Publications

  1. 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. Scientific Reports 13: 21927. PMID: 38081834: PubMed Link
  2. 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: 843. PMID: 37375533: PubMed Link
  3. Marras SAE, Vargas-Gold DY, Tyagi S, and Kramer FR. MULTIPLEX NUCLEIC ACID ASSAY METHODS CAPABLE OF DETECTING CLOSELY RELATED ALLELES, AND REAGENTS THEREFOR. (January 2023) United States patent no. 11,542,547.
  4. 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(24): 1575223. PMID: 36555395: PubMed Link
  5. Tyagi S and Marras SAE. TARGET MEDIATED IN SITU SIGNAL AMPLIFICATION WITH DUAL INTERACTING HAIRPIN PROBES. (October 2022) United States patent no. 11,459,603.
  6. 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
  7. 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
  8. 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
  9. Parveen N and Marras SAE. MULTIPLEX DIAGNOSTIC ASSAY FOR LYME DISEASE AND OTHER TICK-BORNE DISEASES. (May 2022) United States Patent No. 11,326,215.
  10. 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
  11. Marras SAE, Vargas-Gold DY, Tyagi S, and Kramer FR. HIGHLY SELECTIVE NUCLEIC ACID AMPLIFICATION PRIMERS. (September 2021) United States Patent No. 11,111,515.
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. Mustaev A and Marras SAE. DUAL SENSITIZER CONTAINING LUMINESCENT COMPOUNDS, CONJUGATES AND USES THEREOF. (August 2016) United States Patent No. 9,415,111.
  19. Day X, Marras SAE, and Libera M. GEL-TETHERED MOLECULAR BEACONS. (May 2016) United States Patent No. 9,340,831.
  20. 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
  21. 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
  22. Mustaev A, Kozlov M, Marras SAE, Krasnopero L, Wirpsza L, and Pillai S. FLUOROPHORE CHELATED LANTHANIDE LUMINESCENT PROBES WITH IMPROVED QUANTUM EFFICIENCY. (December 2015) United States Patent No. 9,221,759.
  23. 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
  24. 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
  25. 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
  26. 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.
  27. Dai X, Yang W, Firlar E, Marras SAE, and Libera M (2012) Surface-patterned microgel-tethered molecular beacons. Soft Matter 8: 3067-3076.
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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.
  35. 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
  36. 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
  37. Marras SAE (2008) Interactive fluorophore and quencher pairs for labeling fluorescent nucleic acid hybridization probes. Molecular Biotechnology 38: 247-255. PMID: 17985254: PubMed Link
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. Kramer FR, Tyagi S, Marras SAE, and Trunfio H. OPTICALLY DECODABLE MICROCARRIERS, ARRAYS AND METHODS. (March 2004) United States Patent No. 7,741,031.
  48. 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
  49. Marras SAE, Kramer FR, and Tyagi S (2003) Genotyping SNPs with molecular beacons. Methods in Molecular Biology 212: 111-128. PMID: 12491906: PubMed Link
  50. Marras SAE (2003) Development of molecular beacons for nucleic acid detection. Doctoral Dissertation, Leiden University, Leiden, the Netherlands.
  51. 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
  52. 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
  53. 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
  54. 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.
  55. 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
  56. 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.
  57. 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
  58. 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.
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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.
  64. Tyagi S, Marras SAE, and Kramer FR (2000) Wavelength-shifting molecular beacons. Nature Biotechnology 18: 1191-1196. PMID: 11062440: PubMed Link
  65. Tyagi S, Kramer FR, and Marras SAE. WAVELENGTH-SHIFTING PROBES AND PRIMERS AND THEIR USE IN ASSAYS AND KITS. (March 2000) United States Patent No. 6,037,130.
  66. 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
  67. 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
  68. 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
  69. Vet JAM, Hessels D, Marras SAE, van de Kaa CA, van der Poel HG, Michalides RJ, Debruyne FM, and Schalken JA (1998) Comparative analysis of p53 mutations in bladder washings and histologic specimens. American Journal of Clinical Pathology 110: 647-652. PMID: 9802351: PubMed Link
  70. Vet JAM, Witjes JA, Marras SAE, Hessels D, van der Poel HG, Debruyne FM, and Schalken JA (1996) Predictive value of p53 mutations analyzed in bladder washings for progression of high-risk superficial bladder cancer. Clinical Cancer Research 2: 1055-1061. PMID: 9816267: PubMed Link
  71. Teunissen MJ, Marras SAE, Op den Camp HJ, and Vogels GD (1989) Improved method for simultaneous determination of alcohols, volatile fatty acids, lactic acid or 2,3-butanediol in biological samples. Journal of Microbiological Methods 10: 247-254.