1. Meyenburg Prize in 2002
2. Co-recipient (with Craig Mello) of National Academy of Sciences Award in Molecular Biology in 2003
3. Co-recipient (with Craig Mello, Thomas Tuschl and David Baulcombe) of the Wiley Prize in the Biomedical Sciences from Rockefeller University in 2003
4. Elected member National Academy of Sciences in 2004
5. Co-recipient (with Victor Ambros, Craig Mello, and Gary Ruvkun) of Brandeis University’s Lewis S. Rosenstiel Award for Distinguished Work in Medical Research in 2005
6. Co-recipient (with Craig Mello) of the Gairdner Foundation International Award in 2005
7. Co-recipient (with Craig Mello and David Baulcombe) of Massry Prize in 2005
8. Co-recipient (with Craig Mello) of the Paul Ehrlich and Ludwig Darmstaedter Prize in 2006
9. Co-recipient (with Craig Mello) of the Nobel Prize in Physiology or Medicine in 2006
1. EGO-1, a C. elegans RdRP, modulates gene expression via production of mRNA-templated short antisense RNAs. Maniar JM, Fire AZ. Curr Biol. 2011; 21 (6): 449-59
2. Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Lamm AT, Stadler MR, Zhang H, Gent JI, Fire AZ. Genome Res. 2011; 21 (2): 265-75
3. On the nature of in vivo requirements for rde-4 in RNAi and developmental pathways in C. elegans. Blanchard D, Parameswaran P, Lopez-Molina J, Gent J, Saynuk JF, Fire A. RNA Biol. 2011; 8 (3)
4. An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo. Gracey LE, Chen ZY, Maniar JM, Valouev A, Sidow A, Kay MA, Fire AZ. Epigenetics Chromatin. 2010; 3 (1): 13
5. Cell autonomous specification of temporal identity by Caenorhabditis elegans microRNA lin-4. Zhang H, Fire AZ. Dev Biol. 2010; 344 (2): 603-10
6. Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. Gent JI, Lamm AT, Pavelec DM, Maniar JM, Parameswaran P, Tao L, Kennedy S, Fire AZ. Mol Cell. 2010; 37 (5): 679-89
7. Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans. Sha K, Gu SG, Pantalena-Filho LC, Goh A, Fleenor J, Blanchard D, Krishna C, Fire A. BMC Genomics. 2010: 11 465
8. Human tRNA-derived small RNAs in the global regulation of RNA silencing. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA. RNA. 2010; 16 (4): 673-95
9. Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Collins AM. J Immunol. 2010; 184 (12): 6986-92
10. Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning. Gu SG, Fire A. Chromosoma. 2010; 119 (1): 73-87
11. Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems. Parameswaran P, Sklan E, Wilkins C, Burgon T, Samuel MA, Lu R, Ansel KM, Heissmeyer V, Einav S, Jackson W, Doukas T, Paranjape S, Polacek C, dos Santos FB, Jalili R, Babrzadeh F, Gharizadeh B, Grimm D, Kay M, Koike S, Sarnow P, Ronaghi M, Ding SW, Harris E, Chow M, Diamond MS, Kirkegaard K, Glenn JS, Fire AZ. PLoS Pathog. 2010; 6 (2): e1000764
12. Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls. Witten D, Tibshirani R, Gu SG, Fire A, Lui WO. BMC Biol. 2010: 8 58
13. A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. Gent JI, Schvarzstein M, Villeneuve AM, Gu SG, Jantsch V, Fire AZ, Baudrimont A. Genetics. 2009; 183 (4): 1297-314
14. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Fire AZ. Sci Transl Med. 2009; 1 (12): 12ra23
15. Profiling and discovery of novel miRNAs from formalin-fixed, paraffin-embedded melanoma and nodal specimens. Ma Z, Lui WO, Fire A, Dadras SS. J Mol Diagn. 2009; 11 (5): 420-9
16. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM. Genome Res. 2008; 18 (7): 1051-63
17. Capped small RNAs and MOV10 in human hepatitis delta virus replication. Haussecker D, Cao D, Huang Y, Parameswaran P, Fire AZ, Kay MA. Nat Struct Mol Biol. 2008; 15 (7): 714-21
18. MicroRNA expression signature of human sarcomas. Subramanian S, Lui WO, Lee CH, Espinosa I, Nielsen TO, Heinrich MC, Corless CL, Fire AZ, van de Rijn M. Oncogene. 2008; 27 (14): 2015-26
19. Transmission dynamics of heritable silencing induced by double-stranded RNA in Caenorhabditis elegans. Alcazar RM, Lin R, Fire AZ. Genetics. 2008; 180 (3): 1275-88
20. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ. Nucleic Acids Res. 2007; 35 (19): e130
21. Connector inversion probe technology: a powerful one-primer multiplex DNA amplification system for numerous scientific applications. Akhras MS, Unemo M, Thiyagarajan S, Nyrén P, Davis RW, Fire AZ, Pourmand N. PLoS One. 2007; 2 (9): e915
22. Distinct populations of primary and secondary effectors during RNAi in C. elegans. Pak J, Fire A. Science. 2007; 315 (5809): 241-4
23. Gene silencing by double-stranded RNA (Nobel Lecture). Fire AZ, Angew Chem Int Ed Engl. 2007; 46 (37): 6966-84
24. Patterns of known and novel small RNAs in human cervical cancer. Lui WO, Pourmand N, Patterson BK, Fire A. Cancer Res. 2007; 67 (13): 6031-43
25. A differential cytolocalization assay for analysis of macromolecular assemblies in the eukaryotic cytoplasm. Blanchard D, Hutter H, Fleenor J, Fire A. Mol Cell Proteomics. 2006; 5 (11): 2175-84
26. An antagonistic role for the C. elegans Schnurri homolog SMA-9 in modulating TGFbeta signaling during mesodermal patterning. Foehr ML, Lindy AS, Fairbank RC, Amin NM, Xu M, Yanowitz J, Fire AZ, Liu J. Development. 2006; 133 (15): 2887-96
27. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. Genome Res. 2006; 16 (12): 1505-16
28. Structural analysis of hyperperiodic DNA from Caenorhabditis elegans. Moreno-Herrero F, Seidel R, Johnson SM, Fire A, Dekker NH. Nucleic Acids Res. 2006; 34 (10): 3057-66
29. Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans. Fire A, Alcazar R, Tan F. Genetics. 2006; 173 (3): 1259-73
30. Cyclin D involvement demarcates a late transition in C. elegans embryogenesis. Yanowitz J, Fire A. Dev Biol. 2005; 279 (1): 244-51
31. Imprinting capacity of gamete lineages in Caenorhabditis elegans. Sha K, Fire A. Genetics. 2005; 170 (4): 1633-52
32. Nucleic acid structure and intracellular immunity: some recent ideas from the world of RNAi. Fire A, Q Rev Biophys. 2005; 38 (4): 303-9
33. UNC-39, the C. elegans homolog of the human myotonic dystrophy-associated homeodomain protein Six5, regulates cell motility and differentiation. Yanowitz JL, Shakir MA, Hedgecock E, Hutter H, Fire AZ, Lundquist EA. Dev Biol. 2004; 272 (2): 389-402
34. Inducible systemic RNA silencing in Caenorhabditis elegans. Timmons L, Tabara H, Mello CC, Fire AZ. Mol Biol Cell. 2003; 14 (7): 2972-83
35. Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Simmer F, Tijsterman M, Parrish S, Koushika SP, Nonet ML, Fire A, Ahringer J, Plasterk RH. Curr Biol. 2002; 12 (15): 1317-9
36. Rescue of polyglutamine-mediated cytotoxicity by double-stranded RNA-mediated RNA interference. Caplen NJ, Taylor JP, Statham VS, Tanaka F, Fire A, Morgan RA. Hum Mol Genet. 2002; 11 (2): 175-84
37. The T-box factor MLS-1 acts as a molecular switch during specification of nonstriated muscle in C. elegans. Kostas SA, Fire A. Genes Dev. 2002; 16 (2): 257-69
38. Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans. Parrish S, Fire A. RNA. 2001; 7 (10): 1397-402
39. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. Cell. 2001; 106 (1): 23-34
40. Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Timmons L, Court DL, Fire A. Gene. 2001; 263 (1-2): 103-12
41. On the role of RNA amplification in dsRNA-triggered gene silencing. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A. Cell. 2001; 107 (4): 465-76
42. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA. Proc Natl Acad Sci U S A. 2001; 98 (17): 9742-7
43. Caenorhabditis elegans twist plays an essential role in non-striated muscle development. Corsi AK, Kostas SA, Fire A, Krause M. Development. 2000; 127 (10): 2041-51
44. Essential roles for Caenorhabditis elegans lamin gene in nuclear organization, cell cycle progression, and spatial organization of nuclear pore complexes. Liu J, Rolef Ben-Shahar T, Riemer D, Treinin M, Spann P, Weber K, Fire A, Gruenbaum Y. Mol Biol Cell. 2000; 11 (11): 3937-47
45. Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. Parrish S, Fleenor J, Xu S, Mello C, Fire A. Mol Cell. 2000; 6 (5): 1077-87
46. Identification and molecular-genetic characterization of a LAMP/CD68-like protein from Caenorhabditis elegans. Kostich M, Fire A, Fambrough DM. J Cell Sci. 2000: 113 ( Pt 14) 2595-606
47. Overlapping roles of two Hox genes and the exd ortholog ceh-20 in diversification of the C. elegans postembryonic mesoderm. Liu J, Fire A. Development. 2000; 127 (23): 5179-90
48. Recognition and silencing of repeated DNA. Hsieh J, Fire A. Annu Rev Genet. 2000: 34 187-204
49. The MADS-Box factor CeMEF2 is not essential for Caenorhabditis elegans myogenesis and development. Dichoso D, Brodigan T, Chwoe KY, Lee JS, Llacer R, Park M, Corsi AK, Kostas SA, Fire A, Ahnn J, Krause M. Dev Biol. 2000; 223 (2): 431-40
50. dsRNA-mediated gene silencing in cultured Drosophila cells: a tissue culture model for the analysis of RNA interference. Caplen NJ, Fleenor J, Fire A, Morgan RA. Gene. 2000; 252 (1-2): 95-105
51. Evolutionary conservation of MyoD function and differential utilization of E proteins. Zhang JM, Chen L, Krause M, Fire A, Paterson BM. Dev Biol. 1999; 208 (2): 465-72
52. RNA-triggered gene silencing. Fire A, Trends Genet. 1999; 15 (9): 358-63
53. The RING finger/B-box factor TAM-1 and a retinoblastoma-like protein LIN-35 modulate context-dependent gene silencing in Caenorhabditis elegans. Hsieh J, Liu J, Kostas SA, Chang C, Sternberg PW, Fire A. Genes Dev. 1999; 13 (22): 2958-70
54. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Tabara H, Sarkissian M, Kelly WG, Fleenor J, Grishok A, Timmons L, Fire A, Mello CC. Cell. 1999; 99 (2): 123-32
55. Two-color GFP expression system for C. elegans. Miller DM, Desai NS, Hardin DC, Piston DW, Patterson GH, Fleenor J, Xu S, Fire A. Biotechniques. 1999; 26 (5): 914-8, 920-1
56. Analysis of a Caenorhabditis elegans Twist homolog identifies conserved and divergent aspects of mesodermal patterning. Harfe BD, Vaz Gomes A, Kenyon C, Liu J, Krause M, Fire A. Genes Dev. 1998; 12 (16): 2623-35
57. Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans. Kelly WG, Fire A. Development. 1998; 125 (13): 2451-6
58. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Montgomery MK, Fire A. Trends Genet. 1998; 14 (7): 255-8
59. Muscle and nerve-specific regulation of a novel NK-2 class homeodomain factor in Caenorhabditis elegans. Harfe BD, Fire A. Development. 1998; 125 (3): 421-9
60. MyoD and the specification of muscle and non-muscle fates during postembryonic development of the C. elegans mesoderm. Harfe BD, Branda CS, Krause M, Stern MJ, Fire A. Development. 1998; 125 (13): 2479-88
61. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Nature. 1998; 391 (6669): 806-11
62. RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Montgomery MK, Xu S, Fire A. Proc Natl Acad Sci U S A. 1998; 95 (26): 15502-7
63. Specific interference by ingested dsRNA. Timmons L, Fire A. Nature. 1998; 395 (6705): 854
64. A C. elegans E/Daughterless bHLH protein marks neuronal but not striated muscle development. Krause M, Park M, Zhang JM, Yuan J, Harfe B, Xu SQ, Greenwald I, Cole M, Paterson B, Fire A. Development. 1997; 124 (11): 2179-89
65. Caenorhabditis elegans levamisole resistance genes lev-1, unc-29, and unc-38 encode functional nicotinic acetylcholine receptor subunits. Fleming JT, Squire MD, Barnes TM, Tornoe C, Matsuda K, Ahnn J, Fire A, Sulston JE, Barnard EA, Sattelle DB, Lewis JA. J Neurosci. 1997; 17 (15): 5843-57
66. Distinct requirements for somatic and germline expression of a generally expressed Caernorhabditis elegans gene. Kelly WG, Xu S, Montgomery MK, Fire A. Genetics. 1997; 146 (1): 227-38
67. Genetically targeted cell disruption in Caenorhabditis elegans. Harbinder S, Tavernarakis N, Herndon LA, Kinnell M, Xu SQ, Fire A, Driscoll M. Proc Natl Acad Sci U S A. 1997; 94 (24): 13128-33
68. The Caenorhabditis elegans NK-2 homeobox gene ceh-22 activates pharyngeal muscle gene expression in combination with pha-1 and is required for normal pharyngeal development. Okkema PG, Ha E, Haun C, Chen W, Fire A. Development. 1997; 124 (20): 3965-73
69. An inductive interaction in 4-cell stage C. elegans embryos involves APX-1 expression in the signalling cell. Mickey KM, Mello CC, Montgomery MK, Fire A, Priess JR. Development. 1996; 122 (6): 1791-8
70. Repression of gene expression in the embryonic germ lineage of C. elegans. Seydoux G, Mello CC, Pettitt J, Wood WB, Priess JR, Fire A. Nature. 1996; 382 (6593): 713-6
71. DNA transformation. Mello C, Fire A. Methods Cell Biol. 1995: 48 451-82
72. Rolling replication of short DNA circles. Fire A, Xu SQ. Proc Natl Acad Sci U S A. 1995; 92 (10): 4641-5
73. Whole-mount in situ hybridization for the detection of RNA in Caenorhabditis elegans embryos. Seydoux G, Fire A. Methods Cell Biol. 1995: 48 323-37
74. A four-dimensional digital image archiving system for cell lineage tracing and retrospective embryology. Fire A, Comput Appl Biosci. 1994; 10 (4): 443-7
75. A screen for genetic loci required for body-wall muscle development during embryogenesis in Caenorhabditis elegans. Ahnn J, Fire A. Genetics. 1994; 137 (2): 483-98
76. Combinatorial structure of a body muscle-specific transcriptional enhancer in Caenorhabditis elegans. Jantsch-Plunger V, Fire A. J Biol Chem. 1994; 269 (43): 27021-8
77. Elements regulating cell- and stage-specific expression of the C. elegans MyoD family homolog hlh-1. Krause M, Harrison SW, Xu SQ, Chen L, Fire A. Dev Biol. 1994; 166 (1): 133-48
78. Soma-germline asymmetry in the distributions of embryonic RNAs in Caenorhabditis elegans. Seydoux G, Fire A. Development. 1994; 120 (10): 2823-34
79. The Caenorhabditis elegans MYOD homologue HLH-1 is essential for proper muscle function and complete morphogenesis. Chen L, Krause M, Sepanski M, Fire A. Development. 1994; 120 (6): 1631-41
80. The Caenorhabditis elegans NK-2 class homeoprotein CEH-22 is involved in combinatorial activation of gene expression in pharyngeal muscle. Okkema PG, Fire A. Development. 1994; 120 (8): 2175-86
81. Molecular characterization of the her-1 gene suggests a direct role in cell signaling during Caenorhabditis elegans sex determination. Perry MD, Li W, Trent C, Robertson B, Fire A, Hageman JM, Wood WB. Genes Dev. 1993; 7 (2): 216-28
82. Sequence requirements for myosin gene expression and regulation in Caenorhabditis elegans. Okkema PG, Harrison SW, Plunger V, Aryana A, Fire A. Genetics. 1993; 135 (2): 385-404
83. The novel metallothionein genes of Caenorhabditis elegans. Structural organization and inducible, cell-specific expression. Freedman JH, Slice LW, Dixon D, Fire A, Rubin CS. J Biol Chem. 1993; 268 (4): 2554-64
84. Histochemical techniques for locating Escherichia coli beta-galactosidase activity in transgenic organisms. Fire A, Genet Anal Tech Appl. 1992 Oct-Dec; 9 (5-6): 151-8
85. Body-wall muscle formation in Caenorhabditis elegans embryos that lack the MyoD homolog hlh-1. Chen L, Krause M, Draper B, Weintraub H, Fire A. Science. 1992; 256 (5054): 240-3
86. Functional conservation of nematode and vertebrate myogenic regulatory factors. Krause M, Fire A, White-Harrison S, Weintraub H, Tapscott S. J Cell Sci Suppl. 1992: 16 111-5
87. Production of antisense RNA leads to effective and specific inhibition of gene expression in C. elegans muscle. Fire A, Albertson D, Harrison SW, Moerman DG. Development. 1991; 113 (2): 503-14
88. A modular set of lacZ fusion vectors for studying gene expression in Caenorhabditis elegans. Fire A, Harrison SW, Dixon D. Gene. 1990; 93 (2): 189-98
89. CeMyoD accumulation defines the body wall muscle cell fate during C. elegans embryogenesis. Krause M, Fire A, Harrison SW, Priess J, Weintraub H. Cell. 1990; 63 (5): 907-19
90. Vectors for low copy transformation of C. elegans. Fire A, Kondo K, Waterston R. Nucleic Acids Res. 1990; 18 (14): 4269-70
91. 5,6-Dichloro-1-beta-D-ribofuranosylbenzimidazole inhibits transcription elongation by RNA polymerase II in vitro. Chodosh LA, Fire A, Samuels M, Sharp PA. J Biol Chem. 1989; 264 (4): 2250-7
92. Proper expression of myosin genes in transgenic nematodes. Fire A, Waterston RH. EMBO J. 1989; 8 (11): 3419-28
93. Integrative transformation of Caenorhabditis elegans. Fire A, EMBO J. 1986; 5 (10): 2673-80
94. Dinucleotide priming of transcription mediated by RNA polymerase II. Samuels M, Fire A, Sharp PA. J Biol Chem. 1984; 259 (4): 2517-25
95. Interactions between RNA polymerase II, factors, and template leading to accurate transcription. Fire A, Samuels M, Sharp PA. J Biol Chem. 1984; 259 (4): 2509-16
96. Characterization of tRNA precursor splicing in mammalian extracts. Laski FA, Fire AZ, RajBhandary UL, Sharp PA. J Biol Chem. 1983; 258 (19): 11974-80
97. In vitro transcription: whole-cell extract. Manley JL, Fire A, Samuels M, Sharp PA. Methods Enzymol. 1983: 101 568-82
98. Separation and characterization of factors mediating accurate transcription by RNA polymerase II. Samuels M, Fire A, Sharp PA. J Biol Chem. 1982; 257 (23): 14419-27
99. In vitro transcription of adenovirus. Fire A, Baker CC, Manley JL, Ziff EB, Sharp PA. J Virol. 1981; 40 (3): 703-19
100.Inhibition of transcription factor activity by poliovirus. Crawford N, Fire A, Samuels M, Sharp PA, Baltimore D. Cell. 1981; 27 (3 Pt 2): 555-61
101.DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. Manley JL, Fire A, Cano A, Sharp PA, Gefter ML. Proc Natl Acad Sci U S A. 1980; 77 (7): 3855-9
102.Regulation of adenovirus mRNA synthesis. Sharp PA, Manley J, Fire A, Gefter M. Ann N Y Acad Sci. 1980: 354 1-15
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