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Publications

  • Biancalani, T., L. DeVille, and N. Goldenfeld.  Multi-dimensional niche construction and diversification in trait-based Lotka-Volterra models Physical Review E, 91, 052107 – Published (7 May 2015). PDF  http://journals.aps.org/pre/abstract/10.1103/PhysRevE.91.052107  
  • DeVille, L. and M. Gagliardi.    Finite-size effects and switching times for Moran dynamics with mutation, Journal of Mathematical Biology (Dec 2015)  PDF   https://www.researchgate.net/publication/288060641_Finite-size_effects_and_switching_times_for_Moran_dynamics_with_mutation
  • Zhang C1, She Q2, Bi H3, Whitaker RJ4. (2016 May 2); 82(10):3070-81. doi: 10.1128/AEM.00455-16. The apt/6-Methylpurine Counterselection System and Its Applications in Genetic Studies of the Hyperthermophilic Archaeon Sulfolobus islandicus. Print (2016 May 15).     PDF    http://aem.asm.org/content/82/10/3070.long http://nai.nasa.gov/articles/2016/5/26/genetic-studies-of-a-hyperthermophilic-archaeon/
  • W. H.H. Reeder IV, M.B. Hirst, S.C. Dawson, J Sanck, and Gordon V. Wolfe. (2015)   The Food Web of Boiling Springs Lake is Dominated by the Heterolobosean Tetramitus thermacidophilus strain BSL. Journal of Eukaryotic Microbiology (62): 374-390.  PDF  http://onlinelibrary.wiley.com/doi/10.1111/jeu.12193/abstract
  • Moore JM, Magnan D, Mojica AK, Bravo Núñez MA, Bates D, Rosenberg SM, Hastings PJ.  (2015).  Roles of nucleoid-associated proteins in stress-induced mutagenic break repair in starving Escherichia coliGenetics doi: 10.1534/ genetics.115.178970. PMID: 26500258. (2015)   PDF    http://www.ncbi.nlm.nih.gov/pubmed/26500258
  • Singh, R., Sanford, R., Katz, L., Fouke, B.W., and Werth, C.J., 2015. Metabolism Induced CaCO3 Biomineralization during Reactive Transport in a Micromodel: Implications for Porosity Alteration. Environmental Science and Technology. Vol. Vol. 49, 12094−12104, (2015).     PDF  http://pubs.acs.org/doi/full/10.1021/acs.est.5b00152
  • Brettin, T., J. J. Davis, T. Disz, R. A. Edwards, S. Gerdes, G. J. Olsen, R. Olson, R. Overbeek, B. Parrello, G. D. Pusch, M. Shukla, J. A. Thomason, III, R. Stevens, V. Vonstein, A. R. Wattam, and F. Xia (2015) RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Science Reports 5: 8365; doi: 10.1038/srep08365.  http://www.nature.com/articles/srep08365  PDF
  • Neil H. Kim, Gloria Lee, Nicholas A. Sherer, K. Michael Martini, Nigel Goldenfeld, and Thomas E. Kuhlman. Real-time transposable element activity in individual live cells. Proc. Natl. Acad. Sci. Early edition June 2016. (16 pages) ( PDF) https://doi.org/10.1073/pnas.1601833113
  • Barge, L.M., Branscomb, E., Brucato, J.R., Cardoso, S.S.S., Cartwright, J.H.E., Danielache, S.O., Galante, D., Kee, T.P., Miguel, Y., Mojzsis, S. and Robinson, K.J., 2016.   Thermodynamics, Disequilibrium, Evolution: Far-From-Equilibrium Geological and Chemical Considerations for Origin-Of-Life Research.   Origins of Life and Evolution of Biospheres, pp.1-18.  (2016)  DOI: 10.1007/s11084-016-9508-z  http://link.springer.com/article/10.1007/s11084-016-9508-z  PDF
  • Davis, J. J., S. Gerdes, G. J. Olsen, R. Olson, G. D. Pusch, M. Shukla, V. Vonstein, A. R. Wattam, and H. Yoo (2016) PATtyFams: Protein families for the microbial genomes in the PATRIC database. Frontiers in Microbiology 7: 118; doi: 10.3389/fmicb.2016.00118.  http://journal.frontiersin.org/article/10.3389/fmicb.2016.00118/full   PDF
  • Dong, Y., Sanford, R.A., Boyanov, M.I., Kemner, K.M., Flynn, T.M., O’Loughlin, E.J., Locke, R.A. II, Weber, J.R., Egan, S.R., and Fouke, B.W. (Nov 2016) Orenia metallireducens sp. nov. strain Z6, a Novel Metal-reducing Firmicutes from 2.0 KM Deep Subsurface. Applied and Environmental Microbiology, 82 (21) 6440-6453. doi: 10.1128/AEM.02382-16  PDF  http://aem.asm.org/content/82/21/6440.full.pdf+html 
  • Dong, Y., Sanford, R.A., Boyanov, M.I., Kemner, K.M., Flynn, T.M., O’Loughlin, E.J., Locke, R.A. II, Weber, J.R., Egan, S.R., and Fouke, B.W. (Oct 2016) Tepidibacillus decaturensis sp. Nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater. International Journal of Systematic and Evolutionary Microbiology. doi: 10.1099/ijsem.0.001295    http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem…  PDF
  • Dong, Y., Sanford, R.A., Chang, Y., Fouke, B.W. (2016) Draft Genome Sequence of Tepidibacillus decaturensis strain Z9, an Anaerobic, Moderately Thermophilic and Heterotrophic Bacterium from Deep Subsurface. Genome Announcement, 4 (2). doi: 10.1128/genomeA.00190-16     http://genomea.asm.org/content/4/2/e00190-16.full   PDF
  • Fitzgerald, D., Hastings, P.J., Rosenberg, S.M. (2017) Stress-induced mutagenesis: implications in cancer and drug resistance. Annual Reviews, Cancer Biology 1, 6.1-6.22. doi: 10.1146/annurev-cancerbio-050216-121919  PDF  http://www.annualreviews.org/doi/abs/10.1146/annurev-cancerbio-050216-121919 
  • Peterson, J.R., Thor, S., Kohler, L., Kohler, P.R.A., Metcalf, W.W., and Luthey-Schulten, Z. (2016) Genome-wide Gene Expression and RNA half-life measurements allow Predictions Regulation and Metabolic Behavior in Methanosarcina acetivorans. BMC Genomics. Accepted for Publication. doi: 10.1186/s12864-016-3219-8  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3219-8  PDF
  • Xia, J., Chen, L-T., Mei, Q., Ma, C-H., Halliday, J.A., Lin, H-Y., Magnan, D., Pribis, J.P., Fitzgerald, D.M., Hamilton, H.M., Richters, M., Nehring, R., Shen, X., Li, L., Bates, D., Hastings, P.J., Herman, C., Jayaram, M., and Rosenberg, S.M. (2016) Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase. Science Advances AAAS 2, e1601605. doi: 10.1126/sciadv.1601605  PDF  http://advances.sciencemag.org/content/2/11/e1601605 
  • Tommaso Biancalani, Farshid Jafarpour, Nigel Goldenfeld. Giant amplification of noise in fluctuation-induced pattern formation. Phys. Rev. Lett. 118, 018101 (5 pages) (2017). (PDF). https://doi.org/10.1103/PhysRevLett.118.018101 
  • Chi Xue and Nigel Goldenfeld.  Stochastic predator-prey dynamics of transposons in the human genome. Phys. Rev. Lett. 117, 208101 (2016). (PDF). 
  • S. Thor, J.R. Peterson, Z. Luthey-Schulten Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function Archaea, 2017, Jan 4, vol. 2017, Article ID: 9763848, 18 pages, doi: 10.1155/2017/9763848  https://www.hindawi.com/journals/archaea/2017/9763848/  PDF
  • J.R. Peterson, S. Thor, L. Kohler, P.R.A. Kohler, W.W. Metcalf, Z. Luthey-Schulten 
  • Genome-Wide Gene Expression and RNA Half-Life Measurements allow Predictions of Regulation and Metabolic Behavior in Methanosarcina acetivorans BMC Genomics, 2016, Nov 16, 17(1):924 doi: 10.1186/s12864-016-3219-8   PDF https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112694/ 
  • Peterson, J.R., Thor, S., Kohler, L., Kohler, P.R.A., Metcalf, W.W., and Luthey-Schulten, Z. (2016) Genome-wide Gene Expression and RNA half-life measurements allow Predictions Regulation and Metabolic Behavior in Methanosarcina acetivorans. BMC Genomics. Accepted for Publication. doi: 10.1186/s12864-016-3219-8 PDF
  • Rogers, E., Bravo Núñez, M.A., Hastings, P.J., and Rosenberg, S.M. (2016) Stress and Environmental Control of Gene Expression and Adaptation in Bacteria. Chapter 9.3, How a large gene network couples mutagenic DNA break repair to stress in Escherichia coli. Chapter 9.3. de Bruijn, F.J. (Ed), Wiley & Sons Publisher, Hoboken, N.J. USA, pp.570-576. ISBN: 978-1-119-00488-2
  • Rogers, E., Correa, R., Barreto, B., Bravo Núñez, M.A., Minnick, P.J., Vera Cruz, D., Xia, J., Hastings, P.J., and Rosenberg, S.M. (2016) Stress and Environmental Control of Gene Expression and Adaptation in Bacteria. Chapter 2.14, Double-strand-break repair, mutagenesis and stress. de Bruijn, F.J. (Ed.), Wiley & Sons Publisher, Hoboken, N.J. USA, pp. 185-195. ISBN: 978-1-119-00488-2
  • E. Branscomb, T. Biancalani, N. Goldenfeld, M. Russell (2017), Escapement Mechanisms and the Conversion of Disequilibria; the engines of creation.  Physics Reports (in press). PDF http://www.sciencedirect.com/science/article/pii/S0370157317300455
  • Changyi Zhang, Qunxin She, Hongkai Bi, and Rachel J. Whitaker The apt/6-Methylpurine Counterselection System and Its Applications in Genetic Studies of the Hyperthermophilic Archaeon Sulfolobus islandicus    PDF Appl. Environ. Microbiol. May 2016 82:10 12 3070-3081; Accepted manuscript posted online 11 March 2016, doi:10.1128/AEM.00455-16 
  • Shiraishi M, Ishino S, Yoshida K, Yamagami T, Cann I, Ishino Y. 2016. PDF PCNA is involved in the EndoQ-mediated DNA repair process in Thermococcales. Sci Rep. 2016 May 6;6:25532. doi: 10.1038/srep25532.
  • Shiraishi M, Ishino S, Cann I, Ishino Y.  2017. A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus. Biosci Biotechnol Biochem. 2017 Jan 18:1-7. doi: 10.1080/09168451.2016.1277946. [Epub ahead of print] PMID: 28095753