; Kim Ø. Rasmussen; Amarda Shehu; Anny Usheva; Alan R. Bishop; Boian S. Alexandrov (Bioinform., 2023)

TopicTag: Automatic Annotation of NMF Topic Models Using Chain of Thought and Prompt Tuning with LLMs. - Selma Wanna; Nicholas Solovyev 001; Ryan Barron; Maksim Ekin Eren; Manish Bhattarai; Kim Ø. Rasmussen; Boian S. Alexandrov (DocEng, 2024)

Domain-Specific Retrieval-Augmented Generation Using Vector Stores, Knowledge Graphs, and Tensor Factorization. - Ryan Barron; Ves Grantcharov; Selma Wanna; Maksim Ekin Eren; Manish Bhattarai; Nicholas Solovyev 001; George Tompkins; Charles Nicholas; Kim Ø. Rasmussen; Cynthia Matuszek; Boian S. Alexandrov (ICMLA, 2024)

Cyber-Security Knowledge Graph Generation by Hierarchical Nonnegative Matrix Factorization. - Ryan Barron; Maksim Ekin Eren; Manish Bhattarai; Selma Wanna; Nick Solovyev 001; Kim Ø. Rasmussen; Boian S. Alexandrov; Charles Nicholas; Cynthia Matuszek (ISDFS, 2024)

Catch'em all: Classification of Rare, Prominent, and Novel Malware Families. - Maksim Ekin Eren; Ryan Barron; Manish Bhattarai; Selma Wanna; Nicholas Solovyev 001; Kim Ø. Rasmussen; Boian S. Alexandrov; Charles Nicholas (ISDFS, 2024)

Tensor Network Space-Time Spectral Collocation Method for Time Dependent Convection-Diffusion-Reaction Equations. - Dibyendu Adak; Duc P. Truong; Gianmarco Manzini; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2024)

High-order Tensor-Train Finite Volume Method for Shallow Water Equations. - Mustafa Engin Danis; Duc P. Truong; Derek DeSantis; Mark Petersen; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2024)

LaFA: Latent Feature Attacks on Non-negative Matrix Factorization. - Minh N. Vu; Ben Nebgen; Erik Skau; Geigh Zollicoffer; Juan Castorena; Kim Ø. Rasmussen; Boian S. Alexandrov; Manish Bhattarai (CoRR, 2024)

Space-Time Spectral Element Tensor Network Approach for Time Dependent Convection Diffusion Reaction Equation with Variable Coefficients. - Dibyendu Adak; Duc P. Truong; Radoslav G. Vuchkov; Saibal De; Derek DeSantis; Nathan V. Roberts; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2024)

HEAL: Hierarchical Embedding Alignment Loss for Improved Retrieval and Representation Learning. - Manish Bhattarai; Ryan Barron; Maksim Ekin Eren; Minh Vu; Ves Grantcharov; Ismael Boureima; Valentin G. Stanev; Cynthia Matuszek; Vladimir I. Valtchinov; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2024)

Tensor networks for solving the time-independent Boltzmann neutron transport equation. - Duc P. Truong; Mario I. Ortega; Ismael Boureima; Gianmarco Manzini; Kim Ø. Rasmussen; Boian S. Alexandrov (J. Comput. Phys., 2024)

Generating Hidden Markov Models from Process Models Through Nonnegative Tensor Factorization. - Erik Skau; Andrew Hollis; Stephan J. Eidenbenz; Kim Ø. Rasmussen; Boian S. Alexandrov (ACM Trans. Model. Comput. Simul., 2024)

Tensor-train WENO scheme for compressible flows. - Mustafa Engin Danis; Duc P. Truong; Ismael Boureima; Oleg Korobkin; Kim Ø. Rasmussen; Boian S. Alexandrov (J. Comput. Phys., 2025)

Tensor Network Space-Time Spectral Collocation Method for Solving the Nonlinear Convection Diffusion Equation. - Dibyendu Adak; Mustafa Engin Danis; Duc P. Truong; Kim Ø. Rasmussen; Boian S. Alexandrov (J. Sci. Comput., 2025)