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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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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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Random resistor-diode networks and the crossover from isotropic to directed percolation.

Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics

Janssen HK, Stenull O.
PMID: 11088812
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Sep;62(3):3173-85. doi: 10.1103/physreve.62.3173.

By employing the methods of renormalized field theory, we show that the percolation behavior of random resistor-diode networks near the multicritical line belongs to the universality class of isotropic percolation. We construct a mesoscopic model from the general epidemic...

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Janssen HK, Stenull O. Random resistor-diode networks and the crossover from isotropic to directed percolation. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000;62(3):3173-85doi: 10.1103/physreve.62.3173.
Janssen, H. K., & Stenull, O. (2000). Random resistor-diode networks and the crossover from isotropic to directed percolation. Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, 62(3), 3173-85. https://doi.org/10.1103/physreve.62.3173
Janssen, and Stenull. "Random resistor-diode networks and the crossover from isotropic to directed percolation." Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics vol. 62,3 (2000): 3173-85. doi: https://doi.org/10.1103/physreve.62.3173
Janssen HK, Stenull O. Random resistor-diode networks and the crossover from isotropic to directed percolation. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Sep;62(3):3173-85. doi: 10.1103/physreve.62.3173. PMID: 11088812.
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Nonlinear random resistor diode networks and fractal dimensions of directed percolation clusters.

Physical review. E, Statistical, nonlinear, and soft matter physics

Stenull O, Janssen HK.
PMID: 11461359
Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jul;64(1):016135. doi: 10.1103/PhysRevE.64.016135. Epub 2001 Jun 28.

We study nonlinear random resistor diode networks at the transition from the nonpercolating to the directed percolating phase. The resistor-like bonds and the diode-like bonds under forward bias voltage obey a generalized Ohm's law V approximately I(r). Based on...

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Stenull O, Janssen HK. Nonlinear random resistor diode networks and fractal dimensions of directed percolation clusters. Phys Rev E Stat Nonlin Soft Matter Phys. 2001;64(1):016135doi: 10.1103/PhysRevE.64.016135.
Stenull, O., & Janssen, H. K. (2001). Nonlinear random resistor diode networks and fractal dimensions of directed percolation clusters. Physical review. E, Statistical, nonlinear, and soft matter physics, 64(1), 016135. https://doi.org/10.1103/PhysRevE.64.016135
Stenull, O, and Janssen, H K. "Nonlinear random resistor diode networks and fractal dimensions of directed percolation clusters." Physical review. E, Statistical, nonlinear, and soft matter physics vol. 64,1 (2001): 016135. doi: https://doi.org/10.1103/PhysRevE.64.016135
Stenull O, Janssen HK. Nonlinear random resistor diode networks and fractal dimensions of directed percolation clusters. Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jul;64(1):016135. doi: 10.1103/PhysRevE.64.016135. Epub 2001 Jun 28. PMID: 11461359.
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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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Multifractal properties of resistor diode percolation.

Physical review. E, Statistical, nonlinear, and soft matter physics

Stenull O, Janssen HK.
PMID: 11909182
Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar;65(3):036124. doi: 10.1103/PhysRevE.65.036124. Epub 2002 Feb 27.

Focusing on multifractal properties we investigate electric transport on random resistor diode networks at the phase transition between the nonpercolating and the directed percolating phase. Building on first principles such as symmetries and relevance we derive a field theoretic...

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Stenull O, Janssen HK. Multifractal properties of resistor diode percolation. Phys Rev E Stat Nonlin Soft Matter Phys. 2002;65(3):036124doi: 10.1103/PhysRevE.65.036124.
Stenull, O., & Janssen, H. K. (2002). Multifractal properties of resistor diode percolation. Physical review. E, Statistical, nonlinear, and soft matter physics, 65(3), 036124. https://doi.org/10.1103/PhysRevE.65.036124
Stenull, Olaf, and Janssen, Hans-Karl. "Multifractal properties of resistor diode percolation." Physical review. E, Statistical, nonlinear, and soft matter physics vol. 65,3 (2002): 036124. doi: https://doi.org/10.1103/PhysRevE.65.036124
Stenull O, Janssen HK. Multifractal properties of resistor diode percolation. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar;65(3):036124. doi: 10.1103/PhysRevE.65.036124. Epub 2002 Feb 27. PMID: 11909182.
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Viability of competing field theories for the driven lattice gas.

Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics

Schmittmann B, Janssen HK, Tauber UC, Zia RK, Leung K, Cardy JL.
PMID: 11031662
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 May;61(5):5977-80. doi: 10.1103/physreve.61.5977.

It has recently been suggested that the driven lattice gas should be described by an alternate field theory in the limit of infinite drive. We review the original and the alternate field theory, invoking several well-documented key features of...

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Schmittmann B, Janssen HK, Tauber UC, et al. Viability of competing field theories for the driven lattice gas. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000;61(5):5977-80doi: 10.1103/physreve.61.5977.
Schmittmann, B., Janssen, H. K., Tauber, U. C., Zia, R. K., Leung, K., & Cardy, J. L. (2000). Viability of competing field theories for the driven lattice gas. Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, 61(5), 5977-80. https://doi.org/10.1103/physreve.61.5977
Schmittmann, et al. "Viability of competing field theories for the driven lattice gas." Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics vol. 61,5 (2000): 5977-80. doi: https://doi.org/10.1103/physreve.61.5977
Schmittmann B, Janssen HK, Tauber UC, Zia RK, Leung K, Cardy JL. Viability of competing field theories for the driven lattice gas. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 May;61(5):5977-80. doi: 10.1103/physreve.61.5977. PMID: 11031662.
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Showing 1 to 12 of 268 entries