-
1
-
-
30944469304
-
Mutation discovery in bacterial genomes: Metronidazole resistance in Helicobacter pylori
-
Albert, T.J., Dailidiene, D., Dailide, G., Norton, J.E., Kalia, A., Richmond, T.A., Molla, M., Singh, J., Green, R.D., Berg, D.E. 2005. Mutation discovery in bacterial genomes: Metronidazole resistance in Helicobacter pylori. Nature Methods. 2:951-953.
-
(2005)
Nature Methods
, vol.2
, pp. 951-953
-
-
Albert, T.J.1
Dailidiene, D.2
Dailide, G.3
Norton, J.E.4
Kalia, A.5
Richmond, T.A.6
Molla, M.7
Singh, J.8
Green, R.D.9
Berg, D.E.10
-
2
-
-
40549120596
-
The RAST server: Rapid annotations using subsystems technology
-
Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., Meyer, F., Olsen, G.J., Olson, R., Osterman, A.L., Overbeek, R.A., McNeil, L.K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G.D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., Zagnitko, O. 2008. The RAST server: Rapid annotations using subsystems technology. BMC Genomics. 9:75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
Formsma, K.7
Gerdes, S.8
Glass, E.M.9
Kubal, M.10
Meyer, F.11
Olsen, G.J.12
Olson, R.13
Osterman, A.L.14
Overbeek, R.A.15
McNeil, L.K.16
Paarmann, D.17
Paczian, T.18
Parrello, B.19
Pusch, G.D.20
Reich, C.21
Stevens, R.22
Vassieva, O.23
Vonstein, V.24
Wilke, A.25
Zagnitko, O.26
more..
-
4
-
-
24144502463
-
Disease and health management in Asian aquaculture
-
Bondad-Reantaso, M.G., Subasinghe, R.P., Arthur, J.R., Ogawa, K., Chinabut, S., Adlard, R., Tan, Z., Shariff, M. 2005. Disease and health management in Asian aquaculture. Veterinary Parasitology. 132:249-272.
-
(2005)
Veterinary Parasitology
, vol.132
, pp. 249-272
-
-
Bondad-Reantaso, M.G.1
Subasinghe, R.P.2
Arthur, J.R.3
Ogawa, K.4
Chinabut, S.5
Adlard, R.6
Tan, Z.7
Shariff, M.8
-
6
-
-
33746809569
-
AGMIAL: Implementing an annotation strategy for prokaryote genomes as a distributed system
-
Bryson, K., Loux, V., Bossy, R., Nicolas, P., Chaillou, S., van de Guchte, M., Penaud, S., Maguin, E., Hoebeke, M., Bessieres, P., Gibrat, J.F. 2006. AGMIAL: Implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Research. 34:3533-3545.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 3533-3545
-
-
Bryson, K.1
Loux, V.2
Bossy, R.3
Nicolas, P.4
Chaillou, S.5
Van de Guchte, M.6
Penaud, S.7
Maguin, E.8
Hoebeke, M.9
Bessieres, P.10
Gibrat, J.F.11
-
7
-
-
77951983076
-
The Economic Effects of Rainbow Trout Stocking by Fish andWildlife Service Hatcheries in FY 2004
-
U.S. Fish and Wildlife Service DoE, Arlington, VA
-
Caudill, J. 2005. The Economic Effects of Rainbow Trout Stocking by Fish andWildlife Service Hatcheries in FY 2004. U.S. Fish and Wildlife Service DoE, Arlington, VA.
-
(2005)
-
-
Caudill, J.1
-
8
-
-
0033485517
-
Improved microbial gene identification with GLIMMER
-
Delcher, A.L., Harmon, D., Kasif, S., White, O., Salzberg, S.L. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Research. 27:4636-4641.
-
(1999)
Nucleic Acids Research
, vol.27
, pp. 4636-4641
-
-
Delcher, A.L.1
Harmon, D.2
Kasif, S.3
White, O.4
Salzberg, S.L.5
-
9
-
-
34447297799
-
Complete genome sequence of the fish pathogen Flavobacterium psychrophilum
-
Duchaud, E., Boussaha, M., Loux, V., Bernardet, J.F., Michel, C., Kerouault, B., Mondot, S., Nicolas, P., Bossy, R., Caron, C., Bessieres, P., Gibrat, J.F., Claverol, S., Dumetz, F., Le Henaff, M., Benmansour, A. 2007. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nature Biotechnology. 25:763-769.
-
(2007)
Nature Biotechnology
, vol.25
, pp. 763-769
-
-
Duchaud, E.1
Boussaha, M.2
Loux, V.3
Bernardet, J.F.4
Michel, C.5
Kerouault, B.6
Mondot, S.7
Nicolas, P.8
Bossy, R.9
Caron, C.10
Bessieres, P.11
Gibrat, J.F.12
Claverol, S.13
Dumetz, F.14
Le Henaff, M.15
Benmansour, A.16
-
10
-
-
0031978181
-
Base-calling of automated sequencer traces using Phred. II. Error probabilities
-
Ewing, B., Green, P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research. 8:186-194.
-
(1998)
Genome Research
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
11
-
-
0031955518
-
Base-calling of automated sequencer traces using Phred. I. Accuracy assessment
-
Ewing, B., Hillier, L.,Wendl, M.C., Green, P. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Research. 8:175-185.
-
(1998)
Genome Research
, vol.8
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.C.3
Green, P.4
-
12
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., McKenney, K., Sutton, G., FitzHugh, W., Fields, C., Gocayne, J., Scott, J., Shirley, R., Liu, L., Glodek, A., Kelley, J., Weidman, J., Phillips, C., Spriggs, T., Hedblom, E., Cotton, M., Utterback, T., Hanna, M., Nguyen, D., Saudek, D., Brandon, R., Fine, L., Fritchman, J., Fuhrmann, J., Geoghagen, N., Gnehm, L., McDonald, L., Small, K., Fraser, C., Smith, H., Venter, J. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:496-512.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
Kerlavage, A.R.6
Bult, C.J.7
Tomb, J.F.8
Dougherty, B.A.9
Merrick, J.M.10
McKenney, K.11
Sutton, G.12
FitzHugh, W.13
Fields, C.14
Gocayne, J.15
Scott, J.16
Shirley, R.17
Liu, L.18
Glodek, A.19
Kelley, J.20
Weidman, J.21
Phillips, C.22
Spriggs, T.23
Hedblom, E.24
Cotton, M.25
Utterback, T.26
Hanna, M.27
Nguyen, D.28
Saudek, D.29
Brandon, R.30
Fine, L.31
Fritchman, J.32
Fuhrmann, J.33
Geoghagen, N.34
Gnehm, L.35
McDonald, L.36
Small, K.37
Fraser, C.38
Smith, H.39
Venter, J.40
more..
-
13
-
-
0036889014
-
The value of complete microbial genome sequencing (you get what you pay for)
-
Fraser, C.M., Eisen, J.A., Nelson, K.E., Paulsen, I.T., Salzberg, S.L. 2002. The value of complete microbial genome sequencing (you get what you pay for). Journal of Bacteriology. 184:6403-6405.
-
(2002)
Journal of Bacteriology
, vol.184
, pp. 6403-6405
-
-
Fraser, C.M.1
Eisen, J.A.2
Nelson, K.E.3
Paulsen, I.T.4
Salzberg, S.L.5
-
14
-
-
34547912489
-
DoriC: A database of oriC regions in bacterial genomes
-
Gao, F., Zhang, C.T. 2007. DoriC: A database of oriC regions in bacterial genomes. Bioinformatics. 23:1866-1867.
-
(2007)
Bioinformatics
, vol.23
, pp. 1866-1867
-
-
Gao, F.1
Zhang, C.T.2
-
15
-
-
41349112730
-
Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes
-
Gao, F., Zhang, C.T. 2008. Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics. 9:79.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 79
-
-
Gao, F.1
Zhang, C.T.2
-
16
-
-
0031955116
-
Consed: A graphical tool for sequence finishing
-
Gordon, D., Abajian, C., Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Research. 8:195-202.
-
(1998)
Genome Research
, vol.8
, pp. 195-202
-
-
Gordon, D.1
Abajian, C.2
Green, P.3
-
17
-
-
0035054380
-
Automated finishing with autofinish
-
Gordon, D., Desmarais, C., Green, P. 2001. Automated finishing with autofinish. Genome Research. 11:614-625.
-
(2001)
Genome Research
, vol.11
, pp. 614-625
-
-
Gordon, D.1
Desmarais, C.2
Green, P.3
-
18
-
-
28044463174
-
Genometrics as an essential tool for the assembly of whole genome sequences: The example of the chromosome of Bifidobacterium longum NCC2705
-
Guy, L., Karamata, D.,Moreillon, P.,Roten, C.A. 2005. Genometrics as an essential tool for the assembly of whole genome sequences: The example of the chromosome of Bifidobacterium longum NCC2705. BMC Microbiology. 5:60.
-
(2005)
BMC Microbiology
, vol.5
, pp. 60
-
-
Guy, L.1
Karamata, D.2
Moreillon, P.3
Roten, C.A.4
-
19
-
-
5444276316
-
Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication
-
Guy, L., Roten, C.A. 2004. Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication. Gene. 340:45-52.
-
(2004)
Gene
, vol.340
, pp. 45-52
-
-
Guy, L.1
Roten, C.A.2
-
20
-
-
33947546580
-
Gene flow, effective population size and selection at major histocompatibility complex genes: Brown trout in the Hardanger Fjord, Norway
-
Hansen, M.M., Skaala, O., Jensen, L.F., Bekkevold, D., Mensberg, K.L. 2007. Gene flow, effective population size and selection at major histocompatibility complex genes: Brown trout in the Hardanger Fjord, Norway. Molecular Ecology. 16:1413-1425.
-
(2007)
Molecular Ecology
, vol.16
, pp. 1413-1425
-
-
Hansen, M.M.1
Skaala, O.2
Jensen, L.F.3
Bekkevold, D.4
Mensberg, K.L.5
-
21
-
-
4944254822
-
Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis
-
Hendrickson, E.L., Kaul, R., Zhou, Y., Bovee, D., Chapman, P., Chung, J., Conway de Macario, E., Dodsworth, J.A., Gillett, W.,Graham, D.E.,Hackett, M.,Haydock, A.K., Kang, A., Land, M.L., Levy, R., Lie, T.J., Major, T.A., Moore, B.C., Porat, I., Palmeiri, A., Rouse, G., Saenphimmachak, C., Soll, D., Van Dien, S., Wang, T., Whitman, W.B., Xia, Q., Zhang, Y., Larimer, F.W., Olson, M.V., Leigh, J.A. 2004. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. Journal of Bacteriology. 186:6956-6969.
-
(2004)
Journal of Bacteriology
, vol.186
, pp. 6956-6969
-
-
Hendrickson, E.L.1
Kaul, R.2
Zhou, Y.3
Bovee, D.4
Chapman, P.5
Chung, J.6
Conway De Macario, E.7
Dodsworth, J.A.8
Gillett, W.9
Graham, D.E.10
Hackett, M.11
Haydock, A.K.12
Kang, A.13
Land, M.L.14
Levy, R.15
Lie, T.J.16
Major, T.A.17
Moore, B.C.18
Porat, I.19
Palmeiri, A.20
Rouse, G.21
Saenphimmachak, C.22
Soll, D.23
Van Dien, S.24
Wang, T.25
Whitman, W.B.26
Xia, Q.27
Zhang, Y.28
Larimer, F.W.29
Olson, M.V.30
Leigh, J.A.31
more..
-
22
-
-
36148979374
-
An evaluation of comparative genome sequencing (CGS) by comparing two previously-sequenced bacterial genomes
-
Herring, C.D., Palsson, B.O. 2007. An evaluation of comparative genome sequencing (CGS) by comparing two previously-sequenced bacterial genomes. BMC Genomics. 8:274.
-
(2007)
BMC Genomics
, vol.8
, pp. 274
-
-
Herring, C.D.1
Palsson, B.O.2
-
23
-
-
43549087573
-
Developing antibacterial vaccines in genomics and proteomics era
-
Kaushik, D.K., Sehgal, D. 2008. Developing antibacterial vaccines in genomics and proteomics era. Scandinavian Journal of Immunology. 67:544-552.
-
(2008)
Scandinavian Journal of Immunology
, vol.67
, pp. 544-552
-
-
Kaushik, D.K.1
Sehgal, D.2
-
24
-
-
37249056994
-
Declining wild salmon populations in relation to parasites from farm salmon
-
Krkosek, M., Ford, J.S., Morton, A., Lele, S., Myers, R.A., Lewis, M.A. 2007. Declining wild salmon populations in relation to parasites from farm salmon. Science. 318:1772-1775.
-
(2007)
Science
, vol.318
, pp. 1772-1775
-
-
Krkosek, M.1
Ford, J.S.2
Morton, A.3
Lele, S.4
Myers, R.A.5
Lewis, M.A.6
-
25
-
-
35648988889
-
Optical mapping as a routine tool for bacterial genome sequence finishing
-
Latreille, P., Norton, S., Goldman, B.S., Henkhaus, J., Miller, N., Barbazuk, B., Bode, H.B., Darby, C., Du, Z., Forst, S., Gaudriault, S., Goodner, B., Goodrich-Blair, H., Slater, S. 2007. Optical mapping as a routine tool for bacterial genome sequence finishing. BMC Genomics. 8:321.
-
(2007)
BMC Genomics
, vol.8
, pp. 321
-
-
Latreille, P.1
Norton, S.2
Goldman, B.S.3
Henkhaus, J.4
Miller, N.5
Barbazuk, B.6
Bode, H.B.7
Darby, C.8
Du, Z.9
Forst, S.10
Gaudriault, S.11
Goodner, B.12
Goodrich-Blair, H.13
Slater, S.14
-
26
-
-
33747822277
-
REGANOR: A gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes
-
Linke, B., McHardy, A.C., Neuweger, H., Krause, L., Meyer, F. 2006. REGANOR: A gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Applied Bioinformatics. 5:193-198.
-
(2006)
Applied Bioinformatics
, vol.5
, pp. 193-198
-
-
Linke, B.1
McHardy, A.C.2
Neuweger, H.3
Krause, L.4
Meyer, F.5
-
27
-
-
42549149636
-
Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions
-
Mandel, M.J., Stabb, E.V., Ruby, E.G. 2008. Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions. BMC Genomics. 9:138.
-
(2008)
BMC Genomics
, vol.9
, pp. 138
-
-
Mandel, M.J.1
Stabb, E.V.2
Ruby, E.G.3
-
28
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., Dewell, S.B., Du, L., Fierro, J.M., Gomes, X.V., Godwin, B.C., He, W., Helgesen, S., Ho, C.H., Irzyk, G.P., Jando, S.C., Alenquer, M.L., Jarvie, T.P., Jirage, K.B., Kim, J.B., Knight, J.R., Lanza, J.R., Leamon, J.H., Lefkowitz, S.M., Lei, M., Li, J., Lohman, K.L., Lu, H., Makhijani, V.B., McDade, K.E., McKenna, M.P., Myers, E.W., Nickerson, E., Nobile, J.R., Plant, R., Puc, B.P., Ronan, M.T., Roth, G.T., Sarkis, G.J., Simons, J.F., Simpson, J.W., Srinivasan, M., Tartaro, K.R., Tomasz, A., Vogt, K.A., Volkmer, G.A., Wang, S.H., Wang, Y., Weiner, M.P., Yu, P., Begley, R.F., Rothberg, J.M. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437:376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.J.9
Chen, Z.10
Dewell, S.B.11
Du, L.12
Fierro, J.M.13
Gomes, X.V.14
Godwin, B.C.15
He, W.16
Helgesen, S.17
Ho, C.H.18
Irzyk, G.P.19
Jando, S.C.20
Alenquer, M.L.21
Jarvie, T.P.22
Jirage, K.B.23
Kim, J.B.24
Knight, J.R.25
Lanza, J.R.26
Leamon, J.H.27
Lefkowitz, S.M.28
Lei, M.29
Li, J.30
Lohman, K.L.31
Lu, H.32
Makhijani, V.B.33
McDade, K.E.34
McKenna, M.P.35
Myers, E.W.36
Nickerson, E.37
Nobile, J.R.38
Plant, R.39
Puc, B.P.40
Ronan, M.T.41
Roth, G.T.42
Sarkis, G.J.43
Simons, J.F.44
Simpson, J.W.45
Srinivasan, M.46
Tartaro, K.R.47
Tomasz, A.48
Vogt, K.A.49
Volkmer, G.A.50
Wang, S.H.51
Wang, Y.52
Weiner, M.P.53
Yu, P.54
Begley, R.F.55
Rothberg, J.M.56
more..
-
29
-
-
33644873697
-
The integrated microbial genomes (IMG) system
-
Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., Werner, G., Padki, A., Zhao, X., Dubchak, I., Hugenholtz, P., Anderson, I., Lykidis, A., Mavromatis, K., Ivanova, N., Kyrpides, N.C. 2006. The integrated microbial genomes (IMG) system. Nucleic Acids Research. 34:D344-D348.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Markowitz, V.M.1
Korzeniewski, F.2
Palaniappan, K.3
Szeto, E.4
Werner, G.5
Padki, A.6
Zhao, X.7
Dubchak, I.8
Hugenholtz, P.9
Anderson, I.10
Lykidis, A.11
Mavromatis, K.12
Ivanova, N.13
Kyrpides, N.C.14
-
30
-
-
38549101119
-
The integrated microbial genomes (IMG) system in 2007: Data content and analysis tool extensions
-
Markowitz, V.M., Szeto, E., Palaniappan, K., Grechkin, Y., Chu, K., Chen, I.M., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K., Ivanovam, N.N., Kyrpidesm, N.C. 2008. The integrated microbial genomes (IMG) system in 2007: Data content and analysis tool extensions. Nucleic Acids Research. 36:D528-D533.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Markowitz, V.M.1
Szeto, E.2
Palaniappan, K.3
Grechkin, Y.4
Chu, K.5
Chen, I.M.6
Dubchak, I.7
Anderson, I.8
Lykidis, A.9
Mavromatis, K.10
Ivanovam, N.N.11
Kyrpidesm, N.C.12
-
31
-
-
34547641574
-
Going from functional genomics to biological significance
-
McCarthy, F.M., Bridges, S.M., Burgess, S.C. 2007a. Going from functional genomics to biological significance. Cytogenetic and Genome Research. 117:278-287.
-
(2007)
Cytogenetic and Genome Research
, vol.117
, pp. 278-287
-
-
McCarthy, F.M.1
Bridges, S.M.2
Burgess, S.C.3
-
32
-
-
33846081387
-
AgBase: A unified resource for functional analysis in agriculture
-
McCarthy, F.M., Bridges, S.M., Wang, N., Magee, G.B., Williams, W.P., Luthe, D.S., Burgess, S.C. 2007b. AgBase: A unified resource for functional analysis in agriculture. Nucleic Acids Research. 35:D599-D603.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
McCarthy, F.M.1
Bridges, S.M.2
Wang, N.3
Magee, G.B.4
Williams, W.P.5
Luthe, D.S.6
Burgess, S.C.7
-
33
-
-
33750483615
-
AgBase: A functional genomics resource for agriculture
-
McCarthy, F.M., Wang, N., Magee, G.B., Nanduri, B., Lawrence, M.L., Camon, E.B., Barrell, D.G., Hill, D.P., Dolan, M.E.,Williams,W.P., Luthe, D.S., Bridges, S.M., Burgess, S.C. 2006. AgBase: A functional genomics resource for agriculture. BMC Genomics. 7:229.
-
(2006)
BMC Genomics
, vol.7
, pp. 229
-
-
McCarthy, F.M.1
Wang, N.2
Magee, G.B.3
Nanduri, B.4
Lawrence, M.L.5
Camon, E.B.6
Barrell, D.G.7
Hill, D.P.8
Dolan, M.E.9
Williams, W.P.10
Luthe, D.S.11
Bridges, S.M.12
Burgess, S.C.13
-
34
-
-
33846119130
-
The national microbial pathogen database resource (NMPDR): A genomics platform based on subsystem annotation
-
McNeil, L.K., Reich, C., Aziz, R.K., Bartels, D., Cohoon, M., Disz, T., Edwards, R.A., Gerdes, S., Hwang, K., Kubal, M., Margaryan, G.R., Meyer, F., Mihalo, W., Olsen, G.J., Olson, R., Osterman, A., Paarmann, D., Paczian, T., Parrello, B., Pusch, G.D., Rodionov, D.A., Shi, X., Vassieva, O., Vonstein, V., Zagnitko, O., Xia, F., Zinner, J., Overbeek, R., Stevens, R. 2007. The national microbial pathogen database resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Research. 35:D347-D353.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
McNeil, L.K.1
Reich, C.2
Aziz, R.K.3
Bartels, D.4
Cohoon, M.5
Disz, T.6
Edwards, R.A.7
Gerdes, S.8
Hwang, K.9
Kubal, M.10
Margaryan, G.R.11
Meyer, F.12
Mihalo, W.13
Olsen, G.J.14
Olson, R.15
Osterman, A.16
Paarmann, D.17
Paczian, T.18
Parrello, B.19
Pusch, G.D.20
Rodionov, D.A.21
Shi, X.22
Vassieva, O.23
Vonstein, V.24
Zagnitko, O.25
Xia, F.26
Zinner, J.27
Overbeek, R.28
Stevens, R.29
more..
-
35
-
-
43849099955
-
Microbiology in the post-genomic era
-
Medini, D., Serruto, D., Parkhill, J.,Relman, D.A., Donati,C., Moxon, R., Falkow, S., Rappuoli, R. 2008. Microbiology in the post-genomic era. Nature Reviews in Microbiology. 6:419-430.
-
(2008)
Nature Reviews in Microbiology
, vol.6
, pp. 419-430
-
-
Medini, D.1
Serruto, D.2
Parkhill, J.3
Relman, D.A.4
Donati, C.5
Moxon, R.6
Falkow, S.7
Rappuoli, R.8
-
36
-
-
0037561991
-
GenDB-an open source genome annotation system for prokaryote genomes
-
Meyer, F., Goesmann, A., McHardy, A.C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R., Puhler, A. 2003. GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Research. 31:2187-2195.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 2187-2195
-
-
Meyer, F.1
Goesmann, A.2
McHardy, A.C.3
Bartels, D.4
Bekel, T.5
Clausen, J.6
Kalinowski, J.7
Linke, B.8
Rupp, O.9
Giegerich, R.10
Puhler, A.11
-
37
-
-
33846016960
-
Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1
-
Mongodin, E.F., Shapir, N., Daugherty, S.C., DeBoy, R.T., Emerson, J.B., Shvartzbeyn, A., Radune, D., Vamathevan, J., Riggs, F., Grinberg, V., Khouri, H., Wackett, L.P., Nelson, K.E., Sadowsky, M.J. 2006. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genetics. 2:e214.
-
(2006)
PLoS Genetics
, vol.2
-
-
Mongodin, E.F.1
Shapir, N.2
Daugherty, S.C.3
DeBoy, R.T.4
Emerson, J.B.5
Shvartzbeyn, A.6
Radune, D.7
Vamathevan, J.8
Riggs, F.9
Grinberg, V.10
Khouri, H.11
Wackett, L.P.12
Nelson, K.E.13
Sadowsky, M.J.14
-
38
-
-
48849091840
-
New ways to identify novel bacterial antigens for vaccine development
-
Movahedi, A.R., Hampson, D.J. 2008. New ways to identify novel bacterial antigens for vaccine development. Veterinary Microbiology. 131:1-13.
-
(2008)
Veterinary Microbiology
, vol.131
, pp. 1-13
-
-
Movahedi, A.R.1
Hampson, D.J.2
-
39
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M. 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
Gerstein, M.6
Snyder, M.7
-
40
-
-
43349084767
-
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
-
Nagarajan, N., Read, T.D., Pop, M. 2008. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics. 24:1229-1235.
-
(2008)
Bioinformatics
, vol.24
, pp. 1229-1235
-
-
Nagarajan, N.1
Read, T.D.2
Pop, M.3
-
41
-
-
84856609558
-
Trout Production
-
NASS
-
NASS. 2007. Trout Production. (http://usda.mannlib.cornell.edu/MannUsda/viewDocument Info.do?documentID=1172)
-
(2007)
-
-
-
42
-
-
18744383009
-
Aquaculture and ocean resources: Raising tigers of the sea
-
Naylor, R., Burke, M. 2005. Aquaculture and ocean resources: Raising tigers of the sea. Annual Review of Environmental Resources. 30:185-218.
-
(2005)
Annual Review of Environmental Resources
, vol.30
, pp. 185-218
-
-
Naylor, R.1
Burke, M.2
-
43
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek, R., Begley, T., Butler, R.M., Choudhuri, J.V., Chuang, H.Y., Cohoon, M., de Crecy-Lagard, V., Diaz, N., Disz, T., Edwards, R., Fonstein, M., Frank, E.D., Gerdes, S., Glass, E.M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., Krause, L., Kubal, M., Larsen, N., Linke, B.,McHardy, A.C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy,V., Pusch, G.D.,Rodionov, D.A., Ruckert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O., Vonstein, V. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research. 33:5691-5702.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
De Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
Fonstein, M.11
Frank, E.D.12
Gerdes, S.13
Glass, E.M.14
Goesmann, A.15
Hanson, A.16
Iwata-Reuyl, D.17
Jensen, R.18
Jamshidi, N.19
Krause, L.20
Kubal, M.21
Larsen, N.22
Linke, B.23
McHardy, A.C.24
Meyer, F.25
Neuweger, H.26
Olsen, G.27
Olson, R.28
Osterman, A.29
Portnoy, V.30
Pusch, G.D.31
Rodionov, D.A.32
Ruckert, C.33
Steiner, J.34
Stevens, R.35
Thiele, I.36
Vassieva, O.37
Ye, Y.38
Zagnitko, O.39
Vonstein, V.40
more..
-
44
-
-
0037208159
-
The ERGO genome analysis and discovery system
-
Overbeek, R., Larsen, N., Walunas, T., D'Souza, M., Pusch, G., Selkov, E., Jr., Liolios, K., Joukov, V., Kaznadzey, D., Anderson, I., Bhattacharyya, A., Burd, H., Gardner, W., Hanke, P., Kapatral, V., Mikhailova, N., Vasieva, O., Osterman, A., Vonstein, V., Fonstein, M., Ivanova, N., Kyrpides, N. 2003. The ERGO genome analysis and discovery system. Nucleic Acids Research. 31:164-171.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 164-171
-
-
Overbeek, R.1
Larsen, N.2
Walunas, T.3
D'Souza, M.4
Pusch, G.5
Selkov Jr., E.6
Liolios, K.7
Joukov, V.8
Kaznadzey, D.9
Anderson, I.10
Bhattacharyya, A.11
Burd, H.12
Gardner, W.13
Hanke, P.14
Kapatral, V.15
Mikhailova, N.16
Vasieva, O.17
Osterman, A.18
Vonstein, V.19
Fonstein, M.20
Ivanova, N.21
Kyrpides, N.22
more..
-
45
-
-
0035166979
-
The comprehensive microbial resource
-
Peterson, J.D., Umayam, L.A., Dickinson, T., Hickey, E.K.,White, O. 2001. The comprehensive microbial resource. Nucleic Acids Research. 29:123-125.
-
(2001)
Nucleic Acids Research
, vol.29
, pp. 123-125
-
-
Peterson, J.D.1
Umayam, L.A.2
Dickinson, T.3
Hickey, E.K.4
White, O.5
-
46
-
-
45549109750
-
Genome assembly forensics: Finding the elusive mis-assembly
-
Phillippy, A.M., Schatz, M.C., Pop, M. 2008. Genome assembly forensics: Finding the elusive mis-assembly. Genome Biology. 9:R55.
-
(2008)
Genome Biology
, vol.9
-
-
Phillippy, A.M.1
Schatz, M.C.2
Pop, M.3
-
47
-
-
37749016899
-
New insights into animal pathogenic oomycetes
-
Phillips, A.J., Anderson, V.L., Robertson, E.J., Secombes, C.J., van West, P. 2008. New insights into animal pathogenic oomycetes. Trends in Microbiology. 16:13-19.
-
(2008)
Trends in Microbiology
, vol.16
, pp. 13-19
-
-
Phillips, A.J.1
Anderson, V.L.2
Robertson, E.J.3
Secombes, C.J.4
Van West, P.5
-
48
-
-
0034629284
-
Identification of vaccine candidates against serogroup B Meningococcus by whole-genome sequencing
-
Pizza, M., Scarlato, V., Masignani, V., Giuliani, M., Arico, B., Comanducci, M., Jennings, G., Baldi, L., Bartolini, E., Capecchi, B., Galeotti, C., Luzzi, E., Manetti, R., Marchetti, E., Mora, M., Nuti, S., Ratti, G., Santini, L., Savino, S., Scarselli, M., Storni, E., Zuo, P., Broeker, M., Hundt, E., Knapp, B., Blair, E., Mason, T., Tettelin, H., Hood, D., Jeffries, A., Saunders, N., Granoff, D., Venter, J.,Moxon, E., Grandi, G.,Rappuoli, R. 2000. Identification of vaccine candidates against serogroup B Meningococcus by whole-genome sequencing. Science. 287:1816-1820.
-
(2000)
Science
, vol.287
, pp. 1816-1820
-
-
Pizza, M.1
Scarlato, V.2
Masignani, V.3
Giuliani, M.4
Arico, B.5
Comanducci, M.6
Jennings, G.7
Baldi, L.8
Bartolini, E.9
Capecchi, B.10
Galeotti, C.11
Luzzi, E.12
Manetti, R.13
Marchetti, E.14
Mora, M.15
Nuti, S.16
Ratti, G.17
Santini, L.18
Savino, S.19
Scarselli, M.20
Storni, E.21
Zuo, P.22
Broeker, M.23
Hundt, E.24
Knapp, B.25
Blair, E.26
Mason, T.27
Tettelin, H.28
Hood, D.29
Jeffries, A.30
Saunders, N.31
Granoff, D.32
Venter, J.33
Moxon, E.34
Grandi, G.35
Rappuoli, R.36
more..
-
49
-
-
16644381328
-
Comparative genome assembly
-
Pop, M., Phillippy, A., Delcher, A.L., Salzberg, S.L. 2004. Comparative genome assembly. Briefs in Bioinformatics. 5:237-248.
-
(2004)
Briefs in Bioinformatics
, vol.5
, pp. 237-248
-
-
Pop, M.1
Phillippy, A.2
Delcher, A.L.3
Salzberg, S.L.4
-
50
-
-
39649084637
-
Bioinformatics challenges of new sequencing technology
-
Pop, M., Salzberg, S.L. 2008. Bioinformatics challenges of new sequencing technology. Trends in Genetics. 24:142-149.
-
(2008)
Trends in Genetics
, vol.24
, pp. 142-149
-
-
Pop, M.1
Salzberg, S.L.2
-
51
-
-
34147162107
-
Genome re-annotation: A wiki solution?
-
Salzberg, S.L. 2007. Genome re-annotation: A wiki solution? Genome Biology. 8:102.
-
(2007)
Genome Biology
, vol.8
, pp. 102
-
-
Salzberg, S.L.1
-
52
-
-
84885709306
-
Tools for gene finding and whole genome comparison
-
In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Humana Press, Totowa, NJ
-
Salzberg, S.L., Delcher, A.L. 2004. Tools for gene finding and whole genome comparison. In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Microbial Genomics. Humana Press, Totowa, NJ, pp. 19-31.
-
(2004)
Microbial Genomics
, pp. 19-31
-
-
Salzberg, S.L.1
Delcher, A.L.2
-
53
-
-
0032518163
-
Microbial gene identification using interpolated Markov models
-
Salzberg, S.L., Delcher, A.L., Kasif, S., White, O. 1998a. Microbial gene identification using interpolated Markov models. Nucleic Acids Research. 26:544-548.
-
(1998)
Nucleic Acids Research
, vol.26
, pp. 544-548
-
-
Salzberg, S.L.1
Delcher, A.L.2
Kasif, S.3
White, O.4
-
54
-
-
0032517137
-
Skewed oligomers and origins of replication
-
Salzberg, S.L., Salzberg, A.J., Kerlavage, A.R., Tomb, J.F. 1998b. Skewed oligomers and origins of replication. Gene. 217:57-67.
-
(1998)
Gene
, vol.217
, pp. 57-67
-
-
Salzberg, S.L.1
Salzberg, A.J.2
Kerlavage, A.R.3
Tomb, J.F.4
-
55
-
-
28944439470
-
Beware of mis-assembled genomes
-
Salzberg, S.L., Yorke, J.A. 2005. Beware of mis-assembled genomes. Bioinformatics. 21:4320-4321.
-
(2005)
Bioinformatics
, vol.21
, pp. 4320-4321
-
-
Salzberg, S.L.1
Yorke, J.A.2
-
56
-
-
0017367852
-
Nucleotide sequence of bacteriophage phi X174 DNA
-
Sanger, F., Air, G.M., Barrell, B.G., Brown, N.L., Coulson, A.R., Fiddes, C.A., Hutchison, C.A., Slocombe, P.M., Smith, M. 1977. Nucleotide sequence of bacteriophage phi X174 DNA. Nature. 265:687-695.
-
(1977)
Nature
, vol.265
, pp. 687-695
-
-
Sanger, F.1
Air, G.M.2
Barrell, B.G.3
Brown, N.L.4
Coulson, A.R.5
Fiddes, C.A.6
Hutchison, C.A.7
Slocombe, P.M.8
Smith, M.9
-
57
-
-
46249095809
-
Overlapping protein-encoding genes in Pseudomonas fluorescens Pf0-1
-
Silby, M.W., Levy, S.B. 2008. Overlapping protein-encoding genes in Pseudomonas fluorescens Pf0-1. PLoS Genetics. 4:e1000094.
-
(2008)
PLoS Genetics
, vol.4
-
-
Silby, M.W.1
Levy, S.B.2
-
58
-
-
33745172816
-
History of microbial genomics
-
In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Humana Press, Totowa, NJ
-
Smith, H.O. 2004. History of microbial genomics. In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Microbial Genomics. Humana Press, Totowa, NJ, pp. 3-16.
-
(2004)
Microbial Genomics
, pp. 3-16
-
-
Smith, H.O.1
-
59
-
-
33947398002
-
Minimus:Afast, lightweight genome assembler
-
Sommer, D.D., Delcher, A.L., Salzberg, S.L., Pop, M. 2007. Minimus:Afast, lightweight genome assembler. BMC Bioinformatics. 8:64.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 64
-
-
Sommer, D.D.1
Delcher, A.L.2
Salzberg, S.L.3
Pop, M.4
-
60
-
-
4344568000
-
Genome update: Annotation quality in sequenced microbial genomes
-
Ussery, D.W., Hallin, P.F. 2004. Genome update: Annotation quality in sequenced microbial genomes. Microbiology. 150:2015-2017.
-
(2004)
Microbiology
, vol.150
, pp. 2015-2017
-
-
Ussery, D.W.1
Hallin, P.F.2
-
61
-
-
38049076500
-
Bacterial genome annotation at TIGR
-
In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Humana Press, Totowa, NJ
-
White, O. 2004. Bacterial genome annotation at TIGR. In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Microbial Genomics. Humana Press, Totowa, NJ, pp. 33-46.
-
(2004)
Microbial Genomics
, pp. 33-46
-
-
White, O.1
-
62
-
-
55749113393
-
The genome sequence of the fish pathogen Renibacterium salmoninarum suggests reductive evolution away from an environmental Arthrobacter ancestor
-
Wiens, G.D., Rockey, D.D.,Wu, Z., Chang, J., Levy, R. Crane, S., Chen, D., Capri, G.R., Burnett, J.R., Sudheesh, P.S., Schipma, M.J.,Burd, H.,Bhattacharyya, A., Rhodes, L.D., Kaul, R., Strom, M.S. 2008. The genome sequence of the fish pathogen Renibacterium salmoninarum suggests reductive evolution away from an environmental Arthrobacter ancestor. Journal of Bacteriology. 190:6970-6982.
-
(2008)
Journal of Bacteriology
, vol.190
, pp. 6970-6982
-
-
Wiens, G.D.1
Rockey, D.D.2
Wu, Z.3
Chang, J.4
Levy, R.5
Crane, S.6
Chen, D.7
Capri, G.R.8
Burnett, J.R.9
Sudheesh, P.S.10
Schipma, M.J.11
Burd, H.12
Bhattacharyya, A.13
Rhodes, L.D.14
Kaul, R.15
Strom, M.S.16
-
63
-
-
0035114563
-
Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection
-
Wizemann, T.M., Heinrichs, J.H., Adamou, J.E., Erwin, A.L., Kunsch, C., Choi, G.H., Barash, S., Rosen, C., Masure, H., Tuomanen, E., Gayle, A., Brewah, Y., Walsh, W., Barren, P., Lathigra, R., Hanson, M., Langermann, S., Johnson, S., Koenig, S. 2001. Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection. Infectious Immunity. 69:1593-1598.
-
(2001)
Infectious Immunity
, vol.69
, pp. 1593-1598
-
-
Wizemann, T.M.1
Heinrichs, J.H.2
Adamou, J.E.3
Erwin, A.L.4
Kunsch, C.5
Choi, G.H.6
Barash, S.7
Rosen, C.8
Masure, H.9
Tuomanen, E.10
Gayle, A.11
Brewah, Y.12
Walsh, W.13
Barren, P.14
Lathigra, R.15
Hanson, M.16
Langermann, S.17
Johnson, S.18
Koenig, S.19
-
64
-
-
0035861496
-
The genome of the natural genetic engineer Agrobacterium tumefaciens C58
-
Wood, D.W., Setubal, J.C., Kaul, R., Monks, D.E., Kitajima, J.P., Okura, V.K., Zhou, Y., Chen, L., Wood, G.E., Almeida, N.F., Jr., Woo, L., Chenm, Y., Paulsenm, I.T., Eisen, J.A., Karp, P.D., Bovee, D., Sr., Chapman, P., Clendenning, J., Deatherage, G., Gillet, W., Grant, C., Kutyavin, T., Levy, R., Li, M.J., McClelland, E., Palmieri, A., Raymond, C., Rouse, G., Saenphimmachak, C., Wu, Z., Romero, P., Gordon, D., Zhang, S., Yoo, H., Tao, Y., Biddle, P., Jung, M., Krespan, W., Perry, M., Gordon-Kamm, B., Liao, L., Kim, S., Hendrick, C., Zhao, Z.Y., Dolan, M., Chumley, F., Tingey, S.V., Tomb, J.F., Gordon, M.P., Olson, M.V., Nester, E.W. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science. 294:2317-2323.
-
(2001)
Science
, vol.294
, pp. 2317-2323
-
-
Wood, D.W.1
Setubal, J.C.2
Kaul, R.3
Monks, D.E.4
Kitajima, J.P.5
Okura, V.K.6
Zhou, Y.7
Chen, L.8
Wood, G.E.9
Almeida Jr., N.F.10
Woo, L.11
Chenm, Y.12
Paulsenm, I.T.13
Eisen, J.A.14
Karp, P.D.15
Bovee Sr., D.16
Chapman, P.17
Clendenning, J.18
Deatherage, G.19
Gillet, W.20
Grant, C.21
Kutyavin, T.22
Levy, R.23
Li, M.J.24
McClelland, E.25
Palmieri, A.26
Raymond, C.27
Rouse, G.28
Saenphimmachak, C.29
Wu, Z.30
Romero, P.31
Gordon, D.32
Zhang, S.33
Yoo, H.34
Tao, Y.35
Biddle, P.36
Jung, M.37
Krespan, W.38
Perry, M.39
Gordon-Kamm, B.40
Liao, L.41
Kim, S.42
Hendrick, C.43
Zhao, Z.Y.44
Dolan, M.45
Chumley, F.46
Tingey, S.V.47
Tomb, J.F.48
Gordon, M.P.49
Olson, M.V.50
Nester, E.W.51
more..
|