molecular beacons

Publications

(co-authored by inventors of the molecular beacon technology)


  1. Tyagi S and Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14: 303-308. PMID: 9630890: PubMed Link

  2. Blok HJ and Kramer FR (1997) Amplifiable hybridization probes containing a molecular switch. Mol Cell Probes 11: 187-194. PMID: 9232617: PubMed Link

  3. Gao W, Tyagi S, Kramer FR, and Goldman E (1997) Messenger RNA release from ribosomes during 5'-translational blockage by consecutive low-usage arginine but not leucine codons in Escherichia coli. Mol Microbiol 25: 707-716. PMID: 9379900: PubMed Link

  4. Giesendorf BA, Vet JA, Tyagi S, Mensink EJ, Trijbels FJ, and Blom HJ (1998) Molecular beacons: a new approach for semiautomated mutation analysis. Clin Chem 44: 482-486. PMID: 9510851: PubMed Link

  5. Kostrikis LG, Tyagi S, Mhlanga MM, Ho DD, and Kramer FR (1998) Spectral genotyping of human alleles. Science 279: 1228-1229. PMID: 9508692: PubMed Link

  6. Leone G, van Schijndel H, van Gemen B, Kramer FR, and Schoen CD (1998) Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Res 26: 2150-2155. PMID: 9547273: PubMed Link

  7. Ortiz E, Estrada G, and Lizardi PM (1998) PNA molecular beacons for rapid detection of PCR amplicons. Mol Cell Probes 12: 219-226. PMID: 9727198: PubMed Link

  8. Piatek AS, Tyagi S, Pol AC, Telenti A, Miller LP, Kramer FR, and Alland D (1998) Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat Biotechnol 16: 359-363. PMID: 9555727: PubMed Link

  9. Tyagi S, Bratu DP, and Kramer FR (1998) Multicolor molecular beacons for allele discrimination. Nat Biotechnol 16: 49-53. PMID: 9447593: PubMed Link

  10. Bonnet G, Tyagi S, Libchaber A, and Kramer FR (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc Natl Acad Sci U S A 96: 6171-6176. PMID: 10339560: PubMed Link

  11. Gonzalez E, Bamshad M, Sato N, Mummidi S, Dhanda R, Catano G, Cabrera S, McBride M, Cao XH, Merrill G, O'Connell P, Bowden DW, Freedman BI, Anderson SA, Walter EA, Evans JS, Stephan KT, Clark RA, Tyagi S, Ahuja SS, Dolan MJ, and Ahuja SK (1999) Race-specific HIV-1 disease-modifying effects associated with CCR5 haplotypes. Proc Natl Acad Sci U S A 96: 12004-12009. PMID: 10518566: PubMed Link

  12. Manganelli R, Dubnau E, Tyagi S, Kramer FR, and Smith I (1999) Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis. Mol Microbiol 31: 715-724. PMID: 10027986: PubMed Link

  13. Marras SAE, Kramer FR, and Tyagi S (1999) Multiplex detection of single-nucleotide variations using molecular beacons. Genetic Analysis: Biomolecular Engineering 14: 151-156. PMID: 10084107: PubMed Link

  14. Rhee JT, Piatek AS, Small PM, Harris LM, Chaparro SV, Kramer FR, and Alland D (1999) Molecular epidemiologic evaluation of transmissibility and virulence of Mycobacterium tuberculosis. J Clin Microbiol 37: 1764-1770. PMID: 10325321: PubMed Link

  15. Vet JAM, Majithia AR, Marras SAE, Tyagi S, Dube S, Poiesz BJ, and Kramer FR (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons. Proceedings of the National Academy of Sciences USA 96: 6394-6399. PMID: 10339598: PubMed Link

  16. Park S, Wong M, Marras SAE, Cross EW, Kiehn TE, Chaturvedi V, Tyagi S, and Perlin DS (2000) Rapid identification of Candida dubliniensis using a species-specific molecular beacon. Journal of Clinical Microbiology 38: 2829-2836. PMID: 10921935: PubMed Link

  17. Piatek AS, Telenti A, Murray MR, El-Hajj H, Jacobs WR, Jr., Kramer FR, and Alland D (2000) Genotypic analysis of Mycobacterium tuberculosis in two distinct populations using molecular beacons: implications for rapid susceptibility testing. Antimicrob Agents Chemother 44: 103-110. PMID: 10602730: PubMed Link

  18. Tyagi S, Marras SAE, and Kramer FR (2000) Wavelength-shifting molecular beacons. Nature Biotechnology 18: 1191-1196. PMID: 11062440: PubMed Link

  19. Tyagi S, Marras SAE, Vet JAM, and Kramer FR (2000) Molecular beacons: hybridization probes for detection of nucleic acids in homogeneous solutions. In Kessler C (ed.), Nonradioactive Analysis of Biomolecules, second edition. Springer Verlag, Berlin, Germany, pp. 606-616.

  20. van Schie RC, Marras SAE, Conroy JM, Nowak NJ, Catanese JJ, and de Jong PJ (2000) Semiautomated clone verification by real-time PCR using molecular beacons. Biotechniques 29: 1296-1300, 1302-1294, 1306 passim. PMID: 11126133: PubMed Link

  21. Xiao G, Chicas A, Olivier M, Taya Y, Tyagi S, Kramer FR, and Bargonetti J (2000) A DNA damage signal is required for p53 to activate gadd45. Cancer Res 60: 1711-1719. PMID: 10749144: PubMed Link

  22. Bourdon V, Mhlanga M, Massimi A, Tyagi S, Kucherlapati R, and Chaganti R (2001) A 12p array to identify amplified and overexpressed sequences in testicular germ cell tumors. Nature Genetics 27: 44-44. PMID: PubMed Link

  23. Dracheva S, Marras SAE, Elhakem SL, Kramer FR, Davis KL, and Haroutunian V (2001) N-methyl-D-aspartic acid receptor expression in the dorsolateral prefrontal cortex of elderly patients with schizophrenia. American Journal of Psychiatry 158: 1400-1410. PMID: 11532724: PubMed Link

  24. El-Hajj HH, Marras SAE, Tyagi S, Kramer FR, and Alland D (2001) Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. Journal of Clinical Microbiology 39: 4131-4137. PMID: 11682541: PubMed Link

  25. Gold B, Rodriguez GM, Marras SAE, Pentecost M, and Smith I (2001) The Mycobacterium tuberculosis IdeR is a dual functional regulator that controls transcription of genes involved in iron acquisition, iron storage and survival in macrophages. Molecular Microbiology 42: 851-865. PMID: 11722747: PubMed Link

  26. Jones M, Alland D, Marras SAE, El-Hajj H, Taylor MT, and McMillan W (2001) Rapid and sensitive detection of Mycobacterium DNA using cepheid SmartCycler (R) and tube lysis system. Clinical Chemistry 47: 1917-1918. PMID: PubMed Link

  27. Manganelli R, Tyagi S, and Smith I (2001) Real Time PCR Using Molecular Beacons : A New Tool to Identify Point Mutations and to Analyze Gene Expression in Mycobacterium tuberculosis. Methods Mol Med 54: 295-310. PMID: 21341083: PubMed Link

  28. Molenaar C, Marras SAE, Slats JC, Truffert JC, Lemaitre M, Raap AK, Dirks RW, and Tanke HJ (2001) Linear 2' O-Methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Research 29: E89-89. PMID: 11522845: PubMed Link

  29. Smit ML, Giesendorf BA, Vet JA, Trijbels FJ, and Blom HJ (2001) Semiautomated DNA mutation analysis using a robotic workstation and molecular beacons. Clin Chem 47: 739-744. PMID: 11274026: PubMed Link

  30. Van Beuningen R, Marras SAE, Kramer FR, Oosterlaken T, Weusten J, Borst G, and Van de Wiel P (2001) Development of a high-throughput detection system for HIV-1 using real-time NASBA based on molecular beacons. Proceedings - SPIE the International Society for Optical Engineering 4264: 66-71. PMID: PubMed Link

  31. Fang Y, Wu WH, Pepper JL, Larsen JL, Marras SAE, Nelson EA, Epperson WB, and Christopher-Hennings J (2002) Comparison of real-time, quantitative PCR with molecular beacons to nested PCR and culture methods for detection of Mycobacterium avium subsp. paratuberculosis in bovine fecal samples. Journal of Clinical Microbiology 40: 287-291. PMID: 11773135: PubMed Link

  32. Larsen MH, Vilcheze C, Kremer L, Besra GS, Parsons L, Salfinger M, Heifets L, Hazbon MH, Alland D, Sacchettini JC, and Jacobs WR, Jr. (2002) Overexpression of inhA, but not kasA, confers resistance to isoniazid and ethionamide in Mycobacterium smegmatis, M. bovis BCG and M. tuberculosis. Mol Microbiol 46: 453-466. PMID: 12406221: PubMed Link

  33. Marras SAE (2002) Artificial hybridization probes. In Khudyakov YE and Fields HA (eds.), Artificial DNA: Methods and Applications. CRC Press, Boca Raton, FL, pp. 71-89.

  34. Marras SAE, Kramer FR, and Tyagi S (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Research 30: e122. PMID: 12409481: PubMed Link

  35. Mathema B, Bifani PJ, Driscoll J, Steinlein L, Kurepina N, Moghazeh SL, Shashkina E, Marras SAE, Campbell S, Mangura B, Shilkret K, Crawford JT, Frothingham R, and Kreiswirth BN (2002) Identification and evolution of an IS6110 low-copy-number Mycobacterium tuberculosis cluster. Journal of Infectious Diseases 185: 641-649. PMID: 11865421: PubMed Link

  36. Phadtare S, Tyagi S, Inouye M, and Severinov K (2002) Three amino acids in Escherichia coli CspE surface-exposed aromatic patch are critical for nucleic acid melting activity leading to transcription antitermination and cold acclimation of cells. J Biol Chem 277: 46706-46711. PMID: 12324471: PubMed Link

  37. Vet JA, Van der Rijt BJ, and Blom HJ (2002) Molecular beacons: colorful analysis of nucleic acids. Expert Rev Mol Diagn 2: 77-86. PMID: 11963813: PubMed Link

  38. Bratu DP, Cha BJ, Mhlanga MM, Kramer FR, and Tyagi S (2003) Visualizing the distribution and transport of mRNAs in living cells. Proc Natl Acad Sci U S A 100: 13308-13313. PMID: 14583593: PubMed Link

  39. Kuckleburg CJ, Chase CC, Nelson EA, Marras SAE, Dammen MA, and Christopher-Hennings J (2003) Detection of bovine leukemia virus in blood and milk by nested and real-time polymerase chain reactions. Journal of Veterinary Diagnostic Investigation 15: 72-76. PMID: 12580302: PubMed Link

  40. Marras SAE, Kramer FR, and Tyagi S (2003) Genotyping SNPs with molecular beacons. Methods in Molecular Biology 212: 111-128. PMID: 12491906: PubMed Link

  41. Nascimento AM, Goldman GH, Park S, Marras SAE, Delmas G, Oza U, Lolans K, Dudley MN, Mann PA, and Perlin DS (2003) Multiple resistance mechanisms among Aspergillus fumigatus mutants with high-level resistance to itraconazole. Antimicrobial Agents and Chemotherapy 47: 1719-1726. PMID: 12709346: PubMed Link

  42. Shi L, Jung YJ, Tyagi S, Gennaro ML, and North RJ (2003) Expression of Th1-mediated immunity in mouse lungs induces a Mycobacterium tuberculosis transcription pattern characteristic of nonreplicating persistence. Proc Natl Acad Sci U S A 100: 241-246. PMID: 12506197: PubMed Link

  43. Zhu G, Xiao H, Mohan VP, Tanaka K, Tyagi S, Tsen F, Salgame P, and Chan J (2003) Gene expression in the tuberculous granuloma: analysis by laser capture microdissection and real-time PCR. Cell Microbiol 5: 445-453. PMID: 12814435: PubMed Link

  44. Hazbon MH and Alland D (2004) Hairpin primers for simplified single-nucleotide polymorphism analysis of Mycobacterium tuberculosis and other organisms. J Clin Microbiol 42: 1236-1242. PMID: 15004082: PubMed Link

  45. Marras SAE, Gold B, Kramer FR, Smith I, and Tyagi S (2004) Real-time measurement of in vitro transcription. Nucleic Acids Research 32: e72. PMID: 15155820: PubMed Link

  46. Tyagi S and Alsmadi O (2004) Imaging native beta-actin mRNA in motile fibroblasts. Biophys J 87: 4153-4162. PMID: 15377515: PubMed Link

  47. Varma-Basil M, El-Hajj H, Colangeli R, Hazbon MH, Kumar S, Bose M, Bobadilla-del-Valle M, Garcia LG, Hernandez A, Kramer FR, Osornio JS, Ponce-de-Leon A, and Alland D (2004) Rapid detection of rifampin resistance in Mycobacterium tuberculosis isolates from India and Mexico by a molecular beacon assay. J Clin Microbiol 42: 5512-5516. PMID: 15583274: PubMed Link

  48. Varma-Basil M, El-Hajj H, Marras SAE, Hazbon MH, Mann JM, Connell ND, Kramer FR, and Alland D (2004) Molecular beacons for multiplex detection of four bacterial bioterrorism agents. Clinical Chemistry 50: 1060-1062. PMID: 15161722: PubMed Link

  49. Mhlanga MM, Vargas DY, Fung CW, Kramer FR, and Tyagi S (2005) tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells. Nucleic Acids Res 33: 1902-1912. PMID: 15809226: PubMed Link

  50. Sinsimer D, Leekha S, Park S, Marras SAE, Koreen L, Willey B, Naidich S, Musser KA, and Kreiswirth BN (2005) Use of a multiplex molecular beacon platform for rapid detection of methicillin and vancomycin resistance in Staphylococcus aureus. Journal of Clinical Microbiology 43: 4585-4591. PMID: 16145111: PubMed Link

  51. Vargas DY, Raj A, Marras SAE, Kramer FR, and Tyagi S (2005) Mechanism of mRNA transport in the nucleus. Proceedings of the National Academy of Sciences USA 102: 17008-17013. PMID: 16284251: PubMed Link

  52. Vet JA and Marras SAE (2005) Design and optimization of molecular beacon real-time polymerase chain reaction assays. Methods in Molecular Biology 288: 273-290. PMID: 15333910: PubMed Link

  53. Waltz TL, Marras SAE, Rochford G, Nolan J, Lee E, Melegari M, and Pollack H (2005) Development of a molecular-beacon assay to detect the G1896A precore mutation in hepatitis B virus-infected individuals. Journal of Clinical Microbiology 43: 254-258. PMID: 15634980: PubMed Link

  54. Carroll KD, Bu W, Palmeri D, Spadavecchia S, Lynch SJ, Marras SAE, Tyagi S, and Lukac DM (2006) Kaposi's Sarcoma-associated herpesvirus lytic switch protein stimulates DNA binding of RBP-Jk/CSL to activate the Notch pathway. Journal of Virology 80: 9697-9709. PMID: 16973574: PubMed Link

  55. Hazbon MH, Brimacombe M, Bobadilla del Valle M, Cavatore M, Guerrero MI, Varma-Basil M, Billman-Jacobe H, Lavender C, Fyfe J, Garcia-Garcia L, Leon CI, Bose M, Chaves F, Murray M, Eisenach KD, Sifuentes-Osornio J, Cave MD, Ponce de Leon A, and Alland D (2006) Population genetics study of isoniazid resistance mutations and evolution of multidrug-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 50: 2640-2649. PMID: 16870753: PubMed Link

  56. Marras SAE (2006) Selection of fluorophore and quencher pairs for fluorescent nucleic acid hybridization probes. Methods in Molecular Biology 335: 3-16. PMID: 16785616: PubMed Link

  57. Marras SAE, Tyagi S, and Kramer FR (2006) Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clinica Chimica Acta 363: 48-60. PMID: 16111667: PubMed Link

  58. Mhlanga MM and Tyagi S (2006) Using tRNA-linked molecular beacons to image cytoplasmic mRNAs in live cells. Nat Protoc 1: 1392-1398. PMID: 17406426: PubMed Link

  59. Raj A, Peskin CS, Tranchina D, Vargas DY, and Tyagi S (2006) Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4: e309. PMID: 17048983: PubMed Link

  60. Chakravorty S, Helb D, Burday M, Connell N, and Alland D (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69: 330-339. PMID: 17391789: PubMed Link

  61. Colangeli R, Helb D, Vilcheze C, Hazbon MH, Lee CG, Safi H, Sayers B, Sardone I, Jones MB, Fleischmann RD, Peterson SN, Jacobs WR, Jr., and Alland D (2007) Transcriptional regulation of multi-drug tolerance and antibiotic-induced responses by the histone-like protein Lsr2 in M. tuberculosis. PLoS Pathog 3: e87. PMID: 17590082: PubMed Link

  62. Chakravorty S, Aladegbami B, Motiwala AS, Dai Y, Safi H, Brimacombe M, Helb D, and Alland D (2008) Rifampin resistance, Beijing-W clade-single nucleotide polymorphism cluster group 2 phylogeny, and the Rv2629 191-C allele in Mycobacterium tuberculosis strains. J Clin Microbiol 46: 2555-2560. PMID: 18550732: PubMed Link

  63. Hazbon MH, Motiwala AS, Cavatore M, Brimacombe M, Whittam TS, and Alland D (2008) Convergent evolutionary analysis identifies significant mutations in drug resistance targets of Mycobacterium tuberculosis. Antimicrob Agents Chemother 52: 3369-3376. PMID: 18591265: PubMed Link

  64. Marras SAE (2008) Interactive fluorophore and quencher pairs for labeling fluorescent nucleic acid hybridization probes. Molecular Biotechnology 38: 247-255. PMID: 17985254: PubMed Link

  65. Safi H, Sayers B, Hazbon MH, and Alland D (2008) Transfer of embB codon 306 mutations into clinical Mycobacterium tuberculosis strains alters susceptibility to ethambutol, isoniazid, and rifampin. Antimicrob Agents Chemother 52: 2027-2034. PMID: 18378710: PubMed Link

  66. Sinsimer D, Huet G, Manca C, Tsenova L, Koo MS, Kurepina N, Kana B, Mathema B, Marras SAE, Kreiswirth BN, Guilhot C, and Kaplan G (2008) The phenolic glycolipid of Mycobacterium tuberculosis differentially modulates the early host cytokine response but does not in itself confer hypervirulence. Infection and Immunity 76: 3027-3036. PMID: 18443098: PubMed Link

  67. El-Hajj HH, Marras SAE, Tyagi S, Shashkina E, Kamboj M, Kiehn TE, Glickman MS, Kramer FR, and Alland D (2009) Use of sloppy molecular beacon probes for identification of mycobacterial species. Journal of Clinical Microbiology 47: 1190-1198. PMID: 19171684: PubMed Link

  68. Kramer FR, Marras SAE, and Tyagi S (2009) Inventing molecular beacons. In Bustin SA (ed.), The PCR Revolution. Cambridge University Press, Cambridge, pp. 19 - 47.

  69. Kumar P, Nath K, Rath B, Sen MK, Vishalakshi P, Chauhan DS, Katoch VM, Singh S, Tyagi S, Sreenivas V, and Prasad HK (2009) Visual format for detection of Mycobacterium tuberculosis and M. bovis in clinical samples using molecular beacons. J Mol Diagn 11: 430-438. PMID: 19661384: PubMed Link

  70. Saidac DS, Marras SAE, and Parveen N (2009) Detection and quantification of Lyme spirochetes using sensitive and specific molecular beacon probes. BMC Microbiololgy 9: 43. PMID: 19239692: PubMed Link

  71. Tyagi S (2009) Imaging intracellular RNA distribution and dynamics in living cells. Nat Methods 6: 331-338. PMID: 19404252: PubMed Link

  72. van den Bogaard PT and Tyagi S (2009) Using molecular beacons to study dispersal of mRNPs from the gene locus. Methods Mol Biol 464: 91-103. PMID: 18951181: PubMed Link

  73. Banada PP, Sivasubramani SK, Blakemore R, Boehme C, Perkins MD, Fennelly K, and Alland D (2010) Containment of bioaerosol infection risk by the Xpert MTB/RIF assay and its applicability to point-of-care settings. J Clin Microbiol 48: 3551-3557. PMID: 20720033: PubMed Link

  74. Blakemore R, Story E, Helb D, Kop J, Banada P, Owens MR, Chakravorty S, Jones M, and Alland D (2010) Evaluation of the analytical performance of the Xpert MTB/RIF assay. J Clin Microbiol 48: 2495-2501. PMID: 20504986: PubMed Link

  75. Boehme CC, Nabeta P, Hillemann D, Nicol MP, Shenai S, Krapp F, Allen J, Tahirli R, Blakemore R, Rustomjee R, Milovic A, Jones M, O'Brien SM, Persing DH, Ruesch-Gerdes S, Gotuzzo E, Rodrigues C, Alland D, and Perkins MD (2010) Rapid molecular detection of tuberculosis and rifampin resistance. N Engl J Med 363: 1005-1015. PMID: 20825313: PubMed Link

  76. Chakravorty S, Aladegbami B, Burday M, Levi M, Marras SAE, Shah D, El-Hajj HH, Kramer FR, and Alland D (2010) Rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique. Journal of Clinical Microbiology 48: 258-267. PMID: 19923485: PubMed Link

  77. Helb D, Jones M, Story E, Boehme C, Wallace E, Ho K, Kop J, Owens MR, Rodgers R, Banada P, Safi H, Blakemore R, Lan NT, Jones-Lopez EC, Levi M, Burday M, Ayakaka I, Mugerwa RD, McMillan B, Winn-Deen E, Christel L, Dailey P, Perkins MD, Persing DH, and Alland D (2010) Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology. J Clin Microbiol 48: 229-237. PMID: 19864480: PubMed Link

  78. Krasnoperov LN, Marras SAE, Kozlov M, Wirpsza L, and Mustaev A (2010) Luminescent probes for ultrasensitive detection of nucleic acids. Bioconjugate Chemistry 21: 319-327. PMID: 20085336: PubMed Link

  79. Veith R, Sorkalla T, Baumgart E, Anzt J, Haberlein H, Tyagi S, Siebrasse JP, and Kubitscheck U (2010) Balbiani ring mRNPs diffuse through and bind to clusters of large intranuclear molecular structures. Biophys J 99: 2676-2685. PMID: 20959109: PubMed Link

  80. Blakemore R, Nabeta P, Davidow AL, Vadwai V, Tahirli R, Munsamy V, Nicol M, Jones M, Persing DH, Hillemann D, Ruesch-Gerdes S, Leisegang F, Zamudio C, Rodrigues C, Boehme CC, Perkins MD, and Alland D (2011) A multisite assessment of the quantitative capabilities of the Xpert MTB/RIF assay. Am J Respir Crit Care Med 184: 1076-1084. PMID: 21836139: PubMed Link

  81. Boehme CC, Nicol MP, Nabeta P, Michael JS, Gotuzzo E, Tahirli R, Gler MT, Blakemore R, Worodria W, Gray C, Huang L, Caceres T, Mehdiyev R, Raymond L, Whitelaw A, Sagadevan K, Alexander H, Albert H, Cobelens F, Cox H, Alland D, and Perkins MD (2011) Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study. Lancet 377: 1495-1505. PMID: 21507477: PubMed Link

  82. Bratu DP, Catrina IE, and Marras SAE (2011) Tiny molecular beacons for in vivo mRNA detection. Methods in Molecular Biology 714: 141-157. PMID: 21431739: PubMed Link

  83. Chakravorty S, Aladegbami B, Thoms K, Lee JS, Lee EG, Rajan V, Cho EJ, Kim H, Kwak H, Kurepina N, Cho SN, Kreiswirth B, Via LE, Barry CE, 3rd, and Alland D (2011) Rapid detection of fluoroquinolone-resistant and heteroresistant Mycobacterium tuberculosis by use of sloppy molecular beacons and dual melting-temperature codes in a real-time PCR assay. J Clin Microbiol 49: 932-940. PMID: 21191047: PubMed Link

  84. Vadwai V, Boehme C, Nabeta P, Shetty A, Alland D, and Rodrigues C (2011) Xpert MTB/RIF: a new pillar in diagnosis of extrapulmonary tuberculosis? J Clin Microbiol 49: 2540-2545. PMID: 21593262: PubMed Link

  85. Vargas DY, Shah K, Batish M, Levandoski M, Sinha S, Marras SAE, Schedl P, and Tyagi S (2011) Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147: 1054-1065. PMID: 22118462: PubMed Link

  86. Altan-Bonnet G and Kramer FR (2012) Nucleic acid hybridization: Robust sequence discrimination. Nat Chem 4: 155-157. PMID: 22354426: PubMed Link

  87. Banada PP, Chakravorty S, Shah D, Burday M, Mazzella FM, and Alland D (2012) Highly sensitive detection of Staphylococcus aureus directly from patient blood. PLoS One 7: e31126. PMID: 22363564: PubMed Link

  88. Batish M, van den Bogaard P, Kramer FR, and Tyagi S (2012) Neuronal mRNAs travel singly into dendrites. Proc Natl Acad Sci U S A 109: 4645-4650. PMID: 22392993: PubMed Link

  89. Catrina IE, Marras SAE, and Bratu DP (2012) Tiny molecular beacons: LNA/2'-O-methyl RNA chimeric probes for imaging dynamic mRNA processes in living cells. ACS Chemical Biology 7: 1586-1595. PMID: 22738327: PubMed Link

  90. Chakravorty S, Kothari H, Aladegbami B, Cho EJ, Lee JS, Roh SS, Kim H, Kwak H, Lee EG, Hwang SH, Banada PP, Safi H, Via LE, Cho SN, Barry CE, 3rd, and Alland D (2012) Rapid, high-throughput detection of rifampin resistance and heteroresistance in Mycobacterium tuberculosis by use of sloppy molecular beacon melting temperature coding. J Clin Microbiol 50: 2194-2202. PMID: 22535987: PubMed Link

  91. Dai X, Yang W, Firlar E, Marras SAE, and Libera M (2012) Surface-patterned microgel-tethered molecular beacons. Soft Matter 8: 3067-3076. PMID: PubMed Link

  92. Nahid P, Kim PS, Evans CA, Alland D, Barer M, Diefenbach J, Ellner J, Hafner R, Hamilton CD, Iademarco MF, Ireton G, Kimerling ME, Lienhardt C, MacKenzie WR, Murray M, Perkins MD, Posey JE, Roberts T, Sizemore C, Stevens WS, Via L, Williams SD, Yew WW, and Swindells S (2012) Clinical research and development of tuberculosis diagnostics: moving from silos to synergy. J Infect Dis 205 Suppl 2: S159-168. PMID: 22476718: PubMed Link

  93. Pillai S, Kozlov M, Marras SAE, Krasnoperov LN, and Mustaev A (2012) New cross-linking quinoline and quinolone derivatives for sensitive fluorescent labeling. Journal of Fluorescence 22: 1021-1032. PMID: 22450725: PubMed Link

  94. Pillai S, Kozlov M, Marras SAE, Krasnoperov LN, and Mustaev A (2012) The synthesis and characterization of new cross-linkable quinolone and quinoline-based luminescent lanthanide chelates. Progresses in Nanotechnology and Nanomaterials 1: 18-24. PMID: PubMed Link

  95. Wirpsza L, Pillai S, Batish M, Marras SAE, Krasnoperov L, and Mustaev A (2012) Highly bright avidin-based affinity probes carrying multiple lanthanide chelates. Journal of Photochemistry and Photobiology B: Biology 116: 22-29. PMID: 23018156: PubMed Link

  96. Banada PP, Koshy R, and Alland D (2013) Detection of Mycobacterium tuberculosis in blood by use of the Xpert MTB/RIF assay. J Clin Microbiol 51: 2317-2322. PMID: 23678063: PubMed Link

  97. Chan K, Marras SAE, and Parveen N (2013) Sensitive multiplex PCR assay to differentiate Lyme spirochetes and emerging pathogens Anaplasma phagocytophilum and Babesia microti. BMC Microbiology 13: 295. PMID: 24359556: PubMed Link

  98. Feasey NA, Banada PP, Howson W, Sloan DJ, Mdolo A, Boehme C, Chipungu GA, Allain TJ, Heyderman RS, Corbett EL, and Alland D (2013) Evaluation of Xpert MTB/RIF for detection of tuberculosis from blood samples of HIV-infected adults confirms Mycobacterium tuberculosis bacteremia as an indicator of poor prognosis. J Clin Microbiol 51: 2311-2316. PMID: 23678061: PubMed Link

  99. Lawn SD, Mwaba P, Bates M, Piatek A, Alexander H, Marais BJ, Cuevas LE, McHugh TD, Zijenah L, Kapata N, Abubakar I, McNerney R, Hoelscher M, Memish ZA, Migliori GB, Kim P, Maeurer M, Schito M, and Zumla A (2013) Advances in tuberculosis diagnostics: the Xpert MTB/RIF assay and future prospects for a point-of-care test. Lancet Infect Dis 13: 349-361. PMID: 23531388: PubMed Link

  100. Piatek AS, Van Cleeff M, Alexander H, Coggin WL, Rehr M, Van Kampen S, Shinnick TM, and Mukadi Y (2013) GeneXpert for TB diagnosis: planned and purposeful implementation. Glob Health Sci Pract 1: 18-23. PMID: 25276513: PubMed Link

  101. van't Hoog AH, Cobelens F, Vassall A, van Kampen S, Dorman SE, Alland D, and Ellner J (2013) Optimal triage test characteristics to improve the cost-effectiveness of the Xpert MTB/RIF assay for TB diagnosis: a decision analysis. PLoS One 8: e82786. PMID: 24367555: PubMed Link

  102. Blakemore R and Alland D (2014) Described diagnostic inconsistencies were observed with an obsolete version of the Xpert MTB/RIF assay and are unlikely to recur in the current version of the assay. J Clin Microbiol 52: 704. PMID: 24478521: PubMed Link

  103. Jones-Lopez E, Manabe YC, Palaci M, Kayiza C, Armstrong D, Nakiyingi L, Ssengooba W, Gaeddert M, Kubiak R, Almeida Junior P, Alland D, Dietze R, Joloba M, Ellner JJ, and Dorman SE (2014) Prospective cross-sectional evaluation of the small membrane filtration method for diagnosis of pulmonary tuberculosis. J Clin Microbiol 52: 2513-2520. PMID: 24808236: PubMed Link

  104. Ssengooba W, Nakiyingi L, Armstrong DT, Cobelens FG, Alland D, Manabe YC, Dorman SE, Ellner JJ, and Joloba ML (2014) Clinical utility of a novel molecular assay in various combination strategies with existing methods for diagnosis of HIV-related tuberculosis in Uganda. PLoS One 9: e107595. PMID: 25222866: PubMed Link

  105. Chakravorty S, Lee JS, Cho EJ, Roh SS, Smith LE, Lee J, Kim CT, Via LE, Cho SN, Barry CE, 3rd, and Alland D (2015) Genotypic susceptibility testing of Mycobacterium tuberculosis isolates for amikacin and kanamycin resistance by use of a rapid sloppy molecular beacon-based assay identifies more cases of low-level drug resistance than phenotypic Lowenstein-Jensen testing. J Clin Microbiol 53: 43-51. PMID: 25339395: PubMed Link

  106. Dharan NJ, Amisano D, Mboowa G, Ssengooba W, Blakemore R, Kubiak RW, Armstrong DT, Jones M, Manabe YC, Joloba ML, Ellner JJ, Dorman SE, and Alland D (2015) Improving the sensitivity of the Xpert MTB/RIF assay on sputum pellets by decreasing the amount of added sample reagent: a laboratory and clinical evaluation. J Clin Microbiol 53: 1258-1263. PMID: 25653410: PubMed Link

  107. Roh SS, Smith LE, Lee JS, Via LE, Barry CE, 3rd, Alland D, and Chakravorty S (2015) Comparative Evaluation of Sloppy Molecular Beacon and Dual-Labeled Probe Melting Temperature Assays to Identify Mutations in Mycobacterium tuberculosis Resulting in Rifampin, Fluoroquinolone and Aminoglycoside Resistance. PLoS One 10: e0126257. PMID: 25938476: PubMed Link

  108. Stevaert A, Nurra S, Pala N, Carcelli M, Rogolino D, Shepard C, Domaoal RA, Kim B, Alfonso-Prieto M, Marras SAE, Sechi M, and Naesens L (2015) An integrated biological approach to guide the development of metal-chelating inhibitors of influenza virus PA endonuclease. Molecular Pharmacology 87: 323-337. PMID: 25477342: PubMed Link

  109. Banada PP, Naidoo U, Deshpande S, Karim F, Flynn JL, O'Malley M, Jones M, Nanassy O, Jeena P, and Alland D (2016) A Novel Sample Processing Method for Rapid Detection of Tuberculosis in the Stool of Pediatric Patients Using the Xpert MTB/RIF Assay. PLoS One 11: e0151980. PMID: 27007974: PubMed Link

  110. Catrina IE, Bayer LV, Yanez G, McLaughlin JM, Malaczek K, Bagaeva E, Marras SAE, and Bratu DP (2016) The temporally controlled expression of Drongo, the fruit fly homolog of AGFG1, is achieved in female germline cells via P-bodies and its localization requires functional Rab11. RNA Biology 13: 1117-1132. PMID: 27654348: PubMed Link

  111. Jayakumar A, Savic RM, Everett CK, Benator D, Alland D, Heilig CM, Weiner M, Friedrich SO, Martinson NA, Kerrigan A, Zamudio C, Goldberg SV, Whitworth WC, Davis JL, and Nahid P (2016) Xpert MTB/RIF Assay Shows Faster Clearance of Mycobacterium tuberculosis DNA with Higher Levels of Rifapentine Exposure. J Clin Microbiol 54: 3028-3033. PMID: 27733634: PubMed Link

  112. Luetkemeyer AF, Firnhaber C, Kendall MA, Wu X, Mazurek GH, Benator DA, Arduino R, Fernandez M, Guy E, Johnson P, Metchock B, Sattler F, Telzak E, Wang YF, Weiner M, Swindells S, Sanne IM, Havlir DV, Grinsztejn B, Alland D, A ACTG, and Tuberculosis Trials Consortium Study T (2016) Evaluation of Xpert MTB/RIF Versus AFB Smear and Culture to Identify Pulmonary Tuberculosis in Patients With Suspected Tuberculosis From Low and Higher Prevalence Settings. Clin Infect Dis 62: 1081-1088. PMID: 26839383: PubMed Link

  113. Shenai S, Ronacher K, Malherbe S, Stanley K, Kriel M, Winter J, Peppard T, Barry CE, Wang J, Dodd LE, Via LE, Barry CE, 3rd, Walzl G, and Alland D (2016) Bacterial Loads Measured by the Xpert MTB/RIF Assay as Markers of Culture Conversion and Bacteriological Cure in Pulmonary TB. PLoS One 11: e0160062. PMID: 27508390: PubMed Link

  114. Vargas DY, Kramer FR, Tyagi S, and Marras SAE (2016) Multiplex Real-Time PCR Assays that Measure the Abundance of Extremely Rare Mutations Associated with Cancer. PLoS One 11: e0156546. PMID: 27244445: PubMed Link

  115. Arrigucci R, Bushkin Y, Radford F, Lakehal K, Vir P, Pine R, Martin D, Sugarman J, Zhao Y, Yap GS, Lardizabal AA, Tyagi S, and Gennaro ML (2017) FISH-Flow, a protocol for the concurrent detection of mRNA and protein in single cells using fluorescence in situ hybridization and flow cytometry. Nat Protoc 12: 1245-1260. PMID: 28518171: PubMed Link

  116. Banada PP, Deshpande S, Chakravorty S, Russo R, Occi J, Meister G, Jones KJ, Gelhaus CH, Valderas MW, Jones M, Connell N, and Alland D (2017) Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System. J Clin Microbiol 55: 291-301. PMID: 27847371: PubMed Link

  117. Banada PP, Deshpande S, Russo R, Singleton E, Shah D, Patel B, Burday M, Koshy R, Wang Q, Jones M, Gall A, Lokhov S, Kwiatkowski R, Persing D, Connell N, and Alland D (2017) Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System. J Clin Microbiol 55: 2964-2971. PMID: 28747367: PubMed Link

  118. Chakravorty S, Roh SS, Glass J, Smith LE, Simmons AM, Lund K, Lokhov S, Liu X, Xu P, Zhang G, Via LE, Shen Q, Ruan X, Yuan X, Zhu HZ, Viazovkina E, Shenai S, Rowneki M, Lee JS, Barry CE, 3rd, Gao Q, Persing D, Kwiatkawoski R, Jones M, Gall A, and Alland D (2017) Detection of Isoniazid-, Fluoroquinolone-, Amikacin-, and Kanamycin-Resistant Tuberculosis in an Automated, Multiplexed 10-Color Assay Suitable for Point-of-Care Use. J Clin Microbiol 55: 183-198. PMID: 27807153: PubMed Link

  119. Chakravorty S, Simmons AM, Rowneki M, Parmar H, Cao Y, Ryan J, Banada PP, Deshpande S, Shenai S, Gall A, Glass J, Krieswirth B, Schumacher SG, Nabeta P, Tukvadze N, Rodrigues C, Skrahina A, Tagliani E, Cirillo DM, Davidow A, Denkinger CM, Persing D, Kwiatkowski R, Jones M, and Alland D (2017) The New Xpert MTB/RIF Ultra: Improving Detection of Mycobacterium tuberculosis and Resistance to Rifampin in an Assay Suitable for Point-of-Care Testing. mBio 8. PMID: 28851844: PubMed Link

  120. Schlachter S, Chan K, Marras SAE, and Parveen N (2017) Detection and Differentiation of Lyme Spirochetes and Other Tick-Borne Pathogens from Blood Using Real-Time PCR with Molecular Beacons. Methods in Molecular Biology 1616: 155-170. PMID: 28600768: PubMed Link

  121. Xie YL, Chakravorty S, Armstrong DT, Hall SL, Via LE, Song T, Yuan X, Mo X, Zhu H, Xu P, Gao Q, Lee M, Lee J, Smith LE, Chen RY, Joh JS, Cho Y, Liu X, Ruan X, Liang L, Dharan N, Cho SN, Barry CE, 3rd, Ellner JJ, Dorman SE, and Alland D (2017) Evaluation of a Rapid Molecular Drug-Susceptibility Test for Tuberculosis. N Engl J Med 377: 1043-1054. PMID: 28902596: PubMed Link

  122. Dorman SE, Schumacher SG, Alland D, Nabeta P, Armstrong DT, King B, Hall SL, Chakravorty S, Cirillo DM, Tukvadze N, Bablishvili N, Stevens W, Scott L, Rodrigues C, Kazi MI, Joloba M, Nakiyingi L, Nicol MP, Ghebrekristos Y, Anyango I, Murithi W, Dietze R, Lyrio Peres R, Skrahina A, Auchynka V, Chopra KK, Hanif M, Liu X, Yuan X, Boehme CC, Ellner JJ, Denkinger CM, and study t (2018) Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective multicentre diagnostic accuracy study. Lancet Infect Dis 18: 76-84. PMID: 29198911: PubMed Link

  123. Vargas DY, Marras SAE, Tyagi S, and Kramer FR (2018) Suppression of Wild-Type Amplification by Selectivity Enhancing Agents in PCR Assays that Utilize SuperSelective Primers for the Detection of Rare Somatic Mutations. The Journal of Molecular Diagnostics 20: 415-427. PMID: 29698835: PubMed Link

  124. Banada PP, Deshpande S, Banik S, Shah D, Koshy R, Patel B, Kwiatkowski R, Persing D, and Alland D (2019) Multiplex Detection of Three Select Agents Directly from Blood by Use of the GeneXpert System. J Clin Microbiol 57. PMID: 30842226: PubMed Link

  125. Cao Y, Parmar H, Simmons AM, Kale D, Tong K, Lieu D, Persing D, Kwiatkowski R, Alland D, and Chakravorty S (2019) Automatic Identification of Individual rpoB Gene Mutations Responsible for Rifampin Resistance in Mycobacterium tuberculosis by Use of Melting Temperature Signatures Generated by the Xpert MTB/RIF Ultra Assay. J Clin Microbiol 58. PMID: 31533985: PubMed Link

  126. Marras SAE, Bushkin Y, and Tyagi S (2019) High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules. Proceedings of the National Academy of Sciences USA 116: 13921-13926. PMID: 31221755: PubMed Link

  127. Marras SAE, Tyagi S, Antson DO, and Kramer FR (2019) Color-coded molecular beacons for multiplex PCR screening assays. PLoS One 14: e0213906. PMID: 30883590: PubMed Link

  128. Oliveira GP, Jr., Zigon E, Rogers G, Davodian D, Lu S, Jovanovic-Talisman T, Jones J, Tigges J, Tyagi S, and Ghiran IC (2020) Detection of Extracellular Vesicle RNA Using Molecular Beacons. iScience 23: 100782. PMID: 31958756: PubMed Link

  129. Safi H, Lingaraju S, Ma S, Husain S, Hoque M, Soteropoulos P, Rustad T, Sherman DR, and Alland D (2020) Rapidly Correcting Frameshift Mutations in the Mycobacterium tuberculosis orn Gene Produce Reversible Ethambutol Resistance and Small-Colony-Variant Morphology. Antimicrob Agents Chemother 64. PMID: 32571828: PubMed Link

  130. Whitfield MG, Marras SAE, Warren RM, Van Rie A, Rice J, Wangh LJ, and Kreiswirth BN (2020) Rapid pyrazinamide drug susceptibility testing using a closed-tube PCR assay of the entire pncA gene. Scientific Reports 10: 4234. PMID: 32144379: PubMed Link

  131. Banada P, Green R, Banik S, Chopoorian A, Streck D, Jones R, Chakravorty S, and Alland D (2021) A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. J Clin Microbiol 59: e0084521. PMID: 34288729: PubMed Link

  132. Cao Y, Parmar H, Gaur RL, Lieu D, Raghunath S, Via N, Battaglia S, Cirillo DM, Denkinger C, Georghiou S, Kwiatkowski R, Persing D, Alland D, and Chakravorty S (2021) Xpert MTB/XDR: a 10-Color Reflex Assay Suitable for Point-of-Care Settings To Detect Isoniazid, Fluoroquinolone, and Second-Line-Injectable-Drug Resistance Directly from Mycobacterium tuberculosis-Positive Sputum. J Clin Microbiol 59. PMID: 33298611: PubMed Link

  133. Kramer FR and Vargas DY (2021) SuperSelective primer pairs for sensitive detection of rare somatic mutations. Sci Rep 11: 22384. PMID: 34789731: PubMed Link

  134. Marras SAE, Chen L, Shashkina E, Davidson RM, Strong M, Daley CL, and Kreiswirth BN (2021) A molecular-beacon-based multiplex real-time PCR assay to distinguish mycobacterium abscessus subspecies and determine macrolide susceptibility. Journal of Clinical Microbiology 59: e0045521. PMID: 33980653: PubMed Link

  135. Badeti S, Jiang Q, Naghizadeh A, Tseng HC, Bushkin Y, Marras SAE, Nisa A, Tyagi S, Chen F, Romanienko P, Yehia G, Evans D, Lopez-Gonzalez M, Alland D, Russo R, Gause W, Shi L, and Liu D (2022) Development of a novel human CD147 knock-in NSG mouse model to test SARS-CoV-2 viral infection. Cell & Bioscience 12: 88. PMID: 35690792: PubMed Link

  136. Dikdan RJ, Marras SAE, Field AP, Brownlee A, Cironi A, Hill DA, and Tyagi S (2022) Multiplex PCR Assays for Identifying all Major Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Journal of Molecular Diagnostics 24: 309-319. PMID: 35121139: PubMed Link

  137. Narang A, Marras SAE, Kurepina N, Chauhan V, Shashkina E, Kreiswirth B, Varma-Basil M, Vinnard C, and Subbian S (2022) Ultrasensitive detection of multidrug-resistant Mycobacterium tuberculosis using SuperSelective primer-based real-time PCR assays. International Journal of Molecular Sciences 23. PMID: 36555395: PubMed Link

  138. Vargas DY, Tyagi S, Marras SAE, Moerzinger P, Abin-Carriquiry JA, Cuello M, Rodriguez C, Martinez A, Makhnin A, Farina A, Patel C, Chuang TL, Li BT, and Kramer FR (2022) Multiplex SuperSelective PCR assays for the detection and quantitation of rare somatic mutations in liquid biopsies. Journal of Molecular Diagnostics 24: 189-204. PMID: 34954118: PubMed Link

  139. Banada PP, Green R, Streck D, Kurvathi R, Reiss R, Banik S, Daivaa N, Montalvan I, Jones R, Marras SAE, Chakravorty S, and Alland D (2023) An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern. Sci Rep 13: 21927. PMID: 38081834: PubMed Link

  140. Ebraham L, Xu C, Wang A, Hernandez C, Siclari N, Rajah D, Walter L, Marras SAE, Tyagi S, Fine DH, Daep CA, and Chang TL (2023) Oral epithelial cells expressing low or undetectable levels of Human Angiotensin-converting Enzyme 2 are susceptible to SARS-CoV-2 virus infection in vitro. Pathogens 12. PMID: 37375533: PubMed Link

  141. Banik S, Ozay B, Trejo M, Zhu Y, Kanna C, Santellan C, Shaw B, Chandrasekaran S, Chaturvedi S, Vejar L, Chakravorty S, Alland D, and Banada P (2024) A simple and sensitive test for Candida auris colonization, surveillance, and infection control suitable for near patient use. J Clin Microbiol 62: e0052524. PMID: 38888304: PubMed Link

  142. Ma MT, Jiang Q, Chen CH, Badeti S, Wang X, Zeng C, Evans D, Bodnar B, Marras SAE, Tyagi S, Bharaj P, Yehia G, Romanienko P, Hu W, Liu SL, Shi L, and Liu D (2024) S309-CAR-NK cells bind the Omicron variants in vitro and reduce SARS-CoV-2 viral loads in humanized ACE2-NSG mice. Journal of Virology: e0003824. PMID: 38767356: PubMed Link

  143. Xie YL, Modi N, Lopez K, Reiss R, Robledo J, Eichberg C, Hapeela N, Nakabugo E, Anyango I, Arora K, Odero R, Van Heerden J, Zemanay W, Kaipilyawar VS, Kennedy S, Banada P, Nakiyingi L, Joloba ML, Centner C, McCarthy K, Ellner J, Salgame P, Alland D, and Dorman SE (2025) Prominence of Mycobacterium tuberculosis biomarkers among sputum culture-negative clinic attendees, independent of Ultra status. J Infect Public Health 18: 102791. PMID: 40315556: PubMed Link

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Recent Publications from our group


Ma MT, Jiang Q, Chen CH, Badeti S, Wang X, Zeng C, Evans D, Bodnar B, Marras SAE, Tyagi S, Bharaj P, Yehia G, Romanienko P, Hu W, Liu SL, Shi L, and Liu D (2024) S309-CAR-NK cells bind the Omicron variants in vitro and reduce SARS-CoV-2 viral loads in humanized ACE2-NSG mice. Journal of Virology: e0003824. PMID: 38767356: PubMed Link

Banada PP, Green R, Streck D, Kurathi R, Reiss R, Banik S, Montalvan I, Jones R, Marras SAE, Chakravorty S, and Alland D (2023) An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern. Scientific Reports 13. 21927. PMID: 38081834: PubMed Link

Ebraham L, Xu C, Wang A, Hernandez C, Siclari N, Rajah D, Walter L, Marras SAE, Tyagi S, Fine DH, Daep CA, and Chang TL (2023) Oral Epithelial cells expressing low or undetectable levels of human angiotensin-converting enzyme 2 are susceptible to SARS-CoV-2 virus infection in vitro. Pathogens 12. PMID: 37375533: PubMed Link


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