Publications
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Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning.
Gu SG,
Fire A.
Chromosoma.
2009
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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
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A Caenorhabditis elegans RNA-directed RNA Polymerase in Sperm Development and Endogenous RNAi.
Gent JI,
Schvarzstein M, Villeneuve AM, Gu SG, Jantsch V, Fire AZ, Baudrimont A.
Genetics.
2009
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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
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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
-
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
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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
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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
-
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
-
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
-
Gene silencing by double-stranded RNA (Nobel Lecture).
Fire AZ,
Angew Chem Int Ed Engl.
2007;
46
(37):
6966-84
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Distinct populations of primary and secondary effectors during RNAi in C. elegans.
Pak J,
Fire A.
Science.
2007;
315
(5809):
241-4
-
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
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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
-
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
-
Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans.
Fire A,
Alcazar R, Tan F.
Genetics.
2006;
173
(3):
1259-73
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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
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Cyclin D involvement demarcates a late transition in C. elegans embryogenesis.
Yanowitz J,
Fire A.
Dev Biol.
2005;
279
(1):
244-51
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Nucleic acid structure and intracellular immunity: some recent ideas from the world of RNAi.
Fire A,
Q Rev Biophys.
2005;
38
(4):
303-9
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Imprinting capacity of gamete lineages in Caenorhabditis elegans.
Sha K,
Fire A.
Genetics.
2005;
170
(4):
1633-52
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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
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Inducible systemic RNA silencing in Caenorhabditis elegans.
Timmons L,
Tabara H, Mello CC, Fire AZ.
Mol Biol Cell.
2003;
14
(7):
2972-83
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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
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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
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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
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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
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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
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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
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Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans.
Parrish S,
Fire A.
RNA.
2001;
7
(10):
1397-402
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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
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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
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Recognition and silencing of repeated DNA.
Hsieh J,
Fire A.
Annu Rev Genet.
2000:
34
187-204
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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
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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
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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
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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
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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
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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
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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
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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
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RNA-triggered gene silencing.
Fire A,
Trends Genet.
1999;
15
(9):
358-63
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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
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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
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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
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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
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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
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Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans.
Kelly WG,
Fire A.
Development.
1998;
125
(13):
2451-6
-
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
-
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
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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
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Specific interference by ingested dsRNA.
Timmons L,
Fire A.
Nature.
1998;
395
(6705):
854
-
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
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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
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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
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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
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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
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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
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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
-
Rolling replication of short DNA circles.
Fire A,
Xu SQ.
Proc Natl Acad Sci U S A.
1995;
92
(10):
4641-5
-
DNA transformation.
Mello C,
Fire A.
Methods Cell Biol.
1995:
48
451-82
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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
-
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
-
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
-
Soma-germline asymmetry in the distributions of embryonic RNAs in Caenorhabditis elegans.
Seydoux G,
Fire A.
Development.
1994;
120
(10):
2823-34
-
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
-
A four-dimensional digital image archiving system for cell lineage tracing and retrospective embryology.
Fire A,
Comput Appl Biosci.
1994;
10
(4):
443-7
-
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
-
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
-
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
-
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
-
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
-
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
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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
-
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
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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
-
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
-
Vectors for low copy transformation of C. elegans.
Fire A,
Kondo K, Waterston R.
Nucleic Acids Res.
1990;
18
(14):
4269-70
-
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
-
Proper expression of myosin genes in transgenic nematodes.
Fire A,
Waterston RH.
EMBO J.
1989;
8
(11):
3419-28
-
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
-
Integrative transformation of Caenorhabditis elegans.
Fire A,
EMBO J.
1986;
5
(10):
2673-2680
-
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
-
Dinucleotide priming of transcription mediated by RNA polymerase II.
Samuels M,
Fire A, Sharp PA.
J Biol Chem.
1984;
259
(4):
2517-25
-
Characterization of tRNA precursor splicing in mammalian extracts.
Laski FA,
Fire AZ, RajBhandary UL, Sharp PA.
J Biol Chem.
1983;
258
(19):
11974-80
-
In vitro transcription: whole-cell extract.
Manley JL,
Fire A, Samuels M, Sharp PA.
Methods Enzymol.
1983:
101
568-82
-
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
-
In vitro transcription of adenovirus.
Fire A,
Baker CC, Manley JL, Ziff EB, Sharp PA.
J Virol.
1981;
40
(3):
703-19
-
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
-
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
-
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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