Google Scholar link for Dr. R. P. Carlson

 

  • McGill, S.L., Yung, Y., Hunt, K.A., Henson, M.A., Hanley, L., Carlson, R.P. (2021) Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy. Scientific Reports. 11, 1457. doi.org/10.1038/s41598-020-80522-8

  • Hunt, K.A. Mallette, N., Peyton, B.M., Carlson, R.P. (2021) In silico analysis of functionalized hydrocarbon production using Ehrlich pathway and fatty acid derivatives in an endophytic fungus. Journal of Fungi. 7(6) 435. https://doi.org/10.3390/jof7060435.

  • Tafur Rangel, A.E., Rios Guzman, W.L. Mejia Perez, D.E., Ojeda Cuellar, C.E., Carlson, R., Gomez Ramirez, J.M., Gonzalez Barrios, A. F. (2021) In silico design for systems-based metabolic engineering for the bioconversion of valuable compounds from industrial by-products. Frontiers in Genetics, 12: 633073.

  • Pulukkody, A. C., Yung, Y.P., Donnarumma, F., Murray, K.K., Carlson, R.P., Hanley, L. (2021) Spatially resolved analysis of Pseudomonas aeruginosa biofilm proteomes measured by laser ablation sample transfer. PLOS One, in press.

  • Patel, A., Carlson, R.P., Henson, M.A. (2021) In silico Analysis of Synthetic Multispecies Biofilms for Cellobiose-to-Isobutanol Conversion Reveals Design Principles for Stable and Productive Communities. Biochemical Engineering Journal. In press.

  • Hammarlund, S.P., Gedeon, T., Carlson, R.P., Harcombe, W. (2021) Limitation by a shared mutualist promotes coexistence of multiple competing partners. Nature Communications. 12, 619. doi.org/10.1038/s41467-021-20922-0.

  • Park, H., Patel, A., Hunt, K.A., Henson, M.A., Carlson, R. P. 2020. Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis. npj Biofilms Microbiomes. 6, 59 (2020). https://doi.org/10.1038/s41522-020-00170-8

  • Mahout, M., Carlson, R.P., Peres, S. (2020) Answer Set Programming for computing constraints-based elementary flux. Processes. 8(12) 1649, doi.org/10.3390/pr8121649.

  • Hulkova, M., Soulkupova, J., Carlson, R.P., Marsalek, B. (2020) Interspecies interactions can enhance Pseudomonas aeruginosa tolerance to surfaces functionalized with silver nanoparticles. in Colloids and Surfaces B: Biointerfaces. 192: 111027. doi.org/10.1016/j.colsurfb.2020.111027

  • Zhang, T. Parker, A., Carlson, R.P., Stewart, P.S., Klapper, I. (2020) Flux-Balance Based Modeling of Biofilm Communities. Processes. Multiscale Model. Simul. 18(2), 1025-1052. doi.org/10.1137/18M1234096

  • Jay, Z.J., Hunt, K.A. Chou, K.J., Schut, G.J., Maness, P.C., Adams, M.W.W., Carlson, R.P. (2020) Integrated thermodynamic analysis of electron bifurcating [FeFe]-hydrogenase to inform anaerobic metabolism and H2 production. Biochemica Biophysica Acta Bioenergetics. 1861; 148087. 10.1016/j.bbabio.2019.148087

  • Park, H., McGill, S.L., Arnold, A. D., Carlson, R.P. (2020) Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor. Cellular and Molecular Life Sciences. 77, 395-413. 10.1007/s00018-019-03377-x

  • Yung, Y., McGill, S.L., Chen, H., Carlson, R.P., Hanley, L. (2019) Reverse Diauxie Phenotype in Pseudomonas aeruginosa Biofilm Revealed by Exometabolomics and Label-Free Proteomics. npj Biofilms and Microbiomes. 5, 31. 10.1038/s41522-019-0104-7

  • Carlson, R.P., Sauro, H.M. (2019) Special Issue: Methods in Computational Biology. Processes 7(4): 205. 10.3390/pr7040205

  • Patel, A., Carlson, R.P., Henson, M. (2019) In silico Metabolic Design of Two-strain Biofilm Systems Predicts Enhanced Biomass Production and Biochemical Synthesis. Biotechnology Journal. 14:7, 1800511. 10.1002/biot.201800511

  • Schepens, D., Carlson, R.P., Heys, J., Beck, A.E., Gedeon, T. (2019) Role of resource allocation and transport in emergence of cross-feeding in microbial consortia. Journal of Theoretical Biology. 467, 150-163. 10.1016/j.jtbi.2019.01.030

  • El-Mansi, M., Stephanopoulos, G., Carlson, R.P. (2019) Chapter 6: Flux Control Analysis and Stoichiometric Network Modeling: Current trends and future prospects. Fermentation Microbiology and Biotechnology 4th ed. pp. 91-116. (eds E. M. T. El-Mansi, Jens Nielsen, David Mousdale, Ross P. Carlson) CRC/Taylor and Francis Inc. London. 10.1201/9780429506987

  • Beck, A.E., Hunt, K.A., Carlson, R.P. (2018) Measuring Cellular Biomass Composition for Computational Biology Applications. Processes 6(5), 38. 10.3390/pr6050038

  • Hunt, K.A., Jennings, R. deM. Inskeep, W.P., Carlson, R. P. (2018) Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PLoS Computational Biology, 14(9):e1006431. 10.1371/journal.pcbi.1006431

  • Gumulya, Y., Boxall, N.J., Khaleque, H.N., Santala, V., Carlson, R.P., Kaksonen, A.H. (2018) In a Quest for Engineering Acidophiles for Biomining Applications: Challenges and Opportunities. Genes, 9(2), 116. 10.3390/genes9020116

  • Carlson, R.P., Beck, A.E., Phalak, P., Fields, M.W., Gedeon, T., Hanley, L., Harcombe, W.R., Henson, M.A., Heys, J.J. (2018) Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross feeding microbial consortia. Biochemical Transactions. 46: 269. 10.1042/BST20170242

  • Beck, A.E., Bernstein, H.C., Carlson, R.P. (2017) Stoichiometric network analysis of cyanobacterial acclimation to photosynthesis-associated stresses identifies heterotrophic niches. Processes 5 (2), 32.

  • Ledbetter, R., Garcia-Costas, A.M., Lubner, C.E., Mulder, D.W., Tokmina-Lukaszewska, M., Artz, J.H.,  Patterson, A., Magnuson, T., Jay, Z. J., Duan, H. D., Miller, J., Plunkett, M.H., Hoben, J.P., Barney, B.M., Carlson, R.P., Miller, A.F., Bothner, B., King, P.W., Peters, J.W., Seefeldt, L.C. (2017) The Electron Bifurcating FixABCX Protein Complex from Azotobacter vinelandii: Generation of Low-Potential Reducing Equivalents for Nitrogenase Catalysis. Biochemistry 56 (32), 4177-4190.

  • El Moustaid, F., Carlson, R.P., Villa, F., Klapper, I. (2017) Photorespiration and Rate Synchronization in a Phototroph-Heterotroph Microbial Consortium. Processes. 5(1), 11.

  • Schepens, D., Beck, A.E., Heys, J.J., Gedeon, T., Carlson, R.P. (2017) The Benefits of Resource Partitioning and Division of Labor in Microbial Consortia. Advances in Systems and Synthetic Biology (editors P. Amar, F. Kepes, V. Norris). EDP Sciences Publishing. pp 137-148. ISBN 978-2-7598-2116-7

  • Schoen, H., Hunt, K.A., Strobel, G., Peyton, B., Carlson, R.P. (2017) Carbon chain length of biofuel- and flavor-relevant hydrocarbons produced by lignocellulolytic fungal endophytes vary with culturing temperature. Mycosciene. In press.

  • Venters, M., Carlson, R.P., Gedeon, T., Heys, J. (2017) Effects of Spatial Localization on Microbial Consortia Growth. PLOS ONE. 12(1) e0168592.

  • Phalak, P., Chen, J., Carlson, R.P., Henson, M.A. (2016) Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species. BMC Systems Biology. 10:90.

  • Phalak, P., Chen, J., Carlson, R.P., Henson, M.A. (2016) Spatiotemporal Metabolic Modeling of a Chronic Wound Biofilm Consortium. IFAC-PapersOnLine. 49:26: 32-37.

  • Salinas, D., Cody, D., McCuthchen, C., Carlson, R.P., Mumey, B., June, R. (2016) Combining Targeted Metabolomic Data with a Model of Glucose Metabolism: Toward Progress in Chondrocyte Mechanotransduction. PLOS ONE. 12(1) E0168326.

  • Hunt, K.A., deM Jennings, R., Inskeep, W.P., Carlson, R.P. (2016) Stoichiometric modelling of assimilatory and dissimilatory biomass utilization in a microbial community. Environmental Microbiology. 18: 4946-4960.

  • Carlson, R.P., Oshota, O., Shipman, M., Caserta, J.A., Hu, P., Saunders, C.W., Xu, J., Reeder, N., Richards, A., Pettigrew, C., Peyton, B.M. (2016) Integrated molecular, physiological and in silico characterization of two Halomonas isolates from industrial brine. In press.

  • Beck, A., Hunt, K.A., Bernstein, H.C, Carlson, R.P. (2016) Interpreting and designing microbial communities for bioprocess applications, from components to interactions to emergent properties. Biotechnologies for Biofuel Production and Optimization. 1: 407-432.

  • Folsom, J.P., Carlson, R.P. (2015) Physiological, elemental composition, and proteomic analyses of Escherichia coli ammonium-limited chemostat growth with comparison to iron- and glucose-limited chemostat growth. Microbiology. 161: 1659-1970.

  • Singh, D.,Carlson, R.P., Fell, D.A., Poolman, M. (2015) Modelling metabolism of the diatom Phaeodactylum tricornutum. Biochemical transactions. 43(6): 1182-1186.

  • Folsom, J.P., Parker, A., Carlson, R.P. (2014) Physiological and Proteomic Analysis of Escherichia coli Iron-Limited Chemostat Growth. Journal of Bacteriology. 196: 2748-2763.

  • Ammons, M.C.B., Tripet, B.P., Carlson, R.P., Kirker, K.R., Gross, M.A., Stanisich, J.J., Copi√© V. (2014) Quantitative NMR Metabolite Profiling of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Discriminates between Biofilm and Planktonic Phenotypes. Journal of Proteome Research. 13(6): 2973-2985.

  • Hunt, K.A., Folsom, J.P., Taffs, R.L.,Carlson, R.P. (2014) Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition. Bioinformatics. 30: 1569-1578.

  • Bernstein, H.C., Carlson, R.P. (2014) Design, construction and characterization methodologies for synthetic microbial consortia. Methods in Molecular Biology. 1151: 49-68.

  • Mallette, N., Pankratz, E.M., Parker, A.E., Strobel, G.A., Busse, S.C., Carlson, R.P., Peyton, B.M. (2014) Evaluation of Cellulose as a Substrate for Hydrocarbon Fuel Production by Ascocoryne sarcoides (NRRL 50072). Journal of Sustainable Bioenergy Systems. 4(1): ID 44247.

  • Bernstein, H.C., Kesaano, M., Moll, K., Smith, T., Gerlach, R., Carlson, R.P., Miller, C.D., Peyton, B.M., Cooksey, K.E., Gardner, R.D., Sims, R.C. (2014) Direct measurement and characterization of active photosynthesis zones inside wastewater remediateing and biofuel producing microalgal biofilms. Bioresource Technology. 156: 206-215.

  • Bhardwaj, C., Cui, Y., Hofstetter, T., Suet, Y. L., Bernstein, H. C., Carlson, R. P., Musahid, A., Hanley, L. (2013) Differentiation of microbial species and strains in coculture biofilms by multivariate analysis of laser desorption postionization mass spectra. The Analyst. 138:6844-6851

  • Cui, Y., Bhardwaj, C., Milasinovic, S., Carlson R. P., Gordon R. J., Hanley L. (2013) Molecular Imaging and Depth Profiling of Biomaterials Interfaces by Femtosecond Laser Desorption Postionization Mass Spectrometry. Applied Materials & Interfaces. 5: 9269-9275.

  • Bhardwaj, C., Moore, J., Gasper, G., Bernstein, H., Carlson, R., Hanley, L. (2013) Laser desorption VUV postionization MS imaging of a cocultured biofilm. Analytical and Bioanalytical Chemistry. 405:6969-6977.

  • Valenzuela, J., Carlson, R. P., Gerlach, R., Cooksey, K., Peyton, B. M., Bothner, B., Fields, M. W. (2013) Nutrient resupplementation arrests bio-oil accumulation in Phaeodactylum tricornutum. Applied Microbiology and Biotechnology. 97:7049-7059.

  • Bernstein, H.C., Beam J.P., Kozubal, M.A., Carlson, R. P., Inskeep, W.P. (2013) In situ Analysis of Oxygen Consumption and Diffusive Transport in High-temperature Acidic Iron Oxide Mats. Environmental Microbiology. 15:2360-2370

  • Mus, F., Toussaint, J.P., Cooksey, K.E., Fields, M.W., Gerlach, R., Peyton, B.M., Carlson, R.P. (2013) Physiological and Molecular Analysis of Carbon Source Supplementation and pH Stress Induced Lipid Accumulation in the Marine Diatom Phaeodactylum tricornutum. Applied Microbiology and Biotechnology. 97:3625-3642

  • Bernstein, H., Carlson, R.P. (2012) Microbial Consortia Engineering for Cellular Factories: in vitro to in silico. Computational and Structural Biotechnology Journal 3(4) e201210017.

  • Carlson, R.P., Oshota, O.J., Taffs, R. (2012) Systems analysis of microbial adaptations to simultaneous stresses. Subcellular Biochemistry. 64: 139-157.

  • Blaze, M.T., Ayin, B., Carlson, R., Hanley, L. (2012) Identification and Imaging of Peptides and Proteins on Enterococcus faecalis Biofilms by Matrix Assisted Laser Desorption Ionization Mass Spectrometry. Analyst. 137:5018.

  • Mallette, N., Knighton, W.B., Strobel, G.A., Carlson, R.P., Peyton B.M. (2012) Resolution of volatile fuel compound profiles from Ascocoryne sarcoides: a comparison by proton transfer reaction-mass spectrometry and solid phase microextraction gas chromatography-mass spectrometry. AMB Express. 2:23.

  • Valenzuela, J., Mazurie, A., Carlson, R.P., Gerlach, R., Cooksey, K., Peyton, B.M., Fields, M.W. (2012) Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum. Biotechnology for Biofuels 5:40.

  • Bernstein, H., Paulson, S., Carlson, R.P. (2012) Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. Journal of Biotechnology, 157: 159-166.

  • Gardner, R., Cooksey, K. Mus, F., Macur, R., Moll, K.,Eustance, E., Carlson, R.P. Gerlach, R., Fields, M.W., Peyton, B.M. (2012) Use of Sodium Bicarbonate to Stimulate Triacylglycerol Accumulation in the Chlorophyte Scenedesmus sp. and the diatom Phaeodactylum tricornutum.Journal of Applied Phycology. 24: 1311-1320.

  • El-Mansi, M., Stephanopoulos, G., Carlson, R.P. (2011) Chapter 7: Flux Control Analysis and Stoichiometric Network Modeling: Basic Principles and Industrial Applications. Fermentation Microbiology and Biotechnology (eds M. El-Mansi, C.F.A. Bryce, A.L. Demain, A.R. Allman) CRC/Taylor and Francis Inc. (invited review).

  • Carlson, R.P., Taffs, R.L. (2010) Molecular-level tradeoffs and metabolic adaptations to simultaneous stressors. Current Opinion in Biotechnology. 21: 1-7. (invited review).

  • Zuroff, T., Bernstein, H., LlyodRandolfi, J., JimenezTaracido, L., Stewart, P.S., Carlson, R.P. (2010) Robustness analysis of culturing perturbations on Escherichia coli colony biofilm betalactam and aminoglycoside antibiotic tolerance. BMC Microbiology. 10:185.

  • Taffs, R., Aston, J.E., Brileya, K., Jay, Z., Klatt, C.G., McGlynn, S., Mallette, N., Montross, S., Gerlach, R., Inskeep, W.P., Ward, D.M., Carlson R.P. (2009) In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. BMC Systems Biology 3:114.

  • Arce, F.T., Carlson, R.P., Monds, R.J., Veeh, R., Hu, F.Z., Stewart, P.S., Lal, R., Ehrlich, G.D., Avci, R. (2009) Nanoscale structural and mechanical properties of nontypeable Haemophilus influenzae biofilms. Journal of Bacteriology. 191:2512

  • Carlson, R.P. (2009) Decomposition of complex microbial behaviors into resourcebased stresses. Bioinformatics. 25:90.

  • Carlson, R.P., Taffs, R., Davison, W.M., Stewart, P.S. (2008) Antibiofilm properties of chitosan coated surfaces. Journal of Biomaterials Science: Polymer Edition. 19:1035.

  • Gasper, G., Carlson, R.P., Akhmetov, A., Moore, J., Hanley, L. (2008) Laser Desorption 7.87eV Postionization Mass Spectrometry of Antibiotics in Staphylococcus epidermidis Bacterial Biofilms. Proteomics. 8:3816.

  • Carlson, R.P. (2007) Metabolic systems cost benefit analysis for interpreting network structure and regulation. Bioinformatics. 23:1258.

  • Carlson, R., Srienc, F. (2006) Gene dosage effects on polyhydroxyalkanoate production in Saccharomyces cerevisiae. Journal of Biotechnology. 124:561573.

  • Trinh, C.T., Carlson, R., Wlaschin, A.P., Srienc, F. (2006) Design, construction, and performance of the most efficient biomass producing E. coli. Metabolic Engineering. 8:628.

  • Wlaschin, A.P., Trinh, C.T., Carlson, R., Srienc, F. (2006) The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies. Metabolic Engineering. 8:338.

  • Kacmar, J., Carlson, R., Balogh, S. Srienc, F. (2006) Automated staining and quantification of poly3hydroxybutyrate (PHB) in Saccharomyces cerevisiae and Ralstonia eutropha cell populations using flow cytometry. Cytometry. 69:2735.

  • Zhang, B., Carlson, R., Srienc, F. (2006) Engineering the monomer composition of polyhydroxyalkanoates synthesized in Saccharomyces cerevisiae. Applied and Environmental Microbiology. 72:536.

  • Carlson, R., Wlaschin, A., Srienc, F. (2005) Kinetic studies and biochemical pathway analysis of anaerobic poly(R)3hydroxybutyric acid synthesis in Escherichia coli.  Applied and Environmental Microbiology. 71:713

  • Zhang, B., Carlson, R., Pederson, E., Witholt, B., Srienc, F. (2005) Novel synthesis routes for polyhydroxyalkanoic acids with unique properties. Polymer Biocatalysis and Biomaterials. 900:292.

  • Vijayasankaran, N., Carlson, R., Srienc, F. (2005) Metabolic pathway structure for recombinant protein synthesis in Escherichia coli. Applied Microbiology and Biotechnology. 68:737.

  • Vijayasankaran, N., Carlson, R., Srienc, F. (2005) Synthesis of Poly[(R)3hydroxybutyric acid] in the Cytoplasm of Pichia pastoris under Oxygen Limitation. Biomacromolecules. 6:604.

  • Carlson, R., Srienc, F. (2004) Fundamental Escherichia coli biochemical pathways for biomass and maintenance energy production: Identification of pathways. Biotechnology and Bioengineering. 85:119.

  • Carlson, R., Srienc, F. (2004) Fundamental Escherichia coli biochemical pathways for biomass and maintenance energy production: Creation of overall flux states. Biotechnology and Bioengineering. 86:49.

  • Kacmar, J., Zamamiri, A., Carlson, R., AbuAbsi, N., Srienc, F. (2004) Singlecell variability in growing Saccharomyces cerevisiae cell populations measured with automated flow cytometry. Journal of Biotechnology. 109:239.

  • Carlson, R., Fell, D., Srienc, F. (2002) Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnology and Bioengineering. 79:121.

  • Srienc, F., Carlson, R. (2000) Metabolic engineering of polyhydroxyalkanoate synthesis in eukaryotic cells. Proceedings of the Agricultural Biotechnology Symposium. 2000:90.