@article{nichols_johnson_chou_kelly_2009, title={Temperature, not LuxS, mediates AI-2 formation in hydrothermal habitats}, volume={68}, ISSN={["1574-6941"]}, DOI={10.1111/j.1574-6941.2009.00662.x}, abstractNote={Quorum sensing provides the basis for coordinating community-wide, microbial behaviors in many mesophilic bacteria. However, little attention has been directed toward the possibility that such phenomena occur in extremely thermal microbial environments. Despite the absence of luxS in hyperthermophile genomes, autoinducer-2 (AI-2), a boronated furanone and proposed 'universal' interspecies mesophilic bacterial communication signal, could be formed by Thermotoga maritima and Pyrococcus furiosus through a combination of biotic and abiotic reaction steps. AI-2 did not, however, induce any detectable quorum-sensing phenotypes in these organisms, although transcriptome-based evidence of an AI-2-induced stress response was observed in T. maritima. The significance, if any, of AI-2 in hydrothermal habitats is not yet clear. Nevertheless, these results show the importance of considering environmental factors, in this case high temperatures, as abiotic causative agents of biochemical and microbiological phenomena.}, number={2}, journal={FEMS MICROBIOLOGY ECOLOGY}, author={Nichols, Jason D. and Johnson, Matthew R. and Chou, Chung-Jung and Kelly, Robert M.}, year={2009}, month={Apr}, pages={173–181} }
 @article{werken_verhaart_vanfossen_willquist_lewis_nichols_goorissen_mongodin_nelson_niel_et al._2008, title={Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus}, volume={74}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.00968-08}, abstractNote={ABSTRACT}, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Werken, Harmen J. G. and Verhaart, Marcel R. A. and VanFossen, Amy L. and Willquist, Karin and Lewis, Derrick L. and Nichols, Jason D. and Goorissen, Heleen P. and Mongodin, Emmanuel F. and Nelson, Karen E. and Niel, Ed W. J. and et al.}, year={2008}, month={Nov}, pages={6720–6729} }
 @article{young_nichols_kelly_deiters_2008, title={Microwave activation of enzymatic catalysis}, volume={130}, ISSN={["0002-7863"]}, DOI={10.1021/ja802404g}, abstractNote={Microwave irradiation can be used to regulate biocatalysis. Herein, the utilization of hyperthermophilic enzymes in a microwave reactor is reported. While these enzymes are inactive at low temperatures, they can be activated with microwave irradiation. To the best of our knowledge, this is the first illustration of a specific microwave effect in enzymatic catalysis.}, number={31}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Young, Douglas D. and Nichols, Jason and Kelly, Robert M. and Deiters, Alexander}, year={2008}, month={Aug}, pages={10048-+} }
 @article{vanfossen_lewis_nichols_kelly_2008, title={Polysaccharide Degradation and Synthesis by Extremely Thermophilic Anaerobes}, volume={1125}, ISBN={["978-1-57331-705-4"]}, ISSN={["0077-8923"]}, DOI={10.1196/annals.1419.017}, abstractNote={Extremely thermophilic fermentative anaerobes (growth Topt ≥ 70°C) have the capacity to use a variety of carbohydrates as carbon and energy sources. As such, a wide variety of glycoside hydrolases and transferases have been identified in these microorganisms. The genomes of three model extreme thermophiles—an archaeon Pyrococcus furiosus (Topt = 98°C), and two bacteria, Thermotoga maritima (Topt = 80°C) and Caldicellulosiruptor saccharolyticus (Topt = 70°C)—encode numerous carbohydrate‐active enzymes, many of which have been characterized biochemically in their native or recombinant forms. In addition to their voracious appetite for polysaccharide degradation, polysaccharide production has also been noted for extremely thermophilic fermentative anaerobes; T. maritima generates exopolysaccharides that aid in biofilm formation, a process that appears to be driven by intraspecies and interspecies interactions.}, number={1}, journal={Annals of the New York Academy of Sciences}, author={VanFossen, A.L. and Lewis, D.L. and Nichols, J.D. and Kelly, R.M.}, year={2008}, month={Mar}, pages={322–337} }
 @article{montero_johnson_chou_conners_geouge_tachdjian_nichols_kelly_2007, title={Responses of wild-type and resistant strains of the hyperthermophilic bacterium Thermotoga maritima to chloramphenicol challenge}, volume={73}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.00453-07}, abstractNote={ABSTRACT}, number={15}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Montero, Clemente I. and Johnson, Matthew R. and Chou, Chung-Jung and Conners, Shannon B. and Geouge, Sarah G. and Tachdjian, Sabrina and Nichols, Jason D. and Kelly, Robert M.}, year={2007}, month={Aug}, pages={5058–5065} }
 @article{montero_lewis_johnson_conners_nance_nichols_kelly_2006, title={Colocation of genes encoding a tRNA-mRNA hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium Thermotoga maritima}, volume={188}, ISSN={["0021-9193"]}, DOI={10.1128/JB.00470-06}, abstractNote={ABSTRACT}, number={19}, journal={JOURNAL OF BACTERIOLOGY}, author={Montero, Clemente I. and Lewis, Derrick L. and Johnson, Matthew R. and Conners, Shannon B. and Nance, Elizabeth A. and Nichols, Jason D. and Kelly, Robert M.}, year={2006}, month={Oct}, pages={6802–6807} }
 @article{brownie_hines_nichols_pollock_hestbeck_1993, title={CAPTURE-RECAPTURE STUDIES FOR MULTIPLE STRATA INCLUDING NON-MARKOVIAN TRANSITIONS}, volume={49}, ISSN={["0006-341X"]}, DOI={10.2307/2532259}, abstractNote={We consider capture-recapture studies where release and recapture data are available from each of a number of strata on every capture occasion. Strata may, for example, be geographic locations or physiological states. Movement of animals among strata occurs with unknown probabilities, and estimation of these unknown transition probabilities is the objective. We describe a computer routine for carrying out the analysis under a model that assumes Markovian transitions and under reducedparameter versions of this model. We also introduce models that relax the Markovian assumption and allow "memory" to operate (i.e., allow dependence of the transition probabilities on the previous state). For these models, we suggest an analysis based on a conditional likelihood approach. Methods are illustrated with data from a large study on Canada geese (Branta canadensis) banded in three geographic regions. The assumption of Markovian transitions is rejected convincingly for these data, emphasizing the importance of the more general models that allow memory.}, number={4}, journal={BIOMETRICS}, author={BROWNIE, C and HINES, JE and NICHOLS, JD and POLLOCK, KH and HESTBECK, JB}, year={1993}, month={Dec}, pages={1173–1187} }
 @article{pollock_nichols_brownie_hines_1990, title={Statistical-inference for capture-recapture experiments}, number={107}, journal={Wildlife Monographs}, author={Pollock, K. H. and Nichols, J. D. and Brownie, C. and Hines, J. E.}, year={1990}, pages={1–97} }