| Year |
Publication |
| 2021 |
2021 Sun, Y., Patel, A., SantaLucia, J., Jr., Roberts, E., Zhao, L.L., Kaye, K., Rao, K., and Bachman, M.A. “Measurement of Klebsiella Intestinal Colonization Density To Assess Infection Risk,” Mpshere 6, e00500-21 (2021). |
| 2021 |
2021 Rao, K., Patel, A.R., Seekatz, A.M., Bassis, C.M., Sun, Y., Henig, O., Albin, O.R., SantaLucia, J., Jr., Woods, R., and Bachman, M.A. “Gut microbiome features are associated with sepsis onset and outcomes,” bioRxiv (2021) doi: https://doi.org/10.1101/2021.01.08.426011. |
| 2020 |
2020 SantaLucia, J., Jr., Sozhamannan, S., Gans, J.D., Koehler, J.W., Soong, R., Lin, N.J., Xie, G., Olson, V. Roth, K., Beck, L.S. “Recommendations for Developing Molecular Assays for Microbial Pathogen Detection Using Modern In Silico Approaches,” J. AOAC Int., 103, 882-899 (2020). |
| 2019 |
David M. Mauger , B. Joseph Cabral, Vladimir Presnyak , Stephen V. Su, David W. Reid , Brooke Goodman , Kristian Link , Nikhil Khatwani, John Reynders, Melissa J. Moore, and Iain J. McFadyen, “mRNA structure regulates protein expression through changes in functional half-life,” PNAS, 24075–24083 |
| 2019 |
Hoshika, S., Leal, N.A., Kim, M.-J., Karalkar, N.B., Kim, M.-S., Bates, A.M., Watkins, N.E., Jr., SantaLucia, H.A., Meyer, A.J., DasGupta, S., Piccirilli, J.A., Ellington, A.D., SantaLucia, J., Jr., Georgiadis, M.M., Benner, S.A. “Hachimoji DNA and RNA: A Genetic System with Eight Building Blocks,” Science, 363, 884-887 (2019). |
| 2018 |
Arjang Hassibi, Arun Manickam, Rituraj Singh, Sara Bolouki, Ruma Sinha, Kshama B Jirage, Mark W McDermott, Babak Hassibi, Haris Vikalo, Gelareh Mazarei, Lei Pei, Luc Bousse, Mark Miller, Mehrdad Heshami, Michael P Savage, Michael T Taylor, Nader Gamini, Nicholas Wood, Pallavi Mantina, Patrick Grogan, Peter Kuimelis, Piyush Savalia, Scott Conradson, Yuan Li, Rich B Meyer, Edmond Ku, Jessica Ebert, Benjamin A Pinsky, Gregory Dolganov, Tran Van, Kirsten A Johnson, Pejman Naraghi-Arani, Robert G Kuimelis & Gary Schoolnik , “Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip,” Nature Biotechnology |
| 2018 |
SantaLucia, J., Jr., “How Much Free Energy is Absorbed Upon Breaking DNA Base Pairs?”, Physics of Life Reviews, (2018) https://doi.org/10.1016/j.plrev.2018.03.008 |
| 2017 |
“RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme,” Miao, Z. et al. RNA, 23, 655-672 (2017). |
| 2014 |
Zemtsova, G. E., Watkins, N. E. Jr.and Levin, M.L. “Multiplex qPCR assay for identification and differentiation of Amblyomma americanum, Amblyomma cajennense, and Amblyomma maculatum (Ixodida:Ixodidae) tick species in the Eastern United States”, J. Med. Entomol., 2014, 51(4), 795-803. PMID: 25118411 |
| 2014 |
Madani, TA, Azhar El, Abuelzein el-TM, Kao M, Al-Bar HM, Farraj, SA, Masri BE, Al-Kaiedi NA, Shakil S, Sohrab, SS, SantaLucia, J. Jr. and Ksiazek TG “Complete genome sequencing and genetic characterization of Alkhumra Hemorrhagic Fever virus isolated from Najron, Saudi Arabia”, Intervirology, 2014, 57(5), 300-310. PMID: 25096447. |
| 2013 |
Jiang, J., Aduri, R., Chow, C.S. and SantaLucia, J. Jr. “Structure modulation of helix 69 from Escherichia Coli 23S ribosomal RNA by pseudouridylations”, Nucleic Acids Research, 2013, 1-11. PMID: 24371282. |
| 2012 |
Sumitaa, M., Jiang, J., SantaLucia, J., Jr., and Chow, C.S. “Comparison of Solution Conformations and Stabilities of Modified Helix 69 rRNA Analogues from Bacteria and Human”, Biopolymers, 97, 94-106. |
| 2012 |
Cruz, J.A., Blanchet, M.-F., et al. (2012) “RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure”, Biopolymers, RNA 18, 610-625. |
| 2012 |
Rothe, J., Watkins, N.E., Jr, Nagy, M. (2012) “New Prediction Model for Probe Specificity in an Allele-Specific Extension Reaction for Haplotype-Specific Extraction (HSE) of Y Chromosome Mixtures”, PLOS ONE, 7(9), e45955. |
| 2011 |
Zazantsev, A.V., Rambo, R.P., Karimpour, S. SantaLucia, J., Jr., Tainer, J.A., and Pace, N.R.(2011) “Solution structure of RNase P RNA”, RNA, 17, 1159-1171. |
| 2011 |
Sijenyi, F., Saro, P., Ouyang, Z., Damm-Ganamet, K., Wood, M., Jiang, J., and SantaLucia, J., Jr. (2011) “The RNA Folding Problems: Different Levels of RNA Structure Prediction”, inRNA 3D Structure Analysis and Prediction (Leontis, N, and Westhof, E., eds.) Series “Nucleic Acids and Molecular Biology”, Springer |
| 2011 |
Watkins, N.E., Kennelly, W.J., Tsay, M.J., Tuin, A., Lee, H.R., Morosyuk, S.M., Hicks, D.A., and SantaLucia, J., Jr. (2011) “Thermodynamic Contributions of Single Internal rA-dA, rC-dC, rG-dG, and rU-dT Mismatches in DNA/RNA Duplexes”, Nucleic Acids Res ., 39, 1894-1902. |
| 2011 |
Medina, R.A., Rojas, M., Tuin, A., Huff, S., Ferres, M., Martines-Valdebenito, C., Godoy, P., Garcia-Sastre, A., Fofanov, Y., and SantaLucia, J., Jr. (2011) “Development and Characterization of a Highly Specific and Sensitive SYBR Green RT-PCR Assay for Detection of the 2009 Pandemic H1N1 Influenza Virus Based on Sequence Signatures”, J. Clin. Microbiol., 49, 335-344. |
| 2010 |
SantaLucia, J., Jr., Boggy, G., Tuin, A., Lee, S. Sekinger, E., and Robertson, G. (2010) “Design Tools for Use in Assay Optimization”, Gen. Eng. Biotech. News 30, 28-29 |
| 2008 |
Desaulniers, J.P., Chang, Y.-C., Aduri, R., Abeysirigunawardena, S.C., SantaLucia, J., Jr., and Chow, C.S. (2008) “Pseudouridines in rRNA Helix Play a Role in Loop Stacking Interactions”, Org. Biomol.Chem., 6, 3892-3895. |
| 2008 |
Saraiya, A.A., Lamichhane, T. N., Chow, C.S., SantaLucia, J., Jr., and Cunningham, P.R. (2008) “Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA”, J. Mol. Biol., 376, 645-657. |
| 2008 |
SantaLucia, J., Jr., Machak, J., and Finzel, B., “Opportunities for RNA-Targeted Therapeutics”, Next Gen. Pharm., Issue 13 (2008) |
| 2007 |
Bevilacqua, P.C., SantaLucia, J., Jr. (2007) “The Biophysics of RNA”, ACS Chem. Biol., 2, 440–444. |
| 2007 |
Aduri, R., Psciuk, B.T., Saro, P., Taniga, H., Schlegel, H.B., SantaLucia, J., Jr. (2007) “AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA”, J. Chem. Theory and Comput., 3, 1464 -1475. |
| 2007 |
SantaLucia, J., Jr. (2007) “Physical Principles and Visual-OMP Software for Optimal PCR Design”, Methods in Molecular Biology: PCR Primer Design, Anton Yuryev, Ed., Humana Press, Totowa, New Jersey, Methods Mol. Biol. |
| 2006 |
Dhimitruka, I., SantaLucia, J., Jr. (2006) “Investigation of the Yamaguchi Esterification Mechanism. Synthesis of a Lux-S Enzyme Inhibitor Using an Improved Esterification Method”, Organic Letters, 2006, 8, 47-50. |
| 2005 |
Watkins, N.E., Jr., SantaLucia, J., Jr. (2005) “Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes”, Nucleic Acids Research, 2005, 33, 6258-6267. |
| 2004 |
SantaLucia, J., Jr., Hicks, D. (2004) “The Thermodynamics of DNA Structural Motifs”, Annu. Rev. Biophys. Biomol. Struct., 33, 415-40. |
| 2004 |
Jang, S.B., Baeyens, K., Jeong, M.S., SantaLucia, J., Jr., Turner, D., Holbrook, S.R. (2004) “Structures of two RNA octamers containing tandem G-A base pairs”, Acta Cryst., 60D, 829-835. |
| 2004 |
Irani, R.J., SantaLucia, J., Jr. (2004) “Efficient preparation of 2-deoxy-3,5-di-O-p-toluoyl-a-D-ribofuranosyl chloride”, SynLett, 2, 335-337. |
| 2002 |
Irani, R.J., SantaLucia, J., Jr. (2002) “The Synthesis of Anti-fixed 3-Methyl-3-deaza-2′-deoxyadenosine and Other 3H-imidazo[4,5-c]pyridine Analogs”, Nucleosides, Nucleotides & Nucleic Acids, 21, 737-751. |
| 2002 |
Chow, C.S., Cunningham, P.R., Lee, K.S., Meroueh, M., SantaLucia, J., Jr., Varma, S. (2002) “Photoinduced cleavage by a rhodium complex at G-U mismatches and exposed guanines in large and small RNAs”, Biochimie, 84, 859-868. |
| 2002 |
Biswas, T., Clos, L.J., Santa Lucia, J., Jr., Mitra, S., Roy, R.J. (2002) “Binding of Specific DNA Base-pair Mismatches by N-Methylpurine-DNA Glycosylase and its implication in Initial Damage Recognition”, Mol. Biol., 320, 503-513. |
| 2001 |
Morosyuk, S.M., SantaLucia, J., Jr., Cunningham, P.R. (2001) “Structure and Function of the Conserved 690 Hairpin in Escherichia coli 16S ribosomal RNA: III. Instant Evolution Studies”, Mol. Biol., 307, 213-221. |
| 2001 |
Morosyuk, S.M., Cunningham, P.R., SantaLucia, J., Jr. (2001) “Structure and Function of the Conserved 690 Hairpin in Escherichia coli 16S ribosomal RNA: II. NMR Solution Structure”, Mol. Biol., 307, 197-211. |
| 2000 |
Morosyuk, S.V., Lee, K., SantaLucia, J., Jr., & Cunningham, P.R. J. (2000) “Structure and Function of the Conserved 690 Hairpin in Escherichia coli 16S ribosomal RNA: Analysis of the stem nucleotides”, Mol. Biol., 300, 113-126. |
| 2000 |
Meroueh, M., Grohar, P.J., Qiu, J., SantaLucia, J., Jr., Scaringe, S.A., Chow, C.S. (2000) “Unique Structural and Stabilizing Roles for the Individual Pseudouridine Residues in the 1920 Region of Escherichia coli 23S rRNA”, Nucleic Acids Res., 28, 2075-2083. |
| 2000 |
Bommarito, S., Peyret, N., SantaLucia, J., Jr. (2000) “Thermodynamic parameters for DNA sequences with dangling ends”, Nucleic Acids Res., 28, 1929-1934. |
| 2000 |
SantaLucia, J., Jr. (2000) “Determination of Nucleic Acid Thermodynamics by UV Absorbance Melting Curves”, in Spectrophotometry and Spectrofluorimetry: A Practical Approach (M.G. Gore, ed.), Oxford U. Press |
| 1999 |
Irani, R., SantaLucia, J., Jr. (1999) “The Synthesis of 5-iodocytidine Phosphoramidite for Heavy Atom Derivatization of RNA”, Tetrahedron Lett., 40, 8961-8964. |
| 1999 |
Blake, R.D., Bizzaro, J.W., Blake, J.D., Day, G.R., Delcourt, S.G., Knowles, J., Marx, K. A., SantaLucia, J., Jr. (1999) “Statistical Mechanical Simulation of Polymeric DNA Melting with MELTSIM”, Bioinformatics, 15, 370-375. |
| 1999 |
Peyret, N., Seneviratne, P.A., Allawi, H.T., SantaLucia, J., Jr. (1999) “Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A-A, C-C, G-G, and T-T Mismatches”, Biochemistry, 38, 3468-3477. |
| 1998 |
Xia, T., SantaLucia, J., Jr., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C., Turner, D.H. (1998) “Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs”, Biochemistry, 37, 14719-14735. |
| 1998 |
Allawi, H.T., SantaLucia, J., Jr. (1998) “NMR Solution Structure of a DNA dodecamer containing single G-T Mismatches”, Nucleic Acids Res., 26, 4925-4934. |
| 1998 |
SantaLucia, J., Jr. (1998) “A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-Neighbor Thermodynamics”, Proc. Natl. Acad. Sci. USA, 95, 1460-1465. |
| 1998 |
Allawi, H.T., SantaLucia, J., Jr. (1998) “Nearest-Neighbor Thermodynamics of Internal A-C Mismatches in DNA: Sequence Dependence and pH Effects”, Biochemistry, 37, 9435-9444. |
| 1998 |
Allawi, H.T., SantaLucia, J., Jr. (1998) “Thermodynamics of Internal C-T Mismatches in DNA”, Nucleic Acids Res., 26, 2694-2701. |
| 1998 |
Allawi, H.T., SantaLucia, J., Jr. (1998) “Nearest Neighbor Thermodynamic Parameters for Internal G-A Mismatches in DNA”, Biochemistry, 37, 2170-2179. |
| 1998 |
Arghavani, M.B., SantaLucia, J., Jr., Romano, L.J. (1998) “Effect of Mismatched Complementary Strands and 5′-Change in Sequence Context on the Thermodynamics and Structure of Benzo[a]pyrene-Modified Oligonucleotides”, Biochemistry, 37, 8575-8583. |
| 1997 |
Leontis, N.B., SantaLucia, J., Jr. (Eds.) (1997) “Molecular Modeling of Nucleic Acids”, ACS Symposium Series, 682, ACS pub., Washington, DC. |
| 1997 |
Wu, M., SantaLucia, J., Jr., Turner, D.H. (1997) “Solution Structure of (rGGCAGGCC)2 by Two-Dimensional NMR and the Iterative Relaxation Matrix Approach”, Biochemistry, 36, 4449-4460. |
| 1997 |
Carter, R.J., Baeyens, K.J., SantaLucia, J., Jr., Turner, D.H., Holbrook, S.R. (1997) “The Crystal Structure of an RNA Oligomer Incorporating Tandem Adenosine-Inosine Mismatches”,Nucleic Acids Res., 25, 4117-4122. |
| 1997 |
SantaLucia, J., Jr., Turner, D.H. (1997) “Measuring the Thermodynamics of RNA Secondary Structure Formation”, Biopolymers, 44, 309-319. |
| 1997 |
Lee, K., Varma, S., SantaLucia, J., Jr., Cunningham, P.R. (1997) “In Vivo Determination of RNA Structure-Function Relationships: Analysis of the 790 Loop in Ribosomal RNA”, J. Mol. Biol., 269, 732-743. |
| 1997 |
Allawi, H.T., SantaLucia, J., Jr. (1997) “Thermodynamics and NMR of Internal G-T Mismatches in DNA”, Biochemistry, 36, 10581-10594. |
| 1996 |
SantaLucia, J., Jr., Allawi, H.T., Seneviratne, P.A. (1996) “Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability”, Biochemistry, 35, 3555-3562. |
| 1995 |
SantaLucia, J., Jr., Shen, L., Cai, Z., Lewis, H., Tinoco, I., Jr. (1995) “Synthesis and NMR of RNA with Isotopic Enrichment in the Bases”, Nucleic Acids Res., 23, 4913-4921. |
| 1994 |
Tinoco, I., Jr., Cai, Z., Chang, K.Y., Chen, X., Hines, J.V., James, J., Jaeger, J.,Molinaro, M., SantaLucia, J., Jr., Shen, L., Variani, G., and Wimberly, B. (1994) “RNA Structural Elements – Loops and Pseudoknots”, FASEB J, 8, A1262. |
| 1993 |
SantaLucia, J., Jr., Turner, D.H. (1993) “Structure of (rGGCGAGCC)2 in Solution from NMR and Restrained Molecular Dynamics”, Biochemistry, 32, 12612-12623. |
| 1993 |
Jaeger, J.A., SantaLucia, J., Jr., Tinoco, I., Jr. (1993) “Determination of RNA Structure and Thermodynamics”, Ann. Rev. Biochem., 62, 255-287. |
| 1992 |
SantaLucia, J., Jr., Kierzek, R., Turner, D.H. (1992) “Context Dependence of Hydrogen Bond Free Energy Revealed by Substitutions in an RNA Hairpin”, Science, 256, 217-219. |
| 1991 |
He, L., Kierzek, R., SantaLucia, J., Jr., Walter, A.E., Turner, D.H. (1991) “Nearest-Neighbor Parameters for GU Mismatches: GU/UG Is Destabilizing in the Contexts CGUG, UGUA, and AGUU but Stabilizing in GGUC”, Biochemistry, 30, 11124-11132. |
| 1991 |
SantaLucia, J., Jr., Kierzek, R., Turner, D.H. (1991) “Stabilities of Consecutive AC, CC, GG, UC, and UU Mismatches in RNA Internal Loops: Evidence for Stable Hydrogen-Bonded UU and CC+ Pairs”, Biochemistry, 30, 8242-8251. |
| 1991 |
SantaLucia, J., Jr., Kierzek, R., Turner, D.H. (1991) “Functional Group Substitutions as Probes of Hydrogen Bonding between GA Mismatches in RNA Internal Loops”, J. Am. Chem. Soc., 113, 4313-4322. |
| 1990 |
SantaLucia, J., Jr., Kierzek, R., Turner, D.H. (1990) “Effects of GA Mismatches on the Structure and Thermodynamics of RNA Internal Loops”, Biochemistry, 29, 8813-8819. |
