NUPACK: Computational Nucleic Acid Analysis and Design

Authors: Fornace, Mark E.^{aff1, aff2, aff3}, Huang, Jining^aff1, Newman, Cody T.^aff1, Nanjundiah, Avinash^aff1, Porubsky, Nicholas J.^aff2, Pierce, Marshall B.^aff5, Pierce, Niles A.^{aff1, aff4}

Source: ACS Synthetic Biology. 15(4):1426-1441

Availability: https://pubs.acs.org/doi/10.1021/acssynbio.5c00817

Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems

Authors: Nanjundiah, Avinash^aff1, Fornace, Mark E.^{aff1, aff2}, Schulte, Samuel J.^aff1, Pierce, Niles A.^{aff1, aff3}

Source: ACS Synthetic Biology. 15(1):74-87

Availability: https://pubs.acs.org/doi/10.1021/acssynbio.5c00470

A Unified Dynamic Programming Framework for the Analysis of Interacting Nucleic Acid Strands: Enhanced Models, Scalability, and Speed

Authors: Fornace, Mark E.^aff1, Porubsky, Nicholas J.^aff1, Pierce, Niles A.^{aff2, aff3, aff4}

Source: ACS Synthetic Biology. 9(10):2665-2678

Availability: https://pubs.acs.org/doi/10.1021/acssynbio.9b00523

Molecular feature and therapeutic perspectives of immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome

Authors: Huang, Qianru, Liu, Xu, Zhang, Yujia, Huang, Jingyao, Li, Dan ^∗, Li, Bin ^∗

Source: In Journal of Genetics and Genomics 20 January 2020 47(1):17-26

Applications of dynamic nucleic acid nanotechnology in closed-loop genetic circuits and detection of viral pathogens

Authors: Huang, Jining

Subject Terms: concentration, analysis, design, synthetic genetic circuits, Bioengineering, dynamic RNA nanotechnology, genetic feedback circuits, complex ensemble, test tube ensemble, equilibrium, multi-tube ensemble, SARS-CoV-2 RNA genome, hybridization chain reaction (HCR), rapid antigen test, reaction pathway engineering, hybridization, base-pairing, ensemble defect, secondary structure, lateral flow assay, DNA, small conditional RNAs, 3. Good health, CRISPR, RNA, synthetic biology