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  1. Zaikova, E., D. A. Walsh, C. P. Stilwell, W.W. Mohn, P. D. Tortell, and S. J. Hallam, 2010. Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet British Columbia, Environmental Microbiology, 12(1):172-91
  2. Walsh, D. A., E. Zaikova, C. G. Howes, Y. C. Song., J.J. Wright, S. Tringe, P. D. Tortell, and S. J. Hallam, 2009. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones, Science, 326(5952):578-82
  3. Schmidtova, J., S. J. Hallam, S.A. Baldwin, 2009. Bacterial community diversity in the transition and anoxic zones of the stratified Nitinat Lake, Environmental Microbiology, 11(12):3233-51
  4. Hartmann, M., S. Lee, S. J. Hallam and W.W. Mohn, 2009. Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands, Environmental Microbiology 11(12):3045-62
  5. Lobban, C. S., S. J. Hallam, P. Mukherjee, and J. W. Petrich. 2007. Photophysics and multifunctionality of hypericin-like pigments in heterotrich ciliates: a phylogenetic perspective. Photochem Photobiol 83:1074-94.
  6. Hallam, S. J., K. T. Konstantinidis, N. Putnam, C. Schleper, Y. Watanabe, J. Sugahara, C. Preston, J. de la Torre, P. M. Richardson, and E. F. DeLong. 2006. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A 103:18296-301.
  7. Yoshinari, S., T. Itoh, S. J. Hallam, E. F. DeLong, S. Yokobori, A. Yamagishi, T. Oshima, K. Kita, and Y. Watanabe. 2006. Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease. Biochem Biophys Res Commun 346:1024-32.
  8. Hallam, S. J., T. J. Mincer, C. Schleper, C. M. Preston, K. Roberts, P. M. Richardson, and E. F. DeLong. 2006. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4:e95.
  9. DeLong, E. F., C. M. Preston, T. Mincer, V. Rich, S. J. Hallam, N. U. Frigaard, A. Martinez, M. B. Sullivan, R. Edwards, B. R. Brito, S. W. Chisholm, and D. M. Karl. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503.
  10. Cubonova, L., K. Sandman, S. J. Hallam, E. F. Delong, and J. N. Reeve. 2005. Histones in crenarchaea. J Bacteriol 187:5482-5.
  11. Salerno, J. L., S. A. Macko, S. J. Hallam, M. Bright, Y. J. Won, Z. McKiness, and C. L. Van Dover. 2005. Characterization of symbiont populations in life-history stages of mussels from chemosynthetic environments. Biol Bull 208:145-55.
  12. Hallam, S. J., N. Putnam, C. M. Preston, J. C. Detter, D. Rokhsar, P. M. Richardson, and E. F. DeLong. 2004. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:1457-62.
  13. Hallam, S. J., P. R. Girguis, C. M. Preston, P. M. Richardson, and E. F. DeLong. 2003. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol 69:5483-91.
  14. Girguis, P. R., V. J. Orphan, S. J. Hallam, and E. F. DeLong. 2003. Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor. Appl Environ Microbiol 69:5472-82.
  15. Goffredi, S. K., L. A. Hurtado, S. J. Hallam, and R. C. Vrijenhoek. 2003. Evolutionary relationships of deep-sea vent and cold seep clams (Mollusca : Vesicomyidae) of the "pacifica/lepta" species complex, p. 311-320. Mar Biol, vol. 142.
  16. Won, Y., S. J. Hallam, G. D. O'Mullan, and R. C. Vrijenhoek. 2003. Cytonuclear disequilibrium in a hybrid zone involving deep-sea hydrothermal vent mussels of the genus Bathymodiolus. Mol Ecol 12:3185-90.
  17. Won, Y. J., S. J. Hallam, G. D. O'Mullan, I. L. Pan, K. R. Buck, and R. C. Vrijenhoek. 2003. Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus Bathymodiolus. Appl Environ Microbiol 69:6785-92.
  18. Hallam, S. J., A. Goncharov, J. McEwen, R. Baran, and Y. Jin. 2002. SYD-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains, specifies axon identity in C. elegans. Nat Neurosci 5:1137-46.
  19. Hallam, S. J., E. Singer, D. Waring, and Y. Jin. 2000. The C. elegans NeuroD homolog cnd-1 functions in multiple aspects of motor neuron fate specification. Development 127:4239-52.
  20. Hallam, S. J., and Y. Jin. 1998. lin-14 regulates the timing of synaptic remodelling in Caenorhabditis elegans. Nature 395:78-82.
  21. Zhou, D. C., S. J. Hallam, S. J. Lee, R. S. Klein, P. H. Wiernik, M. S. Tallman, and R. E. Gallagher. 1998. Constitutive expression of cellular retinoic acid binding protein II and lack of correlation with sensitivity to all-trans retinoic acid in acute promyelocytic leukemia cells. Cancer Res 58:5770-6.
  22. Wadler, S., X. Mao, R. Bajaj, S. J. Hallam, and E. L. Schwartz. 1993. N-(phosphonacetyl)-L-aspartate synergistically enhances the cytotoxicity of 5-fluorouracil/interferon-alpha-2a against human colon cancer cell lines. Mol Pharmacol 44:1070-6.
  23. Schwartz, E. L., S. J. Hallam, R. E. Gallagher, and P. H. Wiernik. 1995. Inhibition of all-trans-retinoic acid metabolism by fluconazole in vitro and in patients with acute promyelocytic leukemia. Biochem Pharmacol 50:923-8.
  24. Sagayadan, G. E., P. H. Wiernik, N. Sun, G. Ahearn, D. Thompson, S. J. Hallam, X. P. Hu, J. P. Dutcher, and R. E. Gallagher. 1994. Effect of retinoic acid and interferon alpha on granulocyte-macrophage colony forming cells in chronic myeloid leukemia: increased inhibition by all-trans- and 13-cis-retinoic acids in advanced stage disease. Leuk Res 18:741-8.
  25. Wadler, S., E. L. Schwartz, H. Haynes, R. Rameau, A. Quish, J. Mandeli, R. Gallagher, S. J. Hallam, A. Fields, G. Goldberg, F. McGill, S. Jennings, R. C. Wallach, and C. D. Runowicz. 1997. All-trans retinoic acid and interferon-alpha-2a in patients with metastatic or recurrent carcinoma of the uterine cervix: clinical and pharmacokinetic studies. New York Gynecologic Oncology Group. Cancer 79:1574-80.

Book Chapters
  1. Taupp, M. and S. J. Hallam. 2009. The “meta-methanoxgenome” Part 23 in the Handbook of Hydrocarbon Microbiology
  2. Taupp, M., L. Constan L., S. J. Hallam. 2009. The biochemistry of anaerobic methane oxidation Part 17 in the Handbook of Hydrocarbon Microbiology

Technical Reports
  1. Ussler W. III, C.K. Paull , S. J. Hallam, T. Lorenson, Y. Chen, and R. Matsumoto. 2005. Microbially-mediated diagenesis of methane carbon across the sulfate-methane interface in a methane-rich core from the Gulf of Mexico. In: Proceedings of the Fifth International Conference on Gas Hydrates, V.3, Exploration, Resources and Environment, Trondheim, Norway, pp. 1056-1062.
  2. Hallam S. J., E.F. DeLong, W. Ussler III and C.K. Paull. 2005. Methanogenic and methanotrophic archaeal diversity in gulf of mexico sediments, USGS Digital Data publication for the July 2002 Marion Dufresne Gulf of Mexico Cruise

On-line Video Protocols
  1. Weidner M, Taupp M, and S. J. Hallam. Expression of recombinant proteins in the methylotrophic yeast Pichia pastoris. J Vis Exp 2010 Feb 25;(36), pii: 1862.
  2. Lee, S and S. J. Hallam. Extraction of high molecular weight genomic DNA from soils and sediments. J Vis Exp. 2009 Nov 10;(33). pii: 1569.
  3. Taupp M, Lee S, Hawley A, Yang J, S. J. Hallam. Large insert environmental genomic library production. J Vis Exp. 2009 Sep 23;(31). pii: 1387.
  4. Wright J.J., Lee S, Zaikova E, Walsh D.A. and S. J. Hallam. DNA extraction from 0.22 µm Sterivex filters and cesium chloride density gradient centrifugation. J Vis Exp. 2009 Sep 18;(31). pii: 1352.
  5. Walsh D.A., Zaikova E, and S. J. Hallam. Small volume filtration of coastal seawater samples. J Vis Exp. 2009 Jun 19;(28). pii: 1163.
  6. Walsh D.A., Zaikova E, and S. J. Hallam. Large volume filtration of coastal seawater samples. J Vis Exp. 2009 Jun 18;(28). pii: 1161.
  7. Zaikova E, Hawley A, Walsh D. A., and S. J. Hallam. Seawater sampling and collection. J Vis Exp. 2009 Jun 17;(28). pii: 1159.
  1. S. J. Hallam and Fanny Kiefer, Oxygen Minimum Zones. Studio 4 - Shaw Television 2010 Apr 6.
  2. BBC World Service, "Science In Action 12/03/2010" (, starting at 13 minutes into the program)
  3. CBC "Quirks and Quarks 04/24/2010" (


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