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A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres.

Frontiers in microbiology

Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P.
PMID: 26779135
Front Microbiol. 2016 Jan 07;6:1469. doi: 10.3389/fmicb.2015.01469. eCollection 2015.

The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named....

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Abdul Rahman N, Parks DH, Vanwonterghem I, et al. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Front Microbiol. 2016;6:1469doi: 10.3389/fmicb.2015.01469.
Abdul Rahman, N., Parks, D. H., Vanwonterghem, I., Morrison, M., Tyson, G. W., & Hugenholtz, P. (2015). A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Frontiers in microbiology, 61469. https://doi.org/10.3389/fmicb.2015.01469
Abdul Rahman, Nurdyana, et al. "A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres." Frontiers in microbiology vol. 6 (2015): 1469. doi: https://doi.org/10.3389/fmicb.2015.01469
Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Front Microbiol. 2016 Jan 07;6:1469. doi: 10.3389/fmicb.2015.01469. eCollection 2015. PMID: 26779135; PMCID: PMC4704652.
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Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics.

PeerJ

Rinke C, Low S, Woodcroft BJ, Raina JB, Skarshewski A, Le XH, Butler MK, Stocker R, Seymour J, Tyson GW, Hugenholtz P.
PMID: 27688978
PeerJ. 2016 Sep 22;4:e2486. doi: 10.7717/peerj.2486. eCollection 2016.

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass...

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Rinke C, Low S, Woodcroft BJ, et al. Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ. 2016;4:e2486doi: 10.7717/peerj.2486.
Rinke, C., Low, S., Woodcroft, B. J., Raina, J. B., Skarshewski, A., Le, X. H., Butler, M. K., Stocker, R., Seymour, J., Tyson, G. W., & Hugenholtz, P. (2016). Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4e2486. https://doi.org/10.7717/peerj.2486
Rinke, Christian, et al. "Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics." PeerJ vol. 4 (2016): e2486. doi: https://doi.org/10.7717/peerj.2486
Rinke C, Low S, Woodcroft BJ, Raina JB, Skarshewski A, Le XH, Butler MK, Stocker R, Seymour J, Tyson GW, Hugenholtz P. Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ. 2016 Sep 22;4:e2486. doi: 10.7717/peerj.2486. eCollection 2016. PMID: 27688978; PMCID: PMC5036114.
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Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains.

Standards in genomic sciences

Whitman WB, Woyke T, Klenk HP, Zhou Y, Lilburn TG, Beck BJ, De Vos P, Vandamme P, Eisen JA, Garrity G, Hugenholtz P, Kyrpides NC.
PMID: 26203337
Stand Genomic Sci. 2015 May 17;10:26. doi: 10.1186/s40793-015-0017-x. eCollection 2015.

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach...

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Whitman WB, Woyke T, Klenk HP, et al. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci. 2015;10:26doi: 10.1186/s40793-015-0017-x.
Whitman, W. B., Woyke, T., Klenk, H. P., Zhou, Y., Lilburn, T. G., Beck, B. J., De Vos, P., Vandamme, P., Eisen, J. A., Garrity, G., Hugenholtz, P., & Kyrpides, N. C. (2015). Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Standards in genomic sciences, 1026. https://doi.org/10.1186/s40793-015-0017-x
Whitman, William B, et al. "Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains." Standards in genomic sciences vol. 10 (2015): 26. doi: https://doi.org/10.1186/s40793-015-0017-x
Whitman WB, Woyke T, Klenk HP, Zhou Y, Lilburn TG, Beck BJ, De Vos P, Vandamme P, Eisen JA, Garrity G, Hugenholtz P, Kyrpides NC. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci. 2015 May 17;10:26. doi: 10.1186/s40793-015-0017-x. eCollection 2015. PMID: 26203337; PMCID: PMC4511459.
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JTD special edition 'Hot Topics in COPD'-The microbiome in COPD.

Journal of thoracic disease

Chambers DC, Gellatly SL, Hugenholtz P, Hansbro PM.
PMID: 25478194
J Thorac Dis. 2014 Nov;6(11):1525-31. doi: 10.3978/j.issn.2072-1439.2014.11.08.

The pathogenesis of chronic obstructive pulmonary disease (COPD) and its exacerbations, are intricately linked to colonisation and infection with bacteria and other microbes. Despite their undeniable importance, we have a poor understanding of the complex relationships between COPD phenotypes,...

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Chambers DC, Gellatly SL, Hugenholtz P, et al. JTD special edition 'Hot Topics in COPD'-The microbiome in COPD. J Thorac Dis. 2014;6(11):1525-31doi: 10.3978/j.issn.2072-1439.2014.11.08.
Chambers, D. C., Gellatly, S. L., Hugenholtz, P., & Hansbro, P. M. (2014). JTD special edition 'Hot Topics in COPD'-The microbiome in COPD. Journal of thoracic disease, 6(11), 1525-31. https://doi.org/10.3978/j.issn.2072-1439.2014.11.08
Chambers, Daniel C, et al. "JTD special edition 'Hot Topics in COPD'-The microbiome in COPD." Journal of thoracic disease vol. 6,11 (2014): 1525-31. doi: https://doi.org/10.3978/j.issn.2072-1439.2014.11.08
Chambers DC, Gellatly SL, Hugenholtz P, Hansbro PM. JTD special edition 'Hot Topics in COPD'-The microbiome in COPD. J Thorac Dis. 2014 Nov;6(11):1525-31. doi: 10.3978/j.issn.2072-1439.2014.11.08. PMID: 25478194; PMCID: PMC4255167.
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[Non-directive therapy].

Nederlands tijdschrift voor de psychologie en haar grensgebieden

HUGENHOLTZ PT.
PMID: 14403823
Ned Tijdschr Psychol. 1959;14:533-42.

No abstract available.

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HUGENHOLTZ PT. [Non-directive therapy]. Ned Tijdschr Psychol. 1959;14:533-42
HUGENHOLTZ, P. T. (1959). [Non-directive therapy]. Nederlands tijdschrift voor de psychologie en haar grensgebieden, 14533-42.
HUGENHOLTZ, P T. "[Non-directive therapy]." Nederlands tijdschrift voor de psychologie en haar grensgebieden vol. 14 (1959): 533-42.
HUGENHOLTZ PT. [Non-directive therapy]. Ned Tijdschr Psychol. 1959;14:533-42. Dutch. PMID: 14403823.
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[Phenomenological anthropology].

Nederlands tijdschrift voor de psychologie en haar grensgebieden

HUGENHOLTZ PT.
PMID: 13387932
Ned Tijdschr Psychol. 1956;11(4):297-311.

No abstract available.

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HUGENHOLTZ PT. Phenomenologische anthropologie. [Phenomenological anthropology]. Ned Tijdschr Psychol. 1956;11(4):297-311
HUGENHOLTZ, P. T. (1956). Phenomenologische anthropologie. [Phenomenological anthropology]. Nederlands tijdschrift voor de psychologie en haar grensgebieden, 11(4), 297-311.
HUGENHOLTZ, P T. "Phenomenologische anthropologie." [Phenomenological anthropology]. Nederlands tijdschrift voor de psychologie en haar grensgebieden vol. 11,4 (1956): 297-311.
HUGENHOLTZ PT. Phenomenologische anthropologie. [Phenomenological anthropology]. Ned Tijdschr Psychol. 1956;11(4):297-311. Dutch. PMID: 13387932.
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[Experience and the world of experience].

Nederlands tijdschrift voor de psychologie en haar grensgebieden

HUGENHOLTZ PT.
PMID: 14919879
Ned Tijdschr Psychol. 1951;6(6):384-410.

No abstract available.

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HUGENHOLTZ PT. Over het beleven en de belevingswereld. [Experience and the world of experience]. Ned Tijdschr Psychol. 1951;6(6):384-410
HUGENHOLTZ, P. T. (1951). Over het beleven en de belevingswereld. [Experience and the world of experience]. Nederlands tijdschrift voor de psychologie en haar grensgebieden, 6(6), 384-410.
HUGENHOLTZ, P T. "Over het beleven en de belevingswereld." [Experience and the world of experience]. Nederlands tijdschrift voor de psychologie en haar grensgebieden vol. 6,6 (1951): 384-410.
HUGENHOLTZ PT. Over het beleven en de belevingswereld. [Experience and the world of experience]. Ned Tijdschr Psychol. 1951;6(6):384-410. Undetermined. PMID: 14919879.
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[ON HOLDING RESPONSIBLE AND RESPONSIBILITY].

Nederlands tijdschrift voor de psychologie en haar grensgebieden

HUGENHOLTZ PT.
PMID: 14259623
Ned Tijdschr Psychol. 1964 Nov-Dec;19:551-70.

No abstract available.

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HUGENHOLTZ PT. OVER TOEREKENEN EN TOEREKENBAARHEID. [ON HOLDING RESPONSIBLE AND RESPONSIBILITY]. Ned Tijdschr Psychol. 1964;19:551-70
HUGENHOLTZ, P. T. (1964). OVER TOEREKENEN EN TOEREKENBAARHEID. [ON HOLDING RESPONSIBLE AND RESPONSIBILITY]. Nederlands tijdschrift voor de psychologie en haar grensgebieden, 19551-70.
HUGENHOLTZ, P T. "OVER TOEREKENEN EN TOEREKENBAARHEID." [ON HOLDING RESPONSIBLE AND RESPONSIBILITY]. Nederlands tijdschrift voor de psychologie en haar grensgebieden vol. 19 (1964): 551-70.
HUGENHOLTZ PT. OVER TOEREKENEN EN TOEREKENBAARHEID. [ON HOLDING RESPONSIBLE AND RESPONSIBILITY]. Ned Tijdschr Psychol. 1964 Nov-Dec;19:551-70. Dutch. PMID: 14259623.
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Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6).

Standards in genomic sciences

Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.
PMID: 21677850
Stand Genomic Sci. 2011 Apr 29;4(2):131-43. doi: 10.4056/sigs.1463589.

Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability...

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Zeytun A, Sikorski J, Nolan M, et al. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Stand Genomic Sci. 2011;4(2):131-43doi: 10.4056/sigs.1463589.
Zeytun, A., Sikorski, J., Nolan, M., Lapidus, A., Lucas, S., Han, J., Tice, H., Cheng, J. F., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Ngatchou-Djao, O. D., Land, M., Hauser, L., Jeffries, C. D., Han, C., Detter, J. C., Ubler, S., Rohde, M., Tindall, B. J., Göker, M., Wirth, R., Woyke, T., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Klenk, H. P., & Kyrpides, N. C. (2011). Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Standards in genomic sciences, 4(2), 131-43. https://doi.org/10.4056/sigs.1463589
Zeytun, Ahmet, et al. "Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6)." Standards in genomic sciences vol. 4,2 (2011): 131-43. doi: https://doi.org/10.4056/sigs.1463589
Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Stand Genomic Sci. 2011 Apr 29;4(2):131-43. doi: 10.4056/sigs.1463589. PMID: 21677850; PMCID: PMC3111988.
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Complete genome sequence of Oceanithermus profundus type strain (506).

Standards in genomic sciences

Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Jeffries CD, Brambilla EM, Röhl A, Mwirichia R, Rohde M, Tindall BJ, Sikorski J, Wirth R, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M.
PMID: 21677858
Stand Genomic Sci. 2011 Apr 29;4(2):210-20. doi: 10.4056/sigs.1734292.

Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite....

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Pati A, Zhang X, Lapidus A, et al. Complete genome sequence of Oceanithermus profundus type strain (506). Stand Genomic Sci. 2011;4(2):210-20doi: 10.4056/sigs.1734292.
Pati, A., Zhang, X., Lapidus, A., Nolan, M., Lucas, S., Del Rio, T. G., Tice, H., Cheng, J. F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Hauser, L., Jeffries, C. D., Brambilla, E. M., Röhl, A., Mwirichia, R., Rohde, M., Tindall, B. J., Sikorski, J., Wirth, R., Göker, M., Woyke, T., Detter, J. C., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C., Klenk, H. P., & Land, M. (2011). Complete genome sequence of Oceanithermus profundus type strain (506). Standards in genomic sciences, 4(2), 210-20. https://doi.org/10.4056/sigs.1734292
Pati, Amrita, et al. "Complete genome sequence of Oceanithermus profundus type strain (506)." Standards in genomic sciences vol. 4,2 (2011): 210-20. doi: https://doi.org/10.4056/sigs.1734292
Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Jeffries CD, Brambilla EM, Röhl A, Mwirichia R, Rohde M, Tindall BJ, Sikorski J, Wirth R, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. Complete genome sequence of Oceanithermus profundus type strain (506). Stand Genomic Sci. 2011 Apr 29;4(2):210-20. doi: 10.4056/sigs.1734292. PMID: 21677858; PMCID: PMC3111992.
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Cell Wall-Associated Proteases of Streptococcus cremoris Wg2.

Applied and environmental microbiology

Hugenholtz J, van Sinderen D, Kok J, Konings WN.
PMID: 16347329
Appl Environ Microbiol. 1987 Apr;53(4):853-9. doi: 10.1128/aem.53.4.853-859.1987.

Two components of the proteolytic system, proteins A and B (J. Hugenholtz, F. Exterkate, and W. N. Konings, Appl. Environ. Microbiol. 48:1105-1110, 1984), have been studied in Streptococcus cremoris Wg2 by immunological methods. The components could not be separated...

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Hugenholtz J, van Sinderen D, Kok J, et al. Cell Wall-Associated Proteases of Streptococcus cremoris Wg2. Appl Environ Microbiol. 1987;53(4):853-9doi: 10.1128/aem.53.4.853-859.1987.
Hugenholtz, J., van Sinderen, D., Kok, J., & Konings, W. N. (1987). Cell Wall-Associated Proteases of Streptococcus cremoris Wg2. Applied and environmental microbiology, 53(4), 853-9. https://doi.org/10.1128/aem.53.4.853-859.1987
Hugenholtz, J, et al. "Cell Wall-Associated Proteases of Streptococcus cremoris Wg2." Applied and environmental microbiology vol. 53,4 (1987): 853-9. doi: https://doi.org/10.1128/aem.53.4.853-859.1987
Hugenholtz J, van Sinderen D, Kok J, Konings WN. Cell Wall-Associated Proteases of Streptococcus cremoris Wg2. Appl Environ Microbiol. 1987 Apr;53(4):853-9. doi: 10.1128/aem.53.4.853-859.1987. PMID: 16347329; PMCID: PMC203768.
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Complete genome sequence of Saccharomonospora viridis type strain (P101).

Standards in genomic sciences

Pati A, Sikorski J, Nolan M, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Chain P, D'haeseleer P, Chen A, Palaniappan K, Ivanova N, Mavromatis K, Mikhailova N, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.
PMID: 21304650
Stand Genomic Sci. 2009 Sep 24;1(2):141-9. doi: 10.4056/sigs.20263.

Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified among the usually...

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Pati A, Sikorski J, Nolan M, et al. Complete genome sequence of Saccharomonospora viridis type strain (P101). Stand Genomic Sci. 2009;1(2):141-9doi: 10.4056/sigs.20263.
Pati, A., Sikorski, J., Nolan, M., Lapidus, A., Copeland, A., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Pitluck, S., Cheng, J. F., Chertkov, O., Brettin, T., Han, C., Detter, J. C., Kuske, C., Bruce, D., Goodwin, L., Chain, P., D'haeseleer, P., Chen, A., Palaniappan, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Rohde, M., Tindall, B. J., Göker, M., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C., & Klenk, H. P. (2009). Complete genome sequence of Saccharomonospora viridis type strain (P101). Standards in genomic sciences, 1(2), 141-9. https://doi.org/10.4056/sigs.20263
Pati, Amrita, et al. "Complete genome sequence of Saccharomonospora viridis type strain (P101)." Standards in genomic sciences vol. 1,2 (2009): 141-9. doi: https://doi.org/10.4056/sigs.20263
Pati A, Sikorski J, Nolan M, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Chain P, D'haeseleer P, Chen A, Palaniappan K, Ivanova N, Mavromatis K, Mikhailova N, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Saccharomonospora viridis type strain (P101). Stand Genomic Sci. 2009 Sep 24;1(2):141-9. doi: 10.4056/sigs.20263. PMID: 21304650; PMCID: PMC3035233.
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Showing 1 to 12 of 239 entries