• 6,291,743 - Transgenic plants expressing mutant geminivirus AC1 or C1 genes, granted Sep 2001.
• 5,869,287 - Method of producing particles containing nucleic acid sequences in yeast, granted Feb 1999.
• 5,846,795 - RNA transformation vector, granted Dec 1998.
• 5,804,439 - Plasmid encoding hybrid RNA virus, granted Sep 1998.

• "Systematic Identification of Novel, Essential Host Genes Affecting Bromovirus RNA Replication"

Gancarz BL, Hao LH, He QL, PLoS One 6(8): e23988 Aug 2011. To systematically identify novel, essential host genes affecting BMV RNA replication, we tested a collection of similar to 900 yeast strains.

• "Organelle-like membrane compartmentalization of positive-strand RNA virus replication factories"

den Boon JA, Ahlquist P, Annual Review of Microbiology 13 (64): 241-256 Oct 2010.  Understanding of these complexes is growing, providing substantial new insights into the organization, coordination, and potential control of crucial processes in virus replication.  PubMed/NLM.

• "Cytoplasmic viral replication complexes"

den Boon JA, Diaz A, Ahlquist P, Cell Host & Microbe 8 (1): 77-85 Jul 2010.  The structure, function, and assembly of some positive-strand RNA virus replication complexes have parallels and potential evolutionary links with the replicative cores of double-strand RNA virus and retrovirus virions and more general similarities with the replication factories of cytoplasmic DNA viruses.  PubMed/NLM.

• "Statistical use of argonaute expression and RISC assembly in microRNA target identification"

Stanhope SA, Sengupta S, den Boon J, et al., PLoS Comput Biol 5 (9): e1000516 Sep 2009. We demonstrate that regression models accommodating RISC abundance and controlling for other mediating factors fit the expression profiles of known target pairs substantially better than models based on m/miRNA expressions alone, and lead to verifications of computational target pair predictions that are more sensitive than those based on marginal expression levels. Pubmed/NLM.

• National Cancer Institute, NIH, Bethesda
• National Center for Microscopy and Imaging Research, University of California - San Diego
• McArdle Laboratory for Cancer Research