202320222021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011



Dynamic Phaeodactylum tricornutum exometabolites shape surrounding bacterial communities.
V. Brisson, C. Swink, J. Kimbrel, X. Mayali, T. Samo, S.M. Kosina, M. Thelen, T.R. Northen, R.K. Stuart
New Phytologist (2023). 

Prolonging Genetic Circuit Stability through Adaptive Evolution of Overlapping Genes.
J.L. Chlebek, S.P. Leonard, C.S. Kang-Yun, M.C. Yung, D.P. Ricci, Y. Jiao, D.M. Park 
Nucleic Acids Research (2023).

Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer.
J. A. Mattocks, J.J. Jung, C.-Y. Lin, Z. Dong, N.H. Yennawar, E.R. Featherston, C.S. Kang-Yun, T.A. Hamilton, D.M. Park, A.K. Boal, J.A Cotruvo
Nature (2023). vol 618, 87–93. 

Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system.
J. Thompson, C. Barr, L.C. Babcock-Adams, L. Bird, L. Eugenio, A. Garber, Y. Hongoh, M. Liu, K.H. Nealson, A. Okamoto, D. Repeta, S. Suzuki, C. Tacto, M. Tashjian, N. Merino.
Frontiers in Microbiology (2023). Volume 14.

Electrogenetic signaling and information propagation for controlling microbial sonsortia via programmed lysis.
E. VanArsdale, A. Navid, M.J. Chu, T.M. Halvorsen, G.F. Payne, Y. Jiao, W.E. Bentley, M.C. Yung
Biotechnology and Bioengineering (2023). vol 120, 1366–1381. 

Terabase-Scale Coassembly of a Tropical Soil Microbiome.
R. Riley, R.M. Bowers, A. P. Camargo, A. Campbell, R. Egan, E. A. Eloe-Fadrosh, B. Foster, S. H., M. Huntemann, M. Kellom, J.A. Kimbrel, L. Oliker, K. Yelick, J. Pett-Ridge, A. Salamov, N.J. Varghese, A. Clum. Microbiology Spectrum (2023). doi:10.1128/spectrum.00200-23

Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils.
F. Maillard, T.J. Michaud, C.R. See, L.C. DeLancey, S.J. Blazewicz, J.A. Kimbrel, J. Pett-Ridge, P.G. Kennedy.
mSystems (2023).

Temporal evolution of Pu and Cs sediment contamination in a seasonally stratified pond.
F. Coutelot, J. Wheeler, N. Merino, D.I Kaplan, S. Owings, M. Taillefert, M., et al.
Science of The Total Environment (2023). vol 857, 159320.

The Western Lake Erie Culture Collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome.
C.E. Yancey, E. A. Kiledal, S.R. Chaganti, V.J. Denef, R.M. Errera, J.T. Evans, L.N. Hart, D. Isailovic, W.S James, J.K. Kharbush, J.A. Kimbrel, W. Li, X. Mayali, H. Nitschky, C.A. Polik, M.A. Powers, S.H. Premathilaka, N.A. Rappuhn, L.A. Reitz, S.R. Rivera, C.C. Zwiers, G.J. Dick. 
Harmful Algae (2023). Vol 126, 102440.

Active populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands.
M.M. Foley, S.J. Blazewicz, K.J. McFarlane, A. Greenlon, M. Hayer, J.A. Kimbrel, B.J. Koch, V.L. Monsaint-Queeney, K. Morrison, E. Morrissey, B.A. Hungate, J. Pett-Ridge.
Soil Biology and Biochemistry (2023). Volume 177, 108886.


Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape
T.M. Halvorsen, D.P. Ricci, D.M. Park, Y. Jiao, and M.C. Yung.
ACS Synthetic Biology (2022), vol 11 (11), 3785–3796.

Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples
J. Kimbrel, J. Moon, A. Avila-Herrera, J.M. Martí, J. Thissen, N. Mulakken, S.H. Sandholtz, T. Ferrell, C. Daum, S. Hall, B. Segelke, K. T Arrildt, S. Messenger, D.A. Wadford, C. Jaing, J.E. Allen, M.K. Borucki
Viruses (2022), vol 14 (12), 2775

Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity.
M. Windler, R. Stuart, J.S. Deutzmann, X. Mayali, A. Navid, P. D’haeseleer, O.E. Marcu, M. Lipton, C. Nicora, A.M. Spormann.
FEMS Microbial Ecology (2022), vol 98 (9). 

Plutonium mobilization from contaminated estuarine sediments, Esk Estuary (UK).
E. Balboni, N. Merino, J.D. Begg, K.M. Samperton, F.E. Zengotita, G.T.W. Law, A.B. Kersting, M. Zavarin.
Chemosphere (2022), vol 308, 136240.

Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina
M.M. Morris, J.A. Kimbrel, H. Geng, M.B.Tran-Gyamfi, E.T. Yu, K.L. Sale, T.W. Lane, X. Mayali.
mSphere (2022), vol 7 (4).

Microbial Carbonation of Monocalcium Silicate
M.S. Guzman, J. Iyer, P. Kim, D. Kopp, Z. Dong, P. Foroughi, M.C. Yung, R.E. Riman*, and Y. Jiao*
ACS Omega (2022) vol 7 (15) 12524–12535.

Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow
N. Merino, T. R. Jackson, J.H. Campbell, A.B. Kersting, J. Sacket, J.C. Fisher, J.C. Bruckner, M. Zavarin, S.D. Hamilton-Brehm, D.P. Moser
Science of The Total Environment (2022). Vol 842, 156768

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate
H. Kim, J.A. Kimbrel, C.A. Vaiana, J.R. Wollard, X. Mayali, C.R. Buie
The ISME Journal (2022). Vol 16, 1036–1045.

Complete Genome Sequence of Acidithiobacillus ferriphilus GT2, Isolated from Gold Mill Tailings
M. Guzman, D. Reed, Y, Fujita., Y. Jiao., D.M. Park.
Microbiology Resource Announcements. (2022) Vol 11, No 2.

Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in Teosinte and a Modern Maize Cultivar
V. L. Brisson, J. Richardy, S. M. Kosina, T. R. Northen, J. P. Vogel, A. C. M. Gaudin.
Phytobiomes Journal (2022). 6 (1).

Plant-associated fungi support bacterial resilience following water limitation.
R. Hestrin, M. Kan, M. Lafler, J. Wollard, J.A. Kimbrel, P. Ray, S. Blazewicz, R. Stuart, K. Craven, M. Firestone, E. Nuccio, J. Pett-Ridge.
The ISME Journal (2022), vol 16, 2752–2762.

Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems
A. Greenlon, E. Sieradzki, O. Zablocki, B.J. Koch, M.M Foley, J.A. Kimbrel, B.A. Hungate, S.J. Blazewicz, E.E. Nuccio, C.L. Sun, A. Chew, C. Mancilla, M.B. Sullivan, M. Firestone, J. Pett-Ridge, J.F. Banfield.
mSystems (2022), vol 7 (6).

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi
E.E. Nuccio, S.J. Blazewicz, M. Lafler, A.N. Campbell, A. Kakouridis, J.A. Kimbrel, J. Wollard, D. Vyshenska, R. Riley, A. Tomatsu, R. Hestrin, R.R. Malmstrom, M. Firestone, J. Pett-Ridge
Microbiome (2022), vol 10 (1).

Life and death in the soil microbiome: how ecological processes influence biogeochemistry
N. W. Sokol*, LLNL Soil Microbiome Consortium (R. Stuart, Y. Jiao, J. Kimbrel, etc)….., J. Pett-Ridge*
Nature Reviews Microbiology (2022). 20, 415-430


Comparative Genomics Reveals Insights into Induction of Violacein Biosynthesis and Adaptive Evolution in Janthinobacterium
X. Wu, A.E. Kazakov, S. Gushgari-Doyle, X. Yu, V. Trotter, R. K. Stuart, R. Chakraborty
Microbiology Spectrum (2021) Vol 9(3).

Prokaryotic Genome Annotation
J. A. Kimbrel, B. M. Jeffrey, C. S. Ward
Microbial Systems Biology (2022) 193-214.

Identification of effector metabolites using exometabolite profiling of diverse
V. Brisson, M. Mayali, B. Bowen, A. Golini, M. Thelen, R. K. Stuart, T. R Northen
mSystems (2021) 6:e00835-21.

Capturing an elusive but critical element: Natural protein enables actinium chemistry
G.J.-P. Deblonde
, J. Mattocks, Z. Dong, P. Wooddy, J. Cotruvo Jr., M. Zavarin. 
Science Advances, (2021), 7(43), eabk0273.

Bridging Hydrometallurgy and Biochemistry: A Protein-based Process for Recovery and Separation of Rare Earth Elements
Z. Dong, J. A. Mattocks, G. J.P. Deblonde, D. Hu, Y. Jiao, J. A Cotruvo, Park, D.M.
ACS Central Science (2021). 7(11), 1798–1808.

Janthinobacter additions reduce rotifer grazing of microalga Microchloropsis salina in biotically complex communities
C. S. Ward, K. Rolison, M. Li, S. Rozen, C. L. Fisher, T. W. Lane, M. P. Thelen, R. K. Stuart
Algal Research (2021). 58, 102400.

Microbe-Encapsulated Silica Gel Biosorbents for Selective Extraction of Scandium from Coal Byproducts
Z. Dong, G. J.P. Deblonde, A. Middleton, D. Hu, A. Dohnalkova, L. Kovarik, O. Qafoku, V. Shutthanandan, H. Jin, H. Hsu-Kim, N. Theaker, Y. Jiao, D. M. Park
Environmental Science and Technology (2021). 55, 9, 6320–6328.

Projection Microstereolithographic Microbial Bioprinting for Engineered Biofilms
K. Dubbin, Z. Dong, D. M. Park, J. Alvarado, J. Su, E. Wasson, C. Robertson, J. Jackson, A. Bose, M. Moya, Y. Jiao, W. F. Hynes
Nano Letters (2021) 21, 1352-1359.

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
S. M.D. Seaver, F. Liu, Q. Zhang, J. Jeffryes, J.P. Faria, J. N. Edirisinghe, M. Mundy, N. Chia, E. Noor, M. E. Beber, A. A. Best, M. DeJongh, J. A. Kimbrel, P. D’haeseleer, S. R. McCorkle, J. R. Bolton, E. Pearson, S. Canon, E. M. Wood-Charlson, R. W. Cottingham, A. P. Arkin, C. S. Henry
Nucleic Acids Research (2021) 49, D1, D575-D588.

MultiPhATE2: code for functional annotation and comparison of phage genomes
Z. Ecale, L Carol, J. A. Kimbrel, R. Edwards, K. McNair, B. Souza. S. Malfatti
G3 (2021) 11, 5.

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate
H. Kim; J. A. Kimbrel, C.A. Vaiana, A. Christopher, J. R. Wollard, X. Mayali, C. R. Buie
The ISME Journal (2021).
Behind the paper blog post 

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
G. Trubl, J. A. Kimbrel, J. Liquet-Gonzalez, E. E. Nuccio, P. K. Weber, J. Pett-Ridge, J. K. Jansson, M. P. Waldrop, S. J. Blazewicz
Microbiome (2021) 9, 1.


A biosorption-based approach for selective extraction of rare earth elements from coal byproducts
D. M. Park, A. Middleton, R. Smith, G. Deblonde, D. Laudal, N. Theaker, H. Hsu-Kim, Y. Jiao.
Separation and Purification Technology (2020) 241, 116726.

Selective and Efficient Biomacromolecular Extraction of Rare-Earth Elements using Lanmodulin
G. J.P. Deblonde, J. A. Mattocks, D. M. Park, D. W. Reed, J. A. Cotruvo, Y. Jiao
ACS Inorganic Chemistry (2020) 59, 17, 11855–11867.

Selective Biosorption of Valuable Rare Earth Elements Among Co-occurring Lanthanides
E. Chang, A. W. Brewer, D. M. Park, Y. Jiao, and L. N. Lammers
Environmental Engineering Science. (2020) 38, 3.

Major element composition controls rare earth element solubility during leaching of coal fly ash and coal by-products
A. Middleton, D. M. Park, Y. Jiao, H. Hsu-Kim
International Journal of Coal Geology (2020). 227, 103532. 

Techno-economic and Life Cycle Assessments for Sustainable Rare Earth Recovery from Coal Byproducts using Biosorption
M. Alipanah, D. M. Park, A. Middleton, Z. Dong, H. Hsu-Kim, Y. Jiao, H. Jin
ACS Sustainable Chemistry and Engineering (2020) 8, 49, 17914–17922.

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
A. I. Garber, K. H. Nealson, A. Okamoto, S. M. McAllister, C. S. Chan, R. A. Barco, N. Merino
Frontiers in Microbiology (2020) 11, 37.

Surface complexation model of rare earth element adsorption onto bacterial surfaces with lanthanide binding tags
E. Chang, A. Brewer, D. M. Park, Y. Jiao, Lammers L.N.
Applied Chemistry (2020) Vol 112:10448. Doi: 10.1016/j.apgeochem.2019.104478

Metabolomic Analysis Reveals Contributions of Citric and Citramalic Acids to Rare Earth Bioleaching by a Paecilomyces fungus
V. Brisson, W.-Q. Zhuang, L. Avarez-Cohen
Frontiers in Microbiology (2020) 10, 3008.

Selective collection of iron-rich dust particles by natural Trichodesmium colonies
N. Kessler, R. Armoza-Zvuloni, S. Wang, S. Basu, P. K. Weber, R. K. Stuart, Y. Shaked
The ISME Journal (2020) 14, 91-103.

Encapsulin carrier proteins for enhanced expression of antimicrobial peptides
T-H. Lee, T. S. Carpenter, P. D'haeseleer, D. F. Savage, M. C. Yung
Biotechnology and Bioengineering (2020) 117, 603-613.


Microbe encapsulation for selective rare-earth recovery from electronic waste leachates
A. Brewer, A. Dohnalkova, V. Shutthanandan, L. Kovarik, E. Chang, A. M. Sawvel, H. E. Mason, D. Reed, C. Ye, W. F. Hynes, L. N. Lammers, D. M. ParkY. Jiao
Environmental Science and Technology (2019) 53, 13888-13897.

Bio- and mineral acid leaching of rare earth elements from synthetic phosphogypsum
P. J. Antonick, Z. C. Hu, Y. Fujita, D. W. Reed, G. Das, L. L. Wu, R. Shivaramaiah, P. Kim, A. Eslamimanesh, M. M. Lencka, Y. Jiao, A. Anderko, A. Navrotsky, R. E. Riman
J Chem Thermodyn (2019) 132, 491-496.

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling
J. E. Schmidt, A. D. Kent, V. L. Brisson, A. C. M. Gaudin
Microbiome (2019) 7, 146.

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil
V. Brisson, J. E. Schmidt, T. R. Northen, J. P. Vogel, A. C. M. Gaudin
Scientific Reports (2019) 9, 15611.

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
C. E. Zhou, S. Malfatti, J. A. Kimbrel, C. Philipson, K. McNair, T. Hamilton, R. Edwards, B. Souza
Bioinformatics (2019) 35, 4402-2204.

Recovery of rare earth elements from geothermal fluids through bacterial cell surface adsorption
A. Brewer, E. Chang, D. M. Park, T. Kou, Y. Li, L. N. Lammers, Y. Jiao
Environmental Science and Technology (2019) 53, 7714-7723.

The UzcRS two-component system in Caulobacter crescentus integrates regulatory input from diverse auxiliary regulators
D. M. Park, K. W. Overton, Y. Jiao.
Mol Microbiol. (2019) 111(3):678-699. doi: 10.1111/mmi.14180

System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris
A. Navid, Y. Jiao, S. E. Wong, J. Pett-Ridge
BMC Bioinformatics (2019) 20, 233.

Guanidine-riboswitch-regulated efflux transporters protect bacteria against ionic liquid toxicity
D. A. Higgins
, J. Gladden, J. A. Kimbrel, B. A. Simmons, S. W. Singer, M. P. Thelen
Journal of Bacteriology (2019) 201, e00069-19.

A combinatorial sensor design in Caulobacter crescentus for selective environmental uranium detection
D. M. Park, M. J. Taffet  
ACS Synthetic Biology (2019) 8, 807-817.

A new method to correct for habitat filtering in microbial correlation networks
V. Brisson, J. Schmidt, T. R. Northen, J. P. Vogel, A. C. M. Gaudin
Frontiers in Microbiology (2019) 10, 585.

Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context
N. Merino, H. S. Aronson, D. P. Bojanova, J. Feyhl-Buska, M. L. Wong, S. Zhang, D. Giovannelli
Frontiers in Microbiology (2019) 10, 780.

Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis
C. L. Fisher, C. S. Ward, P. D. Lane, J. A. Kimbrel, K. L. Sale, R. K. Stuart, X. Mayali, T. W. Lane
Algal Research (2019) 40, 101500.

Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere
J. A. Kimbrel, T. J. Samo, C. Ward, D. Nilson, M. P. Thelen, A. Siccardi, P. Zimba, T. W. Lane, X. Mayali
Algal Research (2019) 40, 101489.

Reaction of Owith a diiron protein generates a mixed-valent Fe2+/Fe3+ center and peroxide
J. M. Bradley, D. A. Svistunenko, J. Pullin, N. Hill, R. K. Stuart, B. Palenik, M. T. Wilson, A. M. Hemmings, G. R. Moore, N. E. Le Brun
PNAS (2019) 116, 2058-67.


Pervasive iron limitation at subsurface chlorophyll maxima of the California Current
S. L. Hogle, C. L. Dupont, B. M. Hopkinson, A. L. King, K. N. Buck, K. L. Roe, R. K. Stuart, A. E. Allen, E. L. Mann, Z. I. Johnson and K. A. Barbeau
PNAS (2018) 115, 13300-05.

Combining multiple functional annotation tools increases coverage of metabolic annotation
M. Griesemer, J. Kimbrel, C. E. Zhou, A. NavidP. D'haeseleer
BMC Genomics (2018) 19, 948.

The UzcRS two-component system in Caulobacter crescentus integrates regulatory input from diverse auxiliary regulators
D. M. ParkK. W. Overton,Y. Jiao
Mol. Microbiol. (2018) 111, 678–99.

Reduction of plutonium (VI) to (V) by hydroxamate compounds at environmentally relevant pH  
K. D. Morrison, Y. Jiao, A. B. Kersting, M. Zavarin
Environ. Sci. Technol. (2018) 52, 6448–56.

Microbial community structure and functional potential along a hypersaline gradient
J. A. Kimbrel, N. Ballor, Y.-W. Wu, M. M. David, T. C. Hazen, B. A. Simmons, et al.
Front. Microbiol. (2018) 9, 533.

Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions
T. J. Samo, J. A. Kimbrel, D. J. Nilson, J. Pett-Ridge, P. K. Weber, X. Mayali
Environ. Microbiol. (2018) 20, 4385–400.

Proteomic profiling of Burkholderia thailandensis during host infection using Bio-Orthogonal Noncanonical Amino acid Tagging (BONCAT)
M. Franco, P. M. D'haeseleer, S. S. Branda, M. J. Liou, Y. Haider, B. W. Segelke, S. H. El-Etr
Front. Cell Infect. Microbiol. (2018) 8, 370.

Jungle Express: A versatile bacterial repressor for tight transcriptional control
T. L. Ruegg, J. H. Pereira, J. C. Chen, A. DeGiovanni, P. Novichkov, V. K. Mutalik,  G. P. Tomaleri, S. Singer, N. J. Hillson, B. A. Simmons, P. Adams, M. P. Thelen
Nature Communications (2018) 9, 3617.    

Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast
D. A. Higgins, M. K. Young, M. Tremaine, M. Sardi, J. M. Fletcher, M. Agnew, L. Liu, Q. Dickinson, D. Peris, R. L. Wrobel, C. T. Hittinger, A. P. Gasch, S. W. Singer, B. A. Simmons,
R. Landick, M. P. Thelen*, T. K. Sato*. 
Genetics (2018) 210, 219-34.

Techno-economic and life cycle analysis for bioleaching rare earth elements from waste materials
V. Thompson, M. Gupta, H. Jin, E. Vahidi, M. Jindra, V. Nguyen, Y. Fujita, J. Sutherland, Y. Jiao, D. Reed
ACS Sustainable Chem. Eng. (2018) 6, 1602-09.


Development and characterization of a thermophilic, lignin degrading microbiota
S. J. Ceballos, C.-W. Yu, J. Claypool, S. W. Singer, B. A. Simmons, M. P. Thelen, C. W. Simmons, and J. S. VanderGheynst
Process Biochemistry (2017) 63, 193-203.

Recovery of Rare Earth Elements from Low-Grade Feedstock Leachates using Engineered Bacteria
D. M. ParkA. Brewer, D. W. Reed, L. N. Lammers, Y. Jiao
Environmental Science and Technology (2017) 51 (22), 13471-13480.

Techno-economic assessment for integrating biosorption into rare earth recovery process
H. Jin, D. M. Park, M. Gupta, A. W. Brewer, L. Ho, S. L. Singer, W. L. Bourcier, S. Woods, D. W. Reed, L. N. Lammers, J. W. Sutherland, Y. Jiao 
ACS Sustainable Chem. Eng. (2017) 5, 10148-55.

Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM)
R. K. Stuart
, X. Mayali, M. P. Thelen, J. Pett-Ridge, and P. K. Weber 
Bio-protocol (2017) 7, e2263.

Re-directing bacterial microcompartment systems to enhance recombinant expression of lysis protein E from bacteriophage ϕX174 in Escherichia coli
M. C. Yung, F. A. Bourguet, T. S. Carpenter, M. A. Coleman
Microb. Cell Fact. (2017) 16, 71.

Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus
D. M. Park, K. W. Overton, M. J. Liou, Y. Jiao
Molecular Microbiology (2017) 104, 46-64. 

Long-term diffusion of U(VI) in bentonite: Dependence on density 
C. Joseph, J. Mibus, P. Trepte, C. Müller, V. Brendler, D. M. Park, Y. Jiao, A. B. Kersting, M. Zavarin 
Sci. Total Environ. (2017) 575, 207-218. 


Interactions of Plutonium with Pseudomonas sp. Strain EPS-1W and Its Extracellular Polymeric Substances
M. A. Boggs, Y. Jiao, Z. Dai, M. Zavarin, A. B. Kersting
Appl. Environ. Microbiol. (2016) 82, 7093-7101.

Two outer membrane proteins contribute to Caulobacter crescentus cellular fitness by preventing intracellular S-layer protein accumulation
K. W. Overton
, D. Park, M. Yung, A. Dohnalkova, J. Smit, Y. Jiao
Appl. Environ. Microbiol. (2016) 82, 6961–6972.

Microbially Mediated Leaching of Rare Earth Elements from Recyclable Materials.
D.W. Reed, Y. Fujita, D.L. Daubaras, D.F. Bruhn, J.H. Reiss, V.S. Thompson and Y. Jiao
Proceedings of the XXVIII International Mineral Processing Congress (IMPC 2016), 2016, Québec City, Canadian Institute of Mining, Metallurgy and Petroleum.

Permanent Draft Genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria
R. C. Everroad, R. K. Stuart, B. M. Bebout, A. M. Detweiler, J. Z. Lee, D. Woebken, L. Prufert-Bebout, J. Pett-Ridge
SIGS (2016) 11, 1-8. 

Bioleaching of Rare Earth Elements from Waste Phosphors and Cracking Catalysts
D. W. Reed, Y. Fujita, D. L. Daubaras, Y. Jiao, V. S. Thompson
Hydrometallurgy (2016) 166, 34–40.

Microbial mercury methylation in Antarctic sea ice 
C. M. Gionfriddo, M. T. Tate, R. R. Wick, M. B. Schultz, A. Zemla, M. P. Thelen, R. Schofield, D. P. Krabbenhoft, K. E. Holt, J. W. Moreau
Nature Microbiology (2016) 1, 16127.

Light regimes shape utilization of extracellular organic C and N in a cyanobacterial biofilm
R. K. Stuart, X. Mayali, A. Boaro, A. Zemla, R. C. Everroad, D. Nilson, P.K. Weber, M. Lipton, B. Bebout, J. Pett-Ridge, M. P. Thelen
mBio (2016) 7, e00650-16.

Bioadsorption of Rare Earth Elements through Cell Surface Display of Lanthanide Binding Tags
D. M. Park, D. W. Reed, M. C. Yung, A. Eslamimanesh, M. M. Lencka, A. Anderko, Y. Fujita, R. E. Riman, A. Navrotsky, Y. Jiao
Environ Sci Technol. (2016) 50, 2735-42.

Application of a physiologically-based pharmacokinetic model to study theophylline metabolism and its interactions with ciprofloxacin and caffeine
A. Navid, D. M. Ng, S. E. Wong, F. C. Lightstone
CPT: Pharmacometrics & Systems Pharmacology (2016) 5, 74-81.


Impact of anaerobiosis on expression of the iron-responsive Fur and RyhB regulons
N. A. Beauchene, K. S. Myers, D. Chung, D. M. Park, A. M. Weisnicht, S. Keleş, P. J. Kiley
mBio (2015) 6, e01947-15.

Cyanobacterial reuse of extracellular organic carbon in microbial mats
R. K. Stuart, X. Mayali, J. Z. Lee, R. C. Everroad, M. Hwang, B. M. Bebout, P. K. Weber, J. Pett-Ridge, M. P. Thelen
The ISME Journal (2015) 101240–1251.

Do Genome-scale Models Need Exact Solvers or Clearer Standards?
A. Ebrahim, E. Almaas, E. Bauer, A. Bordbar, A. P. Burgard, R. L. Chang, A. Dräger, I. Famili, A. M. Feist, R. M. T. Fleming, S. S. Fong, V. Hatzimanikatis, M. J. Herrgård, A. Holder, M. Hucka, D. Hyduke, N. Jamshidi, S. Y. Lee, N. Le Novère, J. A. Lerman, N. E. Lewis, D. Ma, R. Mahadevan, C. Maranas, H. Nagarajan, A. Navid, J. Nielsen, L. K. Nielsen, J. Nogales, A. Noronha, C. Pal, B. O. Palsson, J. A. Papin, K. R. Patil, N. D. Price, J. L. Reed, M. Saunders, R. S. Senger, N. Sonnenschein, Y. Sun, I. Thiele
Molecular Systems Biology (2015) 11, 831.

Transposon mutagenesis paired with deep sequencing of Caulobacter crescentus under uranium stress reveals genes essential for detoxification and stress tolerance
M. C. Yung, D. M. Park, K. W. Overton, M. J. Blow, C. A. Hoover, J. Smit, S. R. Murray, D. P. Ricci, B. Christen, G. R. Bowman, Y. Jiao
Journal of Bacteriology (2015) 197, 3160-72.


Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw
C. W. Simmons, A. P. Reddy, P. D’haeseleer, J. Khudyakov, K. Billis, A. Pati, B. A. Simmons, M. P. Thelen, J. S. VanderGheynst
Biotechnology for Biofuels (2014) 7, 495.

Modulation of Medium pH by Caulobacter crescentus Facilitates Recovery from Uranium-Induced Growth Arrest
D. M. Park and Y. Jiao
Applied and Environmental Microbiology (2014) 80, 5680-88.

Development of a native Escherichia coli induction system for ionic liquid tolerance
M. Frederix, K. Hutter, J. Leu, T. S. Batth, W. J. Turner, T. L. Ruegg, H. Blanch, B. A. Simmons, P. D. Adams, J. D. Keasling, M. P. Thelen, M. J. Dunlop, C. J. Petzold, A. Mukhopadhyay
PLoS ONE (2014) 9, e101115.

Photoenhanced Electrochemical Interaction between Shewanella and a Hematite Nanowire Photoanode
F. Qian, H. Wang, Y. Ling, G. Wang, M. P. Thelen, and Y. Li
Nano Letters (2014) 14(6), 3688-93.

Biomineralization of uranium by PhoY phosphatase activity aids cell survival in Caulobacter crescentus
M. C. Yung and Y. Jiao
Applied and Environmental Microbiology (2014) 80, 4795-804.

An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production
T. L. Ruegg, E.-M. Kim, B. A. Simmons, J. D. Keasling, S. W. Singer, T. S. Lee, M. P. Thelen 
Nature Communications (2014) 5, 3490.

Shotgun Proteomic Analysis Unveils Survival and Detoxification Strategies byCaulobacter crescentus during Exposure to Uranium, Chromium, and Cadmium
M. C. Yung
, J. Ma, M. Salemi, B. S. Phinney, G. R. Bowman, and Y. Jiao 
Journal of Proteome Research (2014) 13, 1833-47.


Quantitative in silico analysis of transient metabolism of acetaminophen and associated causes of hepatotoxicity in humans
A. Navid, D. M. Ng, B. J. Stewart, S. E. Wong, and F. C. Lightstone
In Silico Pharmacology (2013) 1, 14.

Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses
A. P. Reddy, C. W. Simmons, P. D'haeseleer, J. Khudyakov, H. Burd, M. Hadi, B. A. Simmons, S. W. Singer, M. P. Thelen, J. S. VanderGheynst 
PLoS ONE (2013) 8, e77985.

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
P. D'haeseleer, J. M. Gladden, M. Allgaier, P. S. Chain, S. G. Tringe, S. A. Malfatti, J. T. Aldrich, C. D. Nicora, E. W. Robinson, L. Paša-Tolić, P. Hugenholtz, B. A. Simmons, S. W. Singer 
PLoS ONE (2013) 8, e68465.

Lignin depletion enhances the digestibility of cellulose in cultured xylem cells
C. I. Lacayo, M. S. Hwang, S.-Y. Ding, M. P. Thelen
PLoS ONE (2013) 8, e68266.

Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction
S. Chaudhury, M. D. M. Abdulhameed, N. Singh, G. J. Tawa, P. M. D’haeseleer, A. T. Zemla, A. Navid, C. E. Zhou, M. C. Franklin, J. Cheung, M. J. Rudolph, J. Love, J. F. Graf, D. A. Rozak, J. L. Dankmeyer, K. Amemiya, S. Daefler, A. Wallqvist
PLoS ONE (2013) 8, e63369.

D-Lactate production as a function of glucose metabolism in Saccharomyces cerevisiae
B. J. Stewart, A. Navid, K. S. Kulp, J. L. S. Knaack, and G. Bench
Yeast (2013) 30, 81–91.


Genome-Level Transcription Data of Yersina Pestis Analyzed With A New Metabolic Constraint-Based Approach
A. Navid, E. Almaas
BMC Systems Biology (2012) 6, 150.

Characterization of axial and proximal histidine mutations of the decaheme cytochrome MtrA from Shewanella str. ANA-3: Implications for the electron transport mechanism.
C. Reyes, F. Qian, A. Zhang, S. Bondarev, A. Welch, M. P. Thelen, C. W. Saltikov
Journal of Bacteriology (2012) 194, 5840-47.

Enhanced cellulose degradation using cellulase-nanosphere complexes
C. Blanchette, C. I. Lacayo, N. O. Fischer, M. Hwang, M. P. Thelen
PLoS One (2012) 7, e42116.

Syntrophic metabolism of a co-culture containing Clostridium cellulolyticum and Rhodopseudomonas palustris for hydrogen production
Y. Jiao, A. Navid, B. J. Stewart, J. McKinlay, M. P. Thelen, J. Pett-Ridge
International Journal of Hydrogen Energy (2012) 37, 11719-26.

Global transcriptome response to ionic liquid by a tropical rainforest soil bacterium, Enterobacter lignolyticus
J. Khudyakov, P. D’haeseleer, S. Borglin, K. DeAngelis, H. Woo, E. Lindquist, T. C. Hazen, B. A. Simmons, M. P. Thelen
PNAS (2012) 109, e2173-82.

Tracing determinants of dual substrate specificity in glycoside hydrolase family 5
Z. Chen, G. D. Friedland, J. H. Pereira, S. A. Reveco, R. Chan, J. I. Park, M. P. Thelen, P. D. Adams, A. P. Arkin, J. D. Keasling, H. W. Blanch, B. A. Simmons, K. L. Sale, D. Chivian, S. R. Chhabra
Journal of Biological Chemistry (2012) 287, 25335-43.

"Development of constraint-based system-level models of microbial metabolism
A. Navid (2012) in Microbial Systems Biology, Methods in Molecular Biology, Vol. 881, ISBN: 9781617798269, ed. Navid, A., Chapter 18, 531-549.

"Yersinia pestis Metabolic Network"
A. Navid and E. Almaas (2012) in Yersinia: Systems Biology and Control, ISBN: 9781908230058, eds. Carniel, E, Hinnebusch, BJ. Chapter 6, 83-108.

Metal affinity enrichment increases the MS proteomics identification of extracellular microbial proteins
K. E. Wheeler
, B. Erickson, R. Mueller, S. W. Singer, N. C. VerBerkmoes, M. Hwang, M. P. Thelen, R. L. Hettich
Journal of Proteome Research (2012) 11, 861-70


Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targets
A. NavidBriefings in Functional Genomics (2011) 10, 354-64.

A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated Bacterial and Archaeal genes
A. Yelton, B. Thomas, S. Simmons, P. Wilmes, A. Zemla, M. P. Thelen, N. Justice, J. F. Banfield
PLoS Computional Biology (2011) 7, e1002230.

ATM controls meiotic double-strand break formation
J. Lange, J. Pan, F. Cole, M. P. Thelen, M. Jasin, S. Keeney 
Nature (2011) 479, 237-40.