Publications

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

 

Surface complexation model of rare earth element adsorption onto bacterial surfaces with lanthanide binding tags
Chang E., Brewer A., Park, D.M., Jiao, Y., 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) In press.

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.

2019

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 (2019) online.

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
Antonick, P. J.;  Hu, Z. C.;  Fujita, Y.;  Reed, D. W.;  Das, G.;  Wu, L. L.;  Shivaramaiah, R.;  Kim, P.;  Eslamimanesh, A.;  Lencka, M. M.;  Jiao, Y.;  Anderko, A.;  Navrotsky, A.; Riman, R. E.,
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
Park DM, Overton KW, Jiao Y., .
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.

2018

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.

2017

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. 

2016

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.

2015

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.

2014

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.

2013

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.

2012

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

2011

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.