A New Class of Cellular Automata. - Hosna Jabbari; Jon C. Muzio; Lin Sun (DSD, 2007)

HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding. - Hosna Jabbari; Anne Condon; Ana Pop; Cristina Pop 004; Yinglei Zhao (WABI, 2007)

Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding. - Hosna Jabbari; Anne Condon; Shelly Zhao (J. Comput. Biol., 2008)

An O(n5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids. - Ho-Lin Chen; Anne Condon; Hosna Jabbari (J. Comput. Biol., 2009)

Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges. - Anne Condon; Hosna Jabbari (Theor. Comput. Sci., 2009)

A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures. - Hosna Jabbari; Anne Condon (BMC Bioinform., 2014)

Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction. - Sebastian Will; Hosna Jabbari (WABI, 2015)

Sparse RNA folding revisited: space-efficient minimum free energy structure prediction. - Sebastian Will; Hosna Jabbari (Algorithms Mol. Biol., 2016)

Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice. - Hosna Jabbari; Ian Wark; Carlo Montemagno; Sebastian Will (WABI, 2017)

Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. - Hosna Jabbari; Ian Wark; Carlo Montemagno; Sebastian Will (Bioinform., 2018)

Viz23: web server for visualization of gene expression and locational information. - Luke Trinity; Andrew Hollar; Haley Greenyer; Hosna Jabbari; Ulrike Stege (CASCON, 2021)

Identification of conserved and evolving RNA secondary structures in SARS-CoV-2 and related viruses. - Alison Ziesel; Hosna Jabbari (CASCON, 2021)

In silico prediction of COVID-19 test efficiency with DinoKnot. - Tara Newman; Hiu Fung Kevin Chang; Hosna Jabbari (ICHI, 2021)

SARS-CoV-2 Ribosomal Frameshifting Pseudoknot: Detection of Inter-viral Structural Similarity. - Luke Trinity; Lance Lansing; Hosna Jabbari; Ulrike Stege (ICHI, 2021)

A QUBO model of the RNA folding problem optimized by variational hybrid quantum annealing. - Tristan Zaborniak; Juan Giraldo; Hausi A. Müller; Hosna Jabbari; Ulrike Stege (QCE, 2022)

KnotAli: informed energy minimization through the use of evolutionary information. - Mateo Gray; Sean Chester; Hosna Jabbari (BMC Bioinform., 2022)

Supervised promoter recognition: a benchmark framework. - Raul I. Perez Martell; Alison Ziesel; Hosna Jabbari; Ulrike Stege (BMC Bioinform., 2022)

AI-powered aptamer generation. - Majid Khabbazian; Hosna Jabbari (Nat. Comput. Sci., 2022)

SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles. - Mateo Gray; Sebastian Will; Hosna Jabbari (WABI, 2023)

Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot. - Luke Trinity; Ian Wark; Lance Lansing; Hosna Jabbari; Ulrike Stege (PLoS Comput. Biol., 2023)

Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot. - Luke Trinity; Ulrike Stege; Hosna Jabbari (PLoS Comput. Biol., 2024)

DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots. - Tara Newman; Hiu Fung Kevin Chang; Hosna Jabbari (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration. - Mateo Gray; Sebastian Will; Hosna Jabbari (Algorithms Mol. Biol., 2024)

Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. - Mateo Gray; Sebastian Will; Hosna Jabbari (WABI, 2025)