TY - STD TI - National Energy Technology Laboratory. DOE’s unconventional gas research programs 1976–1995. An archive of important results. Washington, D.C.: US Department of Energy. 2007. ID - ref1 ER - TY - BOOK PY - 2013 DA - 2013// TI - Technically recoverable shale oil and shale gas resources: an assessment of 137 shale formations in 41 countries outside the United States PB - US Department of Energy CY - Washington, D.C. ID - ref2 ER - TY - CHAP AU - Solomon, S. AU - Qin, D. AU - Manning, M. AU - Alley, R. AU - Berntsen, T. AU - Bindoff, N. AU - Chen, Z. AU - Chidthaison, A. AU - Gregory, J. AU - Hegerl, G. ED - Solomon, S. ED - Qin, D. ED - Manning, M. ED - Chen, Z. ED - Marquis, M. ED - Averyt, K. ED - Tignor, M. ED - Miller, H. PY - 2007 DA - 2007// TI - Technical summary BT - Climate change 2007: the physical science basis contribution of working group I to the fourth assessment report for the intergovernmental panel on climate change PB - Cambridge University Press CY - Cambridge, New York ID - Solomon2007 ER - TY - JOUR AU - Conrado, R. J. AU - Gonzalez, R. PY - 2014 DA - 2014// TI - Envisioning the bioconversion of methane to liquid fuels JO - Science VL - 343 UR - https://doi.org/10.1126/science.1246929 DO - 10.1126/science.1246929 ID - Conrado2014 ER - TY - JOUR AU - Wood, D. A. AU - Nwaoha, C. AU - Towler, B. F. PY - 2012 DA - 2012// TI - Gas-to-liquids (GTL): a review of an industry offering several routes for monetizing natural gas JO - J Nat Gas Sci Eng VL - 9 UR - https://doi.org/10.1016/j.jngse.2012.07.001 DO - 10.1016/j.jngse.2012.07.001 ID - Wood2012 ER - TY - JOUR AU - Haynes, C. A. AU - Gonzalez, R. PY - 2014 DA - 2014// TI - Rethinking biological activation of methane and conversion to liquid fuels JO - Nat Chem Biol VL - 10 UR - https://doi.org/10.1038/nchembio.1509 DO - 10.1038/nchembio.1509 ID - Haynes2014 ER - TY - JOUR AU - Knittel, K. AU - Boetius, A. PY - 2009 DA - 2009// TI - Anaerobic oxidation of methane: progress with an unknown process JO - Annu Rev Microbiol VL - 63 UR - https://doi.org/10.1146/annurev.micro.61.080706.093130 DO - 10.1146/annurev.micro.61.080706.093130 ID - Knittel2009 ER - TY - JOUR AU - Dale, A. W. AU - Cappellen, P. AU - Aguilera, D. R. AU - Regnier, P. PY - 2008 DA - 2008// TI - Methane efflux from marine sediments in passive and active margins: estimations from bioenergetic reaction-transport simulations JO - Earth Planet Sci Lett VL - 265 UR - https://doi.org/10.1016/j.epsl.2007.09.026 DO - 10.1016/j.epsl.2007.09.026 ID - Dale2008 ER - TY - JOUR AU - Nauhaus, K. AU - Albrecht, M. AU - Elvert, M. AU - Boetius, A. AU - Widdel, F. PY - 2007 DA - 2007// TI - In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate JO - Environ Microbiol VL - 9 UR - https://doi.org/10.1111/j.1462-2920.2006.01127.x DO - 10.1111/j.1462-2920.2006.01127.x ID - Nauhaus2007 ER - TY - JOUR AU - Hallam, S. J. AU - Putnam, N. AU - Preston, C. M. AU - Detter, J. C. AU - Rokhsar, D. AU - Richardson, P. M. AU - DeLong, E. F. PY - 2004 DA - 2004// TI - Reverse methanogenesis: testing the hypothesis with environmental genomics JO - Science VL - 305 UR - https://doi.org/10.1126/science.1100025 DO - 10.1126/science.1100025 ID - Hallam2004 ER - TY - JOUR AU - Scheller, S. AU - Goenrich, M. AU - Boecher, R. AU - Thauer, R. K. AU - Jaun, B. PY - 2010 DA - 2010// TI - The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane JO - Nature VL - 465 UR - https://doi.org/10.1038/nature09015 DO - 10.1038/nature09015 ID - Scheller2010 ER - TY - JOUR AU - Moran, J. J. AU - House, C. H. AU - Freeman, K. H. AU - Ferry, J. G. PY - 2005 DA - 2005// TI - Trace methane oxidation studied in several Euryarchaeota under diverse conditions JO - Archaea VL - 1 UR - https://doi.org/10.1155/2005/650670 DO - 10.1155/2005/650670 ID - Moran2005 ER - TY - JOUR AU - Moran, J. J. AU - House, C. H. AU - Thomas, B. AU - Freeman, K. H. PY - 2007 DA - 2007// TI - Products of trace methane oxidation during nonmethyltrophic growth by Methanosarcina JO - J Geophys Res VL - 112 ID - Moran2007 ER - TY - JOUR AU - Meyerdierks, A. AU - Kube, M. AU - Kostadinov, I. AU - Teeling, H. AU - Glockner, F. O. AU - Reinhardt, R. AU - Amann, R. PY - 2010 DA - 2010// TI - Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group JO - Environ Microbiol VL - 12 UR - https://doi.org/10.1111/j.1462-2920.2009.02083.x DO - 10.1111/j.1462-2920.2009.02083.x ID - Meyerdierks2010 ER - TY - JOUR AU - Shima, S. AU - Krueger, M. AU - Weinert, T. AU - Demmer, U. AU - Kahnt, J. AU - Thauer, R. K. AU - Ermler, U. PY - 2012 DA - 2012// TI - Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically JO - Nature VL - 481 UR - https://doi.org/10.1038/nature10663 DO - 10.1038/nature10663 ID - Shima2012 ER - TY - JOUR AU - Galagan, J. E. AU - Nusbaum, C. AU - Roy, A. AU - Endrizzi, M. G. AU - Macdonald, P. AU - FitzHugh, W. AU - Calvo, S. AU - Engels, R. AU - Smirnov, S. AU - Atnoor, D. PY - 2002 DA - 2002// TI - The genome of M. acetivorans reveals extensive metabolic and physiological diversity JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.223902 DO - 10.1101/gr.223902 ID - Galagan2002 ER - TY - JOUR AU - Kohler, P. R. AU - Metcalf, W. W. PY - 2012 DA - 2012// TI - Genetic manipulation of Methanosarcina spp JO - Front Microbiol VL - 3 UR - https://doi.org/10.3389/fmicb.2012.00259 DO - 10.3389/fmicb.2012.00259 ID - Kohler2012 ER - TY - JOUR AU - Macauley, S. R. AU - Zimmerman, S. A. AU - Apolinario, E. E. AU - Evilia, C. AU - Hou, Y. -. M. AU - Ferry, J. G. AU - Sowers, K. R. PY - 2009 DA - 2009// TI - The archetype γ-class carbonic anhydrase (Cam) contains iron when synthesized in vivo JO - Biochemistry VL - 48 UR - https://doi.org/10.1021/bi802246s DO - 10.1021/bi802246s ID - Macauley2009 ER - TY - JOUR AU - Beal, E. J. AU - House, C. H. AU - Orphan, V. J. PY - 2009 DA - 2009// TI - Manganese- and iron-dependent marine methane oxidation JO - Science VL - 325 UR - https://doi.org/10.1126/science.1169984 DO - 10.1126/science.1169984 ID - Beal2009 ER - TY - JOUR AU - Moran, J. J. AU - Beal, E. J. AU - Vrentas, J. M. AU - Orphan, V. J. AU - Freeman, K. H. AU - House, C. H. PY - 2008 DA - 2008// TI - Methyl sulfides as intermediates in the anaerobic oxidation of methane JO - Environ Microbiol VL - 10 ID - Moran2008 ER - TY - JOUR AU - Vepachedu, V. R. AU - Ferry, J. G. PY - 2012 DA - 2012// TI - Role of the fused corrinoid/methyl transfer protein CmtA during CO-dependent growth of Methanosarcina acetivorans JO - J Bacteriol VL - 194 UR - https://doi.org/10.1128/JB.00593-12 DO - 10.1128/JB.00593-12 ID - Vepachedu2012 ER - TY - JOUR AU - Lienard, T. AU - Becher, B. AU - Marschall, M. AU - Bowien, S. AU - Gottschalk, G. PY - 1996 DA - 1996// TI - Sodium ion translocation by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase from Methanosarcina mazei Gö1 reconstituted in ether lipid liposomes JO - Eur J Biochem VL - 239 UR - https://doi.org/10.1111/j.1432-1033.1996.0857u.x DO - 10.1111/j.1432-1033.1996.0857u.x ID - Lienard1996 ER - TY - JOUR AU - Raybuck, S. A. AU - Ramer, S. E. AU - Abbanat, D. R. AU - Peters, J. W. AU - Ormejohnson, W. H. AU - Ferry, J. G. AU - Walsh, C. T. PY - 1991 DA - 1991// TI - Demonstration of carbon-carbon bond cleavage of acetyl coenzyme A by using isotopic exchange catalyzed by the CO dehydrogenase complex from acetate-grown Methanosarcina thermophila JO - J Bacteriol VL - 173 ID - Raybuck1991 ER - TY - JOUR AU - Abbanat, D. R. AU - Ferry, J. G. PY - 1990 DA - 1990// TI - Synthesis of acetyl coenzyme A by carbon monoxide dehydrogenase complex from acetate-grown Methanosarcina thermophila JO - J Bacteriol VL - 172 ID - Abbanat1990 ER - TY - JOUR AU - Terlesky, K. C. AU - Ferry, J. G. PY - 1988 DA - 1988// TI - Ferredoxin requirement for electron transport from the carbon monoxide dehydrogenase complex to a membrane-bound hydrogenase in acetate-grown Methanosarcina thermophila JO - J Biol Chem VL - 263 ID - Terlesky1988 ER - TY - JOUR AU - Matschiavelli, N. AU - Rother, M. PY - 2015 DA - 2015// TI - Role of a putative tungsten-dependent formylmethanofuran dehydrogenase in Methanosarcina acetivorans JO - Arch Microbiol VL - 197 UR - https://doi.org/10.1007/s00203-014-1070-3 DO - 10.1007/s00203-014-1070-3 ID - Matschiavelli2015 ER - TY - JOUR AU - Wang, M. AU - Tomb, J. F. AU - Ferry, J. G. PY - 2011 DA - 2011// TI - Electron transport in acetate-grown Methanosarcina acetivorans JO - BMC Microbiol VL - 11 UR - https://doi.org/10.1186/1471-2180-11-165 DO - 10.1186/1471-2180-11-165 ID - Wang2011 ER - TY - JOUR AU - Metcalf, W. W. AU - Zhang, J. -. K. AU - Shi, X. AU - Wolfe, R. S. PY - 1996 DA - 1996// TI - Molecular, genetic, and biochemical characterization of the serC gene of Methanosarcina barkeri Fusaro JO - J Bacteriol VL - 178 ID - Metcalf1996 ER - TY - JOUR AU - Gibson, D. G. AU - Young, L. AU - Chuang, R. Y. AU - Venter, J. C. AU - Hutchison, C. A. AU - Smith, H. O. PY - 2009 DA - 2009// TI - Enzymatic assembly of DNA molecules up to several hundred kilobases JO - Nat Methods VL - 6 UR - https://doi.org/10.1038/nmeth.1318 DO - 10.1038/nmeth.1318 ID - Gibson2009 ER - TY - JOUR AU - Weil, C. F. AU - Cram, D. S. AU - Sherf, B. A. AU - Reeve, J. N. PY - 1988 DA - 1988// TI - Structure and comparative analysis of the genes encoding component C of methyl coenzyme M reductase in the extremely thermophilic archaebacterium Methanothermus fervidus JO - J Bacteriol VL - 170 ID - Weil1988 ER - TY - JOUR AU - Metcalf, W. W. AU - Zhang, J. K. AU - Apolinario, E. AU - Sowers, K. R. AU - Wolfe, R. S. PY - 1997 DA - 1997// TI - A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors JO - Proc Natl Acad Sci USA VL - 94 UR - https://doi.org/10.1073/pnas.94.6.2626 DO - 10.1073/pnas.94.6.2626 ID - Metcalf1997 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows-Wheeler transform JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - DePristo, M. A. AU - Banks, E. AU - Poplin, R. AU - Garimella, K. V. AU - Maguire, J. R. AU - Hartl, C. AU - Philippakis, A. A. AU - Angel, G. AU - Rivas, M. A. AU - Hanna, M. PY - 2011 DA - 2011// TI - A framework for variation discovery and genotyping using next-generation DNA sequencing data JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.806 DO - 10.1038/ng.806 ID - DePristo2011 ER - TY - JOUR AU - Danecek, P. AU - Auton, A. AU - Abecasis, G. AU - Albers, C. A. AU - Banks, E. AU - DePristo, M. A. AU - Handsaker, R. E. AU - Lunter, G. AU - Marth, G. T. AU - Sherry, S. T. PY - 2011 DA - 2011// TI - The variant call format and VCFtools JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr330 DO - 10.1093/bioinformatics/btr330 ID - Danecek2011 ER - TY - JOUR AU - Angel, R. AU - Claus, P. AU - Conrad, R. PY - 2012 DA - 2012// TI - Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions JO - ISME J VL - 6 UR - https://doi.org/10.1038/ismej.2011.141 DO - 10.1038/ismej.2011.141 ID - Angel2012 ER - TY - STD TI - Lane DJ. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. Chichester: Wiley. 1991. pp. 115–147. ID - ref36 ER - TY - JOUR AU - Ohtsu, I. AU - Wiriyathanawudhiwong, N. AU - Morigasaki, S. AU - Nakatani, T. AU - Kadokura, H. AU - Takagi, H. PY - 2010 DA - 2010// TI - The l-cysteine/l-cystine shuttle system provides reducing equivalents to the periplasm in Escherichia coli JO - J Biol Chem VL - 285 UR - https://doi.org/10.1074/jbc.M109.081356 DO - 10.1074/jbc.M109.081356 ID - Ohtsu2010 ER - TY - JOUR AU - Ruebush, S. S. AU - Brantley, S. L. AU - Tien, M. PY - 2006 DA - 2006// TI - Reduction of soluble and insoluble iron forms by membrane fractions of Shewanella oneidensis grown under aerobic and anaerobic conditions JO - Appl Environ Microbiol VL - 72 UR - https://doi.org/10.1128/AEM.72.4.2925-2935.2006 DO - 10.1128/AEM.72.4.2925-2935.2006 ID - Ruebush2006 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. AU - Batut, P. AU - Chaisson, M. AU - Gingeras, T. R. PY - 2013 DA - 2013// TI - STAR: ultrafast universal RNA-seq aligner JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Trapnell, C. AU - Roberts, A. AU - Goff, L. AU - Pertea, G. AU - Kim, D. AU - Kelley, D. R. AU - Pimentel, H. AU - Salzberg, S. L. AU - Rinn, J. L. AU - Pachter, L. PY - 2012 DA - 2012// TI - Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2012.016 DO - 10.1038/nprot.2012.016 ID - Trapnell2012 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. A. AU - Pertea, G. AU - Mortazavi, A. AU - Kwan, G. AU - Baren, M. J. AU - Salzberg, S. L. AU - Wold, B. J. AU - Pachter, L. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER -