Research Publications
This bibliography contains publications from research funded by the Genomic Science Program. Most publications are from FY 2021 and beyond, though older publications appear in some cases. If you are a GSP-funded researcher and don’t see your publications listed below, contact Marissa Mills ([email protected]) to get your publications added.
| Year | DOI | Authors | Title | Journal | Volume/Pages |
|---|---|---|---|---|---|
| 10.1002/9781119312994.apr0348 | Ding, L., J.-G. Chen, A. M. Jones and S. M. Assmann | Heterotrimeric G-Protein-Coupled Signaling in Higher Plants | Annual Plant Reviews online | 30–63 | |
| 2000 | 10.1128/AEM.66.8.3616-3620.2000 | Marsh, T. L., P. Saxman, J. Cole and J. Tiedje | Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis | Applied and Environmental Microbiology | 66(8) 3616–20 |
| 2004 | 10.1126/science.1093857 | Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, et al. | Environmental genome shotgun sequencing of the Sargasso Sea | Science | 304(5667) 66–74 |
| 2004 | 10.1073/pnas.0401526101 | Lindell, D., M. B. Sullivan, Z. I. Johnson, A. C. Tolonen, F. Rohwer and S. W. Chisholm | Transfer of photosynthesis genes to and from Prochlorococcus viruses | Proceedings of the National Academy of Sciences of the United States of America | 101(30) 11013–8 |
| 2004 | 10.1128/JB.186.14.4457-4465.2004 | Friedman, L. and R. Kolter | Two genetic loci produce distinct carbohydrate-rich structural components of the Pseudomonas aeruginosa biofilm matrix | Journal of Bacteriology | 186(14) 4457–65 |
| 2004 | 10.1046/j.1365-2958.2003.03877.x | Friedman, L. and R. Kolter | Genes involved in matrix formation in Pseudomonas aeruginosa PA14 biofilms | Molecular Microbiology | 51(3) 675–90 |
| 2005 | 10.1093/bioinformatics/bti613 | Xing, Y. and C. Lee | Assessing the application of Ka/Ks ratio test to alternatively spliced exons | Bioinformatics | 21(19) 3701-3703 |
| 2005 | 10.1371/journal.pbio.0030144 | Sullivan, M. B., M. L. Coleman, P. Weigele, F. Rohwer and S. W. Chisholm | Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations | PLoS Biology | 3(5) e144 |
| 2005 | 10.1128/JB.187.3.940-948.2005 | Romano, J. D. and R. Kolter | Pseudomonas-Saccharomyces interactions: influence of fungal metabolism on bacterial physiology and survival | Journal of Bacteriology | 187(3) 940–8 |
| 2005 | 10.1128/JB.187.10.3551-3555.2005 | Reguera, G. and R. Kolter | Virulence and the environment: a novel role for Vibrio cholerae toxin-coregulated pili in biofilm formation on chitin | Journal of Bacteriology | 187(10) 3551–5 |
| 2005 | 10.1016/j.str.2005.01.019 | Johnson, E., D. Cascio, M. R. Sawaya, M. Gingery and I. Schröder | Crystal structures of a tetrahedral open pore ferritin from the hyperthermophilic Archaeon Archaeoglobus fulgidus | Structure | 13(4) 637-648 |
| 2005 | 10.1093/bioinformatics/bti346 | Garrity, G. M. and T. G. Lilburn | Self-organizing and self-correcting classifications of biological data | Bioinformatics | 21(10) 2309-2314 |
| 2005 | 10.1093/nar/gki038 | Cole, J. R., B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity and J. M. Tiedje | The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis | Nucleic Acids Research | 33(Suppl_1) D294–6 |
| 2006 | 10.1021/ja058831y | Xu, Q., H. Guo, A. Wlodawer and H. Guo | The importance of dynamics in substrate-assisted catalysis and specificity | Journal of the American Chemical Society | 128(18) 5994–5 |
| 2006 | 10.1093/nar/gkl396 | Xing, Y., T. Yu, Y. N. Wu, M. Roy, J. Kim and C. Lee | An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs | Nucleic Acids Research | 34(10) 3150-3160 |
| 2006 | 10.1002/qua.20810 | Walewski, Ł., D. Krachtus, S. Fischer, J. C. Smith, P. Bała and B. Lesyng | SCC-DFTB energy barriers for single and double proton transfer processes in the model molecular systems malonaldehyde and porphycene | International Journal of Quantum Chemistry | 106(3) 636–40 |
| 2006 | 10.1371/journal.pbio.0040234 | Sullivan, M. B., D. Lindell, J. A. Lee, L. R. Thompson, J. P. Bielawski and S. W. Chisholm | Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts | PLoS Biology | 4(8) e234 |
| 2006 | 10.1016/j.str.2006.02.001 | Smith, J. C. | Tight in titin | Structure | 14(3) 389–90 |
| 2006 | 10.1021/bi052433q | Schwarzl, S. M., J. C. Smith and S. Fischer | Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism | Biochemistry | 45(18) 5830–47 |
| 2006 | 10.1021/jp055314t | Moritsugu, K. and J. C. Smith | Temperature-dependent protein dynamics: a simulation-based probabilistic diffusion-vibration Langevin description | Journal of Physical Chemistry B | 110(11) 5807–16 |
| 2006 | 10.1155/JAMDS/2006/16018 | Moffat, J. | Mathematical modelling of information age conflict | Journal of Applied Mathematics and Decision Sciences | 2006 |
| 2006 | 10.1002/prot.20981 | Mesentean, S., S. Fischer and J. C. Smith | Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping | Proteins | 64(1) 210–8 |
| 2006 | 10.1021/ja055962q | Kurkal-Siebert, V. and J. C. Smith | Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k | Journal of the American Chemical Society | 128(7) 2356–64 |
| 2006 | 10.1016/j.jnoncrysol.2006.01.115 | Kurkal-Siebert, V., R. M. Daniel, J. L. Finney, M. Tehei, R. V. Dunn and J. C. Smith | Enzyme hydration, activity and flexibility: A neutron scattering approach | Journal of Non-Crystalline Solids | 352(42–49) 4387–93 |
| 2006 | 10.1016/j.jmb.2006.06.022 | Koppole, S., J. C. Smith and S. Fischer | Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke | Journal of Molecular Biology | 361(3) 604–16 |
| 2006 | 10.1021/ct600092c | Imhof, P., F. Noe, S. Fischer and J. C. Smith | AM1/d Parameters for Magnesium in Metalloenzymes | Journal of Chemical Theory and Computation | 2(4) 1050–6 |
| 2006 | 10.1021/bi060461i | Guo, H., A. Wlodawer, T. Nakayama, Q. Xu and H. Guo | Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase | Biochemistry | 45(30) 9129–37 |
| 2006 | 10.1073/pnas.0510013103 | Glass, J. I., N. Assad-Garcia, N. Alperovich, S. Yooseph, M. R. Lewis, M. Maruf, C. A. Hutchison, 3rd, H. O. Smith and J. C. Venter | Essential genes of a minimal bacterium | Proceedings of the National Academy of Sciences of the United States of America | 103(2) 425–30 |
| 2006 | 10.1038/sj.cdd.4401807 | Efferth, T., S. M. Schwarzl, J. Smith and R. Osieka | Role of glucose-6-phosphate dehydrogenase for oxidative stress and apoptosis | Cell Death and Differentiation | 13(3) 527–8 |
| 2006 | 10.1039/b516451f | Bondar, A. N., J. C. Smith and S. Fischer | Structural and energetic determinants of primary proton transfer in bacteriorhodopsin | Photochemical and Photobiological Sciences | 5(6) 547–52 |
| 2006 | 10.1021/ja060731k | Baudry, J. | Van der waals interactions and decrease of the rotational barrier of methyl-sized rotators: a theoretical study | Journal of the American Chemical Society | 128(34) 11088–93 |
| 2006 | 10.1039/b610075a | Balog, E., J. C. Smith and D. Perahia | Conformational heterogeneity and low-frequency vibrational modes of proteins | Physical Chemistry Chemical Physics | 8(47) 5543–8 |
| 2007 | 10.1016/j.inffus.2005.04.003 | Zheng, Y., E. A. Essock, B. C. Hansen and A. M. Haun | A new metric based on extended spatial frequency and its application to DWT based fusion algorithms | Information Fusion | 8(2 SPEC. ISS.) 177-192 |
| 2007 | 10.1021/bi061737p | Xu, Q., H. B. Guo, A. Wlodawer, T. Nakayama and H. Guo | The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As | Biochemistry | 46(12) 3784–92 |
| 2007 | 10.1021/jp0670743 | Xu, Q., H. Guo, A. Gorin and H. Guo | Stabilization of a transition-state analogue at the active site of yeast cytosine deaminase: importance of proton transfers | Journal of Physical Chemistry B | 111(23) 6501–6 |
| 2007 | 10.1529/biophysj.105.079723 | Topham, C. M. and J. C. Smith | Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form | Biophysical Journal | 92(3) 769–86 |
| 2007 | Smith, J. C., A. N. Bondar, S. Suhai and P. T. Frangopol | Computer Simulations of Local Anesthetic Mechanisms Quantum Chemical Investigation of Procaine | Romanian Reports in Physics | 59(2) 289–99 | |
| 2007 | 10.1117/12.727781 | Privitera, G., S. Tudisco, L. Lanzanò, F. Musumeci, S. Privitera, A. Scordino, D. Tudisco, M. Mazzillo and G. Condorelli | Single photon spectrometer for biomedical application: New developments | Progress in Biomedical Optics and Imaging - Proceedings of SPIE | 6628 |
| 2007 | 10.1039/9781847557773-00099 | Nutt, D. R. and J. C. Smith | Choosing an Appropriate Water Model for Use in Biomolecular Simulations | Physics and Chemistry of Ice | 451–8 |
| 2007 | 10.1021/ct700053u | Nutt, D. R. and J. C. Smith | Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? | Journal of Chemical Theory and Computation | 3(4) 1550–60 |
| 2007 | 10.1093/bioinformatics/btm241 | Newberg, L. A., W. A. Thompson, S. Conlan, T. M. Smith, L. A. McCue and C. E. Lawrence | A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction | Bioinformatics | 23(14) 1718-1727 |
| 2007 | 10.1529/biophysj.107.111898 | Moritsugu, K. and J. C. Smith | Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian | Biophysical Journal | 93(10) 3460–9 |
| 2007 | 10.1016/j.jmb.2006.12.058 | Mesentean, S., S. Koppole, J. C. Smith and S. Fischer | The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor | Journal of Molecular Biology | 367(2) 591–602 |
| 2007 | 10.1073/pnas.0708199104 | Meinhold, L., J. C. Smith, A. Kitao and A. H. Zewail | Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation | Proceedings of the National Academy of Sciences of the United States of America | 104(44) 17261–5 |
| 2007 | 10.1002/prot.21246 | Meinhold, L. and J. C. Smith | Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns | Proteins | 66(4) 941–53 |
| 2007 | 10.1103/PhysRevLett.99.138101 | Meinhold, L., F. Merzel and J. C. Smith | Lattice dynamics of a protein crystal | Physical Review Letters | 99(13) 138101 |
| 2007 | Mazzotti, A., E. Stucchi, G. L. Fradelizio, L. Zanzi and P. Scandone | Re-processing of the CROP-04 seismic data | Bollettino della Societa Geologica Italiana, Supplemento | 7 141-153 | |
| 2007 | 10.1016/j.str.2007.06.008 | Koppole, S., J. C. Smith and S. Fischer | The structural coupling between ATPase activation and recovery stroke in the myosin II motor | Structure | 15(7) 825–37 |
| 2007 | 10.1093/bioinformatics/btm343 | Kim, N. and C. Lee | QPRIMER: A quick web-based application for designing conserved PCR primers from multigenome alignments | Bioinformatics | 23(17) 2331-2333 |
| 2007 | 10.1093/nar/gkl884 | Kim, N., A. V. Alekseyenko, M. Roy and C. Lee | The ASAP II database: Analysis and comparative genomics of alternative splicing in 15 animal species | Nucleic Acids Research | 35(SUPPL. 1) D93-D98 |
| 2007 | 10.1186/gb-2007-8-12-r264 | Kannan, N., J. Wu, G. S. Anand, S. Yooseph, A. F. Neuwald, J. C. Venter and S. S. Taylor | Evolution of allostery in the cyclic nucleotide binding module | Genome Biology | 8(12) R264 |
| 2007 | 10.1371/journal.pbio.0050017 | Kannan, N., S. S. Taylor, Y. Zhai, J. C. Venter and G. Manning | Structural and functional diversity of the microbial kinome | PLoS Biology | 5(3) e17 |
| 2007 | 10.1073/pnas.0702981104 | Guo, H. B. and H. Guo | Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity | Proceedings of the National Academy of Sciences of the United States of America | 104(21) 8797–802 |
| 2007 | 10.1016/B978-012374212-4.50049-3 | Fantini, S. and P. Taroni | Optical Mammography | Cancer Imaging | 445-453 |
| 2007 | 10.1128/JB.01343-06 | Earl, A. M., R. Losick and R. Kolter | Bacillus subtilis genome diversity | Journal of Bacteriology | 189(3) 1163–70 |
| 2007 | 10.1002/chem.200700358 | de Hatten, X., Z. Cournia, I. Huc, J. C. Smith and N. Metzler-Nolte | Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics | Chemistry | 13(29) 8139–52 |
| 2007 | 10.1073/pnas.0701401104 | Daidone, I., M. B. Ulmschneider, A. Di Nola, A. Amadei and J. C. Smith | Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding | Proceedings of the National Academy of Sciences of the United States of America | 104(39) 15230–5 |
| 2007 | 10.1021/jp065172i | Cournia, Z., G. M. Ullmann and J. C. Smith | Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study | Journal of Physical Chemistry B | 111(7) 1786–801 |
| 2007 | 10.1093/nar/gkl889 | Cole, J. R., B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, G. M. Garrity and J. M. Tiedje | The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data | Nucleic Acids Research | 35(SUPPL. 1) D169-D172 |
| 2007 | 10.1080/02770900701595568 | Cicutto, L. and M. Ashby | The importance of a community-based asthma helpline | Journal of Asthma | 44(9) 705-710 |
| 2007 | 10.1038/nbt1316 | Chen, F. and R. A. Dixon | Lignin modification improves fermentable sugar yields for biofuel production | Nature Biotechnology | 25(7) 759–61 |
| 2007 | 10.1016/j.cell.2007.10.053 | Bonneau, R., M. T. Facciotti, D. J. Reiss, A. K. Schmid, M. Pan, et al. | A predictive model for transcriptional control of physiology in a free living cell | Cell | 131(7) 1354–65 |
| 2007 | 10.1016/j.jsb.2006.10.007 | Bondar, A. N., S. Suhai, S. Fischer, J. C. Smith and M. Elstner | Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elements | Journal of Structural Biology | 157(3) 454–69 |
| 2007 | 10.1186/1471-2105-8-456 | Bare, J. C., P. T. Shannon, A. K. Schmid and N. S. Baliga | The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications | BMC Bioinformatics | 8 456 |
| 2007 | 10.1093/bioinformatics/btl647 | Alekseyenko, A. V. and C. J. Lee | Nested Containment List (NCList): A new algorithm for accelerating interval query of genome alignment and interval databases | Bioinformatics | 23(11) 1386-1393 |
| 2008 | 10.1002/mrc.2201 | Yelle, D. J., J. Ralph and C. R. Frihart | Characterization of nonderivatized plant cell walls using high-resolution solution-state NMR spectroscopy | Magnetic Resonance in Chemistry | 46(6) 508–17 |
| 2008 | 10.1371/journal.pone.0001456 | Williamson, S. J., D. B. Rusch, S. Yooseph, A. L. Halpern, K. B. Heidelberg, J. I. Glass, C. Andrews-Pfannkoch, D. Fadrosh, C. S. Miller, G. Sutton, M. Frazier and J. C. Venter | The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples | PLoS One | 3(1) e1456 |
| 2008 | 10.1016/j.copbio.2008.02.014 | Weng, J. K., X. Li, N. D. Bonawitz and C. Chapple | Emerging strategies of lignin engineering and degradation for cellulosic biofuel production | Current Opinion in Biotechnology | 19(2) 166–72 |
| 2008 | 10.1002/jcc.20902 | Voltz, K., J. Trylska, V. Tozzini, V. Kurkal-Siebert, J. Langowski and J. Smith | Coarse-grained force field for the nucleosome from self-consistent multiscaling | Journal of Computational Chemistry | 29(9) 1429–39 |
| 2008 | 10.1021/pr800031f | Van, P. T., A. K. Schmid, N. L. King, A. Kaur, M. Pan, K. Whitehead, T. Koide, M. T. Facciotti, Y. A. Goo, E. W. Deutsch, D. J. Reiss, P. Mallick and N. S. Baliga | Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage | Journal of Proteome Research | 7(9) 3755–64 |
| 2008 | 10.1529/biophysj.108.135442 | Tran, L. M., M. L. Rizk and J. C. Liao | Ensemble modeling of metabolic networks | Biophysical Journal | 95(12) 5606–17 |
| 2008 | Shealy, P., R. Mukhopadhyay, S. Smith and H. Valafar | Automated assignment of backbone resonances using residual dipolar couplings acquired from a protein with known structure | Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008 | 646-652 | |
| 2008 | 10.1111/j.1462-2920.2008.01626.x | Shaw, A. K., A. L. Halpern, K. Beeson, B. Tran, J. C. Venter and J. B. Martiny | It's all relative: ranking the diversity of aquatic bacterial communities | Environmental Microbiology | 10(9) 2200–10 |
| 2008 | 10.2993/0278-0771(2008)28[110:HEOMSF]2.0.CO;2 | Sepez, J. | Historical ecology of Makah subsistence foraging patterns | Journal of Ethnobiology | 28(1) 110-133 |
| 2008 | 10.1016/j.bbamem.2008.06.014 | Sengupta, D., J. C. Smith and G. M. Ullmann | Partitioning of amino-acid analogues in a five-slab membrane model | Biochimica et Biophysica Acta (BBA) - Biomembranes | 1778(10) 2234–43 |
| 2008 | 10.1007/s12155-008-9025-7 | Saballos, A., W. Vermerris, L. Rivera and G. Ejeta | Allelic Association, Chemical Characterization and Saccharification Properties of brown midrib Mutants of Sorghum (Sorghum bicolor (L.) Moench) | BioEnergy Research | 1(3–4) 193–204 |
| 2008 | 10.1093/bioinformatics/btm592 | Reiss, D. J., M. T. Facciotti and N. S. Baliga | Model-based deconvolution of genome-wide DNA binding | Bioinformatics | 24(3) 396–403 |
| 2008 | 10.1088/1742-6596/125/1/012055 | Petridis, L. and J. C. Smith | Cellulosic ethanol: progress towards a simulation model of lignocellulosic biomass | Journal of Physics: Conference Series | 125 |
| 2008 | 10.1073/pnas.0809160105 | Oda, Y., F. W. Larimer, P. S. Chain, S. Malfatti, M. V. Shin, L. M. Vergez, L. Hauser, M. L. Land, S. Braatsch, J. T. Beatty, D. A. Pelletier, A. L. Schaefer and C. S. Harwood | Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments | Proceedings of the National Academy of Sciences of the United States of America | 105(47) 18543–8 |
| 2008 | 10.1021/ja8034027 | Nutt, D. R. and J. C. Smith | Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations | Journal of the American Chemical Society | 130(39) 13066–73 |
| 2008 | 10.1103/PhysRevLett.100.188103 | Neusius, T., I. Daidone, I. M. Sokolov and J. C. Smith | Subdiffusion in peptides originates from the fractal-like structure of configuration space | Physical Review Letters | 100(18) 188103 |
| 2008 | 10.1529/biophysj.108.131714 | Moritsugu, K. and J. C. Smith | REACH coarse-grained biomolecular simulation: transferability between different protein structural classes | Biophysical Journal | 95(4) 1639–48 |
| 2008 | 10.1529/biophysj.107.121418 | Meinhold, L., D. Clement, M. Tehei, R. Daniel, J. L. Finney and J. C. Smith | Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering | Biophysical Journal | 94(12) 4812–8 |
| 2008 | 10.1002/anie.200802679 | McLain, S. E., A. K. Soper, I. Daidone, J. C. Smith and A. Watts | Charge-based interactions between peptides observed as the dominant force for association in aqueous solution | Angewandte Chemie International Edition | 47(47) 9059–62 |
| 2008 | Mahrooz, A., M. Nouri, M. R. Rashidi, N. Aslanabadi, D. Qujeq and A. Azari | Paraoxonase and Arylesterase activities of human serum paraoxonase in coronary artery disease | Koomesh | 10(1) 1-6+1 | |
| 2008 | 10.1111/j.1365-313X.2008.03457.x | Li, X., J. K. Weng and C. Chapple | Improvement of biomass through lignin modification | The Plant Journal | 54(4) 569–81 |
| 2008 | 10.1103/PhysRevLett.100.138102 | Kurkal-Siebert, V., R. Agarwal and J. C. Smith | Hydration-dependent dynamical transition in protein: protein interactions at ≈ 240 K | Physical Review Letters | 100(13) 138102 |
| 2008 | 10.1021/jp076641z | Krishnan, M., V. Kurkal-Siebert and J. C. Smith | Methyl group dynamics and the onset of anharmonicity in myoglobin | Journal of Physical Chemistry B | 112(17) 5522–33 |
| 2008 | 10.1007/s12155-008-9004-z | Kim, H., J. Ralph and T. Akiyama | Solution-state 2D NMR of Ball-milled Plant Cell Wall Gels in DMSO-d6 | BioEnergy Research | 1(1) 56–66 |
| 2008 | 10.1007/s12155-008-9020-z | Jackson, L. A., G. L. Shadle, R. Zhou, J. Nakashima, F. Chen and R. A. Dixon | Improving Saccharification Efficiency of Alfalfa Stems Through Modification of the Terminal Stages of Monolignol Biosynthesis | BioEnergy Research | 1(3–4) 180–92 |
| 2008 | 10.1021/bi801685f | Imker, H. J., J. Singh, B. P. Warlick, F. R. Tabita and J. A. Gerlt | Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum | Biochemistry | 47(43) 11171–3 |
| 2008 | 10.1016/j.jmb.2007.12.073 | Grintsevich, E. E., S. A. Benchaar, D. Warshaviak, P. Boontheung, F. Halgand, J. P. Whitelegge, K. F. Faull, R. R. Ogorzalek Loo, D. Sept, J. A. Loo and E. Reisler | Mapping the Cofilin Binding Site on Yeast G-Actin by Chemical Cross-Linking | Journal of Molecular Biology | 377(2) 395-409 |
| 2008 | 10.1093/nar/gkm815 | Faith, J. J., M. E. Driscoll, V. A. Fusaro, E. J. Cosgrove, B. Hayete, F. S. Juhn, S. J. Schneider and T. S. Gardner | Many Microbe Microarrays Database: Uniformly normalized Affymetrix compendia with structured experimental metadata | Nucleic Acids Research | 36(SUPPL. 1) D866-D870 |
| 2008 | 10.1016/j.copbio.2008.10.010 | Cardenas, E. and J. M. Tiedje | New tools for discovering and characterizing microbial diversity | Current Opinion in Biotechnology | 19(6) 544–9 |
| 2008 | 10.1016/j.ijhydene.2008.07.102 | Burrows, E., F. Chaplen and R. Ely | Optimization of media nutrient composition for increased photofermentative hydrogen production by Synechocystis sp. PCC 6803 | International Journal of Hydrogen Energy | 33(21) 6092–9 |
| 2008 | 10.1021/jp801916f | Bondar, A. N., J. Baudry, S. Suhai, S. Fischer and J. C. Smith | Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions | Journal of Physical Chemistry B | 112(47) 14729–41 |
| 2008 | 10.1016/j.ymben.2008.02.001 | Bernstein, J. R., T. Bulter and J. C. Liao | Transfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotin | Metabolic Engineering | 10(45720) 131-140 |
| 2008 | 10.1021/ac800795f | Benton, H. P., D. M. Wong, S. A. Trauger and G. Siuzdak | XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization | Analytical Chemistry | 80(16) 6382–9 |
| 2008 | 10.1021/bi801425e | Becker, V., D. Sengupta, R. Ketteler, G. M. Ullmann, J. C. Smith and U. Klingmuller | Packing density of the erythropoietin receptor transmembrane domain correlates with amplification of biological responses | Biochemistry | 47(45) 11771–82 |
| 2008 | 10.1080/10635150802434394 | Alekseyenko, A. V., C. J. Lee and M. A. Suchard | Wagner and Dollo: A stochastic duet by composing two parsimonious solos | Systematic Biology | 57(5) 772-784 |
| 2009 | 10.1088/0031-9155/54/17/008 | Zhou, J. and J. Qi | Theoretical analysis and simulation study of a high-resolution zoom-in PET system | Physics in Medicine and Biology | 54(17) 5193–208 |
| 2009 | 10.1007/978-3-642-02498-6_3 | Zhou, J. and J. Qi | High-resolution adaptive PET imaging | International Conference on Information Processing in Medical Imaging | 21 26–37 |
| 2009 | 10.1038/hdy.2009.26 | Zakharov, E. V., N. F. Lobo, C. Nowak and J. J. Hellmann | Introgression as a likely cause of mtDNA paraphyly in two allopatric skippers (Lepidoptera: Hesperiidae) | Heredity | 102(6) 590–9 |
| 2009 | 10.1111/j.1469-8137.2008.02663.x | Yin, T. M., X. Y. Zhang, L. E. Gunter, S. X. Li, S. D. Wullschleger, M. R. Huang and G. A. Tuskan | Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome | New Phytologist | 181(2) 498–503 |
| 2009 | 10.1002/chem.200902297 | Xu, Q., Y. Z. Chu, H. B. Guo, J. C. Smith and H. Guo | Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases | Chemistry | 15(46) 12596–9 |
| 2009 | 10.1002/pro.105 | Xu, J., M. F. Crowley and J. C. Smith | Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation | Protein Science | 18(5) 949–59 |
| 2009 | 10.1186/1471-2180-9-149 | Xia, Q., T. Wang, E. L. Hendrickson, T. J. Lie, M. Hackett and J. A. Leigh | Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis | BMC Microbiology | 9 |
| 2009 | 10.1016/j.ymben.2009.08.004 | Wong, W. W. and J. C. Liao | Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters | Metabolic Engineering | 11(6) 409–14 |
| 2009 | 10.1073/pnas.0812874106 | Wikoff, W. R., A. T. Anfora, J. Liu, P. G. Schultz, S. A. Lesley, E. C. Peters and G. Siuzdak | Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites | Proceedings of the National Academy of Sciences of the United States of America | 106(10) 3698–703 |
| 2009 | Widya, I., R. G. A. Bults, M. H. A. Huis In't Veld and M. M. R. Vollenbroek-Hutten | Scenario-based requirements elicitation in a pain-teletreatment application | ICSOFT 2009 - 4th International Conference on Software and Data Technologies, Proceedings | 2 406-413 | |
| 2009 | 10.1371/journal.pone.0005485 | Whitehead, K., M. Pan, K. Masumura, R. Bonneau and N. S. Baliga | Diurnally entrained anticipatory behavior in archaea | PLoS One | 4(5) e5485 |
| 2009 | 10.1186/1471-2229-9-88 | Vogel, J. P., M. Tuna, H. Budak, N. Huo, Y. Q. Gu and M. A. Steinwand | Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon | BMC Plant Biology | 9 88 |
| 2009 | 10.1021/ct900256k | Ulmschneider, J. P., J. P. Doux, J. A. Killian, J. C. Smith and M. B. Ulmschneider | Peptide Partitioning and Folding into Lipid Bilayers | Journal of Chemical Theory and Computation | 5(9) 2202–5 |
| 2009 | 10.1021/ja9064365 | Thukral, L., J. C. Smith and I. Daidone | Common folding mechanism of a β-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations | Journal of the American Chemical Society | 131(50) 18147–52 |
| 2009 | 10.1007/s10933-008-9266-7 | Swindles, G. T., D. J. Charman, H. M. Roe and P. A. Sansum | Environmental controls on peatland testate amoebae (Protozoa: Rhizopoda) in the North of Ireland: Implications for Holocene palaeoclimate studies | Journal of Paleolimnology | 42(1) 123-140 |
| 2009 | Su, X., H. Hou, G. Li, R. Lin and S. Cai | Product distribution of thermal cracking of exo-tetrahydrodicyclopentadiene | Acta Chimica Sinica | 67(7) 587-592 | |
| 2009 | 10.1104/pp.109.137059 | Stewart, J. J., T. Akiyama, C. Chapple, J. Ralph and S. D. Mansfield | The effects on lignin structure of overexpression of ferulate 5-hydroxylase in hybrid poplar | Plant Physiology | 150(2) 621–35 |
| 2009 | 10.1002/prot.22350 | Splettstoesser, T., F. Noe, T. Oda and J. C. Smith | Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state | Proteins | 76(2) 353–64 |
| 2009 | 10.1021/ja809660g | Spies, M. A., J. G. Reese, D. Dodd, K. L. Pankow, S. R. Blanke and J. Baudry | Determinants of catalytic power and ligand binding in glutamate racemase | Journal of the American Chemical Society | 131(14) 5274–84 |
| 2009 | 10.1155/2009/350424 | Sobel, S. G., H. M. Hastings and M. Testa | Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation | Research Letters in Physical Chemistry | 2009 1–4 |
| 2009 | Smith, J. C. | Overcoming Plant Recalcitrance: Supercomputers Tackle Biofuel Production Problems | SciDAC Review | (15) 34–45 | |
| 2009 | 10.1021/ja9034158 | Shen, T., P. Langan, A. D. French, G. P. Johnson and S. Gnanakaran | Conformational flexibility of soluble cellulose oligomers: chain length and temperature dependence | Journal of the American Chemical Society | 131(41) 14786–94 |
| 2009 | 10.1021/ct900292r | Schulz, R., B. Lindner, L. Petridis and J. C. Smith | Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer | Journal of Chemical Theory and Computation | 5(10) 2798–808 |
| 2009 | 10.1016/j.bpj.2008.10.007 | Schulz, R., M. Krishnan, I. Daidone and J. C. Smith | Instantaneous normal modes and the protein glass transition | Biophysical Journal | 96(2) 476–84 |
| 2009 | 10.1126/science.1178534 | Schnable, P. S., D. Ware, R. S. Fulton, J. C. Stein, F. Wei, et al. | The B73 maize genome: complexity, diversity, and dynamics | Science | 326(5956) 1112–5 |
| 2009 | 10.1038/msb.2009.40 | Schmid, A. K., D. J. Reiss, M. Pan, T. Koide and N. S. Baliga | A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability | Molecular Systems Biology | 5 282 |
| 2009 | 10.1104/pp.109.136408 | Sattler, S. E., A. J. Saathoff, E. J. Haas, N. A. Palmer, D. L. Funnell-Harris, G. Sarath and J. F. Pedersen | A nonsense mutation in a cinnamyl alcohol dehydrogenase gene is responsible for the Sorghum brown midrib6 phenotype | Plant Physiology | 150(2) 584–95 |
| 2009 | 10.1534/genetics.108.098996 | Saballos, A., G. Ejeta, E. Sanchez, C. Kang and W. Vermerris | A genomewide analysis of the cinnamyl alcohol dehydrogenase family in sorghum [Sorghum bicolor (L.) Moench] identifies SbCAD2 as the brown midrib6 gene | Genetics | 181(2) 783–95 |
| 2009 | 10.1364/oe.17.012532 | Saar, B. G., G. R. Holtom, C. W. Freudiger, C. Ackermann, W. Hill and X. S. Xie | Intracavity wavelength modulation of an optical parametric oscillator for coherent Raman microscopy | Optics Express | 17(15) 12532–9 |
| 2009 | 10.1016/j.jtice.2009.05.003 | Rizk, M. L. and J. C. Liao | Ensemble modeling and related mathematical modeling of metabolic networks | Journal of the Taiwan Institute of Chemical Engineers | 40(6) 595-601 |
| 2009 | 10.1021/ja809767v | Phatak, P., J. S. Frahmcke, M. Wanko, M. Hoffmann, P. Strodel, J. C. Smith, S. Suhai, A. N. Bondar and M. Elstner | Long-distance proton transfer with a break in the bacteriorhodopsin active site | Journal of the American Chemical Society | 131(20) 7064–78 |
| 2009 | 10.1002/jcc.21075 | Petridis, L. and J. C. Smith | A molecular mechanics force field for lignin | Journal of Computational Chemistry | 30(3) 457–67 |
| 2009 | 10.1080/08927010902995564 | Pérez-Roa, R. E., M. A. Anderson, D. Rittschof, C. G. Hunt and D. R. Noguera | Involvement of reactive oxygen species in the electrochemical inhibition of barnacle (Amphibalanus amphitrite) settlement | Biofouling | 25(6) 563-571 |
| 2009 | 10.1104/pp.109.136804 | Penning, B. W., C. T. Hunter, 3rd, R. Tayengwa, A. L. Eveland, C. K. Dugard, A. T. Olek, W. Vermerris, K. E. Koch, D. R. McCarty, M. F. Davis, S. R. Thomas, M. C. McCann and N. C. Carpita | Genetic resources for maize cell wall biology | Plant Physiology | 151(4) 1703–28 |
| 2009 | 10.1038/ismej.2008.116 | Pearson, A. and D. B. Rusch | Distribution of microbial terpenoid lipid cyclases in the global ocean metagenome | The ISME Journal | 3(3) 352–63 |
| 2009 | 10.1021/ja9016123 | Parks, J. M., H. Guo, C. Momany, L. Liang, S. M. Miller, A. O. Summers and J. C. Smith | Mechanism of Hg-C protonolysis in the organomercurial lyase MerB | Journal of the American Chemical Society | 131(37) 13278–85 |
| 2009 | 10.1111/j.1755-0998.2008.02203.x | Nowak, C., C. M. Brown and J. J. Hellmann | Microsatellite markers for the hybridizing tiger swallowtails, Papilio glaucus and P. canadensis, and their applicability to historic specimens and congeneric species | Molecular Ecology Resources | 9(3) 800–3 |
| 2009 | 10.1103/PhysRevE.80.011109 | Neusius, T., I. M. Sokolov and J. C. Smith | Subdiffusion in time-averaged, confined random walks | Physical Review E | 80(1) 011109 |
| 2009 | 10.1016/j.cpc.2009.01.007 | Moritsugu, K. and J. C. Smith | REACH: A program for coarse-grained biomolecular simulation | Computer Physics Communications | 180(7) 1188–95 |
| 2009 | 10.1016/j.bpj.2009.05.015 | Moritsugu, K., V. Kurkal-Siebert and J. C. Smith | REACH coarse-grained normal mode analysis of protein dimer interaction dynamics | Biophysical Journal | 97(4) 1158–67 |
| 2009 | 10.1007/s00239-009-9290-x | Montague, M., C. Barnes, H. O. Smith, R. Y. Chuang and S. Vashee | The evolution of RecD outside of the RecBCD complex | Journal of Molecular Evolution | 69(4) 360–71 |
| 2009 | 10.1002/cphc.200800502 | Min, W., S. Lu, G. R. Holtom and X. S. Xie | Triple-resonance coherent anti-stokes Raman scattering microspectroscopy | ChemPhysChem | 10(2) 344–7 |
| 2009 | 10.1117/12.809802 | Min, W., C. W. Freudiger, S. J. Lu, C. W. He, J. X. Kang and X. S. Xie | Stimulated Raman scattering microscopy for biomedical imaging | Multiphoton Microscopy in the Biomedical Sciences IX | 7183 718320 |
| 2009 | 10.1016/j.copbio.2009.10.001 | McInerney, M. J., J. R. Sieber and R. P. Gunsalus | Syntrophy in anaerobic global carbon cycles | Current Opinion in Biotechnology | 20(6) 623–32 |
| 2009 | 10.1038/nmeth.1348 | Manichaikul, A., L. Ghamsari, E. F. Hom, C. Lin, R. R. Murray, et al. | Metabolic network analysis integrated with transcript verification for sequenced genomes | Nature Methods | 6(8) 589–92 |
| 2009 | 10.1186/1754-6834-2-30 | Lau, M. W., C. Gunawan and B. E. Dale | The impacts of pretreatment on the fermentability of pretreated lignocellulosic biomass: A comparative evaluation between ammonia fiber expansion and dilute acid pretreatment | Biotechnology for Biofuels | 2(1) 45668 |
| 2009 | 10.1021/ja901276n | Krishnan, M. and J. C. Smith | Response of small-scale, methyl rotors to protein-ligand association: a simulation analysis of calmodulin-peptide binding | Journal of the American Chemical Society | 131(29) 10083–91 |
| 2009 | 10.1063/1.3108363 | Krishnan, M., R. Schulz and J. C. Smith | Protein Dynamical Transition Role of Methyl Dynamics and Local Diffusion | AIP Conference Proceedings | 1102(1) |
| 2009 | 10.1109/NSSMIC.2009.5401623 | Komarov, S., Y. Yin, H. Wu and Y.-C. Tai | Simulation study of charge collection in highly pixilated CdZnTe detector for PET imaging | 2009 IEEE Nuclear Science Symposium Conference Record (NSS/MIC) | 2892–95 |
| 2009 | 10.1038/msb.2009.42 | Koide, T., D. J. Reiss, J. C. Bare, W. L. Pang, M. T. Facciotti, et al. | Prevalence of transcription promoters within archaeal operons and coding sequences | Molecular Systems Biology | 5 285 |
| 2009 | 10.1038/nrmicro2107 | Koide, T., W. L. Pang and N. S. Baliga | The role of predictive modelling in rationally re-engineering biological systems | Nature Reviews Microbiology | 7(4) 297–305 |
| 2009 | 10.1007/s11367-009-0106-4 | Kim, S. and B. E. Dale | Regional variations in greenhouse gas emissions of biobased products in the United States-corn-based ethanol and soybean oil | International Journal of Life Cycle Assessment | 14(6) 540-546 |
| 2009 | 10.1364/ol.34.002051 | Kieu, K., B. G. Saar, G. R. Holtom, X. S. Xie and F. W. Wise | High-power picosecond fiber source for coherent Raman microscopy | Optics Letters | 34(13) 2051–3 |
| 2009 | 10.1080/13504500903336405 | Jiang, Y. and S. M. Swinton | Market interactions, farmers' choices, and the sustainability of growing advanced biofuels: A missing perspective? | International Journal of Sustainable Development and World Ecology | 16(6) 438-450 |
| 2009 | 10.1088/0031-9155/54/14/015 | James, S. S., Y. Yang, Y. Wu, R. Farrell, P. Dokhale, K. S. Shah and S. R. Cherry | Experimental characterization and system simulations of depth of interaction PET detectors using 0.5 mm and 0.7 mm LSO arrays | Physics in Medicine and Biology | 54(14) 4605–19 |
| 2009 | 10.1021/bi900585m | Imhof, P., S. Fischer and J. C. Smith | Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis | Biochemistry | 48(38) 9061–75 |
| 2009 | 10.1093/mp/ssp047 | Hedenstrom, M., S. Wiklund-Lindstrom, T. Oman, F. Lu, L. Gerber, P. Schatz, B. Sundberg and J. Ralph | Identification of lignin and polysaccharide modifications in Populus wood by chemometric analysis of 2D NMR spectra from dissolved cell walls | Molecular Plant | 2(5) 933–42 |
| 2009 | 10.1007/s12539-008-0011-8 | Guo, H., A. Gorin and H. Guo | A peptide-linkage deletion procedure for estimate of energetic contributions of individual peptide groups in a complex environment: Application to parallel β-sheets | Interdisciplinary Sciences: Computational Life Sciences | 1(1) 12–20 |
| 2009 | 10.1038/nmeth.1318 | Gibson, D. G., L. Young, R. Y. Chuang, J. C. Venter, C. A. Hutchison, 3rd and H. O. Smith | Enzymatic assembly of DNA molecules up to several hundred kilobases | Nature Methods | 6(5) 343–5 |
| 2009 | 10.1016/j.copbio.2009.05.003 | da Costa Sousa, L., S. P. Chundawat, V. Balan and B. E. Dale | 'Cradle-to-grave' assessment of existing lignocellulose pretreatment technologies | Current Opinion in Biotechnology | 20(3) 339-347 |
| 2009 | 10.1016/j.ymben.2009.04.002 | Contador, C. A., M. L. Rizk, J. A. Asenjo and J. C. Liao | Ensemble modeling for strain development of L-lysine-producing Escherichia coli | Metabolic Engineering | 11(4–5) 221–33 |
| 2009 | 10.1093/nar/gkn879 | Cole, J. R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity and J. M. Tiedje | The Ribosomal Database Project: improved alignments and new tools for rRNA analysis | Nucleic Acids Research | 37(Suppl_1) D141–5 |
| 2009 | 10.1016/j.bpj.2009.03.018 | Cheng, X., I. Ivanov, H. Wang, S. M. Sine and J. A. McCammon | Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor | Biophysical Journal | 96(11) 4502–13 |
| 2009 | 10.1002/btpr.213 | Burrows, E. H., W. K. Wong, X. Fern, F. W. Chaplen and R. L. Ely | Optimization of pH and nitrogen for enhanced hydrogen production by Synechocystis sp. PCC 6803 via statistical and machine learning methods | Biotechnology Progress | 25(4) 1009–17 |
| 2009 | 10.1038/msb.2009.34 | Brynildsen, M. P. and J. C. Liao | An integrated network approach identifies the isobutanol response network of Escherichia coli | Molecular Systems Biology | 5 277 |
| 2009 | 10.1007/s00214-009-0565-5 | Bondar, A.-N., J. C. Smith and M. Elstner | Mechanism of a proton pump analyzed with computer simulations | Theoretical Chemistry Accounts | 125(3–6) 353–63 |
| 2009 | 10.1560/ijc.49.2.155 | Bondar, A.-N. and J. C. Smith | Water Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton Pumping | Israel Journal of Chemistry | 49(2) 155–61 |
| 2009 | 10.1038/nbt.1586 | Atsumi, S., W. Higashide and J. C. Liao | Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde | Nature Biotechnology | 27(12) 1177–80 |
| 2009 | 10.1038/ismej.2009.45 | Allen, M. A., F. M. Lauro, T. J. Williams, D. Burg, K. S. Siddiqui, et al. | The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: The role of genome evolution in cold adaptation | ISME Journal | 3(9) 1012-1035 |
| 2010 | 10.1073/pnas.1012900107 | Zhou, R., L. Jackson, G. Shadle, J. Nakashima, S. Temple, F. Chen and R. A. Dixon | Distinct cinnamoyl CoA reductases involved in parallel routes to lignin in Medicago truncatula | Proceedings of the National Academy of Sciences of the United States of America | 107(41) 17803–8 |
| 2010 | 10.1128/mBio.00169-10 | Zhou, J., Y. Deng, F. Luo, Z. He, Q. Tu and X. Zhi | Functional molecular ecological networks | mBio | 1(4) |
| 2010 | 10.1073/pnas.1009170107 | Zhao, Q., H. Wang, Y. Yin, Y. Xu, F. Chen and R. A. Dixon | Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch | Proceedings of the National Academy of Sciences of the United States of America | 107(32) 14496–501 |
| 2010 | 10.1111/j.1365-313X.2010.04223.x | Zhao, Q., L. Gallego-Giraldo, H. Wang, Y. Zeng, S. Y. Ding, F. Chen and R. A. Dixon | An NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula | The Plant Journal | 63(1) 100–14 |
| 2010 | 10.1016/j.plaphy.2010.01.023 | Zhao, N., J. Guan, J. L. Ferrer, N. Engle, M. Chern, P. Ronald, T. J. Tschaplinski and F. Chen | Biosynthesis and emission of insect-induced methyl salicylate and methyl benzoate from rice | Plant Physiology and Biochemistry | 48(4) 279–87 |
| 2010 | 10.1016/j.envsoft.2010.05.012 | Zhang, X. and R. Srinivasan | GIS-based spatial precipitation estimation using next generation radar and raingauge data | Environmental Modelling and Software | 25(12) 1781-1788 |
| 2010 | 10.1007/s12155-010-9079-1 | Zeng, Y. N., B. G. Saar, M. G. Friedrich, F. Chen, Y. S. Liu, R. A. Dixon, M. E. Himmel, X. S. Xie and S. Y. Ding | Imaging Lignin-Downregulated Alfalfa Using Coherent Anti-Stokes Raman Scattering Microscopy | BioEnergy Research | 3(3) 272–7 |
| 2010 | 10.1016/j.fcr.2010.03.014 | Zeid, M., J. K. Yu, I. Goldowitz, M. E. Denton, D. E. Costich, C. T. Jayasuriya, M. Saha, R. Elshire, D. Benscher, F. Breseghello, J. Munkvold, R. K. Varshney, G. Belay and M. E. Sorrells | Cross-amplification of EST-derived markers among 16 grass species | Field Crops Research | 118(1) 28–35 |
| 2010 | 10.1016/j.jmb.2010.06.026 | Zahran, M., I. Daidone, J. C. Smith and P. Imhof | Mechanism of DNA recognition by the restriction enzyme EcoRV | Journal of Molecular Biology | 401(3) 415–32 |
| 2010 | 10.1038/nature09530 | Yooseph, S., K. H. Nealson, D. B. Rusch, J. P. McCrow, C. L. Dupont, et al. | Genomic and functional adaptation in surface ocean planktonic prokaryotes | Nature | 468(7320) 60–6 |
| 2010 | 10.1007/s12155-009-9072-8 | Yilmaz, L. S., W. S. Kontur, A. P. Sanders, U. Sohmen, T. J. Donohue and D. R. Noguera | Electron Partitioning During Light-and Nutrient-Powered Hydrogen Production by Rhodobacter sphaeroides | BioEnergy Research | 3(1) 55–66 |
| 2010 | 10.1007/s11240-010-9826-1 | Yang, X., C.-Y. Ye, Z.-M. Cheng, T. J. Tschaplinski, S. D. Wullschleger, W. Yin, X. Xia and G. A. Tuskan | Genomic aspects of research involving polyploid plants | Plant Cell, Tissue and Organ Culture | 104(3) 387–97 |
| 2010 | 10.1073/pnas.0914506107 | Yang, S., M. L. Land, D. M. Klingeman, D. A. Pelletier, T. Y. Lu, S. L. Martin, H. B. Guo, J. C. Smith and S. D. Brown | Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae | Proceedings of the National Academy of Sciences of the United States of America | 107(23) 10395–400 |
| 2010 | 10.1007/s12539-010-0070-5 | Xu, Q., X. Ye, L. Y. Li, Z. M. Cheng and H. Guo | Structural basis for the action of xyloglucan endotransglycosylases/hydrolases: insights from homology modeling | Interdisciplinary Sciences: Computational Life Sciences | 2(2) 133–9 |
| 2010 | 10.1021/jp102785s | Xu, Q., L. Li and H. Guo | Understanding the mechanism of deacylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As: insights from QM/MM free energy simulations | Journal of Physical Chemistry B | 114(32) 10594–600 |
| 2010 | 10.1093/protein/gzq049 | Xu, J. and J. C. Smith | Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants | Protein Engineering, Design and Selection | 23(10) 759–68 |
| 2010 | Xu, J., G. R. Bao, H. Wang, P. Zhu, F. S. Li, Y. Z. Li, S. Luo and S. Y. Li | Experimental study on hydrolysis of rubber seed oil in sub-critical water | Huaxue Gongcheng/Chemical Engineering (China) | 38(1) 46-49 | |
| 2010 | 10.1016/j.enzmictec.2009.11.001 | Ximenes, E., Y. Kim, N. Mosier, B. Dien and M. Ladisch | Inhibition of cellulases by phenols | Enzyme and Microbial Technology | 46(3–4) 170–6 |
| 2010 | 10.1128/mBio.00246-10 | Wilmes, P., B. P. Bowen, B. C. Thomas, R. S. Mueller, V. J. Denef, N. C. VerBerkmoes, R. L. Hettich, T. R. Northen and J. F. Banfield | Metabolome-proteome differentiation coupled to microbial divergence | mBio | 1(5) |
| 2010 | 10.1111/j.1365-313X.2010.04391.x | Weng, J. K., H. Mo and C. Chapple | Over-expression of F5H in COMT-deficient Arabidopsis leads to enrichment of an unusual lignin and disruption of pollen wall formation | The Plant Journal | 64(6) 898–911 |
| 2010 | 10.1105/tpc.109.073528 | Weng, J. K., T. Akiyama, N. D. Bonawitz, X. Li, J. Ralph and C. Chapple | Convergent evolution of syringyl lignin biosynthesis via distinct pathways in the lycophyte Selaginella and flowering plants | The Plant Cell | 22(4) 1033–45 |
| 2010 | 10.1104/pp.110.155119 | Vanholme, R., B. Demedts, K. Morreel, J. Ralph and W. Boerjan | Lignin biosynthesis and structure | Plant Physiology | 153(3) 895–905 |
| 2010 | 10.1016/j.bpj.2010.03.043 | Ulmschneider, M. B., J. C. Smith and J. P. Ulmschneider | Peptide partitioning properties from direct insertion studies | Biophysical Journal | 98(12) L60–2 |
| 2010 | 10.1186/1471-2164-11-600 | Tyler, L., J. N. Bragg, J. Wu, X. Yang, G. A. Tuskan and J. P. Vogel | Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon | BMC Genomics | 11 600 |
| 2010 | 10.1186/1751-0473-5-7 | Tenenbaum, D., J. C. Bare and N. S. Baliga | GTC: A web server for integrating systems biology data with web tools and desktop applications | Source Code for Biology and Medicine | 5 7 |
| 2010 | 10.4056/sigs.651139 | Tanenbaum, D. M., J. Goll, S. Murphy, P. Kumar, N. Zafar, M. Thiagarajan, R. Madupu, T. Davidsen, L. Kagan, S. Kravitz, D. B. Rusch and S. Yooseph | The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data | Standards in Genomic Sciences | 2(2) 229–37 |
| 2010 | 10.1088/0031-9155/55/2/N04 | St James, S., Y. Yang, S. L. Bowen, J. Qi and S. R. Cherry | Simulation study of spatial resolution and sensitivity for the tapered depth of interaction PET detectors for small animal imaging | Physics in Medicine and Biology | 55(2) N63–74 |
| 2010 | 10.1007/s12155-009-9075-5 | Slater, S., K. Keegstra and T. J. Donohue | The US department of energy great lakes bioenergy research center: Midwestern Biomass as a resource for renewable fuels | Bioenergy Research | 3(1) 45721 |
| 2010 | 10.1016/j.pbi.2010.03.001 | Simmons, B. A., D. Loqué and J. Ralph | Advances in modifying lignin for enhanced biofuel production | Current Opinion in Plant Biology | 13(3) 312-319 |
| 2010 | 10.1111/j.1462-2920.2010.02237.x | Sieber, J. R., D. R. Sims, C. Han, E. Kim, A. Lykidis, A. L. Lapidus, E. McDonnald, L. Rohlin, D. E. Culley, R. Gunsalus and M. J. McInerney | The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production | Environmental Microbiology | 12(8) 2289–301 |
| 2010 | 10.1002/biot.201000129 | Schmidt, B. J., X. Lin-Schmidt, A. Chamberlin, K. Salehi-Ashtiani and J. A. Papin | Metabolic systems analysis to advance algal biotechnology | Biotechnology Journal | 5(7) 660–70 |
| 2010 | 10.1007/s12155-009-9074-6 | Santoro, N., S. L. Cantu, C. E. Tornqvist, T. G. Falbel, J. L. Bolivar, S. E. Patterson, M. Pauly and J. D. Walton | A high-throughput platform for screening milligram quantities of plant biomass for lignocellulose digestibility | Bioenergy Research | 3(1) 93-102 |
| 2010 | 10.1021/bk-2010-1052.ch007 | Saharay, M., H.-B. Guo, J. C. Smith and H. Guo | QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates | Computational Modeling in Lignocellulosic Biofuel Production | 1052 135–54 |
| 2010 | 10.1371/journal.pone.0012947 | Saharay, M., H. Guo and J. C. Smith | Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS | PLoS One | 5(10) e12947 |
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| 2011 | 10.1128/AEM.01834-10 | Wang, J., J. D. Van Nostrand, L. Wu, Z. He, G. Li and J. Zhou | Microarray-based evaluation of whole-community genome DNA amplification methods | Applied and Environmental Microbiology | 77(12) 4241–5 |
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| 2011 | Takasuka, T. E., A. J. Brook, C. R. Currie and B. G. Fox | Discovery and characterization of cellulolytic enzymes from the wood wasp symbiont Streptomyces Sp. ActE | Catalysis and Reaction Engineering Division - Core Programming Topic at the 2011 AIChE Annual Meeting | 2 716 | |
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| 2011 | 10.1021/ct200181t | Srinivas, G., X. Cheng and J. C. Smith | A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils | Journal of Chemical Theory and Computation | 7(8) 2539–48 |
| 2011 | 10.1002/prot.23017 | Splettstoesser, T., K. C. Holmes, F. Noe and J. C. Smith | Structural modeling and molecular dynamics simulation of the actin filament | Proteins | 79(7) 2033–43 |
| 2011 | 10.1111/j.1365-313X.2011.04686.x | Sorensen, I., F. A. Pettolino, A. Bacic, J. Ralph, F. Lu, M. A. O'Neill, Z. Fei, J. K. Rose, D. S. Domozych and W. G. Willats | The charophycean green algae provide insights into the early origins of plant cell walls | The Plant Journal | 68(2) 201–11 |
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| 2011 | 10.2174/97816080521961110101 | Smith, J. C., M. Krishnan, L. Petridis and N. Smolin | Integration of Neutron Scattering with Computer Simulation to Study the Structure and Dynamics of Biological Systems | Dynamics of Biological Macromolecules by Neutron Scattering | 99–108 |
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| 2011 | 10.1016/j.biortech.2010.10.033 | Rosenbaum, M. A., H. Y. Bar, Q. K. Beg, D. Segrè, J. Booth, M. A. Cotta and L. T. Angenent | Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor | Bioresource Technology | 102(3) 2623-2628 |
| 2011 | 10.1093/bioinformatics/btq619 | Rosen, G. L., E. R. Reichenberger and A. M. Rosenfeld | NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads | Bioinformatics | 27(1) 127–9 |
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| 2011 | 10.1002/btpr.506 | Rizk, M. L., R. Laguna, K. M. Smith, F. R. Tabita and J. C. Liao | Redox homeostasis phenotypes in RubisCO-deficient Rhodobacter sphaeroides via ensemble modeling | Biotechnology Progress | 27(1) 15–22 |
| 2011 | 10.1128/JB.00325-11 | Reaves, M. L. and J. D. Rabinowitz | Characteristic phenotypes associated with ptsN-null mutants in Escherichia coli K-12 are absent in strains with functional ilvG | Journal of Bacteriology | 193(18) 4576–81 |
| 2011 | 10.1088/0031-9155/56/17/N01 | Qi, J., Y. Yang, J. Zhou, Y. Wu and S. R. Cherry | Experimental assessment of resolution improvement of a zoom-in PET | Physics in Medicine and Biology | 56(17) N165–74 |
| 2011 | 10.1063/1.3592153 | Prinz, J. H., J. D. Chodera, V. S. Pande, W. C. Swope, J. C. Smith and F. Noe | Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics | Journal of Chemical Physics | 134(24) 244108 |
| 2011 | 10.1137/100789191 | Prinz, J.-H., M. Held, J. C. Smith and F. Noé | Efficient Computation, Sensitivity, and Error Analysis of Committor Probabilities for Complex Dynamical Processes | Multiscale Modeling and Simulation | 9(2) 545–67 |
| 2011 | 10.1128/EC.00016-11 | Pomraning, K. R., K. M. Smith and M. Freitag | Bulk segregant analysis followed by high-throughput sequencing reveals the Neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1 | Eukaryotic Cell | 10(6) 724–33 |
| 2011 | 10.1007/978-1-61779-040-9_19 | Plett, J. M., B. Montanini, A. Kohler, S. Ottonello and F. Martin | Tapping genomics to unravel ectomycorrhizal symbiosis | Fungal Genomics | 722 249–81 |
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| 2011 | 10.1074/jbc.M111.263004 | Pingali, S. V., H. M. O'Neill, J. McGaughey, V. S. Urban, C. S. Rempe, L. Petridis, J. C. Smith, B. R. Evans and W. T. Heller | Small angle neutron scattering reveals pH-dependent conformational changes in Trichoderma reesei cellobiohydrolase I: implications for enzymatic activity | Journal of Biological Chemistry | 286(37) 32801–9 |
| 2011 | 10.1093/nar/gkq1091 | Pieper, U., B. M. Webb, D. T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, et al. | ModBase, a database of annotated comparative protein structure models, and associated resources | Nucleic Acids Research | 39(Suppl_1) D465–74 |
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| 2011 | 10.1021/bk-2010-1052.ch003 | Petridis, L., J. Xu, M. F. Crowley, J. C. Smith and X. Cheng | Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes | Computational Modeling in Lignocellulosic Biofuel Production | 1052 55–73 |
| 2011 | 10.1021/ja206839u | Petridis, L., R. Schulz and J. C. Smith | Simulation analysis of the temperature dependence of lignin structure and dynamics | Journal of the American Chemical Society | 133(50) 20277–87 |
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| 2011 | 10.1074/mcp.M110.006049 | Pan, C., C. R. Fischer, D. Hyatt, B. P. Bowen, R. L. Hettich and J. F. Banfield | Quantitative tracking of isotope flows in proteomes of microbial communities | Molecular & Cellular Proteomics | 10(4) M110.006049 |
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| 2011 | 10.1007/s00253-011-3121-x | Newcomb, M., J. Millen, C. Y. Chen and J. H. Wu | Co-transcription of the celC gene cluster in Clostridium thermocellum | Applied Microbiology and Biotechnology | 90(2) 625–34 |
| 2011 | 10.1103/PhysRevE.83.021902 | Neusius, T., I. Daidone, I. M. Sokolov and J. C. Smith | Configurational subdiffusion of peptides: a network study | Physical Review E | 83(2) 021902 |
| 2011 | 10.1016/B978-0-12-386489-5.00004-X | Myrold, D. D., J. Pett-Ridge and P. J. Bottomley | Nitrogen mineralization and assimilation at millimeter scales | Methods in Enzymology | 496 91–114 |
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| 2011 | 10.1016/j.geoderma.2011.07.017 | Muñoz, J. D. and A. Kravchenko | Soil carbon mapping using on-the-go near infrared spectroscopy, topography and aerial photographs | Geoderma | 166(1) 102-110 |
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| 2011 | 10.1007/s12539-011-0111-8 | Mostofian, B., J. C. Smith and X. Cheng | The solvation structures of cellulose microfibrils in ionic liquids | Interdisciplinary Sciences: Computational Life Sciences | 3(4) 308–20 |
| 2011 | 10.1186/gb-2011-12-5-r44 | Miller, C. S., B. J. Baker, B. C. Thomas, S. W. Singer and J. F. Banfield | EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data | Genome Biology | 12(5) R44 |
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| 2011 | 10.1128/mBio.00323-10 | McKinlay, J. B. and C. S. Harwood | Calvin cycle flux, pathway constraints, and substrate oxidation state together determine the H2 biofuel yield in photoheterotrophic bacteria | mBio | 2(2) |
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| 2011 | 10.1371/journal.pone.0025260 | Malone, B. M., F. Tan, S. M. Bridges and Z. Peng | Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data | PLoS One | 6(9) e25260 |
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| 2011 | 10.4056/sigs.1694706 | Lorenzi, H. A., J. Hoover, J. Inman, T. Safford, S. Murphy, L. Kagan and S. J. Williamson | The Viral MetaGenome Annotation Pipeline(VMGAP): an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data | Standards in Genomic Sciences | 4(3) 418–29 |
| 2011 | 10.1016/j.mimet.2011.05.007 | Liang, C., X. Zhang, L. Wei, H. He, A. J. Higbee and T. C. Balser | Investigation of the molecular ion structure for aldononitrile acetate derivatized muramic acid | Journal of Microbiological Methods | 86(2) 224-230 |
| 2011 | 10.1007/s10533-010-9525-3 | Liang, C., G. Cheng, D. L. Wixon and T. C. Balser | An Absorbing Markov Chain approach to understanding the microbial role in soil carbon stabilization | Biogeochemistry | 106(3) 303-309 |
| 2011 | 10.1021/bi2004476 | Li, T., W. G. Choi, I. S. Wallace, J. Baudry and D. M. Roberts | Arabidopsis thaliana NIP7;1: an anther-specific boric acid transporter of the aquaporin superfamily regulated by an unusual tyrosine in helix 2 of the transport pore | Biochemistry | 50(31) 6633–41 |
| 2011 | 10.1007/s12010-010-9136-4 | Li, L., X. Jiang, H. Guan, P. Wang and H. Guo | Three alginate lyases from marine bacterium Pseudomonas fluorescens HZJ216: purification and characterization | Applied Biochemistry and Biotechnology | 164(3) 305–17 |
| 2011 | 10.1016/j.biortech.2011.04.005 | Li, C., G. Cheng, V. Balan, M. S. Kent, M. Ong, S. P. S. Chundawat, L. D. Sousa, Y. B. Melnichenko, B. E. Dale, B. A. Simmons and S. Singh | Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover | Bioresource Technology | 102(13) 6928-6936 |
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| 2011 | 10.1103/PhysRevA.83.013623 | Levine, G. C., B. A. Friedman and M. J. Bantegui | Detecting many-body entanglement in noninteracting ultracold atomic Fermi gases | Physical Review A | 83(1) |
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| 2011 | 10.1007/s00203-010-0652-y | Laguna, R., F. R. Tabita and B. E. Alber | Acetate-dependent photoheterotrophic growth and the differential requirement for the Calvin-Benson-Bassham reductive pentose phosphate cycle in Rhodobacter sphaeroides and Rhodopseudomonas palustris | Archives of Microbiology | 193(2) 151-154 |
| 2011 | 10.1007/s00294-010-0328-9 | Labbe, J., C. Murat, E. Morin, F. Le Tacon and F. Martin | Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers | Current Genetics | 57(2) 75–88 |
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| 2011 | 10.1016/j.copbio.2011.04.018 | Klitgord, N. and D. Segrè | Ecosystems biology of microbial metabolism | Current Opinion in Biotechnology | 22(4) 541-546 |
| 2011 | 10.1063/1.3626274 | Klein, H. C., X. Cheng, J. C. Smith and T. Shen | Transfer matrix approach to the hydrogen-bonding in cellulose Iα fibrils describes the recalcitrance to thermal deconstruction | Journal of Chemical Physics | 135(8) 085106 |
| 2011 | 10.1016/j.enzmictec.2011.01.007 | Kim, Y., E. Ximenes, N. S. Mosier and M. R. Ladisch | Soluble inhibitors/deactivators of cellulase enzymes from lignocellulosic biomass | Enzyme and Microbial Technology | 48(4–5) 408–15 |
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| 2011 | 10.1134/S0021364011120083 | Kagan, M. Y., D. V. Efremov, M. S. Marienko and V. V. Val'kov | Triplet p-Wave Superconductivity in the Low-Density Extended Hubbard Model with Coulomb Repulsion | JETP Letters | 93(12) 725–30 |
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| 2011 | 10.1016/j.jmb.2011.08.042 | Johs, A., I. M. Harwood, J. M. Parks, R. E. Nauss, J. C. Smith, L. Liang and S. M. Miller | Structural characterization of intramolecular Hg2+ transfer between flexibly linked domains of mercuric ion reductase | Journal of Molecular Biology | 413(3) 639–56 |
| 2011 | 10.1104/pp.110.165654 | Jahn, C. E., J. K. McKay, R. Mauleon, J. Stephens, K. L. McNally, D. R. Bush, H. Leung and J. E. Leach | Genetic variation in biomass traits among 20 diverse rice varieties | Plant Physiology | 155(1) 157–68 |
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