-
1
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
-
2
-
-
46249103973
-
Stem cell transcriptome profiling via massive-scale mRNA sequencing
-
Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619.
-
(2008)
Nat Methods
, vol.5
, pp. 613-619
-
-
Cloonan, N.1
Forrest, A.R.2
Kolle, G.3
Gardiner, B.B.4
Faulkner, G.J.5
-
3
-
-
77951917823
-
Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow
-
Wolf JB, Bayer T, Haubold B, Schilhabel M, Rosenstiel P, et al. (2010) Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Mol Ecol 19 Suppl 1: 162-175.
-
(2010)
Mol Ecol
, vol.19
, pp. 162-175
-
-
Wolf, J.B.1
Bayer, T.2
Haubold, B.3
Schilhabel, M.4
Rosenstiel, P.5
-
4
-
-
65549099632
-
Structure and complexity of a bacterial transcriptome
-
Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, et al. (2009) Structure and complexity of a bacterial transcriptome. J Bacteriol 191: 3203-3211.
-
(2009)
J Bacteriol
, vol.191
, pp. 3203-3211
-
-
Passalacqua, K.D.1
Varadarajan, A.2
Ondov, B.D.3
Okou, D.T.4
Zwick, M.E.5
-
5
-
-
77951041162
-
Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity
-
Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, et al. (2010) Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. J Bacteriol 192: 2359-2372.
-
(2010)
J Bacteriol
, vol.192
, pp. 2359-2372
-
-
Filiatrault, M.J.1
Stodghill, P.V.2
Bronstein, P.A.3
Moll, S.4
Lindeberg, M.5
-
6
-
-
68249102779
-
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
-
Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, et al. (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet 5: e1000569.
-
(2009)
PLoS Genet
, vol.5
-
-
Perkins, T.T.1
Kingsley, R.A.2
Fookes, M.C.3
Gardner, P.P.4
James, K.D.5
-
7
-
-
72049125603
-
The plasticity of the mammalian transcriptome
-
Lindberg J, Lundeberg J, (2010) The plasticity of the mammalian transcriptome. Genomics 95: 1-6.
-
(2010)
Genomics
, vol.95
, pp. 1-6
-
-
Lindberg, J.1
Lundeberg, J.2
-
8
-
-
85041131924
-
Antisense RNA control in bacteria, phages, and plasmids
-
Wagner EG, Simons RW, (1994) Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol 48: 713-742.
-
(1994)
Annu Rev Microbiol
, vol.48
, pp. 713-742
-
-
Wagner, E.G.1
Simons, R.W.2
-
10
-
-
79959349542
-
Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation
-
Chatterjee A, Johnson CM, Shu CC, Kaznessis YN, Ramkrishna D, et al. (2011) Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation. Proc Natl Acad Sci U S A.
-
(2011)
Proc Natl Acad Sci U S A.
-
-
Chatterjee, A.1
Johnson, C.M.2
Shu, C.C.3
Kaznessis, Y.N.4
Ramkrishna, D.5
-
11
-
-
0028019410
-
Gene inhibition using antisense oligodeoxynucleotides
-
Wagner RW, (1994) Gene inhibition using antisense oligodeoxynucleotides. Nature 372: 333-335.
-
(1994)
Nature
, vol.372
, pp. 333-335
-
-
Wagner, R.W.1
-
12
-
-
70849119931
-
Transcriptome complexity in a genome-reduced bacterium
-
Guell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, et al. (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268-1271.
-
(2009)
Science
, vol.326
, pp. 1268-1271
-
-
Guell, M.1
van Noort, V.2
Yus, E.3
Chen, W.H.4
Leigh-Bell, J.5
-
13
-
-
77949425194
-
The primary transcriptome of the major human pathogen Helicobacter pylori
-
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250-255.
-
(2010)
Nature
, vol.464
, pp. 250-255
-
-
Sharma, C.M.1
Hoffmann, S.2
Darfeuille, F.3
Reignier, J.4
Findeiss, S.5
-
15
-
-
70350726230
-
Bacillus anthracis physiology and genetics
-
Koehler TM, (2009) Bacillus anthracis physiology and genetics. Mol Aspects Med 30: 386-396.
-
(2009)
Mol Aspects Med
, vol.30
, pp. 386-396
-
-
Koehler, T.M.1
-
16
-
-
33744764304
-
The superoxide dismutases of Bacillus anthracis do not cooperatively protect against endogenous superoxide stress
-
Passalacqua KD, Bergman NH, Herring-Palmer A, Hanna P, (2006) The superoxide dismutases of Bacillus anthracis do not cooperatively protect against endogenous superoxide stress. J Bacteriol 188: 3837-3848.
-
(2006)
J Bacteriol
, vol.188
, pp. 3837-3848
-
-
Passalacqua, K.D.1
Bergman, N.H.2
Herring-Palmer, A.3
Hanna, P.4
-
17
-
-
0942279513
-
Bacillus anthracis requires siderophore biosynthesis for growth in macrophages and mouse virulence
-
Cendrowski S, MacArthur W, Hanna P, (2004) Bacillus anthracis requires siderophore biosynthesis for growth in macrophages and mouse virulence. Mol Microbiol 51: 407-417.
-
(2004)
Mol Microbiol
, vol.51
, pp. 407-417
-
-
Cendrowski, S.1
MacArthur, W.2
Hanna, P.3
-
18
-
-
57049084193
-
Inhibition of Bacillus anthracis spore outgrowth by nisin
-
Gut IM, Prouty AM, Ballard JD, van der Donk WA, Blanke SR, (2008) Inhibition of Bacillus anthracis spore outgrowth by nisin. Antimicrob Agents Chemother 52: 4281-4288.
-
(2008)
Antimicrob Agents Chemother
, vol.52
, pp. 4281-4288
-
-
Gut, I.M.1
Prouty, A.M.2
Ballard, J.D.3
van der Donk, W.A.4
Blanke, S.R.5
-
19
-
-
70349503583
-
Transcriptional profiling of Bacillus anthracis Sterne (34F2) during iron starvation
-
Carlson PE Jr, Carr KA, Janes BK, Anderson EC, Hanna PC, (2009) Transcriptional profiling of Bacillus anthracis Sterne (34F2) during iron starvation. PLoS One 4: e6988.
-
(2009)
PLoS One
, vol.4
-
-
Carlson Jr., P.E.1
Carr, K.A.2
Janes, B.K.3
Anderson, E.C.4
Hanna, P.C.5
-
20
-
-
63349108274
-
Comparative transcriptional profiling of Bacillus cereus sensu lato strains during growth in CO2-bicarbonate and aerobic atmospheres
-
Passalacqua KD, Varadarajan A, Byrd B, Bergman NH, (2009) Comparative transcriptional profiling of Bacillus cereus sensu lato strains during growth in CO2-bicarbonate and aerobic atmospheres. PLoS One 4: e4904.
-
(2009)
PLoS One
, vol.4
-
-
Passalacqua, K.D.1
Varadarajan, A.2
Byrd, B.3
Bergman, N.H.4
-
21
-
-
34249791184
-
The global transcriptional responses of Bacillus anthracis Sterne (34F2) and a Delta sodA1 mutant to paraquat reveal metal ion homeostasis imbalances during endogenous superoxide stress
-
Passalacqua KD, Bergman NH, Lee JY, Sherman DH, Hanna PC, (2007) The global transcriptional responses of Bacillus anthracis Sterne (34F2) and a Delta sodA1 mutant to paraquat reveal metal ion homeostasis imbalances during endogenous superoxide stress. J Bacteriol 189: 3996-4013.
-
(2007)
J Bacteriol
, vol.189
, pp. 3996-4013
-
-
Passalacqua, K.D.1
Bergman, N.H.2
Lee, J.Y.3
Sherman, D.H.4
Hanna, P.C.5
-
22
-
-
34447252169
-
Transcriptional profiling of Bacillus anthracis during infection of host macrophages
-
Bergman NH, Anderson EC, Swenson EE, Janes BK, Fisher N, et al. (2007) Transcriptional profiling of Bacillus anthracis during infection of host macrophages. Infect Immun 75: 3434-3444.
-
(2007)
Infect Immun
, vol.75
, pp. 3434-3444
-
-
Bergman, N.H.1
Anderson, E.C.2
Swenson, E.E.3
Janes, B.K.4
Fisher, N.5
-
23
-
-
33748987913
-
Transcriptional profiling of the Bacillus anthracis life cycle in vitro and an implied model for regulation of spore formation
-
Bergman NH, Anderson EC, Swenson EE, Niemeyer MM, Miyoshi AD, et al. (2006) Transcriptional profiling of the Bacillus anthracis life cycle in vitro and an implied model for regulation of spore formation. J Bacteriol 188: 6092-6100.
-
(2006)
J Bacteriol
, vol.188
, pp. 6092-6100
-
-
Bergman, N.H.1
Anderson, E.C.2
Swenson, E.E.3
Niemeyer, M.M.4
Miyoshi, A.D.5
-
24
-
-
4644309277
-
Order and disorder in bacterial genomes
-
Rocha EP, (2004) Order and disorder in bacterial genomes. Curr Opin Microbiol 7: 519-527.
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 519-527
-
-
Rocha, E.P.1
-
25
-
-
77952274420
-
Bacillus anthracis genome organization in light of whole transcriptome sequencing
-
Martin J, Zhu W, Passalacqua KD, Bergman N, Borodovsky M, (2010) Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics 11 Suppl 3: S10.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Martin, J.1
Zhu, W.2
Passalacqua, K.D.3
Bergman, N.4
Borodovsky, M.5
-
26
-
-
0038752613
-
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
-
Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, et al. (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423: 81-86.
-
(2003)
Nature
, vol.423
, pp. 81-86
-
-
Read, T.D.1
Peterson, S.N.2
Tourasse, N.3
Baillie, L.W.4
Paulsen, I.T.5
-
27
-
-
58149500119
-
The complete genome sequence of Bacillus anthracis Ames "Ancestor"
-
Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, et al. (2009) The complete genome sequence of Bacillus anthracis Ames "Ancestor". J Bacteriol 191: 445-446.
-
(2009)
J Bacteriol
, vol.191
, pp. 445-446
-
-
Ravel, J.1
Jiang, L.2
Stanley, S.T.3
Wilson, M.R.4
Decker, R.S.5
-
28
-
-
57149085481
-
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
-
t Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, et al. (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36: e141.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
t Hoen, P.A.1
Ariyurek, Y.2
Thygesen, H.H.3
Vreugdenhil, E.4
Vossen, R.H.5
-
29
-
-
56649108210
-
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
-
Ondov BD, Varadarajan A, Passalacqua KD, Bergman NH, (2008) Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics 24: 2776-2777.
-
(2008)
Bioinformatics
, vol.24
, pp. 2776-2777
-
-
Ondov, B.D.1
Varadarajan, A.2
Passalacqua, K.D.3
Bergman, N.H.4
-
31
-
-
40449100030
-
Direct multiplexed measurement of gene expression with color-coded probe pairs
-
Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, et al. (2008) Direct multiplexed measurement of gene expression with color-coded probe pairs. Nature biotechnology 26: 317-325.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 317-325
-
-
Geiss, G.K.1
Bumgarner, R.E.2
Birditt, B.3
Dahl, T.4
Dowidar, N.5
-
32
-
-
58449118337
-
The organization of the bacterial genome
-
Rocha EP, (2008) The organization of the bacterial genome. Annu Rev Genet 42: 211-233.
-
(2008)
Annu Rev Genet
, vol.42
, pp. 211-233
-
-
Rocha, E.P.1
-
33
-
-
0344668838
-
Gene essentiality determines chromosome organisation in bacteria
-
Rocha EP, Danchin A, (2003) Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res 31: 6570-6577.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 6570-6577
-
-
Rocha, E.P.1
Danchin, A.2
-
34
-
-
0042667165
-
Essentiality, not expressiveness, drives gene-strand bias in bacteria
-
Rocha EP, Danchin A, (2003) Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat Genet 34: 377-378.
-
(2003)
Nat Genet
, vol.34
, pp. 377-378
-
-
Rocha, E.P.1
Danchin, A.2
-
35
-
-
0028908039
-
Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex
-
Liu B, Alberts BM, (1995) Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science 267: 1131-1137.
-
(1995)
Science
, vol.267
, pp. 1131-1137
-
-
Liu, B.1
Alberts, B.M.2
-
36
-
-
0024276903
-
When polymerases collide: replication and the transcriptional organization of the E. coli chromosome
-
Brewer BJ, (1988) When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 53: 679-686.
-
(1988)
Cell
, vol.53
, pp. 679-686
-
-
Brewer, B.J.1
-
37
-
-
69749123311
-
Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target
-
Figueroa-Bossi N, Valentini M, Malleret L, Fiorini F, Bossi L, (2009) Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev 23: 2004-2015.
-
(2009)
Genes Dev
, vol.23
, pp. 2004-2015
-
-
Figueroa-Bossi, N.1
Valentini, M.2
Malleret, L.3
Fiorini, F.4
Bossi, L.5
-
38
-
-
68349141373
-
RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation
-
Dawid A, Cayrol B, Isambert H, (2009) RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation. Phys Biol 6: 025007.
-
(2009)
Phys Biol
, vol.6
, pp. 025007
-
-
Dawid, A.1
Cayrol, B.2
Isambert, H.3
-
39
-
-
0028106101
-
Genetic and physiological studies of Bacillus subtilis sigma A mutants defective in promoter melting
-
Rong JC, Helmann JD, (1994) Genetic and physiological studies of Bacillus subtilis sigma A mutants defective in promoter melting. J Bacteriol 176: 5218-5224.
-
(1994)
J Bacteriol
, vol.176
, pp. 5218-5224
-
-
Rong, J.C.1
Helmann, J.D.2
-
40
-
-
14844363122
-
Proteomic analysis of Bacillus anthracis Sterne vegetative cells
-
Francis AW, Ruggiero CE, Koppisch AT, Dong J, Song J, et al. (2005) Proteomic analysis of Bacillus anthracis Sterne vegetative cells. Biochim Biophys Acta 1748: 191-200.
-
(2005)
Biochim Biophys Acta
, vol.1748
, pp. 191-200
-
-
Francis, A.W.1
Ruggiero, C.E.2
Koppisch, A.T.3
Dong, J.4
Song, J.5
-
41
-
-
34547640042
-
Structure, assembly, and function of the spore surface layers
-
Henriques AO, Moran CP Jr, (2007) Structure, assembly, and function of the spore surface layers. Annu Rev Microbiol 61: 555-588.
-
(2007)
Annu Rev Microbiol
, vol.61
, pp. 555-588
-
-
Henriques, A.O.1
Moran Jr., C.P.2
-
42
-
-
0030457111
-
Molecular genetics of sporulation in Bacillus subtilis
-
Stragier P, Losick R, (1996) Molecular genetics of sporulation in Bacillus subtilis. Annu Rev Genet 30: 297-241.
-
(1996)
Annu Rev Genet
, vol.30
, pp. 241-297
-
-
Stragier, P.1
Losick, R.2
-
43
-
-
70349309158
-
Display of proteins on Bacillus subtilis endospores
-
Kim J, Schumann W, (2009) Display of proteins on Bacillus subtilis endospores. Cell Mol Life Sci 66: 3127-3136.
-
(2009)
Cell Mol Life Sci
, vol.66
, pp. 3127-3136
-
-
Kim, J.1
Schumann, W.2
-
44
-
-
75149171079
-
A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation
-
Hahne H, Mader U, Otto A, Bonn F, Steil L, et al. (2010) A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation. J Bacteriol 192: 870-882.
-
(2010)
J Bacteriol
, vol.192
, pp. 870-882
-
-
Hahne, H.1
Mader, U.2
Otto, A.3
Bonn, F.4
Steil, L.5
-
45
-
-
0035724157
-
Genome-wide analysis of the general stress response in Bacillus subtilis
-
Price CW, Fawcett P, Ceremonie H, Su N, Murphy CK, et al. (2001) Genome-wide analysis of the general stress response in Bacillus subtilis. Mol Microbiol 41: 757-774.
-
(2001)
Mol Microbiol
, vol.41
, pp. 757-774
-
-
Price, C.W.1
Fawcett, P.2
Ceremonie, H.3
Su, N.4
Murphy, C.K.5
-
46
-
-
33645108507
-
Adaptation of Bacillus subtilis to growth at low temperature: a combined transcriptomic and proteomic appraisal
-
Budde I, Steil L, Scharf C, Volker U, Bremer E, (2006) Adaptation of Bacillus subtilis to growth at low temperature: a combined transcriptomic and proteomic appraisal. Microbiology 152: 831-853.
-
(2006)
Microbiology
, vol.152
, pp. 831-853
-
-
Budde, I.1
Steil, L.2
Scharf, C.3
Volker, U.4
Bremer, E.5
-
47
-
-
0142214662
-
Genome-wide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity
-
Steil L, Hoffmann T, Budde I, Volker U, Bremer E, (2003) Genome-wide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity. J Bacteriol 185: 6358-6370.
-
(2003)
J Bacteriol
, vol.185
, pp. 6358-6370
-
-
Steil, L.1
Hoffmann, T.2
Budde, I.3
Volker, U.4
Bremer, E.5
-
48
-
-
45649084041
-
The mean and noise of stochastic gene transcription
-
Tang M, (2008) The mean and noise of stochastic gene transcription. J Theor Biol 253: 271-280.
-
(2008)
J Theor Biol
, vol.253
, pp. 271-280
-
-
Tang, M.1
-
49
-
-
58549120549
-
Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters
-
Lei J, (2009) Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters. J Theor Biol 256: 485-492.
-
(2009)
J Theor Biol
, vol.256
, pp. 485-492
-
-
Lei, J.1
-
50
-
-
67650319009
-
Single-molecule approaches to stochastic gene expression
-
Raj A, van Oudenaarden A, (2009) Single-molecule approaches to stochastic gene expression. Annu Rev Biophys 38: 255-270.
-
(2009)
Annu Rev Biophys
, vol.38
, pp. 255-270
-
-
Raj, A.1
van Oudenaarden, A.2
-
51
-
-
53549123008
-
Nature, nurture, or chance: stochastic gene expression and its consequences
-
Raj A, van Oudenaarden A, (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216-226.
-
(2008)
Cell
, vol.135
, pp. 216-226
-
-
Raj, A.1
van Oudenaarden, A.2
-
52
-
-
11344293422
-
Spatial patterns of transcriptional activity in the chromosome of Escherichia coli
-
Jeong KS, Ahn J, Khodursky AB, (2004) Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biol 5: R86.
-
(2004)
Genome Biol
, vol.5
-
-
Jeong, K.S.1
Ahn, J.2
Khodursky, A.B.3
-
53
-
-
77951115595
-
RNA dust: where are the genes?
-
Carninci P, (2010) RNA dust: where are the genes? DNA Res 17: 51-59.
-
(2010)
DNA Res
, vol.17
, pp. 51-59
-
-
Carninci, P.1
|