(DoD) U. S. Army Research Laboratory and Office, Grant number W911NF-13-1-0148, to K.R. (3-year non-renewable grant, at City College of NY)

“Conformational sensing by a mammalian olfactory receptor,” M.T. Liu, M. Na, Y. Li, M. Biscoe, and K. Ryan*, Chemistry-A European Journal, 2020, Vol. 26(50), pp 11345-11655 (September 4, 2020 issue) https://doi.org/10.1002/chem.202001390 or https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202003590

Single-neuron comparison of the olfactory receptor response to deuterated and non-deuterated odorants, Mihwa Na, Min Ting Liu, Minh Q. Nguyen and Kevin Ryan*, ACS Chemical Neuroscience. 2019, 10, 1, 552-562 DOI: 10.1021/acschemneuro.8b00416 https://pubs.acs.org/doi/10.1021/acschemneuro.8b00416

“Carbon chain shape selectivity by the mouse olfactory receptor OR-I7,” Min Ting Liu,Jianghai Ho, Jason Liu, Radhanath Purakait, Uriel N. Morzan, Lucky Ahmed, Victor S. Batista, Hiroaki Matsunami,* and Kevin Ryan,* Organic and Biomolecular Chemistry, 2018, 16, 2541-2548. PMCID: PMC6067823. https://doi.org/10.1039/C8OB00205C

Aldehyde Recognition and Discrimination by Mammalian Odorant Receptors via Functional Group-Specific Hydration Chemistry, Li Y, Peterlin Z, Ho J, Yarnitzky T, Liu MT, Fichman M, Niv MY, Matsunami H, Firestein S,* Ryan K.* ACS Chemical Biology. (2014) Vol. 9 (11): 2563-71; PMID: 25181321; PMCID: PMC4245160. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245160/

(NIH) NIGMS, Grant number 5SC1GM083754, to K.R. (3-year non-renewable grant, at City College of NY)

  • Starting and Stopping RNA Polymerase III Transcription on Single-stranded DNA Oligonucleotides Lama, L. and Ryan, K.* RNA. Oct 2022; 28 (10) (epub July 2022). doi:10.1261/rna.078981.121

Small RNA-seq: The RNA 5’ end ligation problem and a method to circumvent it,” L. Lama, J. Cobo, D. Buenaventura and K. Ryan,* Journal of Biological Methods 2019, Vol. 6(1) e108,  DOI: 10.14440/jbm.2019.269. https://doi.org/10.14440/jbm.2019.269

“Optimizing In Vitro Pre-mRNA 3′ Cleavage Efficiency: Reconstitution from Anion-Exchange Separated HeLa Cleavage Factors and from Adherent HeLa Cell Nuclear Extract,” Na, M., Valente, S. and Ryan, K.*Methods in Molecular Biology (2017) Eukaryotic Transcription and Post-Transcription Gene Expression Regulation Vol. 1507, Chapter 14 (Springer Publishing ISBN 978-1-4939-6516-8) November 2016 https://link.springer.com/protocol/10.1007%2F978-1-4939-6518-2_14

“RNA polymerase III initiation on coligo DNA templates containing loops of variable sequence, size and nucleotide chemistry,” Joy Patel, Lodoe Lama, Niklas Hoffmann, Jose Cobo, Christoph Müller and Kevin Ryan,* Gene (2016) 612:49-54 Epub September 2, 2016, DOI: https://doi.org/10.1016/j.gene.2016.09.001 https://pubmed.ncbi.nlm.nih.gov/27593562/

“An investigation into the role of ATP in the mammalian pre-mRNA 3’ cleavage reaction,” Khleborodova, A., Nagre, N., Pan, X., and Ryan, K.* Biochimie 2016 (April 6) 125: 213-222. PMID 27060432; PMCID not yet available. DOI: 10.1016/j.biochi.2016.04.004 OR https://pubmed.ncbi.nlm.nih.gov/27060432/

“Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I,” Lodoe Lama and Kevin Ryan,* RNA 2016 Jan; 22(1):155-61. DOI: 10.1261/rna.054999.115. Epub 2015 Nov 13. PMID: 26567315; PMCID: PMC4691829 https://pubmed.ncbi.nlm.nih.gov/26567315/

“New insights into the promoterless transcription of DNA coligo templates by RNA polymerase III,” Lodoe Lama, Christine I. Seidl and Kevin Ryan,* 2014 Transcription, Vol. 5, Issue 2. Published online 27 January 2014; http://dx.doi.org/10.4161/trns.27913; PMID: 24531370 OR https://pubmed.ncbi.nlm.nih.gov/25764216/

“Analysis of RNA processing reactions using cell free systems: 3′ end cleavage of pre-mRNA substrates in vitro,” Joseph Jablonski, Mark Clementz, Kevin Ryan and Susana T. Valente,* J Vis Exp. (JoVE), 2014 May 3, (87). doi: 10.3791/51309. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030693/

“Structurally diverse low molecular weight activators of the mammalian pre-mRNA 3’ cleavage reaction,” Min Ting Liu, Nagaraja N. Nagre, and Kevin Ryan,* Bioorganic and Medicinal Chemistry 2013 Jan 15; 22(2):834-41. doi: 10.1016/j.bmc.2013.12.006. Published online 2013 Dec. 15. PMID: 24373842 https://doi.org/10.1016/j.bmc.2013.12.006

(NIH) NIGMS grant R21GM073944 to K.R. (2-year non-renewable grant at City College of NY)

“Circularized synthetic oligodeoxynucleotides serve as promoterless RNA polymerase III templates for small RNA generation in human cells,” C.I. Seidl, L. Lama and K. Ryan*, 2012 Nucleic Acids Research 2013 41 (4): 2552-2564. doi: 10.1093/nar/gks1334 First published online: December 28, 2012. PMCID: PMC3575851 https://pubmed.ncbi.nlm.nih.gov/23275570/

“Circular Single-Stranded Synthetic DNA Delivery Vectors for microRNA,” C. Seidl and K. Ryan*, PLoS One, Feb. 2011 6(2): e16925. doi:10.1371/journal.pone.0016925. PMCID: PMC3040211 https://pubmed.ncbi.nlm.nih.gov/21359172/

“Small-molecule activators of pre-mRNA 3’ cleavage,” Kevin Ryan*, Asya Khleborodova, Jingyi Pan, and Xiaozhou P. Ryan RNA, 2009 15, 3, 483-492. PMCID: PMC2657006 https://pubmed.ncbi.nlm.nih.gov/19155323/

“Finishing Touches: Post-Translational Modification of Protein Factors Involved in Mammalian pre-mRNA 3’ End Formation,” Kevin Ryan* and David L.V. Bauer, Int. J. Biochem. & Cell Bio. 2008 40, 11,2384-2396. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2548416/

(NIH) Ruth L. Kirschstein National Research Service Award Fellowship, to K.R. (2-year non-renewable grant, as post-doc, Columbia University)

“Requirements of the RNA Polymerase II C-Terminal Domain for Reconstituting pre-mRNA Cleavage,” Kevin Ryan, Kanneganti G.K. Murthy, Syuzo Kaneko and James L. Manley*, Molecular and Cellular Biology, 2002, 22, 6, 1684-1692. https://pubmed.ncbi.nlm.nih.gov/11865048/

“Phosphorylation of CPEB by Eg2 Mediates the Recruitment of CPSF into an Active Cytoplasmic Polyadenylation Complex,” Raul Mendez, Kanneganti G.K. Murthy, Kevin Ryan, James L. Manley and Joel D. Richter,* Molecular Cell, 2000, Nov; 6(5):1253-9. https://pubmed.ncbi.nlm.nih.gov/11106762/

“A Synthetic Receptor Motif Designed for Extended Peptide Conformations” Kevin Ryan, Leland Gershell, and W. Clark Still,* Tetrahedron, 2000, 21, 3309-3318. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557054/

“Inhibition of Gene Expression in Human Cells Through Small Molecule-RNA Interactions” Seongwoo Hwang, Natarajan Tamilarasu, Kevin Ryan, Ikramul Huq, W. Clark Still, and Tariq M. Rana,* Proceedings of the National Academy of Sciences, USA, 1999, 96, 23, 12997-13002. https://doi.org/10.1073/pnas.96.23.12997

“Construction of Sequence-Selective Peptide Receptors from Conformationally Restricted Eta– and Theta– Amino Acids,” Kevin Ryan and W. Clark Still,* Bioorganic and Medicinal Chemistry Letters, 1999, 9, 2673-2678. https://pubmed.ncbi.nlm.nih.gov/10509914/