2010-present

39. Ver Eecke, H.C., N.H. Akerman, J.A. Huber, D.A. Butterfield, and J.F. Holden (2013) Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions. Environ. Microbiol. Rep. doi:10.1111/1758-2229.12065. [PDF] [supplement]

38. Jung, J.H., D.H. Seo, J.F. Holden, and C.S. Park (2013) Maltose-forming a-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04. Appl. Microbiol. Biotechnol. doi:10.1007/s00253-013-5068-6. [PDF]

37. Lee, J.E., I.H. Kim, J.H. Jung, D.H. Seo, S.G. Kang, J.F. Holden, J. Cha, and C.S. Park (2013) Molecular cloning and enzymatic characterization of cyclomaltodextrinase from hyperthermophilic archaeon Thermococcus sp. CL1. J. Microbiol. Biotechnol. 23:1060-1069 [PDF]

36. Jamieson, J.W., M.D. Hannington, D.A. Clague, D.S. Kelley, J.R. Delaney, J.F. Holden, M.K. Tivey, and L.E. Kimpe (2013) Sulfide geochronology along the Endeavour Segment of the Juan de Fuca Ridge. Geochem. Geophys. Geosyst. 14, doi:10.1002/ggge.20133. [PDF]

35. Ver Eecke, H.C., D.A. Butterfield, J.A. Huber, M.D. Lilley, E.J. Olson, K.K. Roe, L.J. Evans, A.Y. Merkel, H.V. Cantin, and J.F. Holden (2012) Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents. Proc. Natl. Acad. Sci. USA 109:13,674-13,679. [PDF] [supplement]

34. Jung, J.H., J.F. Holden, D.H. Seo, K.H. Park, H. Shin, S. Ryu, J.H. Lee, and C.S. Park (2012) Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain CL1 isolated from a Paralvinella sp. hydrothermal vent polychaete worm. J. Bacteriol. 194:4769-4770. [PDF]

33. Jung, J.H., J.H. Lee, J.F. Holden, D.H. Seo, H. Shin, H.Y. Kim, W. Kim, and C.S. Park (2012) Complete genome sequence of the hyperthermophilic archaeon Pyrococcus sp. strain ST04 isolated from a deep-sea hydrothermal sulfide chimney on the Juan de Fuca Ridge. J. Bacteriol. 194:4434-4435. [PDF]

32. Fornari, D.J., S.E. Beaulieu, J.F. Holden, L. Mullineaux, and M. Tolstoy (2012) Introduction to the special issue: from RIDGE to Ridge 2000. Oceanography 25:12-17.

31. Holden, J.F. (2012) Hot environments. In T. Schmidt and M. Schaechter (ed.), Topics in Ecological and Environmental Microbiology, 1st Ed., Elsevier Publishing, Oxford, UK.

30. Holden, J.F., J.A. Beier, K.L. Rogers, M.D. Schulte, and B.M. Toner (2012) Biogeochemical processes at hydrothermal vents: microbes and minerals, bioenergetics and carbon fluxes. Oceanography 25:196-208.

29. Girguis, P.R., and J.F. Holden (2012) On the potential for bioenergy and biofuels from hydrothermal vent microbes. Oceanography 25:213-217.

28. Kelley, D.S., S.M. Carbotte, D. Clague, D. Caress, J. Delaney, J. Gill, H. Hadaway, J.F. Holden, E.E.E. Hooft, J.P. Kellogg, M.D. Lilley, M. Stoermer, R. Weekly, and W.S.D. Wilcock (2012) The Endeavour Segment of the Juan de Fuca Ridge: one of the most remarkable places on Earth. Oceanography 25:44-61.

27. Shank, T.M., E.T. Baker, R.W. Embley, S. Hammond, J.F. Holden, S. White, S.L. Walker, M. Calderon, S. Herrera, T.J. Lin, C. Munro, T. Heyl, L.C. Stewart, M. Malik, M. Lobecker, and J. Potter (2012) GALREX 2011: Exploration of the deep-water Galápagos region. Oceanography 25 (Online Supplement):50-52.

26. Oslowski, D.M., J.H. Jung, D.H. Seo, C.S. Park, and J.F. Holden (2011) Production of hydrogen from {alpha}-1,4- and {beta}-1,4-linked saccharides by marine hyperthermophilic archaea. Appl. Environ. Microbiol. 77:3169-3173. [PDF] [supplement - Word document]

25. Holden, J.F., A.L. Menon, and M.W.W. Adams (2011) Hyperthermophile-metal interactions in hydrothermal environments, pp. 39-63. In J.F. Stolz and R.S. Oremland (ed.), Microbial Metal and Metalloid Metabolism: Advances and Applications, American Society for Microbiology Press, Washington, DC.

2000s

24. Ver Eecke, H.C., D.S. Kelley, and J.F. Holden (2009) Abundances of hyperthermophilic autotrophic Fe(III) oxide reducers and heterotrophs in deep-sea hydrothermal sulfide chimneys of the northeastern Pacific Ocean. Appl. Environ. Microbiol. 75:242-245. [PDF] [supplement]

23. Holden, J.F. (2009) Extremophiles: hot environments, pp. 127-146. In M. Schaechter (ed.), Encyclopedia of Microbiology, Elsevier Publishing, Oxford, UK.

22. Feinberg, L.F., R. Srikanth, R.W. Vachet, and J.F. Holden (2008) Constraints on anaerobic growth in the hyperthermophilic archaea Pyrobaculum islandicum and Pyrobaculum aerophilum. Appl. Environ. Microbiol. 74:396-402. [PDF] [supplement]

21. Huber, J.A., and J.F. Holden (2008) Modeling the impact of diffuse vent microorganisms along mid-ocean ridges and flanks, pp. 215-231. In R.P. Lowell, M.R. Perfit, J. Seewald, and A. Metaxas (ed.), Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Ridges, Geophysical Monograph vol. 178, American Geophysical Union, Washington, D.C. [PDF]

20. Schrenk, M.O., J.F. Holden, and J.A. Baross (2008) Magma-to-microbe networks in the context of sulfide hosted microbial ecosystems, pp. 233-258. In R.P. Lowell, M.R. Perfit, J. Seewald, and A. Metaxas (ed.), Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Ridges, Geophysical Monograph vol. 178, American Geophysical Union, Washington, D.C. [PDF]

19. Yennaco, L.J., Y. Hu, and J.F. Holden (2007) Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum. Extremophiles 11:741-746. [PDF]

18. Hu, Y., and J.F. Holden (2006) Citric acid cycle in the hyperthermophilic archaeon Pyrobaculum islandicum grown autotrophically, heterotrophically, and mixotrophically with acetate. J. Bacteriol. 188:4350-4355. [PDF]

17. Feinberg, L.F., and J.F. Holden (2006) Characterization of dissimilatory Fe(III) versus NO3- reduction in the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Bacteriol. 188:525-531. [PDF] [erratum]

16. Holden, J.F., and R.M. Daniel (2004) Upper temperature limit of life based on hyperthermophile culture experiments and field observations, pp. 13-24. In W.S.D. Wilcock, E.F. DeLong, D.S. Kelley, J.A. Baross and S.C. Cary (ed.), The Subsurface Biosphere at Mid-Ocean Ridges, Geophysical Monograph vol. 144, American Geophysical Union, Washington, D.C. [[PDF]

15. Daniel, R.M., R. van Eckert, J.F. Holden, J. Truter, and D.A. Cowan (2004) The stability of biomolecules and the implications for life at high temperatures, pp. 25-39. In W.S.D. Wilcock, E.F. DeLong, D.S. Kelley, J.A. Baross and S.C. Cary (ed.), The Subsurface Biosphere at Mid-Ocean Ridges, Geophysical Monograph vol. 144, American Geophysical Union, Washington, D.C. [PDF]

14. Holland, M.E., J.A. Baross, and J.F. Holden (2004) Illuminating subseafloor ecosystems using microbial tracers, pp. 291-303. In W.S.D. Wilcock, E.F. DeLong, D.S. Kelley, J.A. Baross and S.C. Cary (ed.), The Subsurface Biosphere at Mid-Ocean Ridges, Geophysical Monograph vol. 144, American Geophysical Union, Washington, D.C.

13. Lim, H., J. Eng, J.R. Yates III, S.L. Tollaksen, C.S. Giometti, J.F. Holden, M.W.W. Adams, C.I. Reich, G.J. Olsen, and L.G. Hays (2003) Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to µ LC-ESI tandem mass spectrometry. J. Am. Soc Mass Spectrom. 14: 957-970. [PDF]

12. Holden, J.F., and M.W.W. Adams (2003) Microbe-metal interactions in marine hydrothermal environments. Curr. Opin. Chem. Biol. 7:160-165. [PDF]

11. Holden, J.F., and M.W.W. Adams (2002) Unique aspects of the hyperthermophile proteome. In C. Gerday and N. Glansdorff (ed.), Extremophiles, Encyclopedia of Life Support Systems (EOLSS), developed under the auspices of the UNESCO, Eolss Publishers, Oxford, UK.

10. Holden, J.F., F.L. Poole, II, S.L. Tollaksen, C.S. Giometti, H. Lim, J.R. Yates, III, and M.W.W. Adams (2001) Identification and prediction of membrane proteins in the hyperthermophilic archaeon Pyrococcus furiosus using proteomics and prediction programs. Comp. Funct. Genom. 2:275-288. [PDF]

9. Holden, J.F., K. Takai, M. Summit, S. Bolton, J. Zyskowski, and J.A. Baross (2001) Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean. FEMS Microbiol. Ecol. 36:51-60. [PDF]

8. Adams, M.W.W., J.F. Holden, A. Lal Menon, G.J. Schut, A.M. Grunden, C. Hou, A.M. Hutchins, F.E. Jenney, Jr., C. Kim, K. Ma, G. Pan, R. Roy, R. Sapra, S.V. Story, and M.F.J.M. Verhagen (2001) A key role for sulfur in peptide metabolism and in the regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183:716-724. [PDF]

7. Hutchins, A. M., J. F. Holden, and M. W. W. Adams (2001) Phosphoenolpyruvate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183:709-715. [PDF]

1990s

6. Holden, J.F., M. Summit, and J.A. Baross (1998) Thermophilic and hyperthermophilic microorganisms in 3-30°C hydrothermal fluids following a deep-sea volcanic eruption. FEMS Microbiol. Ecol. 25:33-41.[PDF]

5. Butterfield, D.A., I.R. Jonasson, G.J. Massoth, R.A. Feely, K.K. Roe, R.E. Embley, J.F. Holden, R.E. McDuff, M.D. Lilley, and J.R. Delaney (1997) Seafloor eruptions and evolution of hydrothermal fluid chemistry. Phil. Trans. R. Soc. Lond. A 355:369-386.[PDF]

4. Tunnicliffe, V., R.W. Embley, J.F. Holden, D.A. Butterfield, G.J. Massoth, and S.K. Juniper (1997) Biological colonization of new hydrothermal vents following an eruption on Juan de Fuca Ridge. Deep-Sea Res. Part I 44:1627-1644.[PDF]

3. Baross, J.A., and J.F. Holden (1996) Overview of hyperthermophiles and their heat-shock proteins. Adv. Prot. Chem. 48:1-34.

2. Holden, J.F., and J.A. Baross (1995) Enhanced thermotolerance by hydrostatic pressure in the deep-sea hyperthermophile Pyrococcus strain ES4. FEMS Microbiol. Ecol. 18:27-34.

1. Holden, J.F., and J.A. Baross (1993) Enhanced thermotolerance and temperature induced changes in protein composition in the hyperthermophilic archaeon ES4. J. Bacteriol. 175:2839-2843.[PDF]