-
1
-
-
77749296117
-
Genome Update: The Thousandth Genome-A Cautionary Tale
-
10.1099/mic.0.038257-0 20093288
-
Genome Update: The Thousandth Genome-A Cautionary Tale. Lagesen K, Ussery DW, Wassenaar TM, Microbiology 2010 156 603 608 10.1099/mic.0.038257-0 20093288
-
(2010)
Microbiology
, vol.156
, pp. 603-608
-
-
Lagesen, K.1
Ussery, D.W.2
Wassenaar, T.M.3
-
2
-
-
0037387973
-
A survey of small RNA-encoding genes in Escherichia coli
-
DOI 10.1093/nar/gkg297
-
A survey of small RNA-encoding genes in Escherichia coli. Hershberg R, Altuvia S, Margalit H, Nucleic Acids Res 2003 31 1813 1820 10.1093/nar/gkg297 12654996 (Pubitemid 36432687)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.7
, pp. 1813-1820
-
-
Hershberg, R.1
Altuvia, S.2
Margalit, H.3
-
3
-
-
19544390556
-
MtbRegList, a database dedicated to the analysis of transcriptional regulation of Mycobacterium tuberculosis
-
DOI 10.1093/bioinformatics/bti321
-
MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis. Jacques PE, Gervais AL, Cantin M, Lucier JF, Dallaire G, Drouin G, Gaudreau L, Goulet J, Brzezinski R, Bioinformatics 2005 21 2563 2565 10.1093/bioinformatics/bti321 15722376 (Pubitemid 40731630)
-
(2005)
Bioinformatics
, vol.21
, Issue.10
, pp. 2563-2565
-
-
Jacques, P.-E.1
Gervais, A.L.2
Cantin, M.3
Lucier, J.-F.4
Dallaire, G.5
Drouin, G.6
Gaudreau, L.7
Goulet, J.8
Brzezinski, R.9
-
4
-
-
13444262374
-
EcoCyc: A comprehensive database resource for Escherichia coli
-
15608210
-
EcoCyc: a comprehensive database resource for Escherichia coli. Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD, Nucleic Acids Res 2005 33 334 337 15608210
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4334-337
-
-
Keseler, I.M.1
Collado-Vides, J.2
Gama-Castro, S.3
Ingraham, J.4
Paley, S.5
Paulsen, I.T.6
Peralta-Gil, M.7
Karp, P.D.8
-
5
-
-
0347126296
-
DBTBS: Database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
-
10.1093/nar/gkh074 14681362
-
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Makita Y, Nakao M, Ogasawara N, Nakai K, Nucleic Acids Res 2004 32 75 77 10.1093/nar/gkh074 14681362
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 475-77
-
-
Makita, Y.1
Nakao, M.2
Ogasawara, N.3
Nakai, K.4
-
6
-
-
9144270496
-
RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
-
10.1093/nar/gkh140 14681419
-
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, Collado-Vides J, Nucleic Acids Res 2004 32 303 306 10.1093/nar/gkh140 14681419
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 4303-306
-
-
Salgado, H.1
Gama-Castro, S.2
Martinez-Antonio, A.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Peralta-Gil, M.6
Garcia-Alonso, D.7
Jimenez-Jacinto, V.8
Santos-Zavaleta, A.9
Bonavides-Martinez, C.10
Collado-Vides, J.11
-
7
-
-
65549099632
-
Structure and complexity of a bacterial transcriptome
-
10.1128/JB.00122-09 19304856
-
Structure and complexity of a bacterial transcriptome. Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH, J Bacteriol 2009 191 3203 3211 10.1128/JB.00122-09 19304856
-
(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
Bergman, N.H.6
-
8
-
-
74949137952
-
A single-base resolution map of an archaeal transcriptome
-
10.1101/gr.100396.109 19884261
-
A single-base resolution map of an archaeal transcriptome. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R, Genome Res 2010 20 133 141 10.1101/gr.100396.109 19884261
-
(2010)
Genome Res
, vol.20
, pp. 133-141
-
-
Wurtzel, O.1
Sapra, R.2
Chen, F.3
Zhu, Y.4
Simmons, B.A.5
Sorek, R.6
-
9
-
-
77951041162
-
Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity
-
10.1128/JB.01445-09 20190049
-
Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, Grills G, Schweitzer P, Wang W, Schroth GP, Luo S, et al. J Bacteriol 2010 192 2359 2372 10.1128/JB.01445-09 20190049
-
(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
Grills, G.6
Schweitzer, P.7
Wang, W.8
Schroth, G.P.9
Luo, S.10
-
10
-
-
77949425194
-
The primary transcriptome of the major human pathogen Helicobacter pylori
-
10.1038/nature08756 20164839
-
The primary transcriptome of the major human pathogen Helicobacter pylori. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermuller J, Reinhardt R, et al. Nature 2010 464 250 255 10.1038/nature08756 20164839
-
(2010)
Nature
, vol.464
, pp. 250-255
-
-
Sharma, C.M.1
Hoffmann, S.2
Darfeuille, F.3
Reignier, J.4
Findeiss, S.5
Sittka, A.6
Chabas, S.7
Reiche, K.8
Hackermuller, J.9
Reinhardt, R.10
-
11
-
-
0037250153
-
PRODORIC: Prokaryotic database of gene regulation
-
DOI 10.1093/nar/gkg037
-
PRODORIC: prokaryotic database of gene regulation. Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D, Nucleic Acids Res 2003 31 266 269 10.1093/nar/gkg037 12519998 (Pubitemid 36150381)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 266-269
-
-
Munch, R.1
Hiller, K.2
Barg, H.3
Heldt, D.4
Linz, S.5
Wingender, E.6
Jahn, D.7
-
12
-
-
26444432309
-
Detection of single DNA molecules by multicolor quantum-dot end-labeling
-
DOI 10.1093/nar/gni097
-
TRACTOR-DB: a database of regulatory networks in gamma-proteobacterial genomes. Gonzalez AD, Espinosa V, Vasconcelos AT, Perez-Rueda E, Collado-Vides J, Nucleic Acids Res 2005 33 98 102 10.1093/nar/gni097 15608293 (Pubitemid 41430593)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.11
, pp. 1-9
-
-
Crut, A.1
Geron-Landre, B.2
Bonnet, I.3
Bonneau, S.4
Desbiolles, P.5
Escude, C.6
-
13
-
-
33846107772
-
RegTransBase - A database of regulatory sequences and interactions in a wide range of prokaryotic genomes
-
DOI 10.1093/nar/gkl865
-
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I, Nucleic Acids Res 2007 35 407 412 10.1093/nar/gkl865 17142223 (Pubitemid 46056241)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Kazakov, A.E.1
Cipriano, M.J.2
Novichkov, P.S.3
Minovitsky, S.4
Vinogradov, D.V.5
Arkin, A.6
Mironov, A.A.7
Gelfand, M.S.8
Dubchak, I.9
-
14
-
-
33846067980
-
SwissRegulon: A database of genome-wide annotations of regulatory sites
-
DOI 10.1093/nar/gkl857
-
SwissRegulon: a database of genome-wide annotations of regulatory sites. Pachkov M, Erb I, Molina N, van Nimwegen E, Nucleic Acids Res 2007 35 127 131 10.1093/nar/gkl857 17130146 (Pubitemid 46056183)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Pachkov, M.1
Erb, I.2
Molina, N.3
Van Nimwegen, E.4
-
15
-
-
34547576614
-
SCOPE: A web server for practical de novo motif discovery
-
10.1093/nar/gkm310 17485471
-
SCOPE: a web server for practical de novo motif discovery. Carlson JM, Chakravarty A, DeZiel CE, Gross RH, Nucleic Acids Res 2007 35 259 264 10.1093/nar/gkm310 17485471
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 23259-264
-
-
Carlson, J.M.1
Chakravarty, A.2
Deziel, C.E.3
Gross, R.H.4
-
16
-
-
34548100947
-
A novel ensemble learning method for de novo computational identification of DNA binding sites
-
DOI 10.1186/1471-2105-8-249
-
A novel ensemble learning method for de novo computational identification of DNA binding sites. Chakravarty A, Carlson JM, Khetani RS, Gross RH, BMC Bioinformatics 2007 8 249 10.1186/1471-2105-8-249 17626633 (Pubitemid 47287982)
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 249
-
-
Chakravarty, A.1
Carlson, J.M.2
Khetani, R.S.3
Gross, R.H.4
-
17
-
-
32144448660
-
Improved prediction of bacterial transcription start sites
-
DOI 10.1093/bioinformatics/bti771
-
Improved prediction of bacterial transcription start sites. Gordon JJ, Towsey MW, Hogan JM, Mathews SA, Timms P, Bioinformatics 2006 22 142 148 10.1093/bioinformatics/bti771 16287942 (Pubitemid 43205399)
-
(2006)
Bioinformatics
, vol.22
, Issue.2
, pp. 142-148
-
-
Gordon, J.J.1
Towsey, M.W.2
Hogan, J.M.3
Mathews, S.A.4
Timms, P.5
-
18
-
-
0142241306
-
Sequence alignment kernel for recognition of promoter regions
-
DOI 10.1093/bioinformatics/btg265
-
Sequence alignment kernel for recognition of promoter regions. Gordon L, Chervonenkis AY, Gammerman AJ, Shahmuradov IA, Solovyev VV, Bioinformatics 2003 19 1964 1971 10.1093/bioinformatics/btg265 14555630 (Pubitemid 37322341)
-
(2003)
Bioinformatics
, vol.19
, Issue.15
, pp. 1964-1971
-
-
Gordon, L.1
Chervonenkis, A.Ya.2
Gammerman, A.J.3
Shahmuradov, I.A.4
Solovyev, V.V.5
-
19
-
-
33750200659
-
Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs
-
DOI 10.1186/1471-2105-7-423
-
Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. Jacques PE, Rodrigue S, Gaudreau L, Goulet J, Brzezinski R, BMC Bioinformatics 2006 7 423 10.1186/1471-2105-7-423 17014715 (Pubitemid 44604853)
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 423
-
-
Jacques, P.-E.1
Rodrigue, S.2
Gaudreau, L.3
Goulet, J.4
Brzezinski, R.5
-
20
-
-
33846923330
-
A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts
-
10.1093/nar/gkm221 17170007
-
A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts. Mann S, Li J, Chen YP, Nucleic Acids Res 2007 35 12 10.1093/nar/gkm221 17170007
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 512
-
-
Mann, S.1
Li, J.2
Chen, Y.P.3
-
21
-
-
0034740227
-
Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome
-
DOI 10.1016/S0097-8485(01)00099-7, PII S0097848501000997
-
Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Reese MG, Comput Chem 2001 26 51 56 10.1016/S0097-8485(01)00099-7 11765852 (Pubitemid 33034559)
-
(2001)
Computers and Chemistry
, vol.26
, Issue.1
, pp. 51-56
-
-
Reese, M.G.1
-
22
-
-
0042622334
-
PromH: Promoters identification using orthologous genomic sequences
-
DOI 10.1093/nar/gkg525
-
PromH: Promoters identification using orthologous genomic sequences. Solovyev VV, Shahmuradov IA, Nucleic Acids Res 2003 31 3540 3545 10.1093/nar/gkg525 12824362 (Pubitemid 37442194)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3540-3545
-
-
Solovyev, V.V.1
Shahmuradov, I.A.2
-
23
-
-
0037332383
-
54-dependent transcriptional activators
-
DOI 10.1128/JB.185.6.1757-1767.2003
-
Domain architectures of sigma54-dependent transcriptional activators. Studholme DJ, Dixon R, J Bacteriol 2003 185 1757 1767 10.1128/JB.185.6.1757- 1767.2003 12618438 (Pubitemid 36297874)
-
(2003)
Journal of Bacteriology
, vol.185
, Issue.6
, pp. 1757-1767
-
-
Studholme, D.J.1
Dixon, R.2
-
24
-
-
44849092251
-
Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes
-
DOI 10.1186/1471-2105-9-233
-
Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes. Dekhtyar M, Morin A, Sakanyan V, BMC Bioinformatics 2008 9 233 10.1186/1471-2105-9-233 18471287 (Pubitemid 351796655)
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 233
-
-
Dekhtyar, M.1
Morin, A.2
Sakanyan, V.3
-
25
-
-
39049170386
-
Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription
-
DOI 10.1101/gr.6905408
-
Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription. Du Z, Zhao Y, Li N, Genome Res 2008 18 233 241 10.1101/gr.6905408 18096746 (Pubitemid 351240733)
-
(2008)
Genome Research
, vol.18
, Issue.2
, pp. 233-241
-
-
Du, Z.1
Zhao, Y.2
Li, N.3
-
26
-
-
20344396385
-
Structural properties of promoters: Similarities and differences between prokaryotes and eukaryotes
-
DOI 10.1093/nar/gki627
-
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Kanhere A, Bansal M, Nucleic Acids Res 2005 33 3165 3175 10.1093/nar/gki627 15939933 (Pubitemid 41194460)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.10
, pp. 3165-3175
-
-
Kanhere, A.1
Bansal, M.2
-
27
-
-
33745121203
-
Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation
-
10.1101/gr.4508806 16651665
-
Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Rawal P, Kummarasetti VB, Ravindran J, Kumar N, Halder K, Sharma R, Mukerji M, Das SK, Chowdhury S, Genome Res 2006 16 644 655 10.1101/gr.4508806 16651665
-
(2006)
Genome Res
, vol.16
, pp. 644-655
-
-
Rawal, P.1
Kummarasetti, V.B.2
Ravindran, J.3
Kumar, N.4
Halder, K.5
Sharma, R.6
Mukerji, M.7
Das, S.K.8
Chowdhury, S.9
-
28
-
-
33646867391
-
Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress
-
DOI 10.1186/1471-2105-7-248
-
Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. Wang H, Benham CJ, BMC Bioinformatics 2006 7 248 10.1186/1471-2105-7-248 16677393 (Pubitemid 43786591)
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 248
-
-
Wang, H.1
Benham, C.J.2
-
29
-
-
38549092075
-
QuadBase: Genome-wide database of G4 DNA - Occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
-
17962308
-
QuadBase: genome-wide database of G4 DNA - occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes. Yadav VK, Abraham JK, Mani P, Kulshrestha R, Chowdhury S, Nucleic Acids Res 2008 36 381 385 17962308
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 4381-385
-
-
Yadav, V.K.1
Abraham, J.K.2
Mani, P.3
Kulshrestha, R.4
Chowdhury, S.5
-
30
-
-
68549098194
-
A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles
-
10.1093/bioinformatics/btp359 19515962
-
A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles. Gan Y, Guan J, Zhou S, Bioinformatics 2009 25 2006 2012 10.1093/bioinformatics/btp359 19515962
-
(2009)
Bioinformatics
, vol.25
, pp. 2006-2012
-
-
Gan, Y.1
Guan, J.2
Zhou, S.3
-
31
-
-
8844258763
-
BacTregulators: A database of transcriptional regulators in bacteria and archaea
-
DOI 10.1093/bioinformatics/bth330
-
BacTregulators: a database of transcriptional regulators in bacteria and archaea. Martinez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R, Bioinformatics 2004 20 2787 2791 10.1093/bioinformatics/bth330 15166024 (Pubitemid 39530165)
-
(2004)
Bioinformatics
, vol.20
, Issue.16
, pp. 2787-2791
-
-
Martinez-Bueno, M.1
Molina-Henares, A.J.2
Pareja, E.3
Ramos, J.L.4
Tobes, R.5
-
32
-
-
33646242970
-
ExtraTrain: A database of Extragenic regions and Transcriptional information in prokaryotic organisms
-
10.1186/1471-2180-6-29 16539733
-
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms. Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R, BMC Microbiol 2006 6 29 10.1186/1471-2180-6-29 16539733
-
(2006)
BMC Microbiol
, vol.6
, pp. 29
-
-
Pareja, E.1
Pareja-Tobes, P.2
Manrique, M.3
Pareja-Tobes, E.4
Bonal, J.5
Tobes, R.6
-
33
-
-
3242879355
-
PredictRegulon: A web server for the prediction of the regulatory protein in binding sites and operons in prokaryote genomes
-
DOI 10.1093/nar/gkh364
-
PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes. Yellaboina S, Seshadri J, Kumar MS, Ranjan A, Nucleic Acids Res 2004 32 318 320 10.1093/nar/gkh364 15215402 (Pubitemid 38997351)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.WEB SERVER ISS.
-
-
Yellaboina, S.1
Seshadri, J.2
Kumar, M.S.3
Ranjan, A.4
-
34
-
-
13244287791
-
A novel method for prokaryotic promoter prediction based on DNA stability
-
DOI 10.1186/1471-2105-6-1
-
A novel method for prokaryotic promoter prediction based on DNA stability. Kanhere A, Bansal M, BMC Bioinformatics 2005 6 1 10.1186/1471-2105-6- 1 15631638 (Pubitemid 40195436)
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 1
-
-
Kanhere, A.1
Bansal, M.2
-
35
-
-
72949097205
-
Relative stability of DNA as a generic criterion for promoter prediction: Whole genome annotation of microbial genomes with varying nucleotide base composition
-
10.1039/b906535k 19593472
-
Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition. Rangannan V, Bansal M, Mol Biosyst 2009 5 1758 1769 10.1039/b906535k 19593472
-
(2009)
Mol Biosyst
, vol.5
, pp. 1758-1769
-
-
Rangannan, V.1
Bansal, M.2
-
36
-
-
79951736762
-
High Quality Annotation of Promoter Regions for 913 Bacterial Genomes
-
10.1093/bioinformatics/btq577 20956245
-
High Quality Annotation of Promoter Regions for 913 Bacterial Genomes. Rangannan V, Bansal M, Bioinformatics 2010 26 3043 3050 10.1093/bioinformatics/ btq577 20956245
-
(2010)
Bioinformatics
, vol.26
, pp. 3043-3050
-
-
Rangannan, V.1
Bansal, M.2
-
37
-
-
0347627539
-
Transcription-coupled TA and GC strand asymmetries in the human genome
-
DOI 10.1016/S0014-5793(03)01306-1
-
Transcription-coupled TA and GC strand asymmetries in the human genome. Touchon M, Nicolay S, Arneodo A, d'Aubenton-Carafa Y, Thermes C, FEBS Lett 2003 555 579 582 10.1016/S0014-5793(03)01306-1 14675777 (Pubitemid 37532614)
-
(2003)
FEBS Letters
, vol.555
, Issue.3
, pp. 579-582
-
-
Touchon, M.1
Nicolay, S.2
Arneodo, A.3
D'Aubenton-Carafa, Y.4
Thermes, C.5
-
38
-
-
29244434529
-
A study on the correlation of nucleotide skews and the positioning of the origin of replication: Different modes of replication in bacterial species
-
DOI 10.1093/nar/gki988
-
A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species. Nikolaou C, Almirantis Y, Nucleic Acids Res 2005 33 6816 6822 10.1093/nar/gki988 16321966 (Pubitemid 41830487)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.21
, pp. 6816-6822
-
-
Nikolaou, C.1
Almirantis, Y.2
-
39
-
-
25444443669
-
GC-compositional strand bias around transcription start sites in plants and fungi
-
DOI 10.1186/1471-2164-6-26
-
GC-compositional strand bias around transcription start sites in plants and fungi. Fujimori S, Washio T, Tomita M, BMC Genomics 2005 6 26 10.1186/1471-2164-6-26 15733327 (Pubitemid 41357709)
-
(2005)
BMC Genomics
, vol.6
, pp. 26
-
-
Fujimori, S.1
Washio, T.2
Tomita, M.3
-
40
-
-
0029985398
-
Asymmetric substitution patterns in the two DNA strands of bacteria
-
Asymmetric substitution patterns in the two DNA strands of bacteria. Lobry JR, Mol Biol Evol 1996 13 660 665 8676740 (Pubitemid 26131887)
-
(1996)
Molecular Biology and Evolution
, vol.13
, Issue.5
, pp. 660-665
-
-
Lobry, J.R.1
-
41
-
-
0011202428
-
Structural variations observed in DNA crystal structures and their implications for protein-DNA interactions
-
Structural variations observed in DNA crystal structures and their implications for protein-DNA interactions. Bansal M, Biological structure and Dynamics, Proceedings of the Ninth Conversation 1996 I 121 134
-
(1996)
Biological Structure and Dynamics, Proceedings of the Ninth Conversation
, vol.1
, pp. 121-134
-
-
Bansal, M.1
-
42
-
-
0026089491
-
Curved DNA without A-A: Experimental estimation of all 16 DNA wedge angles
-
Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Bolshoy A, McNamara P, Harrington RE, Trifonov EN, Proc Natl Acad Sci USA 1991 88 2312 2316 10.1073/pnas.88.6.2312 2006170 (Pubitemid 21916406)
-
(1991)
Proceedings of the National Academy of Sciences of the United States of America
, vol.88
, Issue.6
, pp. 2312-2316
-
-
Bolshoy, A.1
Mcnamara, P.2
Harrington, R.E.3
Trifonov, E.N.4
-
43
-
-
0028826669
-
Trinucleotide models for DNA bending propensity: Comparison of models based on DNaseI digestion and nucleosome packaging data
-
8579790
-
Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data. Brukner I, Sanchez R, Suck D, Pongor S, J Biomol Struct Dyn 1995 13 309 317 8579790
-
(1995)
J Biomol Struct Dyn
, vol.13
, pp. 309-317
-
-
Brukner, I.1
Sanchez, R.2
Suck, D.3
Pongor, S.4
-
44
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
DOI 10.1016/0022-2836(86)90452-3
-
Sequence periodicities in chicken nucleosome core DNA. Satchwell SC, Drew HR, Travers AA, J Mol Biol 1986 191 659 675 10.1016/0022-2836(86)90452-3 3806678 (Pubitemid 17185964)
-
(1986)
Journal of Molecular Biology
, vol.191
, Issue.4
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.R.2
Travers, A.A.3
-
45
-
-
39049168212
-
Generic eukaryotic core promoter prediction using structural features of DNA
-
DOI 10.1101/gr.6991408
-
Generic eukaryotic core promoter prediction using structural features of DNA. Abeel T, Saeys Y, Bonnet E, Rouze P, Van de Peer Y, Genome Res 2008 18 310 323 10.1101/gr.6991408 18096745 (Pubitemid 351240741)
-
(2008)
Genome Research
, vol.18
, Issue.2
, pp. 310-323
-
-
Abeel, T.1
Saeys, Y.2
Bonnet, E.3
Rouze, P.4
Van De Peer, Y.5
-
46
-
-
80052259511
-
Analysis of DNA sequence dependent structural properties in prokaryotic genomes
-
(Poster E-33) 20976873
-
Analysis of DNA sequence dependent structural properties in prokaryotic genomes. Rangannan V, Bansal M, ECCB10; Ghent, Belgium 2010 (Poster No. E-33) 20976873
-
(2010)
ECCB10; Ghent, Belgium
-
-
Rangannan, V.1
Bansal, M.2
-
47
-
-
0033935187
-
The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes
-
The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. Tillier ER, Collins RA, J Mol Evol 2000 50 249 257 10754068 (Pubitemid 30429979)
-
(2000)
Journal of Molecular Evolution
, vol.50
, Issue.3
, pp. 249-257
-
-
Tillier, E.R.M.1
Collins, R.A.2
-
48
-
-
35348860808
-
A new method for assessing the effect of replication on DNA base composition asymmetry
-
DOI 10.1093/molbev/msm148
-
A new method for assessing the effect of replication on DNA base composition asymmetry. Necsulea A, Lobry JR, Mol Biol Evol 2007 24 2169 2179 10.1093/molbev/msm148 17646257 (Pubitemid 47574719)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.10
, pp. 2169-2179
-
-
Necsulea, A.1
Lobry, J.R.2
-
49
-
-
10944235924
-
Comparative genomic structure of prokaryotes
-
DOI 10.1146/annurev.genet.38.072902.094318
-
Comparative genomic structure of prokaryotes. Bentley SD, Parkhill J, Annu Rev Genet 2004 38 771 792 10.1146/annurev.genet.38.072902.094318 15568993 (Pubitemid 40013745)
-
(2004)
Annual Review of Genetics
, vol.38
, pp. 771-792
-
-
Bentley, S.D.1
Parkhill, J.2
-
50
-
-
33745067721
-
Ten years of bacterial genome sequencing: Comparative-genomics-based discoveries
-
DOI 10.1007/s10142-006-0027-2
-
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW, Funct Integr Genomics 2006 6 165 185 10.1007/s10142-006-0027-2 16773396 (Pubitemid 43885067)
-
(2006)
Functional and Integrative Genomics
, vol.6
, Issue.3
, pp. 165-185
-
-
Binnewies, T.T.1
Motro, Y.2
Hallin, P.F.3
Lund, O.4
Dunn, D.5
La, T.6
Hampson, D.J.7
Bellgard, M.8
Wassenaar, T.M.9
Ussery, D.W.10
-
51
-
-
57149085868
-
Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world
-
10.1093/nar/gkn668 18948295
-
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Koonin EV, Wolf YI, Nucleic Acids Res 2008 36 6688 6719 10.1093/nar/gkn668 18948295
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 6688-6719
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
52
-
-
0014151680
-
Altered base ratios in the DNA of an Escherichia coli mutator strain
-
10.1073/pnas.58.5.1895 4866980
-
Altered base ratios in the DNA of an Escherichia coli mutator strain. Cox EC, Yanofsky C, Proc Natl Acad Sci USA 1967 58 1895 1902 10.1073/pnas.58.5.1895 4866980
-
(1967)
Proc Natl Acad Sci USA
, vol.58
, pp. 1895-1902
-
-
Cox, E.C.1
Yanofsky, C.2
-
53
-
-
3643052747
-
On the genetic basis of variation and heterogeneity of DNA base composition
-
10.1073/pnas.48.4.582 13918161
-
On the genetic basis of variation and heterogeneity of DNA base composition. Sueoka N, Proc Natl Acad Sci USA 1962 48 582 592 10.1073/pnas.48.4.582 13918161
-
(1962)
Proc Natl Acad Sci USA
, vol.48
, pp. 582-592
-
-
Sueoka, N.1
-
54
-
-
0345490693
-
On dynamics of overlapping genes in bacterial genomes
-
DOI 10.1016/j.gene.2003.09.021
-
On dynamics of overlapping genes in bacterial genomes. Fukuda Y, Nakayama Y, Tomita M, Gene 2003 323 181 187 14659892 (Pubitemid 37501098)
-
(2003)
Gene
, vol.323
, Issue.1-2
, pp. 181-187
-
-
Fukuda, Y.1
Nakayama, Y.2
Tomita, M.3
-
55
-
-
47949084234
-
Large gene overlaps in prokaryotic genomes: Result of functional constraints or mispredictions?
-
DOI 10.1186/1471-2164-9-335
-
Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? Palleja A, Harrington ED, Bork P, BMC Genomics 2008 9 335 10.1186/1471-2164-9-335 18627618 (Pubitemid 352044824)
-
(2008)
BMC Genomics
, vol.9
, pp. 335
-
-
Palleja, A.1
Harrington, E.D.2
Bork, P.3
-
56
-
-
68049089607
-
PairWise Neighbours database: Overlaps and spacers among prokaryote genomes
-
10.1186/1471-2164-10-281 19555467
-
PairWise Neighbours database: overlaps and spacers among prokaryote genomes. Palleja A, Reverter T, Garcia-Vallve S, Romeu A, BMC Genomics 2009 10 281 10.1186/1471-2164-10-281 19555467
-
(2009)
BMC Genomics
, vol.10
, pp. 281
-
-
Palleja, A.1
Reverter, T.2
Garcia-Vallve, S.3
Romeu, A.4
-
57
-
-
0036798984
-
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes
-
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. Rogozin IB, Makarova KS, Natale DA, Spiridonov AN, Tatusov RL, Wolf YI, Yin J, Koonin EV, Nucleic Acids Res 2002 30 4264 4271 10.1093/nar/gkf549 12364605 (Pubitemid 35175194)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.19
, pp. 4264-4271
-
-
Rogozin, I.B.1
Makarova, K.S.2
Natale, D.A.3
Spiridonov, A.N.4
Tatusov, R.L.5
Wolf, Y.I.6
Yin, J.7
Koonin, E.V.8
-
58
-
-
0034612277
-
Operons in Escherichia coli: Genomic analyses and predictions
-
DOI 10.1073/pnas.110147297
-
Operons in Escherichia coli: genomic analyses and predictions. Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J, Proc Natl Acad Sci USA 2000 97 6652 6657 10.1073/pnas.110147297 10823905 (Pubitemid 30412769)
-
(2000)
Proceedings of the National Academy of Sciences of the United States of America
, vol.97
, Issue.12
, pp. 6652-6657
-
-
Salgado, H.1
Moreno-Hagelsieb, G.2
Smith, T.F.3
Collado-Vides, J.4
-
59
-
-
33750459412
-
Global analysis of gene transcription regulation in prokaryotes
-
DOI 10.1007/s00018-006-6184-6
-
Global analysis of gene transcription regulation in prokaryotes. Zhou D, Yang R, Cell Mol Life Sci 2006 63 2260 2290 10.1007/s00018-006-6184-6 16927028 (Pubitemid 44653039)
-
(2006)
Cellular and Molecular Life Sciences
, vol.63
, Issue.19-20
, pp. 2260-2290
-
-
Zhou, D.1
Yang, R.2
-
60
-
-
0035282698
-
Prediction of operons in microbial genomes
-
Prediction of operons in microbial genomes. Ermolaeva MD, White O, Salzberg SL, Nucleic Acids Res 2001 29 1216 1221 10.1093/nar/29.5.1216 11222772 (Pubitemid 32186208)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.5
, pp. 1216-1221
-
-
Ermolaeva, M.D.1
White, O.2
Salzberg, S.L.3
-
61
-
-
13944268797
-
A novel method for accurate operon predictions in all sequenced prokaryotes
-
DOI 10.1093/nar/gki232
-
A novel method for accurate operon predictions in all sequenced prokaryotes. Price MN, Huang KH, Alm EJ, Arkin AP, Nucleic Acids Res 2005 33 880 892 10.1093/nar/gki232 15701760 (Pubitemid 41430509)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.3
, pp. 880-892
-
-
Price, M.N.1
Huang, K.H.2
Alm, E.J.3
Arkin, A.P.4
-
62
-
-
0034893454
-
The genome of Mycobacterium leprae: A minimal mycobacterial gene set
-
REVIEWS1023
-
The genome of Mycobacterium leprae: a minimal mycobacterial gene set. Vissa VD, Brennan PJ, Genome Biol 2001 2 REVIEWS1023
-
(2001)
Genome Biol
, vol.2
-
-
Vissa, V.D.1
Brennan, P.J.2
-
63
-
-
79953160460
-
The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons
-
21051341
-
The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons. Muro EM, Mah N, Moreno-Hagelsieb G, Andrade-Navarro MA, Nucleic Acids Res 2010 39 1732 1738 21051341
-
(2010)
Nucleic Acids Res
, vol.39
, pp. 1732-1738
-
-
Muro, E.M.1
Mah, N.2
Moreno-Hagelsieb, G.3
Andrade-Navarro, M.A.4
-
64
-
-
0035701315
-
The decaying genome of mycobacterium leprae
-
The decaying genome of Mycobacterium leprae. Eiglmeier K, Parkhill J, Honore N, Garnier T, Tekaia F, Telenti A, Klatser P, James KD, Thomson NR, Wheeler PR, et al. Lepr Rev 2001 72 387 398 11826475 (Pubitemid 34111833)
-
(2001)
Leprosy Review
, vol.72
, Issue.4
, pp. 387-398
-
-
Eiglmeier, K.1
Parkhill, J.2
Honore, N.3
Garnier, T.4
Tekaia, F.5
Telenti, A.6
Klatser, P.7
James, K.D.8
Thomson, N.R.9
Wheeler, P.R.10
Churcher, C.11
Harris, D.12
Mungall, K.13
Barrell, B.G.14
Cole, S.T.15
Colston, M.J.16
-
65
-
-
22144451439
-
The regional rule for bacterial base composition
-
DOI 10.1016/j.tig.2005.06.002, PII S0168952505001630
-
The regional rule for bacterial base composition. Mitchison G, Trends Genet 2005 21 440 443 10.1016/j.tig.2005.06.002 15978695 (Pubitemid 40981792)
-
(2005)
Trends in Genetics
, vol.21
, Issue.8
, pp. 440-443
-
-
Mitchison, G.1
-
66
-
-
11044225797
-
CBS Genome Atlas database: A dynamic storage for bioinformatic results and sequence data
-
DOI 10.1093/bioinformatics/bth423
-
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Hallin PF, Ussery DW, Bioinformatics 2004 20 3682 3686 10.1093/bioinformatics/bth423 15256401 (Pubitemid 40136816)
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3682-3686
-
-
Hallin, P.F.1
Ussery, D.W.2
-
67
-
-
0037460960
-
The Z curve database: A graphic representation of genome sequences
-
DOI 10.1093/bioinformatics/btg041
-
The Z curve database: a graphic representation of genome sequences. Zhang CT, Zhang R, Ou HY, Bioinformatics 2003 19 593 599 10.1093/bioinformatics/ btg041 12651717 (Pubitemid 36417053)
-
(2003)
Bioinformatics
, vol.19
, Issue.5
, pp. 593-599
-
-
Zhang, C.-T.1
Zhang, R.2
Ou, H.-Y.3
-
68
-
-
13444273442
-
BacMap: An interactive picture atlas of annotated bacterial genomes
-
15608206
-
BacMap: an interactive picture atlas of annotated bacterial genomes. Stothard P, Van Domselaar G, Shrivastava S, Guo A, O'Neill B, Cruz J, Ellison M, Wishart DS, Nucleic Acids Res 2005 33 317 320 15608206
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4317-320
-
-
Stothard, P.1
Van Domselaar, G.2
Shrivastava, S.3
Guo, A.4
O'Neill, B.5
Cruz, J.6
Ellison, M.7
Wishart, D.S.8
|