Publications

2017

F. Qian, C. Huang, Y.-D. Lin, A. N. Ivanovskaya, T. J. O'Hara, R. H. Booth, C. J. Creek, H. A. Enright, D. A. Soscia, A. M. Belle, R. Liao, F. C. Lightstone, K. S. Kulp and E. K. Wheeler (2017) Simultaneous electrical recording of cardiac electrophysiology and contraction on chip.  Lab on a Chip 17, 1732-1739.

B. J. Bennion, N. A. Be, M. W. McNerney, V. Lao, E. M. Carlson, C. A. Valdez, M. A. Malfatti, H. A. Enright, T. H. Nguyen, F. C. Lightstone, and T. S Carpenter (2017) Predicting a Drug’s Membrane Permeability: A Computational Model Validated With In Vitro Permeability Assay Data.  J. Phys. Chem. B.

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

D. Weilhammer, A. D. Dunkle, C. D. Blanchette, N. O. Fischer, M. Corzett, D. Lehman, T. Boone, P. Hoeprich, A. Driks, A. Rasley (2017) Enhancement of antigen-specific CD4+ and CD8+ T cell responses using a self-assembled biologic nanolipoprotein particle vaccine. Vaccine 35 (11), 1475-1481.

D. M. Park, K. W. Overton, M. J. Liou, Y. Jiao (2017) Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus. Molecular Microbiology 104(1), 46-64. 

X. Zhang, H. Perez-Sanchez, F. C. Lightstone (2017) A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding AntithrombinCurrent Topics in Medicinal Chemistry 17, 1-9.

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

2016

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

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

D.W. Reed, Y. Fujita, D.L. Daubaras, D.F. Bruhn, J.H. Reiss, V.S. Thompson and Y. Jiao (2016) Microbially Mediated Leaching of Rare Earth Elements from Recyclable Materials. Proceedings of the XXVIII International Mineral Processing Congress (IMPC 2016), ISBN: 978-1-926872-29-2, September 11-15, 2016, Québec City, Canadian Institute of Mining, Metallurgy and Petroleum.

F. Qian, P. C. Lan, T. Olson, C. Zhu, E. B. Duoss, C. M. Spadaccini, and T. Y.-J. Han (2016) Multiphase Separation of Copper Nanowires, Chem. Commun., 52, 11627.

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

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

T. Carpenter, J. Parkin, and S. Khalid (2016) The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile. J. Phys. Chem. Lett(17), 3446-3451.

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 (2016) Microbial mercury methylation in Antarctic sea iceNature Microbiology 1, 16127.

S. F. Gilmore, C. D. Blanchette, T. M. Scharadin, G. L. Hura, A. Rasley, M. Corzett, C.-X. Pan, N. O. Fischer, P. T. Henderson (2016) Lipid crosslinking of nanolipoprotein particles substantially enhances serum stability and cellular uptakeACS Applied Materials and Interfaces, 8, 20549-20557

H. E. Enright, S. H. Felix, N. O. Fischer, E. Mukerjee, D. Soscia, M. Mcnerney, K. Kulp, J. Zhang, G. Page, P. Miller, A. Ghetti, E. K. Wheeler, S. Pannu (2016) Long-term non-invasive interrogation of human dorsal root ganglion neuronal cultures on an integrated microfluidic multielectrode array platformAnalyst, 141, 5346-5357.

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 (2016) Light regimes shape utilization of extracellular organic C and N in a cyanobacterial biofilm. mBio 7: e00650-00616. 

T. Liu, C. Zhu, T. Kou, M. A. Worsley, F. Qian, C. Condes, E. B. Duoss, C. M. Spadaccini, Y. Li (2016) Ion Intercalation Induced Capacitance Improvement for Graphene-based Supercapacitor ElectrodesChemNanoMat 2, 635-641.

A. Goliaei, E. Y. Lau, U. Adhikari, E. Schwegler, M. L. Berkowitz (2016) Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United-Atom Force-Field. J. Phys. Chem. B 120(33), 8631-8641.

S. Witzke, M. Petersen, T. Carpenter, S. Khalid (2016) Molecular dynamics simulations reveal the conformational flexibility of Lipid II and its loose association with the defensin plectasin in the Staphylococcus aureus membrane. Biochemistry 55(23): 3303-3314.

T. C. Ramalho, A. A. de Castro, D. R. Silva, M C. Silva, T. C. C. Franca, B. J. Bennion and K. Kuca (2016) Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches toward Remediation Technologies of Warfare Agents and Pesticides. Current Medicinal Chemistry 23, 1041-1061.

T. S. Carpenter and F. C. Lightstone (2016) An Electrostatic Funnel in the GABA-Binding Pathway. PLoS Comput. Biol., 12(4): e1004831.

M. A. Coleman, J. A. Cappuccio, C. D. Blanchette, T. Gao, E. S. Arroyo, A. K. Hinz, F. A. Bourguet, B. Segelke, P. D. Hoeprich, T. Huser, T. A. Laurence, V. L. Motin, B. A. Chromy (2016) Expression and Association of the Yersinia pestis Translocon Proteins, YopB and YopD, Are Facilitated by Nanolipoprotein ParticlesPLoS ONE, 11(3), e0150166.

T. A. Pham, S. M. G. Mortuza, B. C. Wood, E. Y. Lau, T. Ogitsu, S. F. Buchsbaum, Z. S. Siwy, F. Fornasiero, and E. Schwegler (2016) Salt Solutions in Carbon Nanotubes: The Role of Cation−π InteractionsJ. Phys. Chem. C 120 (13), 7332–7338.

B. P. Mayer, D. J. Kennedy, E. Y. Lau, C. A. Valdez (2016) Solution-State Structure and Affinities of Cyclodextrin:Fentanyl Complexes by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics SimulationJ. Phys. Chem. B 120(9), 2423-2433.

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 (2016) Bioadsorption of Rare Earth Elements through Cell Surface Display of Lanthanide Binding Tags. Environ Sci Technol. 50(5), 2735–2742.

A. Navid, D. M. Ng, S. E. Wong, F. C. Lightstone (2016) Application of a physiologically-based pharmacokinetic model to study theophylline metabolism and its interactions with ciprofloxacin and caffeine. CPT: Pharmacometrics & Systems Pharmacology, 5 (2), 74-81.

C. Zhu, T. Liu, F. Qian, T. Y-J. Han, E. B. Duoss, J. D. Kuntz, C. M. Spadaccini, M. A. Worsley, and Y. Li (2016) Supercapacitors Based on Three-Dimensional Hierarchical Graphene Aerogels with Periodic MacroporesNano Lett. 16 (6), 3448-3456.

E. Y. Lau, M. L. Berkowitz, E. Schwegler (2016) Shock Wave-Induced Damage of a Protein by Void Collapse. Biophysical Journal, 110, 1, 147–156.

R. A. Kelsey, D. A. Miller, S. R. Parkin, K. Liu, J. E. Remias, Y. Yang, F. C. Lightstone, K. Liu, C. A. Lippert, S. A. Odom, (2016) Carbonic Anhydrase Mimics for Enhanced CO2 Absorption in an Amine-Based Capture Solvent. Dalton Transactions, 45, 324-333.

2015

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

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 (2015) Cyanobacterial reuse of extracellular organic carbon in microbial matsThe ISME J. 101240–1251.

J.-L. Fattebert, E. Y. Lau, B. J. Bennion, P. Huang, and F. C. Lightstone (2015)  Large-scale First-Principles molecular dynamics simulations with electrostatic embedding: application to acetylcholinesterase catalysis. J. Chem. Theory Comput., 11, 5688–5695. 

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 (2015) Do Genome-scale Models Need Exact Solvers or Clearer Standards?  Molecular Systems Biology, 11, 831.

G. K. Feld, M. Heymann, W. H. Benner, T. Pardini, C.-J. Tsai, S. Boutet, M. A. Coleman, M. S. Hunter, X. Li, M. Messerschmidt, A. Opathalage, B. Pedrini, G. J. Williams, B. A. Krantz, S. Fraden, S. Hau-Riege, J. E. Evans, B. W. Segelke, M. Frank (2015) Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography.  J. Appl. Cryst., 48, 1072-1079.

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 (2015) Transposon mutagenesis paired with deep sequencing of Caulobacter crescentus under uranium stress reveals genes essential for detoxification and stress toleranceJ. Bacteriol., 197, 3160-72.

B. J. Bennion, S. G. Essiz, E. Y. Lau, J.-L. Fattebert, A. Emigh, F. C. Lightstone (2015) A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations. PLoS ONE, 10(4): e0121092.

X. Zhang, H. Péréz-Sánchez, and F. C. Lightstone. (2015) Molecular Dynamics Simulations of Ligand Recognition Upon Binding Antithrombin: A MM/GBSA Approach. Bioinformatics and Biomedical Engineering, 9044, 584-593.

S. P. Hau-Riege and B. J. Bennion (2015) Reproducible radiation-damage processes in proteins irradiated by intense x-ray pulsesPhys Rev E91(2), 022705.

F. Qian, M. Bora, T. Y.-J. Han, A. J. Pascall, S. Guo, S. S. Ly, M. A. Worsley, J. D. Kuntz, T. Y. Olson (2015) On-Demand and Location Selective Particle Assembly for Fabricating Structures of High Energy.  Langmuir, 31(12), 3563–3568.

2014

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

G. K. Feld, S. El-Etr, M. H. Corzett, M. S. Hunter, K. Belhocine, D. M. Monack, M. Frank, B. W. Segelke, A. Rasley (2014) Structure and function of REP34 implicates carboxypeptidase activity in Francisella tularensis host-cell invasion. J. Biol. Chem., 289, 30668.

Q. Zhang, G. Li, X. Liu, F. Qian, Y. Li, T. C. Sum, C. M. Lieber, Q. Xiong (2014) A room temperature low-threshold ultraviolet plasmonic nanolaser.  Nature Communications, 5, 4953.

D. M. Park and Y. Jiao (2014) Modulation of Medium pH by Caulobacter crescentus Facilitates Recovery from Uranium-Induced Growth Arrest.  Applied and Environmental Microbiology, 80(18), 5680-5688.

M. X. LaBute, X. Zhang, J. Lenderman, B. J. Bennion, S. E. Wong, F. C. Lightstone (2014) Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines. PLoS ONE, 9(9): e106298.

M. S. Hunter, B. Segelke, M. Messerschmidt, G. J. Williams, N. A. Zatsepin, A. Barty, W. H. Benner, D. B. Carlson, M. Coleman, A. Graf, S. P. Hau-Riege, T. Pardini, M. M. Seibert, J. Evans, S. Boutet and M. Frank (2014) Fixed-target protein serial microcrystallography with an x-ray free electron laserScientific Reports4, 6026.

T. S. Carpenter, D. A. Kirshner, E. Y. Lau, S. E. Wong, J. P. Nilmeier, and F. C. Lightstone (2014) A Method to Predict Blood-Brain Barrier Permeability of Drug-like Compounds Using Molecular Dynamics SimulationsBiophys. J., 107(3), 630-641.

T. A. Laurence, S. Ly, F. Bourguet, N. O. Fischer, M. A. Coleman (2014) Fluorescence Correlation Spectroscopy at micromolar Concentrations without optical nanoconfinement. Journal of Physical Chemistry B, 118, 9662-9667. 

B. Pedrini, C. J. Tsai, G. Capitani, C. Padeste, M. S. Hunter, N. A. Zatsepin, A. Barty, W. H. Benner, S. Boutet, G. K. Feld, S. P. Hau-Riege, R. A. Kirian, C. Kupitz, M. Messerschmitt, J. I. Ogren, T. Pardini, B. Segelke, G. J. Williams, J. C. Spence, R. Abela, M. Coleman, J. E. Evans, G. F. Schertler, M. Frank, X. D. Li (2014) 7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light SourcePhilos Trans R Soc Lond B Biol Sci. 369(1647): 20130500.

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 (2014) Development of a native Escherichia coli induction system for ionic liquid tolerance.  PLoS ONE, 9(7): e101115.

F. Qian, H. Wang, Y. Ling, G. Wang, M. P. Thelen, and Y. Li (2014) Photoenhanced Electrochemical Interaction between Shewanella and a Hematite Nanowire Photoanode. Nano Letters, 14(6), 3688-3693.

M. C. Yung and Y. Jiao (2014) Biomineralization of uranium by PhoY phosphatase activity aids cell survival in Caulobacter crescentus. Appl. Environ. Microbiol., 80(16), 4795-4804.

N. O. Fischer, A. Rasley, C. D. Blanchette (2014) Nanoparticles and antigen delivery: Understanding the benefits and drawbacks of different delivery platforms. Nanomedicine (Lond), 9(4), 373-376.

C. Zhao, S. H. Hwang, B. A. Buchholz , T. S. Carpenter, F. C. Lightstone, J. Yang, B. D. Hammock, J. E. Casida (2014) The GABAA Receptor Target of Tetramethylenedisulfotetramine. Proc. Natl. Acad. Sci. USA, 111(23), 8607-8612.

N. O. Fischer, C. D. Blanchette, A. Rasley (2014) Enhancing the efficacy of innate immune agonists: Could nanolipoprotein particles hold the key? Nanomedicine (Lond), 9(3), 369-372. 

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

N. O. Fischer, D. R. Weilhammer, A. Dunkle, C. Thomas, M. Hwang, M. Corzett, C. Lychak, W. Mayer, S. Urbin, N. Collette, J. Chiun Chang, G. G. Loots, A. Rasley, C. D. Blanchette (2014) Evaluation of Nanolipoprotein Particles (NLPs) as an In Vivo Delivery Platform. PLoS ONE 9(3): e93342.

M. Frank, D. B. Carlson, M. S. Hunter, G. J. Williams, M. Messerschmidt, N. A. Zatsepin, A. Barty, W. H. Benner, K. Chu, A. T. Graf, S. P. Hau-Riege, R. A. Kirian, C. Padeste, T. Pardini, B. Pedrini, B. Segelke, M. M. Seibert, J. C. Spence, C. J. Tsai, S. M. Lane, X. D. Li, G. Schertler, S. Boutet, M. Coleman, J. E. Evans (2014) Femtosecond X-ray diffraction from two-dimensional protein crystals. IUCrJ, 1(Pt 2), 95-100.

M. C. Yung, J. Ma, M. Salemi, B. S. Phinney, G. R. Bowman, and Y. Jiao (2014) Shotgun Proteomic Analysis Unveils Survival and Detoxification Strategies byCaulobacter crescentus during Exposure to Uranium, Chromium, and CadmiumJ. Proteome Res, 13, 1833-1847.

A. J. Pascall, F. Qian, G. Wang, M. A. Worsley, Y. Li, J. D. Kuntz (2014) Light-Directed Electrophoretic Deposition: A New Additive Manufacturing Technique for Arbitrarily Patterned 3D Composites.  Advanced Materials, 26(14), 2252-2256

Y. Yang, S. E. Wong and F. C. Lightstone (2014) Understanding a Substrate’s Product Regioselectivity in a Family of Enzymes:  A Case Study of Acetaminophen Binding in Cytochrome P450s. PLoS ONE, 9(2): e87058.

H. J. Kulik, S. E. Wong, S. E. Baker, C. A. Valdez, J. H. Satcher, R. D. Aines, and F. C. Lightstone (2014) Developing an approach for first-principles catalyst design: application to carbon capture catalysis. Acta Crystallographica, C70, 123-131. 

S. Ly, F. Bourguet, N. O. Fischer, E. Y. Lau, M. A. Coleman, T. A. Laurence (2014) Quantifying Interactions of a Membrane Protein Embedded in a Lipid Nanodisc using Fluorescence Correlation Spectroscopy. Biophys. J., 106(2), L05-L08.

X. Zhang, S. E. Wong, F. C. Lightstone (2014) Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment. J. Chem. Inf. Model., 54(1) 324-337.

2013

L. W. Tari, X. Li, M. Trzoss, D. C. Bensen, Z. Chen, T. Lam, J. Zhang, S. J. Lee, G. Hough, D. Phillipson, S. Akers-Rodriguez, M. L. Cunningham, B. P. Kwan, K. J. Nelson, A. Castellano, J. B. Locke, V. Brown-Driver, T. M. Murphy, V. S. Ong, C. M. Pillar, D. L. Shinabarger, J. Nix, F. C. Lightstone, S. E. Wong, T. B. Nguyen, K. J. Shaw, J. Finn (2013) Tricyclic GyrB/ParE (TriBE) Inhibitors: A New Class of Broad-Spectrum Dual-Targeting Antibacterial AgentsPLoS ONE, 8(12): e84409.

L. Koziol, N. Kumar, S. E. Wong, F. C. Lightstone (2013) Molecular Recognition of Aromatic Rings by Flavin: Electrostatics and Dispersion Determine Ring Positioning Above Isoalloxazine. J. Phys. Chem. A, 117, 12946-12952. 

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

D. R. Weilhammer, C. D. Blanchette, N. O. Fischer, S. Alam, G. G. Loots, M. Corzett, C. Thomas, C. Lychak, A. D. Dunkle, J. J. Ruitenberg, S. A. Ghanekar, A. J. Sant, A. Rasley (2013) The use of nanolipoprotein particles to enhance the immunostimulatory properties of innate immune agonists against lethal influenza challenge. Biomaterials, 34(38),10305-10318.

H. Wang, G. Wang, Y. Ling, F. Qian, Y. Song, X. Lu, S. Chen, Y. Tong and Y. Li (2013) High Power Density Microbial Fuel Cell with Flexible 3D Graphene-Nickel Foam as AnodeNanoscale, 5, 10283-10290.

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 (2013) Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analysesPLoS ONE, 8, e77985.

H. Wang,* F. Qian,* G. Wang, Y. Jiao, Z. He and Y Li (2013) Self-biased Solar-Microbial Device for Sustainable Hydrogen Generation. ACS Nano, 7, 8728-8735. (* equally contributed)

T. S. Carpenter, E. Y. Lau, and F. C. Lightstone (2013) Identification of a Possible Secondary Picrotoxin-Binding Site on the GABAA-Receptor. Chemical Research in Toxicology, 26, 1444-1454.

B. J. Bennion, E. Y.  Lau, J.-L. Fattebert, P. Huang, E. Schwegler, W. Corning, F. C. Lightstone (2013) Modeling the Binding of CWAs to AChE and BuChE. Military Medical Science Letters, vol. 82(3), 102-114.

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 (2013) Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct SwitchgrassPLoS ONE, 8(7), e68465.

C. I. Lacayo, M. S. Hwang, S.-Y. Ding, M. P. Thelen (2013) Lignin depletion enhances the digestibility of cellulose in cultured xylem cells. PLoS ONE, 8(7), e68266.

E. Y. Lau, S. E. Wong, S. E. Baker, J. P. Bearinger, L. Koziol, C. A. Valdez, J. H. Satcher Jr, R. D. Aines and F. C. Lightstone (2013) Comparison and Analysis of Zinc and Cobalt-based Systems as Catalytic Entities for the Hydration of Carbon Dioxide. PLoS ONE, 8(6), e66187.

D. A. Kirshner, J. P. Nilmeier, and F. C. Lightstone (2013) Catalytic Site Identification – A Web Server to Identify Catalytic Site Structural Matches Throughout PDB. Nucleic Acids Research, 41, W256-W265

J. P. Nilmeier, D. A. Kirshner, S. E. Wong, and F. C. Lightstone (2013) Rapid Catalytic Template Searching as an Enzyme Function Prediction ProcedurePLoS ONE, 8(5), e62535.

P. R. Kumaresan, S. Devaraj, W. Huang, E. Y. Lau, R. Liu, K. S. Lam, I. Jialal (2013) Synthesis and characterization of a novel inhibitor of C-reactive protein-mediated proinflammatory effectsMetab. Synd.r Relat. Disord. 11(3),177-184.

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 (2013) Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction. PLoS ONE 8(5), e63369.

G. Wang, Y. Ling, X. Lu, F. Qian, Y. Tong, V. Lordi, C. Rocha Leao and Y. Li (2013) Computational and Photoelectrochemical Study of Hydrogenated Bismuth Vanadate J. Phys. Chem. C, 117, 10957-10964.

X. Zhang, S. E. Wong, F. C. Lightstone (2013) Message Passing Interface and Multithreading Hybrid for Parallel Molecular Docking of Large Databases on Petascale High Performance Computing Machines. J. Comput. Chem., 34, 915-927.

L. Koziol, S. G. Essiz, S. E. Wong, E. Y. Lau, C. A. Valdez, J. H. Satcher, Jr., R. D. Aines, F. C. Lightstone (2013) Computational Analysis of a Zn-bound Tris(imidazolyl) Calix[6]arene Aqua Complex:  Toward Incorporating Second-coordination Sphere Effects into Carbonic Anhydrase Biomimetics. J. Chem. Theory. Comput., 9, 1320-1327.

Y. Yang, F. C. Lightstone, S. E. Wong (2013) Solvents in Structure-Based in Drug Discovery. Expert Opinion On Drug Discovery, 8, 277-287.

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

M. Trzoss, D. C. Bensen, X. Li, Z. Chen, T. Lam, J. Zhang, C. J. Creighton, M. L. Cunningham, B. Kwan, M. Stidham, K. Nelson, V. Brown-Driver, A. Castellano, K. J. Shaw, F. C. Lightstone, S. E. Wong, T. B. Nguyen, J. Finn, L. W. Tari (2013) Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE), Part II: Development of inhibitors with broad spectrum, Gram-negative antibacterial activityBioorg. Med. Chem. Lett., 23, 1537-1543.

L. W. Tari, M. Trzoss, D. C. Bensen, X. Li, Z. Chen, T. Lam, J. Zhang, C. J. Creighton, M. L. Cunningham, B. Kwan, M. Stidham, K. J. Shaw, F. C. Lightstone, S. E. Wong, T. B. Nguyen, J. Nix, J. Finn (2013) Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activityBioorg. Med. Chem. Lett., 23, 1529-1536.

I. Yoon, S. E. Baker, K. Kim, N. O. Fischer, D. Heineck, Y. Wang, S. C. Esener, D. J. Sirbuly (2013) Nanofiber near-field light-matter interactions for enhanced detection of molecular level displacements and dynamics. Nano Letters, 13, 1440-1445.

N. O. Fischer, A. Rasley, M. Corzett, M. H. Hwang, P. D. Hoeprich, C. D. Blanchette (2013) Colocalized delivery of adjuvant and antigen using nanolipoprotein particles enhances the immune response to recombinant antigens. Journal of the American Chemical Society, 135, 2044-2047.

 

2012

A. Navid, E. Almaas (2012) Genome-Level Transcription Data of Yersina Pestis Analyzed With A New Metabolic Constraint-Based Approach. BMC Systems Biology, 6(1), 150.

T. S. Carpenter, E. Y. Lau and F. C. Lightstone (2012) A Role for Loop-F in Modulating GABA Binding Affinity in the GABAA Receptor. J. Mol. Bio., 422, 310-323.

C. Reyes, F. Qian, A. Zhang, S. Bondarev, A. Welch, M. P. Thelen, C. W. Saltikov (2012) Characterization of axial and proximal histidine mutations of the decaheme cytochrome MtrA from Shewanella str. ANA-3: Implications for the electron transport mechanism. J. Bacteriol 194(21), 5840-5847.

C. Blanchette, C. I. Lacayo, N. O. Fischer, M. Hwang, M. P. Thelen (2012) Enhanced cellulose degradation using cellulase-nanosphere complexes. PLoS One 7(8), e42116.

Y. Jiao, A. Navid, B. J. Stewart, J. McKinlay, M. P. Thelen, J. Pett-Ridge (2012) Syntrophic metabolism of a co-culture containing Clostridium cellulolyticum and Rhodopseudomonas palustris for hydrogen production. Int. J. Hydrogen Energy 37, 11719-11726.

J. Khudyakov, P. D’haeseleer, S. Borglin, K. DeAngelis, H. Woo, E. Lindquist, T. C. Hazen, B. A. Simmons, M. P. Thelen (2012) Global transcriptome response to ionic liquid by a tropical rainforest soil bacterium, Enterobacter lignolyticus. PNAS 109(32), e2173-2182.

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  (2012) Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. J. Biol. Chem. 287, 25335-25343.

L. Koziol, C. A. Valdez, S. E. Baker, E. Y. Lau, W. C. Floyd III, S. E. Wong, J. H. Satcher Jr., F. C. Lightstone, R. D. Aines (2012) Towards a small molecule, biomimetic carbonic anhydrase model: theoretical and experimental investigations of a panel of Zinc(II) aza-macrocyclic catalystsInorganic Chemistry51, 6803-6812.

F. Qian, M. Brewster, S. K. Lim, Y. Ling, C. Greene, J. W. Johnson, S. Gradečak, Y. Cao and Y. Li (2012) Controlled synthesis of AlN/GaN multiple quantum well nanowire structures and their optical propertiesNano Lett. 12, 3344.

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

G. Wang, Y. Ling, X. Lu, H. Wang, F. Qian, Y. Tong and Y. Li (2012) Solar Driven Hydrogen Releasing from Urea and Human UrineEnergy. Environ. Sci., 5, 8215-8219.

W. H. Benner, G. S. Lewis, S. V. Hering, B. Segelke, M. Corzett, J. E. Evans and F. C. Lightstone (2012) Re-Electrospraying Splash-Landed Proteins and Nanoparticles. Analytical Chemistry, 84, 2498-2504.

A. Navid and E. Almaas (2012) "Yersinia pestis Metabolic Network" in Yersinia:  Systems Biology and Control, ISBN: 978-1-908230-05-8, eds. Carniel, E ; Hinnebusch, BJ; Caister Academic Press, Norfolk, UK, Chapter 6, 83-108.

C. I. Lacayo, P. A. Giardini, J. Zhu, M. A. Tsuchida, M. J. Footer, F. S. Soo, Y. Lu, Y. Xia, A. Mogilner, and J. A. Theriot (2012) Choosing orientation: influence of cargo geometry and acta polarization on actin tails.  Molecular Biology of the Cell 23: 614-629.

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

2011

A. Navid (2011) Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targetsBriefings in Functional Genomics10(6), 354-364.

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

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

J. H. Satcher Jr., S. E. Baker, H. J. Kulik, C. A. Valdez, R. L. Krueger, F. C. Lightstone, R. D. Aines (2011) Modeling, synthesis and characterization of zinc containing carbonic anhydrase active site mimics. Energy Procedia, 4, 2090-2095.

S. E. Wong, E. Y. Lau, H. J. Kulik, J. H. Satcher, C. Valdez, M. Worsely, F. C. Lightstone, R. D. Aines (2011) Designing small molecule catalysts for CO2 captureEnergy Procedia4, 817-823.

N. O. Fischer, T. M. Tarasow (2011) Identification and optimization of DNA aptamer binding regions using DNA microarrays. Methods in Molecular Biology: Protein Microarray for Disease Analysis, 723, 57-66.

A. Zemla, B. W. Segelke (2011) Practical applications of structural genomics technologies for mutagen research. Mutation Research, 722(2):165-70.

S. E. Wong and F. C. Lightstone (2011) Accounting for water molecules in drug designExpert Opinion On Drug Discovery6, 65-74.