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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/
  • Zhang, Changyi, Qunxin She, Hongkai Bi, and Rachel J. Whitaker. “The apt/6-Methylpurine Counterselection System and Its Applications in Genetic Studies in the Hyperthermophilic Archaeon Sulfolobus Islandicus.” Applied and Environmental Microbiology, March 11, 2016, AEM.00455–16. https://doi.org/10.1128/AEM.00455-16.
  • 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. PDF http://www.nature.com/articles/srep08365 
  • 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  PDF http://link.springer.com/article/10.1007/s11084-016-9508-z 
  • 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.  PDF  http://journal.frontiersin.org/article/10.3389/fmicb.2016.00118/full   
  • 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    PDF http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.001295   
  • 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  PDF  http://genomea.asm.org/content/4/2/e00190-16.full  
  • 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  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3219-8  
  • 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). 
  • 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/ 
  • 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." (2016) BMC Genomics, 17(1):924.  PDF                    https://doi.org/10.1186/s12864-016-3219-8         
  • Galiardi, M. Mathematical models in evolutionary dynamics. Ph.D. thesis, University of Illinois, 2016 PDF  https://www.ideals.illinois.edu/handle/2142/90535 
  • 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 http:/doi.org/10.1002/97811119004813 
  • Rogers, E., Bravo Núñez, M.A., Hastings, P.J., and Rosenberg, S.M. (2016). How a large gene network couples mutagenic DNA break repair to stress in Stress and Environmental Control of Gene Expression and Adaptation in Bacteria, de Bruijn FJ (Ed), Wiley & Sons Publisher, Hoboken, N.J. USA, pp. 570-576. 
  • 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), 677, 17, 1-60  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
  • Moore JM, Correa R, Rosenberg SM, Hastings PJ.  2017. Persistent Damaged Bases in DNA allow Mutagenic Break Repair in Escherichia coli. PLoS Genetics 13:e1006733. https://doi.org/10.1371/journal.pgen.1006733  PDF 
  • Campbell, Kate M., Angela Kouris, Whitney England, Rika E. Anderson, R. Blaine McCleskey, D. Kirk Nordstrom, and Rachel J. Whitaker. “Sulfolobus Islandicus Meta-Populations in Yellowstone National Park Hot Springs.” Environmental Microbiology, March 1, 2017, n/a – n/a. https://doi.org/10.1111/1462-2920.13728.
  • Anderson, Rika E., Angela Kouris, Christopher H. Seward, Kate M. Campbell, and Rachel J. Whitaker. “Structured Populations of Sulfolobus Acidocaldarius with Susceptibility to Mobile Genetic Elements.” Genome Biology and Evolution 9, no. 6 (June 1, 2017): 1699–1710. https://doi.org/10.1093/gbe/evx104.
  • J.R. Peterson, J.A. Cole, Z. Luthey-Schulten. "Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects." (2017) PLoS ONE, 12(8): e0182570. https://doi.org/10.1371/journal.pone.0182570
  • S. Thor, J.R. Peterson, Z. Luthey-Schulten. "Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function." (2017) Archaea, Jan 4, vol. 2017, Article ID: 9763848, 18 pages, doi: 10.1155/2017/9763848  https://www.hindawi.com/journals/archaea/2017/9763848/ 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
  • Nigel Goldenfeld, Tommaso Biancalani, Farshid Jafarpour. Universal biology and the statistical mechanics of early life. Phil. Trans. R. Soc. A 375, 20160341 (14 pages) (2017). (PDF). http://dx.doi.org/10.1098/rsta.2016.0341
  • Chi Xue and Nigel Goldenfeld. Coevolution Maintains Diversity in the Stochastic “Kill the Winner” Model. Phys. Rev. Lett. 119, 268101 (7 pages) (2017). (PDF). https://doi.org/10.1103/PhysRevLett.119.268101 (Interview with authors for general readership)
  • Correa  R, Thornton PC, Rosenberg SM and PJ Hastings 2018. Oxygen and RNA in stress-induced mutation. Curr Genet. (PDF)  https://link.springer.com/article/10.1007/s00294-017-0801-9
  • Oxygen and RNA in stress-induced mutation. Raul Correa, Philip C. Thornton, Susan M. Rosenberg, P.J. Hastings 2018 Jan 2. doi: 10.1007/s00294-017-0801-9 https://www.ncbi.nlm.nih.gov/pubmed/29294174 
  • The essential genome of the crenarchaeal model Sulfolobus islandicus Changyi Zhang, Alex P. R. Phillips, Rebecca L. Wipfler, Gary J. Olsen, Rachel J. Whitaker doi: https://doi.org/10.1101/408351  PDF Oct 2018 

  • Revealing S-layer Functions in the Hyperthermophilic Crenarchaeon Sulfolobus islandicus Changyi Zhang, Rebecca L Wipfler, Yuan Li, Zhiyu Wang, Emily N Hallett, Rachel J Whitaker doi: https://doi.org/10.1101/444406  PDF