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Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation.

mSystems

Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E.
PMID: 27239563
mSystems. 2016 Jan-Feb;1(1). doi: 10.1128/mSystems.00013-15. Epub 2016 Jan 19.

Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms...

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Noecker C, Eng A, Srinivasan S, et al. Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. mSystems. 2016;1(1)doi: 10.1128/mSystems.00013-15.
Noecker, C., Eng, A., Srinivasan, S., Theriot, C. M., Young, V. B., Jansson, J. K., Fredricks, D. N., & Borenstein, E. (2016). Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. mSystems, 1(1), . https://doi.org/10.1128/mSystems.00013-15
Noecker, Cecilia, et al. "Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation." mSystems vol. 1,1 (2016). doi: https://doi.org/10.1128/mSystems.00013-15
Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E. Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. mSystems. 2016 Jan-Feb;1(1). doi: 10.1128/mSystems.00013-15. Epub 2016 Jan 19. PMID: 27239563; PMCID: PMC4883586.
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Simulation of germination of winter annuals in relation to microclimate and microdistribution.

Oecologia

Janssen JG.
PMID: 28308620
Oecologia. 1974 Sep;14(3):197-228. doi: 10.1007/BF01039793.

A simulation program on the germination of winter annuals is written in such a way that the influence of changing environmental conditions on germination characteristics such as the time of germination, the percentage of germination and the distribution function...

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Janssen JG. Simulation of germination of winter annuals in relation to microclimate and microdistribution. Oecologia. 1974;14(3):197-228doi: 10.1007/BF01039793.
Janssen, J. G. (1974). Simulation of germination of winter annuals in relation to microclimate and microdistribution. Oecologia, 14(3), 197-228. https://doi.org/10.1007/BF01039793
Janssen, J G M. "Simulation of germination of winter annuals in relation to microclimate and microdistribution." Oecologia vol. 14,3 (1974): 197-228. doi: https://doi.org/10.1007/BF01039793
Janssen JG. Simulation of germination of winter annuals in relation to microclimate and microdistribution. Oecologia. 1974 Sep;14(3):197-228. doi: 10.1007/BF01039793. PMID: 28308620.
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Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis.

Genome announcements

Köberl M, White RA, Erschen S, Spanberger N, El-Arabi TF, Jansson JK, Berg G.
PMID: 26272562
Genome Announc. 2015 Aug 13;3(4). doi: 10.1128/genomeA.00862-15.

The genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium (PGPR) with broad-spectrum antagonistic activity against plant-pathogenic fungi, bacteria, and nematodes, consists of a single 3.9-Mb circular chromosome. The genome reveals genes putatively responsible for its promising...

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Köberl M, White RA, Erschen S, et al. Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis. Genome Announc. 2015;3(4)doi: 10.1128/genomeA.00862-15.
Köberl, M., White, R. A., Erschen, S., Spanberger, N., El-Arabi, T. F., Jansson, J. K., & Berg, G. (2015). Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis. Genome announcements, 3(4), . https://doi.org/10.1128/genomeA.00862-15
Köberl, Martina, et al. "Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis." Genome announcements vol. 3,4 (2015). doi: https://doi.org/10.1128/genomeA.00862-15
Köberl M, White RA, Erschen S, Spanberger N, El-Arabi TF, Jansson JK, Berg G. Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis. Genome Announc. 2015 Aug 13;3(4). doi: 10.1128/genomeA.00862-15. PMID: 26272562; PMCID: PMC4536673.
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Limits on Anisotropy in the Nanohertz Stochastic Gravitational Wave Background.

Physical review letters

Taylor SR, Mingarelli CM, Gair JR, Sesana A, Theureau G, Babak S, Bassa CG, Brem P, Burgay M, Caballero RN, Champion DJ, Cognard I, Desvignes G, Guillemot L, Hessels JW, Janssen GH, Karuppusamy R, Kramer M, Lassus A, Lazarus P, Lentati L, Liu K, Osłowski S, Perrodin D, Petiteau A, Possenti A, Purver MB, Rosado PA, Sanidas SA, Smits R, Stappers B, Tiburzi C, van Haasteren R, Vecchio A, Verbiest JP.
PMID: 26252674
Phys Rev Lett. 2015 Jul 24;115(4):041101. doi: 10.1103/PhysRevLett.115.041101. Epub 2015 Jul 22.

The paucity of observed supermassive black hole binaries (SMBHBs) may imply that the gravitational wave background (GWB) from this population is anisotropic, rendering existing analyses suboptimal. We present the first constraints on the angular distribution of a nanohertz stochastic...

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Taylor SR, Mingarelli CM, Gair JR, et al. Limits on Anisotropy in the Nanohertz Stochastic Gravitational Wave Background. Phys Rev Lett. 2015;115(4):041101doi: 10.1103/PhysRevLett.115.041101.
Taylor, S. R., Mingarelli, C. M., Gair, J. R., Sesana, A., Theureau, G., Babak, S., Bassa, C. G., Brem, P., Burgay, M., Caballero, R. N., Champion, D. J., Cognard, I., Desvignes, G., Guillemot, L., Hessels, J. W., Janssen, G. H., Karuppusamy, R., Kramer, M., Lassus, A., Lazarus, P., Lentati, L., Liu, K., Osłowski, S., Perrodin, D., Petiteau, A., Possenti, A., Purver, M. B., Rosado, P. A., Sanidas, S. A., Smits, R., Stappers, B., Tiburzi, C., van Haasteren, R., Vecchio, A., Verbiest, J. P. (2015). Limits on Anisotropy in the Nanohertz Stochastic Gravitational Wave Background. Physical review letters, 115(4), 041101. https://doi.org/10.1103/PhysRevLett.115.041101
Taylor, S R, et al. "Limits on Anisotropy in the Nanohertz Stochastic Gravitational Wave Background." Physical review letters vol. 115,4 (2015): 041101. doi: https://doi.org/10.1103/PhysRevLett.115.041101
Taylor SR, Mingarelli CM, Gair JR, Sesana A, Theureau G, Babak S, Bassa CG, Brem P, Burgay M, Caballero RN, Champion DJ, Cognard I, Desvignes G, Guillemot L, Hessels JW, Janssen GH, Karuppusamy R, Kramer M, Lassus A, Lazarus P, Lentati L, Liu K, Osłowski S, Perrodin D, Petiteau A, Possenti A, Purver MB, Rosado PA, Sanidas SA, Smits R, Stappers B, Tiburzi C, van Haasteren R, Vecchio A, Verbiest JP. Limits on Anisotropy in the Nanohertz Stochastic Gravitational Wave Background. Phys Rev Lett. 2015 Jul 24;115(4):041101. doi: 10.1103/PhysRevLett.115.041101. Epub 2015 Jul 22. PMID: 26252674.
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Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens.

Genome announcements

Köberl M, White RA, Erschen S, El-Arabi TF, Jansson JK, Berg G.
PMID: 26251492
Genome Announc. 2015 Aug 06;3(4). doi: 10.1128/genomeA.00860-15.

Streptomyces sp. strain Wb2n-11, isolated from native desert soil, exhibited broad-spectrum antagonism against plant pathogenic fungi, bacteria, and nematodes. The 8.2-Mb draft genome reveals genes putatively responsible for its promising biocontrol activity and genes which enable the soil bacterium...

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Köberl M, White RA, Erschen S, et al. Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens. Genome Announc. 2015;3(4)doi: 10.1128/genomeA.00860-15.
Köberl, M., White, R. A., Erschen, S., El-Arabi, T. F., Jansson, J. K., & Berg, G. (2015). Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens. Genome announcements, 3(4), . https://doi.org/10.1128/genomeA.00860-15
Köberl, Martina, et al. "Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens." Genome announcements vol. 3,4 (2015). doi: https://doi.org/10.1128/genomeA.00860-15
Köberl M, White RA, Erschen S, El-Arabi TF, Jansson JK, Berg G. Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens. Genome Announc. 2015 Aug 06;3(4). doi: 10.1128/genomeA.00860-15. PMID: 26251492; PMCID: PMC4541278.
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Back to the Future of Soil Metagenomics.

Frontiers in microbiology

Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LF, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P.
PMID: 26903960
Front Microbiol. 2016 Feb 10;7:73. doi: 10.3389/fmicb.2016.00073. eCollection 2016.

No abstract available.

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Nesme J, Achouak W, Agathos SN, et al. Back to the Future of Soil Metagenomics. Front Microbiol. 2016;7:73doi: 10.3389/fmicb.2016.00073.
Nesme, J., Achouak, W., Agathos, S. N., Bailey, M., Baldrian, P., Brunel, D., Frostegård, �. �., Heulin, T., Jansson, J. K., Jurkevitch, E., Kruus, K. L., Kowalchuk, G. A., Lagares, A., Lappin-Scott, H. M., Lemanceau, P., Le Paslier, D., Mandic-Mulec, I., Murrell, J. C., Myrold, D. D., Nalin, R., Nannipieri, P., Neufeld, J. D., O'Gara, F., Parnell, J. J., Pühler, A., Pylro, V., Ramos, J. L., Roesch, L. F., Schloter, M., Schleper, C., Sczyrba, A., Sessitsch, A., Sjöling, S., Sørensen, J., Sørensen, S. J., Tebbe, C. C., Topp, E., Tsiamis, G., van Elsas, J. D., van Keulen, G., Widmer, F., Wagner, M., Zhang, T., Zhang, X., Zhao, L., Zhu, Y. G., Vogel, T. M., & Simonet, P. (2016). Back to the Future of Soil Metagenomics. Frontiers in microbiology, 773. https://doi.org/10.3389/fmicb.2016.00073
Nesme, Joseph, et al. "Back to the Future of Soil Metagenomics." Frontiers in microbiology vol. 7 (2016): 73. doi: https://doi.org/10.3389/fmicb.2016.00073
Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LF, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P. Back to the Future of Soil Metagenomics. Front Microbiol. 2016 Feb 10;7:73. doi: 10.3389/fmicb.2016.00073. eCollection 2016. PMID: 26903960; PMCID: PMC4748112.
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HIV service capacity: identifying current and future areas of clinical shortage.

Sexual health

Mallitt KA, Jansson J, Wand H, Crooks L, Wilson DP.
PMID: 24286518
Sex Health. 2014 Mar;11(1):17-23. doi: 10.1071/SH13151.

UNLABELLED: Background The capacity of HIV services to meet the clinical needs of people living with HIV (PLHIV) has not been evaluated. Similarly, whether HIV services are positioned to respond to increases in patient demand outside metropolitan centres over...

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Mallitt KA, Jansson J, Wand H, et al. HIV service capacity: identifying current and future areas of clinical shortage. Sex Health. 2014;11(1):17-23doi: 10.1071/SH13151.
Mallitt, K. A., Jansson, J., Wand, H., Crooks, L., & Wilson, D. P. (2014). HIV service capacity: identifying current and future areas of clinical shortage. Sexual health, 11(1), 17-23. https://doi.org/10.1071/SH13151
Mallitt, Kylie-Ann, et al. "HIV service capacity: identifying current and future areas of clinical shortage." Sexual health vol. 11,1 (2014): 17-23. doi: https://doi.org/10.1071/SH13151
Mallitt KA, Jansson J, Wand H, Crooks L, Wilson DP. HIV service capacity: identifying current and future areas of clinical shortage. Sex Health. 2014 Mar;11(1):17-23. doi: 10.1071/SH13151. PMID: 24286518.
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Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage.

Journal of animal science and biotechnology

Dicksved J, Jansson JK, Lindberg JE.
PMID: 26688727
J Anim Sci Biotechnol. 2015 Dec 18;6:53. doi: 10.1186/s40104-015-0054-8. eCollection 2015.

BACKGROUND: The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community (microbiome) in newly weaned (35 days of age) piglets. The piglets were fed...

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Dicksved J, Jansson JK, Lindberg JE. Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage. J Anim Sci Biotechnol. 2015;6:53doi: 10.1186/s40104-015-0054-8.
Dicksved, J., Jansson, J. K., & Lindberg, J. E. (2015). Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage. Journal of animal science and biotechnology, 653. https://doi.org/10.1186/s40104-015-0054-8
Dicksved, Johan, et al. "Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage." Journal of animal science and biotechnology vol. 6 (2015): 53. doi: https://doi.org/10.1186/s40104-015-0054-8
Dicksved J, Jansson JK, Lindberg JE. Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage. J Anim Sci Biotechnol. 2015 Dec 18;6:53. doi: 10.1186/s40104-015-0054-8. eCollection 2015. PMID: 26688727; PMCID: PMC4683726.
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Monitoring Population Size, Activity, and Distribution of gfp-luxAB-Tagged Pseudomonas fluorescens SBW25 during Colonization of Wheat.

Microbial ecology

Unge A, Jansson J.
PMID: 12032602
Microb Ecol. 2001 Feb;41(4):290-300. doi: 10.1007/s002480000047.

Increasingly, focus has been directed towards the use of microorganisms as biological control agents to combat fungal disease, as an alternative to chemical fungicides. Pseudomonas fluorescens SBW25 is one bacterial strain that has been demonstrated to promote plant growth...

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Unge A, Jansson J. Monitoring Population Size, Activity, and Distribution of gfp-luxAB-Tagged Pseudomonas fluorescens SBW25 during Colonization of Wheat. Microb Ecol. 2001;41(4):290-300doi: 10.1007/s002480000047.
Unge, A., & Jansson, J. (2001). Monitoring Population Size, Activity, and Distribution of gfp-luxAB-Tagged Pseudomonas fluorescens SBW25 during Colonization of Wheat. Microbial ecology, 41(4), 290-300. https://doi.org/10.1007/s002480000047
Unge, A., and Jansson, J.. "Monitoring Population Size, Activity, and Distribution of gfp-luxAB-Tagged Pseudomonas fluorescens SBW25 during Colonization of Wheat." Microbial ecology vol. 41,4 (2001): 290-300. doi: https://doi.org/10.1007/s002480000047
Unge A, Jansson J. Monitoring Population Size, Activity, and Distribution of gfp-luxAB-Tagged Pseudomonas fluorescens SBW25 during Colonization of Wheat. Microb Ecol. 2001 Feb;41(4):290-300. doi: 10.1007/s002480000047. PMID: 12032602.
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A 3D-TEM study of the shape of mesopores in SBA-15 and modified SBA-15 materials.

Chemical communications (Cambridge, England)

Janssen AH, Van der Voort P, Koster AJ, de Jong KP.
PMID: 12170817
Chem Commun (Camb). 2002 Aug 07;(15):1632-3. doi: 10.1039/b204943k.

The mesopores in SBA-15 are curved on a mesoscopic length scale and even more so in the case of modified SBA-15, which implies that using the particle size of these types of materials in diffusion studies may strongly underestimate...

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Janssen AH, Van der Voort P, Koster AJ, et al. A 3D-TEM study of the shape of mesopores in SBA-15 and modified SBA-15 materials. Chem Commun (Camb). 2002;(15):1632-3doi: 10.1039/b204943k.
Janssen, A. H., Van der Voort, P., Koster, A. J., & de Jong, K. P. (2002). A 3D-TEM study of the shape of mesopores in SBA-15 and modified SBA-15 materials. Chemical communications (Cambridge, England), (15), 1632-3. https://doi.org/10.1039/b204943k
Janssen, Andries H, et al. "A 3D-TEM study of the shape of mesopores in SBA-15 and modified SBA-15 materials." Chemical communications (Cambridge, England) vol. ,15 (2002): 1632-3. doi: https://doi.org/10.1039/b204943k
Janssen AH, Van der Voort P, Koster AJ, de Jong KP. A 3D-TEM study of the shape of mesopores in SBA-15 and modified SBA-15 materials. Chem Commun (Camb). 2002 Aug 07;(15):1632-3. doi: 10.1039/b204943k. PMID: 12170817.
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Resistance of Escherichia coli to Penicillins I. Genetic Study of Some Ampicillin-Resistant Mutants.

Journal of bacteriology

Eriksson-Grennberg KG, Boman HG, Jansson JA, Thorén S.
PMID: 16562043
J Bacteriol. 1965 Jul;90(1):54-62. doi: 10.1128/jb.90.1.54-62.1965.

Eriksson-Grennberg, Kerstin G. (University of Uppsala, Uppsala, Sweden), Hans G. Boman, J. A. Torbjörn Jansson, and Sone Thorén. Resistance of Escherichia coli to penicillins. I. Genetic study of some ampicillin-resistant mutants. J. Bacteriol. 90:54-62. 1965.-A number of ampicillin-resistant mutants...

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Eriksson-Grennberg KG, Boman HG, Jansson JA, et al. Resistance of Escherichia coli to Penicillins I. Genetic Study of Some Ampicillin-Resistant Mutants. J Bacteriol. 1965;90(1):54-62doi: 10.1128/jb.90.1.54-62.1965.
Eriksson-Grennberg, K. G., Boman, H. G., Jansson, J. A., & Thorén, S. (1965). Resistance of Escherichia coli to Penicillins I. Genetic Study of Some Ampicillin-Resistant Mutants. Journal of bacteriology, 90(1), 54-62. https://doi.org/10.1128/jb.90.1.54-62.1965
Eriksson-Grennberg, K G, et al. "Resistance of Escherichia coli to Penicillins I. Genetic Study of Some Ampicillin-Resistant Mutants." Journal of bacteriology vol. 90,1 (1965): 54-62. doi: https://doi.org/10.1128/jb.90.1.54-62.1965
Eriksson-Grennberg KG, Boman HG, Jansson JA, Thorén S. Resistance of Escherichia coli to Penicillins I. Genetic Study of Some Ampicillin-Resistant Mutants. J Bacteriol. 1965 Jul;90(1):54-62. doi: 10.1128/jb.90.1.54-62.1965. PMID: 16562043; PMCID: PMC315594.
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Microscopic theory of the quantum Hall hierarchy.

Physical review letters

Bergholtz EJ, Hansson TH, Hermanns M, Karlhede A.
PMID: 18233544
Phys Rev Lett. 2007 Dec 21;99(25):256803. doi: 10.1103/PhysRevLett.99.256803. Epub 2007 Dec 19.

We solve the quantum Hall problem exactly in a limit and show that the ground states can be organized in a fractal pattern consistent with the Haldane-Halperin hierarchy, and with the global phase diagram. We present wave functions for...

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Bergholtz EJ, Hansson TH, Hermanns M, et al. Microscopic theory of the quantum Hall hierarchy. Phys Rev Lett. 2007;99(25):256803doi: 10.1103/PhysRevLett.99.256803.
Bergholtz, E. J., Hansson, T. H., Hermanns, M., & Karlhede, A. (2007). Microscopic theory of the quantum Hall hierarchy. Physical review letters, 99(25), 256803. https://doi.org/10.1103/PhysRevLett.99.256803
Bergholtz, E J, et al. "Microscopic theory of the quantum Hall hierarchy." Physical review letters vol. 99,25 (2007): 256803. doi: https://doi.org/10.1103/PhysRevLett.99.256803
Bergholtz EJ, Hansson TH, Hermanns M, Karlhede A. Microscopic theory of the quantum Hall hierarchy. Phys Rev Lett. 2007 Dec 21;99(25):256803. doi: 10.1103/PhysRevLett.99.256803. Epub 2007 Dec 19. PMID: 18233544.
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