Publications

2023

Barlow, E.V., House, C.H., Liu. M, Wetherington, M.T., Van Kranendonk, M.J., (2023). Distinctive microfossil supports early Paleoproterozoic rise in complex cellular organization. Geobiology.
Brodsky, H., Calderon, R., Hamilton, D. S., Li, L., Miles, A. D., Pavlick, R. P., Gold, K. M., Crandall, S. G., & Mahowald, N. M. (2023). Assessing long-distance atmospheric transport of soilborne plant pathogens. Environmental Research Letters. https://doi.org/10.1088/1748-9326/acf50c
Choi, S.; Knoerdel, A. R.; Sing, C. E.; Keating, C. D. Effect of polypeptide complex coacervate microenvironment on protonation of a guest molecule. Journal of Physical Chemistry B 2023, 127, 5978-5991. https://doi.org/10.1021/acs.jpcb.3c02098
Covington, M. D., Martin, J. B., Toran, L. E., Macalady, J. L., Sekhon, N., Sullivan, P. L., García, A., Heffernan, J. B., & Graham, W. D. (2023). Carbonates in the Critical Zone. Earth’s Future, 11(1), Article e2022EF002765. https://doi.org/10.1029/2022EF002765
Jones, D. S., Schaperdoth, I., Northup, D. E., Gómez-Cruz, R., & Macalady, J. L. (2023). Convergent Community Assembly among Globally Separated Acidic Cave Biofilms. Applied and environmental microbiology, 89(1). https://doi.org/10.1128/aem.01575-22
Meyer, M. O.; Yamagami, R.; Choi, S.; Keating, C. D.; Bevilacqua, P. C. RNA folding studies inside peptide-rich droplets reveal potential roles of modified nucleosides at the origin of life. Science Advances 2023. http://www.science.org/doi/10.1126/sciadv.adh5152
Porras, M.F., Navas, C.A., Agudelo, G., Santiago-Martínez, M.G., Loeschcke, V., Sørensen, J.G., Crandall, S.G., Biddinger, D., Rajotte, E.G. 2023. Extreme heat alters the performance of hosts and pathogen. Frontiers in Ecology and Evolution. Sec. Coevolution. Manuscript ID: 1186452.

2022

Ayala-Muñoz, D., Macalady, J. L., Sánchez-España, J., Falagán, C., Couradeau, E., & Burgos, W. D. (2022). Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake. ISME Journal, 16(12), 2666-2679. https://doi.org/10.1038/s41396-022-01320-w
Ayala-Muñoz, D., Burgos, W. D., Sánchez-España, J., Falagán, C., Couradeau, E., & Macalady, J. L. (2022). Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake. Frontiers in Bioengineering and Biotechnology, 10, Article 867321. https://doi.org/10.3389/fbioe.2022.867321
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides, Global Phage Small Open Reading Frame (GP-SmORF) Consortium (2022). Thousands of small, novel genes predicted in global phage genomes. Cell Reports, 39(12), Article 110984. https://doi.org/10.1016/j.celrep.2022.110984
Calderon, R., Eller, J.A., Brodsky, H.K., Miles, A.D., Crandall S.G., Mahowald N., Pavlick R., Gold K. 2022. An interactive, online web map resource of global Fusarium oxysporum ff. spp. diversity and distribution. Plant Disease. https://doi.org/10.1094/PDIS-04-22-0789-A.
Choi, S.; Meyer, M. O.; Bevilacqua, P. C.; Keating, C. D. Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles. Nature Chemistry 2022, 14, 1110-1117. https://doi.org/10.1038/s41557-022-00980-7
House, C. H., Wong, G. M., Webster, C. R., Flesch, G. J., Franz, H. B., Stern, J. C, Pavlov, A., Atreya, S. K., Eigenbrode, J. L., Gilbert, A., Hofmann, A. E., Millan, M., Steele, A., Malespin, C.A., Mahaffy, P. R (2022), Depleted carbon isotope compositions observed at Gale crater, Mars. Proceedings of the National Academy of Sciences.
Wong, G. M., H. B. Franz, J. V. Clark, A. C. McAdam, J. M. T. Lewis, M. Millan, D. W. Ming, F. Gomez, B. Clark, J. L. Eigenbrode, R. Navarro-González, and C. H. House (2022). Oxidized and reduced sulfur observed by the Sample Analysis at Mars (SAM) instrument suite during the Glen Torridon campaign at Gale crater, Mars. Journal of Geophysical Research: Planets.

2021

Ayala-Muñoz, D., Simister, R. L., Crowe, S. A., Macalady, J. L., & Burgos, W. D. (2021). Functional redundancy imparts process stability to acidic Fe(II)-oxidizing microbial reactors. Environmental microbiology, 23(7), 3682-3694. https://doi.org/10.1111/1462-2920.15259
Cakmak, F. P., Marianelli, A. M., Keating, C. D. Lipid membrane formation templated by coacervate droplets. Langmuir 2021, 37, 10366-10375. https://doi.org/10.1021/acs.langmuir.1c01562
Cron, B., Macalady, J. L., & Cosmidis, J. (2021). Organic Stabilization of Extracellular Elemental Sulfur in a Sulfurovum-Rich Biofilm: A New Role for Extracellular Polymeric Substances? Frontiers in Microbiology, 12, Article 720101. https://doi.org/10.3389/fmicb.2021.720101

2020

Amend, J. P., Aronson, H. S., Macalady, J. L. & LaRowe, D. E. 2020. Another chemolithotrophic metabolism missing in nature: sulfur comproportionation. Environmental microbiology 22(6): 1971-1976. doi:10.1111/1462-2920.14982.
Ayala-Munoz, D., Simister, R., Crowe, S., Macalady, J., & Burgos, W. D. 2020. Functional redundancy imparts process stability to acidic Fe(II)-oxidizing bioreactors. Environmental Microbiology, 00, 13.
Ayala-Muñoz, D., W. D. Burgos, J. Sánchez-España, E. Couradeau, C, Falagán, and J. L. Macalady. 2020. Metagenomic and metatranscriptomic study of microbial metal resistance in an acidic pit lake, Microorganisms 8, 1350.
Bralower, T. J., Cosmidis, J., Heaney, P. J., Kump, L. R., Morgan, J. V., Harper, D. T., & Vajda, V. (2020). Origin of a global carbonate layer deposited in the aftermath of the Cretaceous-Paleogene boundary impact. Earth and Planetary Science Letters, 548, 116476.
Bralower, Timothy J., Julie Cosmidis, Peter J. Heaney, Lee R. Kump, Joanna V. Morgan, Dustin T. Harper, Shelby L. Lyons, Katherine H. Freeman, Kliti Grice, Jens E. Wendler, James C. Zachos, Natalia Artemieva, Si Athena Chen, Sean P.S. Gulick, Christopher H. House, Heather L. Jones, Christopher M. Lowery, Christine Nims, Bettina Schaefer, Ellen Thomas, Vivi Vajda (2020) Origin of a global carbonate layer deposited in the aftermath of the Cretaceous-Paleogene boundary impact, Earth and Planetary Science Letters 548, 116476, ISSN 0012-821X, https://doi.org/10.1016/j.epsl.2020.116476
Cakmak, P. F., Choi, S., Meyer, M. O., Bevilacqua, P. C., Keating, C. D., 2020, Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments. Nature Communications 2020, 11, 5949. https://doi.org/10.1038/s41467-020-19775-w
Castillo-Rogez, J. C., Neveu, M., Scully, J. E., House, C. H., Quick, L. C., Bouquet, A., & Young, E. (2020). Ceres: astrobiological target and possible ocean world. Astrobiology, 20(2), 269-291.
Crandall, S.G., Saarman, N., and G. Gilbert. 2020. Fungal spore diversity, community structure, and traits across a vegetation mosaic. Fungal Ecology. 45: 1-10. https://doi.org/10.1016/j.funeco.2020.100920.
De Sanctis, M. C., Mitri, G., Castillo-Rogez, J., House, C. H., Marchi, S., Raymond, C. A., & Sekine, Y. (2020). Relict Ocean Worlds: Ceres. Space Science Reviews, 216, 1-33.
Edgar, L. A., Fedo, C. M., Gupta, S., Banham, S. G., Fraeman, A. A., Grotzinger, J. P., & Van Beek, J. (2020). A lacustrine paleoenvironment recorded at Vera RubinRidge, Gale crater: Overview of the sedimentology and stratigraphy observed by the Mars ScienceLaboratory Curiosity Rover. Journal of Geophysical Research: Planets, 125(3), e2019JE006307.
Edgett, K. S., Banham, S. G., Bennett, K. A., Edgar, L. A., Edwards, C. S., Fair n, A. G., & Yingst, R. A. (2020). Extraformational sediment recycling on Mars. Geosphere, 16(6), 1508-1537.
Farag, I. F., Biddle, J. F., Zhao, R., Martino, A. J., House, C. H., & Le n-Zayas, R. I. (2020). Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments. The ISME journal, 14(6), 1345-1358.
Fares, H. M., Marras, A. E., Ting, J. M., Tirrell, M. V., Keating, C. D. 2020, Impact of wet-dry cycling on the phase behavior and compartmentalization properties of complex coacervates, Nature Communications, 11, 5423. https://doi.org/10.1038/s41467-020-19184-z
Ferry, J. G. (2020) Methanosarcina acetivorans: A model for mechanistic understanding of aceticlastic and reverse methanogenesis. Frontiers in Microbiol. 11:1806, 10.3389/fmicb.2020.01806.
Fox, Allison C. Jason D. Boettger, James D. Kubicki, and Katherine H. Freeman (2020) Density Functional Theory Predictions of Noncovalent Hydrogen Isotope Effects during Octane Sorption to a Kaolinite Surface, ACS Earth and Space Chemistry 4 (10), 1756-1764, https://doi.org/10.1021/acsearthspacechem.0c00148
Fraeman, A. A., Edgar, L. A., Rampe, E. B., Thompson, L. M., Frydenvang, J., Fedo, C. M., & Wong, G. M. (2020). Evidence for a diagenetic origin of Vera Rubin ridge, Gale crater, Mars: Summary and synthesis of Curiosity’s exploration campaign. Journal of Geophysical Research: Planets, 125(12), e2020JE006527.
Franz, H. B., Mahaffy, P. R., Webster, C. R., Flesch, G. J., Raaen, E., Freissinet, C., & Summons, R. E. (2020). Indigenous and exogenous organics and surface–atmosphere cycling inferred from carbon and oxygen isotopes at Gale crater. Nature Astronomy, 4(5), 526-532.
Frydenvang, J., Mangold, N., Wiens, R. C., Fraeman, A. A., Edgar, L. A., Fedo, C. M., & House, C. H. (2020). The chemostratigraphy of the Murray formation and role of diagenesis at Vera Rubin ridge in Gale crater, Mars, as observed by the ChemCam instrument. Journal of Geophysical Research: Planets, 125(9), e2019JE006320.
Grettenberger, C. L., McCauley Rench, R., Gruen, D. S., Mills, D. B., Carney, C., Brainard, J. Hamasaki, H., Ramirez, R. Watanabe, Y., Amaral-Zettler, L.A., Ohmoto, H., and Macalady, J. L. 2020. Microbial population structure in a stratified, acidic pit lake in the Iberian Pyrite Belt. Geomicrobiology Journal 37(7): 623-634.
Ingalls, M., Blättler, C., Higgins, J., Magyar, J.S., Eiler, J., and Fischer, W.W. (2020) P/Ca in carbonates as a proxy for paleo-Ca:ALK and phosphate levels, Geophysical Research Letters, ?47(21): e2020GL088804. https://doi.org/10.1029/2020GL088804.
Ingalls, M., Frantz, C.M., Snell, K.E., and Trower, E.J., (2020) Carbonate facies-specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT, Geobiology, 18(5): 566-593. https://doi.org/10.1111/gbi.12386
Klatt, Judith M., Gonzalo V. Gomez-Saez, Steffi Meyer, Petra Pop Ristova, Pelin Yilmaz, Michael Granitsiotis, Jennifer L. Macalady, Gaute Lavik, Lubos Polerecky, Solveig I. Bühring. 2020. Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat, ISME Journal 14: 3024-3037. doi.org/10.1038/s41396-020-0734-z.
l’Haridon, J., Mangold, N., Fraeman, A. A., Johnson, J. R., Cousin, A., Rapin, W., & Wiens, R. C. (2020). Iron mobility during diagenesis at Vera Rubin ridge, Gale crater, Mars. Journal of Geophysical Research: Planets, 125(11), e2019JE006299.
McAdam, A. C., Sutter, B., Archer, P. D., Franz, H. B., Wong, G. M., Lewis, J. M., & Johnson, S. S. (2020). Constraints on the Mineralogy and Geochemistry of Vera Rubin Ridge, Gale Crater, Mars, From Mars Science Laboratory Sample Analysis at Mars Evolved Gas Analyses. Journal of Geophysical Research: Planets, 125(11), e2019JE006309.
Neveu, M., House, C. H., & Wieman, S. T. (2020). Phoebe’s carbon isotope composition as evidence for self-shielding in the solar nebula. Icarus, 345, 113714.
Schaefer, Bettina, Kliti Grice, Marco J.L. Coolen, Roger E. Summons, Xingqian Cui, Thorsten Bauersachs, Lorenz Schwark, Michael E. Böttcher, Timothy J. Bralower, Shelby L. Lyons, Katherine H. Freeman, Charles S. Cockell, Sean P.S. Gulick, Joanna V. Morgan, Michael T. Whalen, Christopher M. Lowery, Vivi Vajda (2020) Microbial life in the nascent Chicxulub crater. Geology 48 (4): 328–332. https://doi.org/10.1130/G46799.1
Thomazo, C., E. Couradeau, A. Giraldo-Silva, J. Marin-Carbonne, A. Brayard, M. Homann, P. Sansjofre, S. V. Lalonde, F. Garcia-Pichel (2020) Biological Soil Crusts as Modern Analogs for the Archean Continental Biosphere: Insights from Carbon and Nitrogen Isotopes, Astrobiology 815-819.
Wilpiszeski, R. L., Sherwood Lollar, B., Warr, O., & House, C. H. (2020). In Situ Growth of Halophilic Bacteria in Saline Fracture Fluids from 2.4 km below Surface in the Deep Canadian Shield. Life, 10(12), 307.
Wong, G. M., Lewis, J. M., Knudson, C. A., Millan, M., McAdam, A. C., Eigenbrode, J. L., … & House, C. H. (2020). Detection of reduced sulfur on Vera Rubin ridge by quadratic discriminant analysis of volatiles observed during evolved gas analysis. Journal of Geophysical Research: Planets, 125(8), e2019JE006304.

2019

Bird, LR, Dawson, KS, Chadwick, GL, Fulton, JM, Orphan, VJ, Freeman, KH. (2019) Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane-oxidizing archaea. Geobiology 17: 611– 627. https://doi.org/10.1111/gbi.12354
Cakmak, F. P. ; Grigas, A. T.; Keating, C. D. Langmuir 2019, Lipid vesicle-coated complex coacervates. 35, 7830-7840. https://doi.org/10.1021/acs.langmuir.9b00213
Couradeau, E. , J. Sasse , D. Goudeau, N. Nath , B.P. Bowen, R. Chakraborty, T.C. Hazen, R.R.Malmstrom, T.R. Northen (2019) Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature Communications 10, 2770.
Cron, B., Henri, P., Chan, C. S., Macalady, J. L. & Cosmidis, J. 2019. Elemental Sulfur Formation by Sulfuricurvum kujiense Is Mediated by Extracellular Organic Compounds. Frontiers in microbiology 10: 909
Fox, A. C., Eigenbrode, J. L., & Freeman, K. H. (2019). Radiolysis of macromolecular organic material in Mars-relevant mineral matrices. Journal of Geophysical Research: Planets, 124, 3257– 3266. https://doi.org/10.1029/2019JE006072
Guan, Y., Ngugi, D. K., Vinu, M, Blom, J., Alam, I., Guillot, S., Ferry, J. G. and Stingl, U. (2019) Comparative genomics of the genus Methanohalophilus, including a newly isolated strain from kebrit deep in the Red Sea, Frontiers in Microbiology. 10:839.doi: 10.3389/fmicb.2019.00839
Martino, A., Rhodes, M. E., León-Zayas, R., Valente, I. E., Biddle, J. F., & House, C. H., 2019. Microbial Diversity in Sub-Seafloor Sediments from the Costa Rica Margin. Geosciences, 9, 218.
Nims, C., Cron, B., Wetherington, M., Macalady, J. & Cosmidis, J. 2019. Low frequency Raman Spectroscopy for micron-scale and in vivo characterization of elemental sulfur in microbial samples. Scientific Reports 9: 7971.
Poudyal, R. R.; Guth-Metzler, R. M.; Veenis, A. J.; Frankel, E. A.; Keating, C. D.; Bevilacqua, P. C., 2019, Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates, Nature Communications, 10, 490. https://doi:10.1038/s41467-019-08353-4
Poudyal, R. R.; Keating, C. D. Bevilacqua, P. C. ACS Chemical Biology 2019, Polyanion-assisted ribozyme catalysis inside complex coacervates. 14, 1243-1248. https://doi.org/10.1021/acschembio.9b00205
Prakash, D., Chauhan, S. S., and Ferry, J. G. (2019) Life on the thermodynamic edge: Respiratory growth of an acetotrophic methanogen. Science Advances. 5, 1-6.
Prakash, D., Iyer, P. R., Suharti, S., Walters, K. A., Santiago-Martinez, M. G., Golbeck, J. H., Murakami, K. S., and Ferry, J. G. (2019) Structure and function of an unusual flavodoxin from the domain Archaea. Proceedings of the National Academy of Science U. S. A. 116, 25917-25922.
Rodriguez, L. E., House, C. H., Smith, K. E., Roberts, M. R., & Callahan, M. P., 2019. Nitrogen heterocycles form peptide nucleic acid precursors in complex prebiotic mixtures. Scientific Reports, 9, 9281.
Rodriguez, L. E., House, C. H., Smith, K. E., Roberts, M. R., & Callahan, M. P., (2019). Nitrogen heterocycles form peptide nucleic acid precursors in complex prebiotic mixtures. Scientific Reports, 9, 9281.
Sean P. S. Gulick, Timothy J. Bralower, Jens Ormö, Brendon Hall, Kliti Grice, Bettina Schaefer, Shelby Lyons, Katherine H. Freeman, Joanna V. Morgan, Natalia Artemieva, Pim Kaskes, Sietze J. de Graaff, Michael T. Whalen, Gareth S. Collins, Sonia M. Tikoo, Christina Verhagen, Gail L. Christeson, Philippe Claeys, Marco J. L. Coolen, Steven Goderis, Kazuhisa Goto, Richard A. F. Grieve, Naoma McCall, Gordon R. Osinski, Auriol S. P. Rae, Ulrich Riller, Jan Smit, Vivi Vajda, Axel Wittmann, the Expedition 364 Scientists (2019) The first day of the Cenozoic. Proceedings of the National Academy of Sciences 116 (39) 1934219351. https://doi.org/10.1073/pnas.1909479116
Smith, K. E., House, C. H., Arevalo, R. D., Dworkin, J. P., & Callahan, M. P., 2019. Organometallic compounds as carriers of extraterrestrial cyanide in primitive meteorites. Nature com., 10, 2777.
Sun, V. Z., Stack, K. M., Kah, L. C., 2019. Late-stage diagenetic concretions in the Murray formation, Gale crater, Mars. Icarus, 321, 866-890.
Wilpiszeski, R. L., Zhang, Z., & House, C. H. (2019). Biogeography of thermophiles and predominance of Thermus scotoductus in domestic water heaters. Extremophiles, 23(1), 119-132.

2018

Couradeau, E., V. J. M. N. L. Felde, D. Parkinson, D. Uteau, A. Rochet, C. Cuellar, S. Peth, F.Garcia-Pichel, T. R. Northen (2018) In situ imaging of drying-induced pore microstructure changes of Biological Soil Crusts, Frontiers in Environmental Science, 6:65. doi: 10.3389/fenvs.2018.00065.
Frankel, E. A. & Bevilacqua, P. C. (2018). Complexity in pH-dependent ribozyme kinetics: Dark pKa shifts and wavy rate-pH profiles. Biochemistry 57, 483-488, 10.1021/acs.biochem.7b00784.
Grisewood, M., Ferry, J. G. and Maranas, C. D. (2018) Computationally exploring and alleviating the kinetic bottlenecks of anaerobic methane oxidation, Frontiers in Environmental Science | Microbiotechnology, Ecotoxicology and Bioremediation. 6:84.
Haas, S., de Beer, D., Fink, A., Klatt, J. M., McCauley Rench, R. L., Hamilton, T.L., Kakuk, B., and Macalady, J. L. 2018. Low-light Anoxygenic Photosynthesis and Fe-S-Biogeochemistry in a Microbial Mat. Frontiers in Microbiology 9:858-873.
Hamilton, T.L., Klatt, J. M., de Beer, D., and Macalady, J. L. 2018. Cyanobacterial photosynthesis under sulfidic conditions: insights from the isolate Leptolyngbya sp. strain hensonii. ISME Journal 12: 568-584.
Holmes, D. E ., Rotaru, A.-E., Ueki, T., Shrestha, P. M., Ferry, J. G., and Lovley, D. R. (2018) Electron and proton flux for carbon dioxide reduction in Methanosarcina barkeri during direct interspecies electron transfer, Frontiers in Microbiology. 9:3109.
Nazem-Bokaee, H., Yan, Z., Maranas, C. D., Ferry, J. G. (2018) The biochemistry and physiology of respiratory-driven reversed methanogenesis, pp. 183-197. In Kalyuzhnaya, M.G. and Xing, X.-H. (eds.),
Physical principles and extant Biology reveal roles for RNA-containing membraneless compartments in origins of life chemistry. Poudyal, R.; Pir Cakmak, F.; Keating, C. D.; Bevilacqua, P. C. Biochemistry 2018, 57, 2509-2519.
Prakash, D., Walters, K. A., Martinie, R. J., McCarver, A. C., Kumar, A. K., Lessner, D. J., Krebs, C., Golbeck, J. H., and Ferry, J. G. (2018) Towards a mechanistic and physiological understanding of ferredoxin:disulfide reductase from the domains Archaea and Bacteria, Journal of Biological Chemistry 293, 9198-9209.
Roush, D., E. Couradeau, B. Guida, F. Garcia-Pichel (2018) A new niche for anoxygenic phototrophs as endoliths, Applied and Environmental Microbiology, Vol. 84 no. 4 e02055-17.
Stein, N., et al., 2018. Desiccation cracks provide evidence of lake drying on Mars, Sutton Island member, Murray formation, Gale Crater. Geology, 46, pp.515-518.
Sánchez-España, J., C. Falagán, K. Wan, I. Yusta and W.D. Burgos. 2018. Microbially mediated aluminosilicate formation in acidic anaerobic environments: A cell-scale chemical perspective. Geobiology, 16, 88-103.
Thomazo, C., E. Couradeau, F. Garcia-Pichel (2018) Possible nitrogen fertilization of the early Earth Ocean by microbial continental ecosystems, Nature Communications, volume 9, Article number: 2530.
Webster, C.R., et al., 2018. Background levels of methane in Mars’ atmosphere show strong seasonal variations. Science, 360, 1093-1096.2019.
Yan, Z. and Ferry, J. G. (2018) Electron bifurcation and confurcation in methanogenesis and reverse methanogenesis, Frontiers in Microbiology. 9:1322.
Yan, Z., Joshi, P., Gorski, C. A., and Ferry, J. G. (2018) A biochemical framework for anaerobic oxidation of methane driven by Fe(III)-dependent respiration, Nature Communications. 9, 1642.
Yung, Y. L., Chen, P., Nealson, K., Atreya, S., Beckett, P., Blank, J. G., Ehlmann, B., Eiler, J., Etiope, G., Ferry, J. G., Forget, F., Gao, P., Hu, R., Kleinbohl, A., Klusman, R., Lefevre, F., Miller, C., Mischna, M., Mumma, M., Newman, S., Oehler, D., Okumura, M., Oremland, R., Orphan, V., Popa, R., Russell, M., Shen, L., Lollar, B. S., Staehle, R., Stamenkovic, V., Templeton, A., Vandaele, A. C., Viscardy, S., Webster, C. R., Wennberg, P. O., Wong, M. L., and Worden, J. (2018) Methane on Mars and Habitability: Challenges and Responses. Astrobiology 18, 1221-1242.

2017

Combining catalytic microparticles with droplets formed by phase coexistence: Adsorption and activity of natural clays at the aqueous/aqueous interface. Pir-Cakmak, F.; Keating, C. D. Scientific Reports 2017, 7, 3215.
E. Couradeau, D. Roush, B. S. Guida, F. Garcia-Pichel (2017) Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico), Biogeosciences, 14, 311-324.
Frankel, E. A., Strulson, C., Keating, C. D. & Bevilacqua, P. C. (2017). Cooperative interactions in the hammerhead ribozyme drive pKa shifting of G12 and its stacked base C17. Biochemistry 56, 2537-2548, 10.1021/acs.biochem.7b00174.
Franz, H. B., Fischer, W. W., Grotzinger, J. P., & Farley, K. A., 2017. Large sulfur isotope fractionations in Martian sediments at Gale crater. Nature Geoscience, 10, 658-662.
Hamilton, T. L., P. V. Welander, H. L. Albrecht, J. M. Fulton, I. Schaperdoth, L. Bird, R.E. Summons, K. H. Freeman, and J. L. Macalady. 2017. Microbial communities and organic biomarkers in a Proterozoic-analog sinkhole, Geobiology 15(6): 784-797, DOI:10.1111/gbi.12252.
Mansor, M., K. Harouaka, U. Nguyen, J. L. Macalady, M. S. Fantle. 2017. Sulfur isotopic fractionation on sulfidic cave walls, Frasassi caves, Italy, in press at Astrobiology.
Mansor, M., K. Harouaka, U. Nguyen, J. L. Macalady, M. S. Fantle. 2017. Sulfur isotopic fractionation on sulfidic cave walls, Frasassi caves, Italy. Astrobiology 18 (1): 59-72.
Oehler, D. Z., Walsh, M. M., Sugitani, K., Liu, M. C., House, C. H., 2017. Large and robust lenticular microorganisms on the young Earth. Precambrian Research, 296, 112-119.
Smith, K. E., House, C. H., Dworkin, J. P., & Callahan, M. P., 2017. Spontaneous Oligomerization of Nucleotide Alternatives in Aqueous Solutions. Origins of Life and Evolution of Biospheres, 47, 3-11.
Steinberg, L. M., Kronyak, R. E., & House, C. H., 2017. Coupling of Anaerobic Waste Treatment to Produce Protein-and Lipid-Rich Bacterial Biomass. Life Sciences in Space Research.
Sugitani, K., Van Kranendonk, M. J., Oehler, D. Z., House, C. H., & Walter, M. R. (2017), Archean coastal-plain paleosols and life on land: Comment. Submitted to Gondwana Research.
Sugitani, K., Van Kranendonk, M. J., Oehler, D. Z., House, C. H., Walter, M. R., 2017. Comment: Archean coastal-plain paleosols and life on land. Gondwana Research, (44), 265-269.
Sutter, B., et al., (2017). Evolved gas analyses of sedimentary rocks and eolian sediment in gale crater, mars: results of the curiosity Rover’s Sample Analysis at Mars (SAM) instrument from Yellowknife Bay to the Namib Dune. Journal of Geophysical Research: Planets.

2016

Batalha, N. E., Kopparapu, R. K., Haqq-Misra, J., & Kasting, J. F. (2016). Climate cycling and valley formation on early Mars, Earth Planet. Sci. Lett., 455 7-13.
Brandt, L. D., & House, C. H. (2016). Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments. Archaea.
De Beer, D., Weber, M., Klatt, J., Hamilton, T.L., Lott, C., Chennu, A. and J.L. Macalady. 2016. Oxygenic and anoxygenic photosynthesis in a microbial mat from an anoxic and sulfidic spring, in press, Environmental Microbiology, doi:10.1111/1462-2920.13654.
Grettenberger, C. L., Pearce, A. R., Bibby, K.J., Jones, D.S., Burgos, W. D., and Macalady, J. L. 2016. Efficient low-pH iron removal by a microbial iron oxide mound ecosystem at Scalp Level Run, in press, Applied and Environmental Microbiology.
Haqq-Misra, J., Kopparapu, R. K., Batalha, N. E., Harman, C. E., & Kasting, J. F. (2016). Limit cycles can reduce the width of the habitable zone, Ap J 827, 120, Aug. 20.
Harouaka, K., Mansor, M., Macalady, J. L. and Fantle, M.S. 2016. Calcium isotopic fractionation in microbially mediated gypsum precipitates, Geochimica Cosmochimica Acta 184:114-131, doi:10.1016/j.gca.2016.03.003.
Jones, D.S., Schaperdoth, I. and Macalady, J. L. 2016. Biogeography of Acidithiobacillus populations in extremely acidic subaerial cave biofilms, advance online publication, ISME Journal, doi:
10.1038/ismej.2016.74.
Kopparapu, R. K., Wolf, E. T., Haqq-Misra, J., Yang, J., Kasting, J. F., Meadows, V. S., Terrien, R., & Mahadevan, S. (2016). he inner edge of the habitable zone for synchronously rotating planets around low-mass stars using general circulation models, Ap. J. 819, 84, 14 pp.
Mansor, M., Schaperdoth, I. and Macalady, J. L. 2016. Draft Genome of Lampenflora Chlorobium limicola strain Frasassi in a Sulfidic Cave System, Genome Announcements 4(3): e00357-16.
Payne, R. C., Britt, A. V., Chen, H., Kasting, J. F. & Catling, D. C. (2016). The response of Phanerozoic surface temperature to variations in atmospheric oxygen concentration, J. Geophys. Res., 121, 10,089-10,096.
Sheng, Y., B. Kaley, K. Bibby, C.L. Grettenberger, J. L. Macalady, G. Wang, and W. Burgos. 2016. Geochemical and temporal influences on the enrichment of acidophilic iron-oxidizing bacterial communities. Applied and Environmental Microbiology 82(12): 3611-3621.
Smith, K. E., House, C. H., Dworkin, J. P., & Callahan, M. P. (2016). Spontaneous oligomerization of nucleotide alternatives in aqueous solutions. Origins of Life & Evolution of Biospheres, 1-9.

2015

Batalha, N. E., Domagal-Goldman, S. D., Ramirez, R., & Kasting, J. F. (2015). Testing the early Mars H2-CO2 greenhouse hypothesis with a 1-D photochemical model, Icarus 258: 337-349.
Cui, Y., & Kump, L. R. (2015). Global warming and the end-Permian extinction event: Proxy and modeling perspectives. Earth-Science Reviews, 149, 5–22. doi:10.1016/j.earscirev.2014.04.007.
Hamilton, T. L., Jones, D. S., Schaperdoth, I., & MacAlady, J. L. (2015). Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00756.
Harman, C. E., Schwieterman, E. W., Schottelkotte, J. C., & Kasting, J. F. (2015). Abiotic O2 levels on planets around F, G, K, and M stars: Possible false positives for life?, Ap J 812, Issue 2, ISSN 0004-637X.
House, C. H. (2015). A synthetic standard for the analysis of carbon isotopes of carbon in silicates, and the observation of a significant water-associated matrix effect. Geochemical transactions, 16, 1-8.
House, C. H., Pellegrini, M., & Fitz-Gibbon, S. T. (2015). Genome-wide gene order distances support clustering the gram-positive bacteria. Frontiers in Microbiology, 5, 785.
Jones, D. S., Kohl, C., Grettenberger, C., Larson, L. N., Burgos, W. D., & Macalady, J. L. (2015). Geochemical niches of iron-oxidizing acidophiles in acidic coal mine drainage. Applied and environmental microbiology, 81(4), 1242-1250.
Jones, D. S., Polerecky, L., Galdenzi, S., Dempsey, B. A., & Macalady, J. L. (2015). Fate of sulfide in the Frasassi cave system and implications for sulfuric acid speleogenesis. Chemical Geology, 410, 21-27.
Kasting, J. F., Chen, H., & Kopparapu, R. K. (2015). Stratospheric temperatures and water loss from moist greenhouse atmospheres of earth-like planets, Ap J Lett. 813, L3, Nov. 1.
Klatt, J. M., Meyer, S., Haeusler, S., Macalady, J. L., de Beer, D., and Polerecky, L. 2015. Structure and function of natural sulphide oxidizing microbial mats under dynamic input of light and chemical energy, ISME Journal 10(4): 921–933, doi:10.1038/ismej.2015.167; published online 25 September 2015.
Liermann, L. J., Albert, I., Buss, H. L., Minyard, M., & Brantley, S. L. (2015). Relating microbial community structure and geochemistry in deep regolith developed on volcaniclastic rock in the Luquillo Mountains, Puerto Rico. Geomicrobiology Journal, 32(6), 494-510.
Mansor, M., Hamilton, T.L., Fantle, M.S. and Macalady, J. L. 2015. Metabolic diversity and ecological niche of Achromatium populations revealed with single-cell genomic sequencing, Frontiers in Microbiology 6: 822, Published online 2015 Aug 10. doi:10.3389/fmicb.2015.00822.
Mason, O. U., Case, D. H., Naehr, T. H., Lee, R. W., Thomas, R. B., Bailey, J. V., & Orphan, V. J. (2015). Comparison of archaeal and bacterial diversity in methane seep carbonate nodules and host sediments, Eel River Basin and Hydrate Ridge, USA. Microbial ecology, 70(3), 766-784.
Yesavage, T., Thompson, A., Hausrath, E. M., & Brantley, S. L. (2015). Basalt weathering in an Arctic Mars-analog site. Icarus, 254, 219–232. doi:10.1016/j.icarus.2015.03.011.
Zerkle, A. L., Jones, D.S., Farquhar, J. and Macalady, J.L. 2015. Sulfur isotope values in the sulfidic Frasassi cave system, central Italy: A case study of a chemolitzotrophic S-based ecosystem, Geochimica et Cosmochimica Acta 173 (15): 373–386, doi:10.1016/j.gca.2015.10.028.

2014

Ahn, C., Alexandroff, R., Allende Prieto, C., Anders, F., Anderson, S., et al. (2014). The Tenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Apache Point Observatory Galactic Evolution Experiment, The Astrophysical Journal Supplement, Volume 211, Issue 2, Article ID. 17, 16 pp. (2014). .
Bastien, F. A., Stassun, K. G., Pepper, J., Wright, J. T., Aigrain, S., Basri, G., Johnson, J. A., Howard, A. W., Walkowicz, L. M. (2014).
Radial Velocity Variations of Photometrically Quiet, Chromospherically Inactive Kepler Stars: A Link between RV Jitter and Photometric Flicker,
Astronomical Journal, 147, 29.
Chakraborty, A., Mahadevan, S., Roy, A., Dixit, V., Harvey Richardson, E., Dongre, V., Pathan, F.M., Chaturvedi, P., Shah, V., Ubale, G.P., Anandarao, B.G. (2014). The PRL Stabilized High-Resolution Echelle Fiber-fed Spectrograph: Instrument Description and First Radial Velocity Results, Astronomical Society of the Pacific, Volume 126, Issue 936, pp.133-147
Crepp, J. R., Johnson, J. A., Howard, A. W., Marcy, G. W., Brewer, J., Fischer, D. A., Wright, J. T., Isaacson, H. (2014).
The Trends High-contrast Imaging Survey. V. Discovery of an Old and Cold Benchmark T-dwarf Orbiting the Nearby G-star HD 19467, The Astrophysical Journal, Volume 781, Issue 1, article id. 29, 6 pp.
Galdenzi, S., Jones, D. S., and Macalady, J. L. (2014). Condensation corrosion: measurements and geomorphic evidence in the Frasassi Caves, Karst Waters Institute Special Publication 18 (Hypogene Cave Morphologies): 44-46.
Hamilton, T. L., Bovee, R. J., Thiel, V., Sattin, S.R., Mohr, W., Schaperdoth, I., Vogl, K., Gilhooly, W. P. III, Lyons, T. W., Tomsho, L. P., Schuster, S. C., Overmann, J., Bryant, D.A., Pearson, A., and Macalady, J. L.(2014). Sulfur dynamo in the phototrophic plate of a meromictic lake, Geobiology, accepted with revisions.
Hamilton, T.L., Jones, D.S., Schaperdoth, I., and Macalady, J. L. 2015. Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem, Frontiers in Microbiology 5 (756): 16 pp., doi: 10.3389/fmicb.2014.00756.
Harouaka, K., Eisenhauer, A., and Fantle, M. S., (2014). Experimental investigation of Ca isotopic fractionation during abiotic gypsum precipitation. Geochim Cosmochim Acta 129, 157-176.
Jones, D. S., Kohl, C., Grettenberger, C., Larson, L. N., Burgos, W. D. and Macalady, J. L. 2015. Geochemical niches of Fe-oxidizing acidophiles in an acidic coal mine drainage, Applied and Environmental Microbiology 81(4): xx-xx, doi: 10.1128/AEM.02919-14.
Jones, D. S., Schaperdoth, I. and Macalady, J. L. (2014). Metagenomic evidence for sulfide oxidation in extremely acidic cave biofilms, Geomicrobiology Journal 31: 194-204.
Kane, S. R., Howell, S. B., Horch, E. P., Feng, Y., Hinkel, N. R., Ciardi, D. R., Everett, M. E., Howard, A. W., Wright, J. T. (2014).
Limits on Stellar Companions to Exoplanet Host Stars with Eccentric Planets, The Astrophysical Journal, Volume 785, Issue 2, article id. 93, 10 pp.
Kasting, J. F., (2014). Chapter 6.6. Modeling the Archean atmosphere and climate, in Treatise on Geochemistry, H. Holland and K. Turekian, eds, Elsevier, pp. 157-175.
Klatt, J. M., Meyer, S., Haeusler, S., Macalady, J. L. , de Beer, D., and Polerecky, L. (2014). Availability of light and chemical energy determines the structure of natural sulphide oxidizing biofilms, in review at ISME Journal.
Kump, L.R., (2014). The Geochemistry of Mass Extinction. Chapter 6.12 in Holland, H.D. and Turekian, K. (eds.) Treatise on Geochemistry, 2nd ed., Oxford University Press, UK, Vol. 6, pp. 269-280.
Kump, L.R., (2014). Earth’s Oxygen Unraveled. Nature Geoscience 7: 248.
Mahadevan, S.., Halverson, S., Ramsey, L., Venditti, N. (2014). Suppression of Fiber Modal Noise Induced Radial Velocity Errors for Bright Emission-line Calibration Sources, The Astrophysical Journal, Volume 786, Issue 1, Article ID. 18, 7 pp.
Marlow, J.J., LaRowe, D.E., Ehlmann, B.L., Amend, J.P., and Orphan, V.J., (2014). The Potential for Biologically Catalyzed Anaerobic Methane Oxidation on Ancient Mars. Astrobiology, 14(4), 292-307.
Marlow, J.J, J. A Steele, D. H Case, S. A Connon, L.A Levin and V. J. Orphan (2014). Microbial abundance and diversity patterns associated with sediments and carbonates from the methane seep environments of Hydrate Ridge, OR. Front. Mar. Sci. doi: 10.3389/fmars.2014.00044.
Marlow, JJ., J. A. Steele, W. Ziebis, A. R. Thurber, L.A. Levin, V.J. Orphan (2014). Carbonate-hosted methanotrophy represents and unrecognized methane sink in the deep sea. Nat. Comm. DOI: 10.1038/ncomms6094.
Ramirez, R. M., R. Kopparapu, C. Harman, M. E. Zugger, T. D. Robinson, R. Freedman, and J. F. Kasting, (2014). Warming early Mars with CO2 and H2, Nature Geoscience 7, 59-63.
Schopf, J.W. (2014). Geological Evidence of Oxygenic Photosynthesis and the Biotic Response to the 2400-2200 Ma “Great Oxidation Event.” Biochemistry (Moscow), 2014 79: 165-177 (special Issue devoted to the 100th anniversary of the birth of Academician Alexander A. Krasnovsky; Published in Russian in Biokhimiya, 2014 79: 223-238)
Smith, K.E., Callahan, M.P., Gerakines, P.A., Dworkin, J.P., and House, C.H., (2014). Investigation of Pyridine Carboxylic Acids in CM2 Carbonaceous Chondrites: Potential Precursor Molecules for Ancient Coenzymes. Geochimica et Cosmochimica Acta.
Song, H., Tong, J., Algeo, T.J., Song, H., Qiu, H., Zhu, Y., Tian, L., Bates, S., Lyons, T.W., Luo, G., Kump, L.R., (2014). Early Triassic seawater sulfate drawdown. Geochim. Cosmochim. Acta 128: 95-113.
Terrien, R.C., Mahadevan, S., Deshpande, R., Bender, C.F., Cargile, P.A., Hearty, F.R., Cottaar, M., Allende Prieto, C., Fleming, S.W., Frinchaboy, P.M., Jackson, K.M., Johnson, J.A., Majewski, S.R., Nidever, D.L., Pepper, J., Rodriquez, J.E., Schneider, D.P., Siverd, R.J., Stassun, K.G., Weaver, B.A., Wilson, J.C. (2014). New Red Jewels in Coma Berenices, The Astrophysical Journal, Volume 782, Issue 2, Article ID. 61, 12 pp.
J.T. Wright, B. Mullan, s. Sigurdsson, M.S. Povich, (2014) The G Infrared Search for Extraterrestrial Civilizations with Large Energy Supplies. I. Background and Justification, The Astrophysical Journal Volume 792 Number 1 ApJ 792 26 doi:10.1088/0004-637X/792/1/26

2013

Barnes, R., K. Mullins, C. Goldblatt, V. S. Meadows, J. F. Kasting, R. Heller, (2013). Tidal Venuses: Triggering a climate catastrophe via tidal heating, Astrobiology 13, 225-250.
Blackwood, G., R. Akeson, E. Bendek, R. Belikov, D. Benford, A. Boss, J. Breckinridge, R. A. Brown, K. Cahoy, J. Catanzarite, D. Ciardi, W. Danchi, D. Ebbets, R. Egerman, S. Gaudi, T. Gautier, T. Glassman, T. Greene, O. Guyon, J. Harrington, S. Howell, L. Kaltenegger, S. Kane, J. Kasdin, J. Kasting, S. Kendrick, J. Krist, B. Lane, P. Lawson, M. Levine, J. Lissauer, R. Lyon, V. Makarov, M. Marley, S. Martin, V. Meadows, B. Mennesson, G. Orton, P. Plavchan, R. Polidan, A. Roberge, G. Schneider, E. Serabyn, M. Shao, C. Sotin, A. Sozzetti, D. Tenerelli, J. Trauger, Z. Tsvetanov, W. Traub, M. Turnbull, S. Unwin, (2013). EXO: The Exoplanet Observatory, white paper.
Brantley, S. L., Lebedeva, M., and Bazilevskaya, E. (2013). Relating weathering fronts for acid neutralization and oxidation to pCO2 and pO2. In: Farquhar, J., Kasting, J., and Canfield, D. Eds.), Treatise of Geochemistry, The Atmosphere — History. Elsevier Amsterdam, The Netherlands.
Cahill J.A., Green R.E., Fulton T..L, Stiller M., Jay F., Ovsyanikov N, Salamzade R, St John J, Stirling I, Slatkin M, Shapiro B. 2013. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genetics 9: e1003345.
Canfield, D.E., and Kump, L.R., 2013. Carbon cycle makeover. Science 339: 533-534.
Charles, A.J., Harding, I.C., Dale, A., Dale, B., Marshall, J.E.A., Kump, L., in review. Seawater salinity changes during the Paleocene-Eocene thermal maximum in the Arctic: evidence from dinoflagellate cycst assemblages, Spitsbergen. Palaeogeography, Palaeoclimatology, Palaeoecology.
Choi J., McCarthy C., Marcy G. W., Howard A. W., Fischer D. A., Johnson J. A., Isaacson H., Wright J. T. (2013) Precise Doppler Monitoring of Barnard’s Star. The Astrophysical Journal 764, 131.
Crepp J. R., Johnson J. A., Howard A. W., Marcy G. W., Fischer D. A., Yantek S. M., Wright J. T., Isaacson H., Feng Y. (2013) The TRENDS High-contrast Imaging Survey. II. Direct Detection of the HD 8375 Tertiary. The Astrophysical Journal 771, 46
Crepp J. R., Johnson J. A., Howard A. W., Marcy G. W., Gianninas A., Kilic M., Wright J. T. (2013) The TRENDS High-contrast Imaging Survey. III. A Faint White Dwarf Companion Orbiting HD 114174. The Astrophysical Journal 774, 1.
Cui, Y. & Kump, L.R. (2013). Global warming and the Permian-Triassic extinction event: proxy and modeling perspectives. Earth-Science Reviews.
Cui, Y., Kump, L.R., and Ridgwell, A., Initial assessment on the carbon emission rate and climatic consequences during the Permian-Triassic mass extinction. Palaeogeography, Palaeoclimatology, Palaeoecology, 389(0): 128-136.
Curtis J. L., Wolfgang A., Wright J. T., Brewer J. M., Johnson J. A. (2013) Ruprecht 147: The Oldest Nearby Open Cluster as a New Benchmark for Stellar Astrophysics. The Astronomical Journal 145, 134.
Dawson S. K., Schaperdoth I., Freeman K. H. and J. L. Macalady. 2013. Anaerobic biodegradation of the isoprenoid biomarker analogues pristane and phytane. Organic Geochemistry, Volume: 65, Pages 118-126.
Freeman K. H. and Pancost R. D. (2013) Molecular and isotopic signatures of terrestrial paleoclimate and ecology. In: Organic Biogeochemistry, Treatise on Geochemistry (Falkowski and Freeman, eds), Elsevier.
Fulton T.L., Norris R.W., Graham R.E., Semken H.A. Jr, Shapiro B. 2013. Ancient DNA supports southern survival of Richardson’s collared lemming (Dicrostonyx richardsoni) during the Last Glacial Maximum. Molecular Ecology 22:2540-2548.
Graham H. V., Patzkowsky M. E., Wing S. L., Parker G.G. Fogel M. L. and K. H. Freeman. Isotopic characteristics of canopies in leaf assemblages. Geochimica et Cosmochimica Acta, in review.
Green RE, Shapiro B. 2013. Human evolution: turning back the clock. Current Biology 23:R286-8.
Gill M.S., Lemey P., Faria N.R., Rambuat A., Shapiro B., Suchard M., 2013. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Molecular Biology and Evolution 30: 713-724.
Haluszczak, L.O., Rose, A., and Kump, L.R., 2013. Geochemical evaluation of flowback and production waters from Marcellus gas wells in Pennsylvania. Applied Geochemistry 28: 55-61.
Hedges S.B. (2013). The origin of life. In Oxford Bibliographies in Evolutionary Biology. Ed. Jonathan Losos. New York: Oxford University Press.
Henderson A. K., Graham H., Magill C. R., Fox D., Patzkowsky M. E. and K. H. Freeman. Angiosperm n-alkane distribution patterns and the geologic record of C4 grasslands. Geochimica et Cosmochimica Acta, in review.
House, C.H., Oehler, D.Z. Sugitani, I., & Mimura, K., 2013. Carbon isotopic analyses of ca. 3.0 Ga microstructures imply planktonic autotrophs inhabited Earth’s early oceans. Geology, 41(6), 651-654.
Johnson J. A., Morton T. D., Wright J. T. (2013) Retired A Stars: The Effect of Stellar Evolution on the Mass Estimates of Subgiants. The Astrophysical Journal 763, 53.
Kasting, J. F., (2013). How was early Earth kept warm? Science 339, 44-45.
Kasting, J. F., Chapter 6.6. Modeling the Archean atmosphere and climate, in Treatise on Geochemistry, H. Holland and K. Turekian, eds, Elsevier, pp. 157-175 (2014).
Kasting, J.F. What caused the rise of atmospheric O2? Chemical Geology, 362, 12-25 (2013).
Kasting, J. F., M. Postman, and M. Mountain, Servicing of large space telescopes and geosynchronous satellites, white paper submitted to National Academy of Sciences’ (NAS’s) Study on the Goals and Direction of the U.S. Human Spaceflight Program, July, 2013.
Kasting, J.F., Kopparapu, R., Ramirez, R.M., Harman, C., 2013. Remote life detection criteria, habitable zone boundaries, and the frequency of Earth-like planets around M and late-K stars. PNAS , doi: 10.1073/pnas.1309107110.
Kennett D. J., Hajdas I., Culleton B. J., Belmecheri S., Martin S., Neff H., Awe J., Graham H. V., Freeman K. H., Newsom L., Lentz D. L., Anselmetti F. S., Robinsom M., Marwan N., Southon J., Hodell D. A. and G. H. Haug (2013) Correlating the Ancient Maya and Modern European Calendars with High-Precision AMS 14C Dating. Nature Scientific Reports, SREP-12-04052.3d 25/3/13 18:39:50.
Kopparapu, R., Ramirez, R.M. (co-primary author), Kasting, J., et al., 2013. Habitable zones around main-sequence stars: New Estimates, The Astrophysical Journal, 765, 2, 131.
Kump, L.R., 2013. Sulfur isotopes and the stepwise oxygenation of the biosphere. Elements 8: 410-411.
Larson, L. N., Fitzgerald, M., Singha, K., Gooseff, M. N., Macalady, J. L. and Burgos, W. D. 2013. Hydrogeochemical niches associated with hyporheic exchange beneath an acid mine drainage-contaminated stream. Journal of Hydrology 501: 163-174.
Liermann, L.J., Brantley, S.L., Albert, I., Buss, H.L, Minyard, M. (in review). Relating microbial community structure and geochemistry in deep regolith developed on volcaniclastic rock in the Luquillo Mountains, Puerto Rico. In review for Geomicrobiology Journal.
Loope, G., Kump, L.R., and Arthur, M.A., 2013. Shallow-water redox conditions from Permian-Triassic boundary microbialites. Chemical Geology 351: 195-208.
Luo, G., Lee R. Kump, Junhua Huang, Chao Li, Yuansheng Du, Qinglai Feng, Xiaoyin Shi, Xiao Bai, Shucheng Xie, in revision. Stratified shallow ocean prevailed from late Paleoproterozoic to middle Mesoproterozoic: Evidence from organic carbon isotopic composition. Earth and Planetary Science Letters.
Macalady, J. L., Hamilton, T. L., Grettenberger, C. L., Jones, D. S., Tsao, L. E. and Burgos, W. D. 2013. Energy, ecology, and the distribution of microbial life. Philosophical Transactions Royal Society B 368: 20120383.
Magill C., Ashley G. M., Domingues-Rodrigo M. and K. H. Freeman. Plant biomarker patterns at Olduvai Gorge establish social meat consumption by pre-modern humans. Nature Communications, in revision.
Magill C., Ashley G. M. and K. H. Freeman (2013) Ecosystem variability and early human habitats in eastern Africa. Proceedings of the National Academy of Sciences 110 (4), 1167-1174 (on line publication: 12/24/2012).
Magill C., Ashley G. M. and K. H. Freeman (2013) Water, plants and early human habitats in eastern Africa. Proceedings of the National Academy of Science 110 (4), 1175-1180 (on line publication: 12/24/2012).
Magill C., Denis E. and K. H. Freeman. Sequential in-cell separation of sedimentary lipids using pressurized liquid extraction. Organic Geochemistry, in review.
Molak M., Lorenzen E.D., Shapiro B., Ho S.Y.W. 2013. Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages. Molecular Biology and Evolution 30: 253-262.
Mueller K. E., Eissenstat D. M., Muller C., Oleksyn J. and K.H. Freeman (2013) Lipid concentrations in soil closely track lipid concentrations in plant leaves and roots. Soil Biology and Biochemistry 63, 14-17.
Ohmoto, H., Watanabe, Y., Lasaga, A.C., Naraoka, H., Johnson, I., Brainard, J. & Chorney, A. (2013, In Press). Oxygen-, iron- and sulfur geochemical cycles on early Earth: paradigms and contradictions. Geological Society of America.
Olson, S.L., Kump, L.R., and Kasting, J.F., Quantifying the areal extent and dissolved oxygen concentrations of Archean oxygen oases. Chemical Geology 362, 35-43 (2013).
Orlando L, Finolhac A, Zhang G, Froese D, [49 authors], Shapiro B*, Jun W*, Willerslev E*. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499: 74-78.
Ramirez, R.M., Kopparapu, R., M, Zugger, M., Robinson, T.D.,Freedman, R., Kasting, J.F., 2013. Warming early Mars with CO2 and H2. Nat. Geosc., doi:10.1038/ngeo2000.
Ramirez, R.M., Kopparapu, R., Lindner, V., Kasting, J.F., 2013. Can increased atmospheric CO2 levels trigger a runaway greenhouse? Astrobiology (submitted 2013).
Schneider, L.J., Bralower, T.J., Kump, L.R., and Patzkowsky, M.E., 2013. Calcareous nannoplankton ecology and community change across the Paleocene-Eocene Thermal Maximum. Paleobiology 39: 628-647.
Shi, C.S., Schopf, J.W. & Kudryavtsev, A.B. (2012, Submitted). Characterization of the stem anatomy of the Eocene fern Dennstaedtiopsis aerenchymata (Dennstaedtiaceae) by use of confocal laser scanning microscopy. American Journal of Botany, August 2013, Volume 100, No. 8, 1626-1628.
Teeling E.C., Hedges S.B. (2013). Making the impossible possible: rooting the tree of placental mammals. Mol. Biol. Evol. 30: 1999–2000.
Thalman O, Shapiro B, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpre MB, et al. 2013. Complete mitochondrial genomes of ancient canids suggests a European origin of domestic dogs. Science, 15 November 2013, Volume 342, No. 6160, 871-874.
Vilstrup J.T., Senguin-Orlando A., Stiller M., Ginolhac A., Raghavan M., Nielsen S.C.A., Weinstock J., Friese D., Vasiliev S.K., Ovodov N.D., Clary J., Helgen K.M., Fleischer R.C., Cooper A., Shapiro B., Orlando L. 2013. Mitochondrial phylogenomics of modern and ancient equids. PLoS ONE 8: e55950.
Weiczorek, R., Fantle, M.S., Kump, L.R., and Ravizza, G., 2013. Osmium isotopic evidence for volcanic activity prior to and enhanced terrestrial weathering during the Paleocene Eocene Thermal Maximum. Geochimica et Cosmochimica Acta 119: 391-410.
Williford, K.N., Ushikumo, T., Schopf, J.W., Lepot, K., Kitajima, K. & Valley, J.W. (2012, In Press). Preservation and detection of microstructural and taxonomic correlations in the carbon isotopic compositions of individual Precambrian microfossils. Geochimica et Cosmochimica Acta, Volume 104, 1 March 2013, 165-182.
Worth, R.J., Sigurdsson, S., & House, C.H. 2013. Seeding Life on the Moons of the Outer Planets via Lithopanspermia. Astrobiology, 13(12), 1155-1165.
Wright J. T., Howard A. W. (2013) Erratum: “Efficient Fitting of Multi-planet Keplerian Models to Radial Velocity and Astrometry Data” (2009, ApJS, 182, 205). The Astrophysical Journal Supplement Series 205, 22.
Wright J. T., Roy A., Mahadevan S., Wang S. X., Ford E. B., Payne M., Lee B. L., Wang J., Crepp J. R., Gaudi B. S., Eastman J., Pepper J., Ge J., Fleming S. W., Ghezzi L., González-Hernández J. I., Cargile P., Stassun K. G., Wisniewski J., Dutra-Ferreira L., Porto de Mello G. F., Maia M. A. G., Nicolaci da Costa L., Ogando R. L. C., Santiago B. X., Schneider D. P., Hearty F. R. (2013) MARVELS-1: A Face-on Double-lined Binary Star Masquerading as a Resonant Planetary System and Consideration of Rare False Positives in Radial Velocity Planet Searches. The Astrophysical Journal 770, 119.
Yanagawa, K., Nunoura, T., McAllister, S. M., Hirai, M., Breuker, A., Brandt, L., … & Takai, K., 2013. The first microbiological contamination assessment by deep-sea drilling and coring by the D/V Chikyu at the Iheya North hydrothermal field in the Mid-Okinawa Trough (IODP Expedition 331). Frontiers in microbiology, 4.
Yesavage, T.A., Stinchcomb G.E., Fantle, M., Sak, P., Kasznel, A., and Brantley, S.L. (submitted). How consumption of oxygen drives regolith formation in a Pennsylvania diabase: bulk, redox and isotopic chemistry of Fe. Submitted to Chemical Geology.
Yesavage, T.A. Thompson, A., Hausrath, E.M., Liermann, L.J., and Brantley, S.L. (submitted) Basalt weathering in an arctic Mars analog site. Submitted to Icarus.

2012

Algeo T., Henderson C., Ellwood B., Rowe H., Elswick E., Bates S., Lyons T., Hower J. C., Smith C., Maynard B., Hays L., Summons R. E., Fulton J. M. and K. H. Freeman (2012). Elevated sediment fluxes in the Sverdrup Basin prior to the end-Permian mass extinction: A link to Siberian Traps volcanism? GSA Bulletin 124, 1424-1448.
Bender C. F., Mahadevan S., Deshpande R., Wright J. T., Roy A., Terrien R. C., Sigurdsson S., Ramsey L. W., Schneider D. P., Fleming S. W. (2012) The SDSS-HET Survey of Kepler Eclipsing Binaries: Spectroscopic Dynamical Masses of the Kepler-16 Circumbinary Planet Hosts. The Astrophysical Journal 751, L31.
Cameron, V., House, C. H., & Brantley, S. L., 2012. A First Analysis of Metallome Biosignatures of Hyperthermophilic Archaea. Archea Journal, ID 789278, 12 pp. doi:10.1155/2012/789278.
Close H. G., Shah S. R., Ingalls A. E., Diefendorf A. F., Brodie E. L., Hansman R. L., Freeman K. H., Aluwihare L. I. and A. Pearson (2012) Export of submicron particulate organic matter to mesopelagic depths in an oligotrophic gyre, PNAS, 110 (31), 12565-12570.
Crepp J. R., Johnson J. A., Fischer D. A., Howard A. W., Marcy G. W., Wright J. T., Isaacson H., Boyajian T., von Braun K., Hillenbrand L. A., Hinkley S., Carpenter J. M., Brewer J. M. (2012) The Dynamical Mass and Three-dimensional Orbit of HR7672B: A Benchmark Brown Dwarf with High Eccentricity. The Astrophysical Journal 751, 97.
Crepp J. R., Johnson J. A., Howard A. W., Marcy G. W., Fischer D. A., Hillenbrand L. A., Yantek S. M., Delaney C. R., Wright J. T., Isaacson H. T., Montet B. T. (2012) The TRENDS High-contrast Imaging Survey. I. Three Benchmark M Dwarfs Orbiting Solar-type Stars. The Astrophysical Journal 761, 39.
Cui Y., Kump L. R., Ridgwell A. J., Charles A. J., Junium C. K., Diefendorf A. F., Freeman K. H., Urban N. M. and I. C. Harding (2012) Reply to ‘Constraints on hyperthermals.’ Nature Geoscience 5, 231–232.
Dalén L., Orlando L., Shapiro B., Durling M.B., Quam R., Gilbert M.T.P., Fernández-Lomana J.C.D., Willerslev E, Arsuaga J.L., Götherström A. 2012. Partial genetic turnover in Neandertal: continuity in the east and population replacement in the west. Molecular Biology and Evolution 29: 1893-1897.
Dawson, K.S., Freeman, K.H. & Macalady, J.L. (2012). Molecular characterization of core lipids from halophilic archaea grown under different salinity conditions. Organic Geochemistry, 48(1-8).
Dawson, K. S., Strapoc, D., Huizinga, B., Lidstrom, U., Ashby, M. and Macalady, J. L. 2012. Quantitative FISH analysis of microbial consortia from a biogenic gas field in the Cook Inlet Basin, Alaska. Applied & Environmental Microbiology 78 (10):3599-3610.
Diefendorf A. F., Freeman K. H. and S. L. Wing (2012). Diterpenoids and Triterpenoids in Temperate C3 Trees. Geochimica et Cosmochimica Acta 85, 342-256.
Dragomir D., Kane S. R., Henry G. W., Ciardi D. R., Fischer D. A., Howard A. W., Jensen E. L. N., Laughlin G., Mahadevan S., Matthews J. M., Pilyavsky G., von Braun K., Wang S. X., Wright J. T. (2012) The HD 192263 System: Planetary Orbital Period and Stellar Variability Disentangled. The Astrophysical Journal 754, 37.
Edson A. R., J. F. Kasting, D. Pollard, S. Lee, P. R. and Bannon. The carbonate-silicate cycle and CO2/climate feedbacks on tidally locked terrestrial planets. Astrobiology 12, 562-571 (2012).
Fischer D. A., Gaidos E., Howard A. W., Giguere M. J., Johnson J. A., Marcy G. W., Wright J. T., Valenti J. A., Piskunov N., Clubb K. I., Isaacson H., Apps K., Lepine S., Mann A., Moriarty J., Brewer J., Spronck J. F. P., Schwab C., Szymkowiak A. (2012) M2K. II. A Triple-planet System Orbiting HIP 57274. The Astrophysical Journal 745, 21.
Fischer A., Shapiro B., Muriuki C., Heller M., Schnee C., Bongcam-Rudloff E., Frey J., Jores J. 2012. The origin of the ‘Mycoplasma mycoides cluster’ coincides with domestication of ruminants. PLoS ONE 7:e36150.
Fulton, J., Arthur M. A. and K. H. Freeman (2012) Black Sea nitrogen cycling and the preservation of phytoplankton δ15N signals during the Holocene. Global Biogeochemical Cycles 26, GB2030, doi:10.1029/2011GB004196.
Fulton, J.M., Arthur, M.A. & Freeman, K.H. (2012). Subboreal aridity and scytonemin in the Holocene BlackSea. Organic Geochemistry, 49: 47–55.
Fulton J. M., Arthur M. A. and K. H. Freeman (2012). The cyanobacterial biomarker scytonemin in the Holocene Black Sea. Organic Geochemistry 49, 47-55.
Fulton T., Letts B., Shapiro B. 2012. Multiple losses of flight and recent speciation in steamer ducks. Proceedings of the Royal Society B 279: 2339-2346.
Fulton, T.L., Wagner, S.M., Fisher, C. & Shapiro, B. (2012). Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons. Annals of Anatomy-Anatomischer Anzeiger, 195(1): 52-57.
Fulton T.L., Wagner S.M., Shapiro B. 2012. Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon. Methods in Molecular Biology 840: 29-35.
Giguere M. J., Fischer D. A., Howard A. W., Johnson J. A., Henry G. W., Wright J. T., Marcy G. W., Isaacson H. T., Hou F., Spronck J. (2012) A High-eccentricity Component in the Double-planet System around HD 163607 and a Planet around HD 164509. The Astrophysical Journal 744, 4.
Ginolhac, A., Vilstrup, J., Stenderup, J., Rasmussen, M., Stiller, M., Shapiro, B., Zazula, G., Froese, D., Steinmann, K.E., Thompson, J.D., AL-Rasheid, K.A.S., Gilbert, M.T.P., Willerslev, E. & Orlando, L. (2012). Improving the performance of true single-molecule sequencing for ancient DNA. BMC Genomics, 13(177).
Hedges, S. (2012). Amniote phylogeny and the position of turtles. BMC Biology, 10(64): 1-2.
Higham, T., Compton, T., Stringer, C., Jacobi, R., Shapiro, B., Trinkaus, E., Chandler, B. & et al. (2011). The earliest evidence for anatomically modern humans in northwestern Europe. Nature, 479(7374): 521-524.
Honisch, B., Ridgwell, A., Schmidt, D., Thomas, E., Gibbs, S., Sluijs, A., Zeebe, RE., Kump, L., Martindale, R., Greene, S., Kiessling, W., Ries, J., Zachos, J., Royer, D., Barker, S., Marchitto, T., Moyer, R., Pelejero, C., Ziveri, P., Foster, G., and Williams, B., 2012. The geological record of ocean acidification. Science 335: 1058-1063.
Horodyskyj, L.B., White, T.S. & Kump, L.R. (2012). Substantial biologically mediated phosphorus depletion from the surface of a Middle Cambrian paleosol. Geology, 40: 503-506.
House, C.H., Oehler, D.Z., Sugitani, K. & Minura, K. (2012, Submitted). Carbon isotopic analyses of ~ 3 Ga microfossils imply an autotrophic Archean microbiota, widespread in the Earth’s earliest oceans. Geology.
Jones D. S., Albrecht H. L., Dawson K. S., Schaperdoth I., Freeman K. H., Pi, Y., Pearson A. and J. L. Macalady (2012) Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. The ISME Journal 6, 158–170.
Jones, D. S., I. Schaperdoth, T. S. Stoffer, K. Dawson, K. H. Freeman, H. Albrecht, and Macalady, J. L. 2012. Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. ISME Journal 6:158-170, doi:10.1038/ismej.2011.75.
Kasting, J. F., A delicate balance: Review of “The Goldilocks Planet” by Jan Zalasiewicz and Mark Williams, Nature 483, 537 (2012).
Kasting, J. F., The mystery of atmospheric oxygen, Nature Geoscience 6, 9-10, 2012.
Kasting, J. F. and D. E. Canfield, Chapter 7: The global oxygen cycle, in Fundamentals of Geobiology, A. H. Knoll, D. E. Canfield, and K. Konhauser, eds., Wiley-Blackwell, Oxford, 2012, pp. 93-104.
Kasting, J. F., D. C. Catling, and K. Zahnle, Atmospheric oxygenation and volcanism. Nature 487: E1-E2 (2012).
Kasting, J. F. and J. Kirschvink, Evolution of a habitable planet, in Frontiers of Astrobiology, C. Impey, J. Lunine, and J. Funes, eds., Cambridge Univ. Press, Cambridge, 2012, pp. 115-131.
Kistler, L. & Shapiro, B. (2011). Ancient DNA confirms a local origin of domesticated chenopod in Eastern North America. Journal of Archaeological Sciences, 38: 3549–3554.
Kopparapu, R. and J. F. Kasting, A photochemical model for the carbon-rich planet WASP-12b, Astrophysical Journal, 745, 77 (10pp) (2012).
Kumar, S. & Hedges, S. (2011). TimeTree2: species divergence times on the iPhone. Bioinformatics, 27: 2023-2024.
Letts, B., Fulton, T.L., Stiller, M., Andrews, T., MacKay, G., Popkp, R. & Shapiro, B. (2012). Ancient DNA Reveals Genetic Continuity in Mountain Woodland Caribou of the Mackenzie and Selwyn Mountains, Northwest Territories, Canada. Arctic Institute of North America, 65(5).
Letts, B. & Shapiro, B. (2012). Case Study: Ancient DNA recovered from Pleistocene-age remains of a Florida armadillo. Methods in Molecular Biology, 840: 87-92.
Lorenzen, E.D., Nogues-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K.A., Shapiro, B., Rahbek, C. & Willerslev, E. (2011). Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479: 359–364.
MacDonald G.M., Beilman D.W.. Kuzmin Y.V., Orlova L.A., Kremenetski K.V., Shapiro B., Wayne R.K., Van Valkenburgh B. 2012. Pattern of extinction of the woolly mammoth in Beringia. Nature Communications 3: 893.
Maresca, J., Crowe, S. & MacAlady, J.L. (2012). Anaerobic Photosynthetic Ecosystems. Geobiology, 10(3): 193-195.
Martino, A.J., Rhodes, M.E., Biddle, J.F., Brandt, L.D., Tomsho, L.P. & House, C.H. (2012). Novel degenerate PCR method for whole genome amplification applied to Peru Margin (ODP Leg 201) subsurface samples. Frontiers in Microbiology, 3. Article 17.
Medeiros P.M., Sikes E. L., Thomas B. and K. H. Freeman (2012) Flow discharge influences on input and transport of particulate and sedimentary organic carbon along a small temperate river. Geochimica et Cosmochimica Acta 77, 317-334.
Melezhik, V., Kump, L., Fallick, A., Strauss, H., Hanski, E., Prave, A., Lepland, A. (eds.), 2012. Reading the Archive of Earth’s Oxygenation. Volume 3: Global Events and the Fennoscandian Arctic Russia – Drilling Earth Project. Springer, Heidelberg, 512 pp.
Melezhik, V., Prave, A., Hanski, E., Fallick, A., Lepland, A., Kump, L. & Strauss, H. (2012). Reading the Archive of Earth’s Oxygenation. Volume 1: The Palaeoproterozoic of Fennoscandia as Context for the Fennoscandian Arctic Russia – Drilling Earth Project. Springer, Heidelberg.
Melezhik, V., Prave, A., Fallick, A., Hanski, E., Lepland, A., Kump, L. & Strauss, H. (2012). Reading the Archive of Earth’s Oxygenation. Volume 2: The Core Archive of the Fennoscandian Arctic Russia – Drilling Early Earth Project. Springer, Heidelberg.
Miller B. P., Gallo E., Wright J. T., Dupree A. K. (2012) On the Detectability of Star-Planet Interaction. The Astrophysical Journal 754, 137.
Ming, R. & et al. (2012). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, Volume 14, Issue 5.
Minyard, M.L., Bruns, M.A., Liermann, L.J., Buss, H.L. & Brantley, S.L. (2012). Geomicrobiology Journal. Bacterial Associations with Weathering Minerals at the Regolith-Bedrock Interface, Luquillo Experimental Forest, Puerto Rico. Geomicrobiology, 29.
Mueller K. E., Polissar P. J., Oleksyn J. and K. H. Freeman (2012). Plant lipid biomarkers in leaves, roots, and soils of eleven temperate tree species. Organic Geochemistry 52, 130-141.
Nasdala, L., Beyssac, O., Schopf, J.W. & Bleisteiner, B. (2012). Application of Raman-based images in the Earth sciences. In: Zoubir, A. (Eds.). Optical Sciences. Vol. 168. Raman Imaging.
Nasdala, L., Beyssac, O., Schopf, J.W. & Bleisteiner, B. (2012). Application of Raman-based images in the Earth sciences. In: Zoubir, A. (Eds.). Raman Imaging, Springer Series in Optical Sciences. Vol. 168. Amsterdam: Springer.
Otake, T. & Watanabe, Y. (2011). Using multiple sulfur isotopes to understand the Earth’s surface environments during the Archean era. Geochemical Journal, 45: 251-264.
Pancost R.D., Freeman K. H., Hermann H. D., Patzkowsky M. E., Ainsaar, L. and T. Martma (2012) Reconstructing Late Ordovician carbon cycle variations. Geochimica et Cosmochimica Acta 105, 433–454.
Rhodes, M.E., Oren, A. & House, C.H. (2012). Dynamics and persistence of Dead Sea microbial populations as shown by high-throughput sequencing of rRNA. Applied and Environmental Microbiology, 78(2489-2492).
Sachse D., White J., Kahmen A., Dawson T., West J. B., Sessions A., van der Meer M., Chikaraishi Y., Schmidt H.-L., Feakins S., Robins R., McInerney F., Pedentcouk N., Magill C., Freeman K. H. and Polissar P.J. (2012) Sources of variability in the hydrogen isotopic composition of organic compounds from photosynthetic organisms. Annual Reviews in Earth and Planetary Sciences 40.
Schopf, J.W. & Kudryavtsev, A.B. (2012). Biogenicity of Earth’s earliest fossils: a resolution of the controversy. Gondwana Research, 39: 761-771.
Schopf, J.W. (2012, In Prss). Forward [Book Chapter]. The Flyer: Boris Sokolov: Natural History and 21st Century Russia Sokolov. Indiana University Press.
Schopf, J.W. (2012). The fossil record of cyanobacteria. In: Whitton, B.A. (Eds.). Ecology of Cyanobacteria II. Their Diversity in Space and Time. Berlin Heidelberg New York: Springer.
Schopf, J.W., Farmer, J.D., Foster, I.S., Kudryavtsev, A.B., Gallardo, V.A. & Espinoza, C. (2012). Gypsum-permineralized microfossils and their relevance to the search for life on Mars. Astrobiology, 12: 619-633.
Schopf, J.W. & Kudryavtsev, A.B. (2012, Submitted). Biogenicity of Earth’s earliest fossils. In: Dilek, L. & Furnes, H. (Eds.). Archean Earth and Early Life. Springer.
Vidal, N., Marin, J., Sassi, J., Battistuzzi, F.U., Donnellan, S., Fitch, A.J., Fry, B.G., Vonk, F.J., Rodriguez, R.C., Couloux, A. & Hedges, S.B. (2012). Molecular evidence for an Asian origin of monitor lizards followed by Tertiary dispersals to Africa and Australasia. Biology Letters, 8: 853-855.
Wang X., Sharon, Wright J. T., Cochran W., Kane S. R., Henry G. W., Payne M. J., Endl M., MacQueen P. J., Valenti J. A., Antoci V., Dragomir D., Matthews J. M., Howard A. W., Marcy G. W., Isaacson H., Ford E. B., Mahadevan S., von Braun K. (2012) The Discovery of HD 37605c and a Dispositive Null Detection of Transits of HD 37605b. The Astrophysical Journal 761, 46.
Widga C., Fulton T.L., Martin L.D., Shapiro B. 2012. Homotherium and Cervalces from the Great Lakes region, USA: geochronology, morphology and ancient DNA. Boreas 41: 546-556.
Wright J. T., Marcy G. W., Howard A. W., Johnson J. A., Morton T. D., Fischer D. A. (2012) The Frequency of Hot Jupiters Orbiting nearby Solar-type Stars. The Astrophysical Journal 753, 160.
Zhao M., Milburn J., Barman T., Hinkley S., Swain M. R., Wright J., Monnier J. D. (2012) Detection of KS -band Thermal Emission from WASP-3b. The Astrophysical Journal 748, L8.

2011

Shipboard Scientific Party: Deep Hot Biosphere. Proceedings of the Ocean Drilling Program (2011). Expedition Report.
Bailey, J.V., Salman, V., Rouse, G.W., Schulz-Vogt, H.N., Levin, L.A. & Orphan, V.J. (2011). A dimorphic life cycle in methane seep dwelling ecotypes of the largest known bacteria. ISME, 5: 1926-1935.
Beal, E., Claire, M.W. & House, C.H. (2011). The anaerobic oxidation of methane at low sulfate concentrations and the redox state of Earth’s atmosphere through time. Geobiology, 9: 131-139.
Biddle, J.A., White, J.R., Teske, A.P. & House, C.H. (2011). Metagenomics of the subsurface Brazos-Trinity Basin (IODP Site 1320): comparison with other sedment and pyrosequenced metagenomes. The ISME Journal, doi:10.1038/ismej.2010.199.
Callahan, M.P., Smith, K.E., Cleaves, H.J.,., Ruzicka, J., Stern, J.C., Glavin, D.P., House, C.H. & Dworkin, J.P. (2011). Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases. Proceedings of the National Academy of Sciences, 1106493108v1-13998.
Cohen, P.A., Schopf, J.W., Butterfield, N.J., Kudryavtsev, A.B. & MacDonald, F.A. (2011). Phosphate biomineralization in Mid-Neoproterozoic protists. Geology, 39: 539-542.
Cui Y. Kump L. R., Ridgwell A. J., Charles A. J., Junium C. K., Diefendorf A. F, Freeman K. H., Urban N. M. and Harding I. C. (2011) Slow release of fossil carbon during the Palaeocene-Eocene Thermal Maximum. Nature Geosciences 4, 481-485.
Dauphas, N. and J. F. Kasting, Low pCO2 in the pore water, not in the Archean air (Comment on Rosing et al., 2010), Nature 474, E2-E3 (2011).
Diefendorf A. F., Freeman K. H., Wing S. L. and H. V. Graham (2011) Production of n-alkyl lipids in living plants and implications for the geologic past. Geochimica et Cosmochimica Acta 75, 7472-7485.
Domagal-Goldman, S. D., V.S. Meadows, M.W. Claire, J.F. Kasting, Using biogenic sulfur gases as remotely detectable biosignatures on anoxic planets, Astrobiology, 11, 1-23 (2011).
Dragomir D., Kane S. R., Pilyavsky G., Mahadevan S., Ciardi D. R., Gazak J. Z., Gelino D. M., Payne A., Rabus M., Ramirez S. V., von Braun K., Wright J. T., Wyatt P. (2011) TERMS Photometry of Known Transiting Exoplanets. The Astronomical Journal 142, 115.
Edson, A., S. Lee, P. Bannon, J. F. Kasting, and D. Pollard, Atmospheric circulations of terrestrial planets orbiting low mass stars, Icarus, 212, 1-13 (2011).
Edwards, C.J.E., Suchard, M.A., Lemey, P., Welch, J.J., Barnes, I., Fulton, T.L., Barnett, R., O’Connell, T.C., Coxon, P., Monaghan, N., Valdiosera, C., Lorenzen, E.D., Willerslev, E., Baryshnikov, G.F., Rambaut, A., Thomas, M.G., Bradley, D.G. & Shapiro, B. (2011). Ancient hybridization and a recent Irish origin for the modern polar bear matriline. Current Biology, 21: 1-8.
Fairén, A. G., A. F. Davila, L. Gago-Duport, J. D. Haqq-Misra, C. Gil, C P. McKay and J. F. Kasting, Cold glacial oceans would have inhibited phyllosilicate sedimentation on early Mars, Nature Geosciences 4, 667-670 (2011).
Fleming, S.W., Maxted, P.F.L., Hebb, L., Stassun, K.G., Ge, J., Cargile, P.A., Ghezzi, L., De Lee, N.M., Wisniewski, J., Gary, B., Porto de Mello, G.F., Ferreira, L., Zhao, B., Anderson, D.R., Wan, X., Hellier, C., Guo, P., West, R.G., Mahadevan, S., Pollacco, D., Lee, B., Collier Cameron, A., van Eyken, J.C., Skillen, I., Crepp, J.R., Cuong Nguyen, D., Kane, S.R., Paegert, M., Nicolaci da Costa, L., Maia, M.A.G. & Santiago, B.X. (2011). Eclipsing Binary Science via the Merging of Transit and Doppler Exoplanet Survey Data—A Case Study with the MARVELS Pilot Project and SuperWASP. The Astronomical Journal, 142: 50.
Freeman K. H., Mueller K. E., Diefendorf, A. F., Wing, S. L. and P. L. Koch (2011) Clarifying the influence of water availability and plant types on carbon isotope discrimination by C3 plants. Letter, Proceedings of the National Academies of Science 108, E59-E60.
Gill, B., Lyons, T., Young, S., Kump, L., Knoll, A. & Saltzman, M.R. (2011). Geochemical evidence for widespread euxinia in the Later Cambrian ocean. Nature, 469: 80-83.
Gonzalez, B.C., Iliffe, T.M., Macalady, J.L., Schaperdoth, I. & Kakuk, B. (2011). Microbial hotspots in anchialine blue holes: initial discoveries from the Bahamas. Hydrobiologia, 677: 149-156.
Güdel, M. and J. F. Kasting, The young Sun and its influence on planetary atmospheres, in Origin of Life: an Astrobiology Perspective, M. Gargaud, P. Lopez-Garcia, H. Martin, eds., Cambridge Univ. Press, pp. 167-182 (2011).
Haqq-Misra, J., Kasting, J.F. & Lee, S. (2011). Availability of O2 and H2O2 on the pre-photosynthetic Earth. Astrobiology, 11: 293-302.
Hedges, S. (2011). On the use of high-level taxonomic names. Zootaxa, 2867: 67-68.
House, C.H., Beal, E.J. & Orphan, V.J. (2011). The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy. Life, 1: 19-33.
Howard A. W., Johnson J. A., Marcy G. W., Fischer D. A., Wright J. T., Henry G. W., Isaacson H., Valenti J. A., Anderson J., Piskunov N. E. (2011) The NASA-UC Eta-Earth Program. II. A Planet Orbiting HD 156668 with a Minimum Mass of Four Earth Masses. The Astrophysical Journal 726, 73.
Howard, A.W., Johnson, J.A., Marcy, G.W., Fischer, D.A., Wright, J.T., Henry, G.W., Isaacson, H., Valenti, J.A., Anderson, J. & Piskunov, N.E. (2011). The NASA-UC Eta-Earth Program. III. A Super-Earth Orbiting HD 97658 and a Neptune-mass Planet Orbiting Gl 785. The Astrophysical Journal, 730: 10.
Johnson, J.A., Clanton, C., Howard, A.W., Bowler, B.P., Henry, G.W., Marcy, G.W., Crepp, J.R., Endl, M., Cochran, W.D., MacQueen, P.J., Wright, J.T. & Isaacson, H. (2011). Retired A Stars and Their Companions: Eighteen New Jovian Planets [Online].
Junium, C.K., B.J., Keely, K.H., Arthur, M.A., Freeman (2011) Chlorins in mid-Cretaceous black shales of the Demerara Rise: the oldest known occurrence. Organic Geochemistry 42, 856-859.
Kane, S., Gelino, D., Dragomir, D., Howard, A., Knutson, H., Krick, J., Laughlin, G., Mahadevan, S., von Braun, K. & Wright, J. (2011). Detecting the Signature of Eccentric Exoplanets During Periastron Passage.
Kane, S.R., Dragomir, D., Ciardi, D.R., Lee, J-W., Lo Curto, G., Lovis, C., Naef, D., Mahadevan, S., Pilyavsky, G., Udry, S., Wang, X. & Wright, J. (2011). Stellar Variability of the Exoplanet Hosting Star HD 63454. The Astrophysical Journal, 737: 58.
Kane, S.R., Henry, G.W., Dragomir, D., Fischer, D.A., Howard, A.W., Wang, X. & Wright, J.T. (2011). Revised Orbit and Transit Exclusion for HD 114762b. The Astrophysical Journal Letters, 735: L41.
Kane, S.R., Howard, A.W., Pilyavsky, G., Mahadevan, S., Henry, G.W., von Braun, K., Ciardi, D.R., Dragomir, D., Fischer, D.A., Jensen, E., Laughlin, G., Ramirez, S.V. & Wright, J.T. (2011). Improved Orbital Parameters and Transit Monitoring for HD 156846b. The Astrophysical Journal, 733: 28.
Kasting, J. F., Habitable planets: What are we learning from Kepler and ground-based searches? Astrobiology 11, 363-366 (2011).
Konhauser, K.O., Lalonde, S.V., Planavsky, N.J., Pecoits, E., Lyons, T.W., Mojzsis, S.J., Rouxel, O.J., Barley Carlos Rosìere, M.E., Fralick, P.W., Kump, L.R. & Bekker, A. (2011). Aerobic pyrite oxidation and acid-rock drainage during the Great Oxidation Event. Nature, 478: 369-373.
Kumar, S. & Hedges, S.B. (2011). TimeTree2: species divergence times on the iPhone. Bioinformatics. 27: 2023-2024.
Lee, B.L., Ge, J., Fleming, S.W., Stassun, K.G., Gaudi, B.S., Barnes, R., Mahadevan, S., Eastman, J.D., Wright, J., Siverd, R.J., Gary, B., Ghezzi, L., Laws, C., Wisniewski, J.P., Porto de Mello, G.F., Ogando, R.L.C., Maia, M.A.G., Nicolaci da Costa, L., Sivarani, T., Pepper, J., Cuong Nguyen, D., Hebb, L., De Lee, N., Wang, J., Wan, X., Zhao, B., Chang, L., Groot, J., Varosi, F., Hearty, F., Hanna, K., van Eyken, J.C., Kane, S.R., Agol, E., Bizyaev, D., Bochanski, J.J., Brewington, H., Chen, Z., Costello, E., Dou, L., Eisenstein, D.J., Fletcher, A., Ford, E.B., Guo, P., Holtzman, J.A., Jiang, P., French Leger, R., Liu, J., Long, D.C., Malanushenko, E., Malanushenko, V., Malik, M., Oravetz, D., Pan, K., Rohan, P., Schneider, D.P., Shelden, A., Snedden, S.A., Simmons, A., Weaver, B.A., Weinberg, D.H. & Xie, J-W. (2011). MARVELS-1b: A Short-period, Brown Dwarf Desert Candidate from the SDSS-III Marvels Planet Search. The Astrophysical Journal, 728: 32.
Lippold, S., Knapp, M., Kuznetsova, T., Leonard, J.A., Benecke, N., Ludwig, A., Rasmussen, M., Weinstock, J., Willerslev, E., Shapiro, B. & Hofreiter, M. (2011). Discovery of lost diversity of paternal horse lineages using ancient DNA. Nature Comm, 2(450).
Loveland-Curtze, J., Miteva, V. & Brenchley, J. (2011). Evaluation of a novel fluorimetric DNA-DNA hybridization method. Can. J. Microbiol, 57: 250-257.
Luo, G., Wang, Y., Algeo, T.J., Kump, L.R., Bai, X., Yang, H., Yao, L. & Xie, S. (2011b). Enhanced nitrogen fixation in the immediate aftermath of the latest Permian marine mass extinction. Geology, 39: 647-650.
Luo, G., Wang, Y., Yang, H., Algeo, T.J., Kump, L.R., Huang, J. & Xie, S. (2011a). Stepwise and large-magnitude negative shift in δ13Ccarb preceded the main marine mass extinction of the Permian–Triassic crisis interval. Palaeogeography Palaeoclimatology Palaeoecology, 299: 70-82.
Margesin, R. & Miteva, V. (2011). Diversity and ecology of psychrophilic microorganisms. Res. Microbiol, 162: 346-361.
McCauley, R.L., Jones, D.S., Schaperdoth, I. & Macalady, J.L. (2011). Lago Infinito (Frasassi Caves, Italy) Microbial Community as an Analog for pre-Phototrophic Earth. Astrobiology, 11(4): 367-389.
McInerney F. A., Helliker B. R. and K. H. Freeman (2011). Hydrogen isotope ratios of leaf wax n-alkanes in grasses are insensitive to transpiration. Geochimica et Cosmochimica Acta. 75, 541-554.
Meyer, K., Freeman, K.H., Macalady, J.L., Fulton, J., Schaperdoth, I. & Kump, L. (2011). Carotenoid biomarkers as an imperfect reflection of the anaerobic phototrophic community in meromictic Fayetteville Green Lake. Geobiology, 9: 321-329.
Miteva, V. (2011). Microorganisms associated with glaciers. In: V. P. Singh, U.K.H.a.P.S. (Eds.). Encyclopedia of Snow, Ice and Glaciers. Springer.
Muirhead, P.S., Edelstein, J., Erskine, D.J., Wright, J.T., Muterspaugh, M.W., Covey, K.R., Wishnow, E.H., Hamren, K., Andelson, P., Kimber, D., Mercer, T., Halverson, S.P., Vanderburg, A., Mondo, D., Czeszumska, A. & Lloyd, J.P. (2011). Precise Stellar Radial Velocities of an M Dwarf with a Michelson Interferometer and a Medium-Resolution Near-Infrared Spectrograph. Publications of the Astronomical Society of the Pacific, 123: 709-724.
Norris J. M., Wright J. T., Wade R. A., Mahadevan S., Gettel S. (2011) Non-detection of the Putative Substellar Companion to HD 149382. The Astrophysical Journal 743, 88.
Pilyavsky G., Mahadevan S., Kane S. R., Howard A. W., Ciardi D. R., de Pree C., Dragomir D., Fischer D., Henry G. W., Jensen E. L. N., Laughlin G., Marlowe H., Rabus M., von Braun K., Wright J. T., Wang X. X. (2011) A Search for the Transit of HD 168443b: Improved Orbital Parameters and Photometry. The Astrophysical Journal 743, 162.
Redman, S.L., Lawler, J.E., Nave, G., Ramsey, L.W. & Mahadevan, S. (2011). The Infrared Spectrum of Uranium Hollow Cathode Lamps from 850 nm to 4000 nm: Wavenumbers and Line Identifications from Fourier Transform Spectra. The Astrophysical Journal Supplement Series, 195: 24.
Rhodes, M.E., Spear, J.R., Oren, A. & House, C.H. (2011). Differences in lateral gene transfer in hypersaline versus thermal environments. BMC Evolutionary Biology, 11:199doi:10.1186/1471-2148-11-199.
Roberson, A.L., Roadt, J., Halevy, I. & Kasting, J.F. (2011). Greenhouse warming by nitrous oxide and methane in the Proterozoic Eon. Geobiology, 9(313-320).
Saltzman, M., Young, S., Kump, L., Gill, B., Lyons, T. & Runnegar, B. (2011). A pulse of atmospheric oxygen during the late Cambrian and implications for plankton and animal biodiversification. Proc. Nat’l Acad. Sci., 108.
Sansjofre, P., Ader, M., Trindade, R.I.F., Elie, M., Lyons, J., Cartigny, P., Nogueira, A.C.R. (2011). A carbon isotope challenge to the snowball Earth. Nature, 478: 93-97.
Schopf, J.W. (2011). Pioneers of astrobiology: J.William Schopf. Astrobiology, 11: 1-6.
Schopf, J.W. (2011). The paleobiologic record of photosynthesis. Photosynthesis Research, 107: 87-101.
Schopf, J.W. & Kudryavtsev, A.B. (2011). Biogenicity of Apex Chert Microstructures. Nature Geoscience, 4: 346-347.
Schopf, J.W. & Kudryavtsev, A.B. (2011). Confocal laser scanning microscopy and Raman (and fluorescence) spectroscopic imagery of permineralized Cambrian and Neoproterozoic fossils. In: M. Laflamme, S.D.a.J.S. (Eds.). Quantifying the Evolution of Early Life: Numerical Approaches to the Evaluation of Fossils and Ancient Ecosystems. Amsterdam: Springer.
Shapiro, B., Ho, S.Y.W., Drummond, A.J., Suchard, M.A., Pybus, O. & Rambaut, A. (2011). A Bayesian phylogenetic method to estimate unknown sequence ages. Mol. Biol. Evol., 28: 879-887.
Tian, F., J. F. Kasting, and K. Zahnle, Revisiting HCN formation in Earth’s early atmosphere, Earth Planet. Sci. Lett. 308, 417-423 (2011).
Turich C. H. and K. H. Freeman (2011) Archaea lipids record paleosalinity in hypersaline conditions. Organic Geochemistry 42, 1147-1157.
Workman, C., Dalen, L., Vartanyan, S., Shapiro, B., Kosintev, P., Sher, A., Gotherstrom, A. & Barnes, I. (2011). Population-level genotyping of coat colour polymorphism in woolly mammoth (Mammuthus primigenius). Quat. Sci. Rev., 30: 2304-2308.
Wright, J.T., Fakhouri, O., Marcy, G.W., Han, E., Feng, Y., Johnson, J.A., Howard, A.W., Fischer, D.A., Valenti, J.A., Anderson, J. & Piskunov, N. (2011). The Exoplanet Orbit Database. Publications of the Astronomical Society of the Pacific, 123: 412-422.
Wright, J.T., Veras, D., Ford, E.B., Johnson, J.A., Marcy, G.W., Howard, A.W., Isaacson, H., Fischer, D.A., Spronck, J., Anderson, J. & Valenti, J. (2011). The California Planet Survey. III. A Possible 2:1 Resonance in the Exoplanetary Triple System HD 37124. The Astrophysical Journal, 730: 93.
Zugger, M. E., J. F. Kasting, D. M. Williams, T. J. Kane, C. R. Philbrick, (2011). Erratum: “Light scattering from exoplanet oceans and atmospheres” (2010, ApJ, 723, 1168-1179), Astrophysical Journal 739:55.
Zugger, M. E., J. F. Kasting, D. M. Williams, T. J. Kane, C. R. Philbrick, (2011). Searching for water Earths in the near infrared, Astrophysical Journal 739:12.

2010

Bailey, J.V., Raub, T.D., Meckler, A.N., Harrison, B. K., Raub, T.M.D., Green, A.M., Orphan, V.J. (2010). Pseudofossils in relict methane seep carbonates resemble endemic microbial consortia in Palaeogeography, Palaeoclimatology, Palaeoecology 285 131-142.
Battistuzzi, F. U., Filipski, A., Hedges, S. B., and Kumar, S. (2010). Performance of relaxed clock methods in estimating evolutionary divergence times and their credibility intervals. Mol. Biol. Evol. 27: 1289-1300.
Buss, H.L., Mathur, R., White, A.F. & Brantley, S.L. (2010). Phosphorus and iron cycling in deep saprolite, Luquillo Muntains, Puerto Rico. Chemical Geology, 269: 52-61.
Campos, P., Willerslev, E., Sher, A,, Axelsson, E., Tikhonov, A., Aaris-Sørensen, K., Greenwood, A., Kahlke, R-D., Kosintsev, P., Krakhmalnaya, T., Kuznetsova, T., Lemey, P., MacPhee, R.D., Norris, C.A., Shepherd, K., Suchard, M.A., Zazula, G.D., Shapiro, B., Gilbert, M.T.P. (2010). Ancient DNA analysis excludes humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc. Natl. Acad. Sci. USA 107: 5675-5680.
Chakraborty, A., Anadarao, B.G., Mahadevan, S., Planets, P.T.H., Coudé Du Foresto, V., Gelino, D.M. & Ribas, I. (2010). The Search for Exoplanets in India.
Colón, K.D., Ford, E.B., Lee, B., Mahadevan, S. & Blake, C.H. (2010). Characterizing transiting extrasolar planets with narrow-band photometry and GTC/OSIRIS. 408.
Czaja A. D., Johnson, C. M., Beard, B. L., Eigenbrode, J. L., Freeman, K. H. and Yamaguchi K. E. (2010) Iron and carbon isotope evidence for ecosystem and environmental diversity in the ~2.7 to 2.5 Ga Hamersley Province, Western Australia. Earth and Planetary Science Letters 292, 170-180.
Diefendorf, A.F., Mueller, K.E., Wing, S.L., Koch, P.L. and Freeman, K.H., (2010). Global patterns in leaf 13C discrimination and implications for studies of past and future climate. Proceedings of the National Academies of Science, 107, 5738-5743.
Fantle, M.S. (2010). Evaluating the Ca isotope proxy, Am. J. Sci. 310: 194-230, doi10.2475/03/2010.03.
Hoffman, M. et al. (2010). The impact of conservation on the status of the World’s vertebrates. Science 330: 1503-1509.
Howard, A.W., Johnson, J.A., Marcy, G.W., Fischer, D.A., Wright, J.T., Bernat, D., Henry, G.W., Peek, K.M.G., Isaacson, H., Apps, K., Endl, M., Cochran, W.D., Valenti, J.A., Anderson, J. & Piskunov, N.E. (2010). The California Planet Survey. I. Four New Giant Exoplanets. The Astrophysical Journal, 721: 1467-1481.
Howard, A.W., Marcy, G.W., Johnson, J.A., Fischer, D.A., Wright, J.T., Isaacson, H., Valenti, J.A., Anderson, J., Lin, D.N.C. & Ida, S. (2010). The Occurrence and Mass Distribution of Close-in Super-Earths, Neptunes, and Jupiters. Science, 330: 653.
Johnson, J.A., Howard, A.W., Bowler, B.P., Henry, G.w., Marcy, G.W., Wright, J.T., Fischer, D.A., Isaacson, H. (2010). Retired A Stars and Their Companions IV: Seven Jovian Exoplanets form Keck Observatory. Publications of the Astronomical Society of the Pacific 122, 892, 701-711.
Johnson, J.A., Howard, A.W., Marcy, G.W., Bowler, B.P., Henry, G.W., Fischer, D.A., Apps, K., Isaacson, H., Wright, J.T. (2010). The California Planet Survey II: A Saturn-Mass Planet Orbiting the M Dwarf GI 649. Publications of the Astronomical Society of the Pacific 122, 149.
Kasting, J. F., W. A. Traub, et al., (2010). Exoplanet characterization and the search for life, White paper for Astronomy and Astrophysics Decadal Survey, available at: http://sites.nationalacademies.org/BPA/BPA_050603#planetarysystems
Kasting, J. F. (2010). Faint young Sun redux, Nature 464, 687-689.
Kuhn, T.S., McFarlane, K., Groves, P., Moers, A.O., Shapiro, B. (2010). Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon. Mol. Ecol. 19: 1312-1318.
Kump, L.R., Kasting, J.F., and Crane, R.G. (2010). The Earth System, 3/e. New Jersey: Prentice Hall, 420 pp.
Kuhn, T.S., McFarlane, K., Groves, P., Moers, A.O., Shapiro, B. (2010). Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon. Mol. Ecol. 19: 1312-1318.
Lal, D., Schopf, J. W., Aboott, P.L., Vacher, L., Jull, A. J. T. and McHargue, L. (2010). Nuclear, chemical and biological characterization of formation histories of ironstones from several sites in Southern California: Dominant role of bacterial activity. Earth Planet. Sci. Letters 296: 227-234.
Loveland-Curtze, J., Miteva, V., Brenchley, J. (2001). Novel Ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov. Extremophiles 14: 61-69
Mahadevan, S., Ramsey, L., Redman, S., Zonak, S., Wright, J., Wolszczan, A., Endl, M., Zhao, B., Planets, P.T.H., Coudé Du Foresto, V., Gelino, D.M. & Ribas, I. (2010). The Habitable Zone Planet Finder Project: A Proposed High Resolution NIR Spectrograph for the Hobby Eberly Telescope (HET) to Discover Low Mass Exoplanets around M Stars.
Moczydłowska, M., Schopf, J.W., and Willman, S. (2010). Micro- and nano-scale ultrastructure of cell walls in Cryogenian microfossils: revealing their biological affinity. Lethaia 43: 129-136.
Mueller, K.E., Diefendorf, A.F., Freeman, K.H., and Eissenstat, D.N., (2010) Appraising the roles of nutrient availability, global change, and functional traits during the angiosperm rise to dominance. Ecology Letters, 13, E1-E6.
Narbonne, G.M., Schopf, J.W., and Walter, M.R. (2010). Hans J. Hofmann (1936-2010). Geology 39(2):13-14.
Polissar P. J. and Freeman K. H. (2010) Effects of aridity and vegetation on plant-wax δD in modern lake sediments. Geochimica et Cosmochimica Acta, 74, 5785-5797.
Rhodes, M.E., Fitz-Gibbon, S.T., Oren, A., House, C.H., 2010. Amino Acid Signatures of Salinity on an Environmental Scale with a Focus on the Dead Sea. Environmental Microbiology, 12: 2613-2623.
Schopf, J.W., Kudryavtsev, A.B., and Sergeev, V.N. (2010). Confocal laser scanning microscopy and Raman imagery of the late Neoproterozoic Chichkan microbiota of South Kazakhstan. Journal of Paleontology 84: 402-416.
Schopf, J.W., Kudryavtsev, A.B., Sugitani, K., and Walter, M.R. (2010). Precambrian microbe-like pseudofossils: a promising solution to the problem. Precambrian Research 179: 191-205.
Schopf, J.W., Kudryavtssev, A.B., Tripathi, B., and Czaja, A.D. (2010). Three-dimensional Morphological (CLSM) and Chemical (Raman) Imagery of CellularlyMineralized Fossils. In: P.A. Allison and D.J. Bottjer, (Editors) Taphonomy: Process and Bias Through Time (Amsterdam: Springer), pp. 457-486.
Schopf, J. W. and Kudryavtsev, A. B. (2010). A renaissance in studies of ancient life. Geology Today. 26: 141-146.
Segura, A., L. Walkowicz, V. Meadows, J. F. Kasting, and S. Hawley, (2010). The effect of a strong stellar flare on the atmospheric chemistry of an Earth-like planet orbiting an M dwarf, Astrobiology. 10, 751-771.
Sergeev, V.N. and Schopf, J.W. (2010). Taxonomy, paleoecology and biostratigraphy of the late NeoProterozoic Chichkan microbiota of South Kazakhstan: the marine biosphere on the eve of metazoan radiation. Journal of Paleontology 84: 363-401.
Taylor, P.D., Vinn, O., Kudryavtsev, A.B., and Schopf, J.W. (2010). Raman spectroscopic study of the mineral composition of cirratulid tubes (Annelida, Polychaeta). Journal of Structural Biology 171: 402-405.
Tian, F., Claire, M.W., Haqq-Misra, J.D., Smith, M., Crisp, D.C., Catling, D., Zahnle, K., and Kasting, J. F. (2010). Photochemical and climate consequences of sulfur outgassing on early Mars, Earth Planet. Sci. Lett. 295, 412-418 (2010).
Vidal, N., Marin, J., Morini, M., Donnellan, S., Branch, W.R., Thomas, R., Vences, M., Wynn A., Cruaud, C., and Hedges, S.B. (2010). Blindsnake evolutionary tree reveals long history on Gonwana. Biology Letters 6:558-561.
Zugger, M. E., J. F. Kasting, D. M. Williams, T. J. Kane, C. R. Philbrick, (2010). Light scattering from exoplanet oceans and atmospheres, Astrophysical Journal 723, 1168-1179.

2009

Barnett, R., Shapiro, B., Ho, S.Y.W., Barnes, I., Burger, J., Yamaguchi, N., Higham, T., Wheeler, H.T., Rosendhal, W., Sher, A.V., Baryshnikov, G., Coooper, A. (2009). Phylogeography of lions (Panthera leo) reveals three distinct taxa and a Late Pleistocene reduction in genetic diversity. Mol. Ecol. 18: 1668-1677.`
Battistuzzi, F.U., and Hedges, S.B. (2009). A major clade of prokaryotes with ancient adaptations to life on land. Mol. Biol. Evol. 26:335-344.
Battistuzzi, F. U., Hedges, S. B. (2009). Archaebacteria. Pp. 101-105 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Battistuzzi, F. U., Hedges, S. B. (2009). Eubacteria. Pp. 106-115 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Beal, E.J., House, C.H., and Orphan, V.J. (2009) Manganese- and Iron-Dependent Marine Methane Oxidation. Science 325: 184-187.
Bhattacharya, D., Yoon, H.-S., Hedges, S. B., Hackett, J. D. (2009). Eukaryotes (Eukaryota). Pp. 116-120 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Bunce, M. Worthy, T., Phillips, M., Holdaway, R., Willerslev, E., Haile, J., Shapiro, B., Scofield, P., Drummond, A., Kamp, R., Cooper A. (2009). The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogegraphy. Pro. Natl. Acad. Sci. USA 106: 20646-20651.
Butler R. P., Howard A. W., Vogt S. S., Wright J. T. (2009) Nondetection of the Neptune-Mass Planet Reported Around GJ 176. The Astrophysical Journal 691, 1738-1743.
Cameron, V., Vance, D. Archer, C. House, C.H., 2009. Nickel Stable Isotopes: A Novel Isotope Biomarker. Proceeding of the National Academy of Sciences, 106: 10944-10948.
Collins, J.J., Penkman, K.E.H., Rohald, N., Shapiro, B., Dobberstein, R.C., Rotz-Timme, A., Hofretier, M. (2009). Is amino acid racemization a useful tool for screening for ancient DNA in bone? Proc. Roy. Soc. B 276:2971-2977.
Czaja, A.D., Kudryavtsev, A.B., Cody G.D., and Schopf, J.W. (2009). Characterization of permineralized kerogen from an Eocene fossil fern. Organic Geochemistry 40: 353-364.
Fischer, D., Driscoll, P., Isaacson, H., Giguere, M., Marcy, G.W., Valenti, J., Wright, J.T., Henry, G.W., Johnson, J.A., Howard, A., Peek, K., McCarthy, C. (2009). Five Planets and an Independent Confirmation of HD 196885Ab from Lick Observatory. Astrophysical Journal 703, 1545.
Goyne, K., Brantley, S.L., et al. (2009) Rare earth element release from phosphate minerals in the presence of organic acids. Chemical Geology. 10.1016/j.chemgeo.2010.03.011.
Hausrath, E.M., Neaman, A., and Brantley, S.L. (2009). Elemental release rates from dissolving basalt and granite with and without organic ligands. American Journal of Science, Volume 309, No. 8, 633-660.
Hedges, S. B., Kumar, S. (Eds.), (2009). The Timetree of Life. Oxford University Press, Oxford, UK. 551 p.
Hedges, S. B., Kumar, S. (2009). Discovering the timetree of life. Pp. 3-18 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Hedges, S. B. (2009). Life. Pp. 89-98 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Hedges, S. B. (2009). Vertebrates (Vertebrata). Pp. 309-314 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Hedges, S. B., Vidal, N. (2009). Lizards, snakes, and amphisbaenians (Squamata). Pp. 383-389 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Heinicke, M. P., Naylor, J. P., Hedges, S. B. (2009). Cartilaginous fishes (Chondrichthyes). Pp. 320-327 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Heinicke, M. P., Sander, J. M., Hedges, S. B. (2009). Lungfishes (Dipnoi). Pp. 348-350 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
Hoashi, M., Bevacqua, D.C., Otake, T., Watanabe, Y., Hickman, A.H., Utsunomiya, S., and Ohmoto, H. (2009). Primary haematite formation in an oxygenated sea 3.46 billion years ago. Nature Geosciences 2, 301-306.
House, C.H. (2009). The Tree of Life viewed through the contents of genomes. Methods in Molecular Biology, 532: 141-161.
House, C.H., Orphan, V.O., Turk, K.A., Thomas, B., Pernthaler, A., Vrentas, J. M., Joye, S.B., (2009). Extensive carbon isotopic heterogeneity among methane seep microbiota. Environmental Microbiology, 11: 2207-2215.
Howard A. W., Johnson J. A., Marcy G. W., Fischer D. A., Wright J. T., Henry G. W., Giguere M. J., Isaacson H., Valenti J. A., Anderson J., Piskunov N. E. (2009) The NASA-UC Eta-Earth Program. I. A Super-Earth Orbiting HD 7924. The Astrophysical Journal 696, 75-83.
Jang, J.-H., Brantley, S. L. (2009) Investigation of Wustite (FeO) dissolution: implications for reductive dissolution of ferric oxides. Environmental Science Technology 43:4, 1086-1090. Supplementl Information.
Kasting, J. F., W. A. Traub, et al., Exoplanet characterization and the search for life, White paper for Astronomy and Astrophysics Decadal Survey, available at: http://sites.nationalacademies.org/BPA/BPA_050603#planetarysystems
Kato, Y., Suzuki, K., Nakamura, K., Hickman, A. H., Nedachi, M., Kusakae, M., Bevacqua, D.C., and Ohmoto. H. (2009). Hematite formation by oxygenated groundwater more than 2.76 billion years ago. Earth & Planetary Science Letters 278, 40-49.
Kump, L.R. (2009) Tipping pointedly colder. Science (Perspectives) 323: 1175-1176.
Kump, L.R., Bralower, T.J., and Ridgwell, A. (2009). Ocean acidification in deep time. Oceanography 22: 94-107.
Lal, A.K. (2008). Origin of life. Astrophysics and Space Science 317: 267-278. Loveland-Curtze, J., Miteva, V., and Brenchley, J.E. (2009b). Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice. . Intern. J. Syst. Evol. Microbiol. 59: 1272 – 1277.
Lyons, J. R. (2009). Atmospherically-derived mass-independent sulfur isotope signatures, and incorporation into sediments. Chemical Geology 267, 164-174 (2009).
Lyons, J. R., Lewis, R.S., Clayton, R.N. (2009). Comment on “Experimental Test of Self-shielding in Vacuum Ultraviolet Photodissociation of CO”. Science 324, 1516-a.
Miteva, V., Teacher, C., Sowers, T., and Brenchley, J. (2009). Comparison of the microbial diversity at different depths of the GISP2 Greenland icecore in relationship to deposition climates. Environmental Microbiology 11 (3), 640-656. Moody, K (2009). “Three Body Dynamics in Dense Gravitational Systems” Ph.D, Dissertation, Department of Astronomy, The Pennsylvania State University, Aug. 2009.
Orphan, V.J., and House, C.H. (2009). Geobiological investigations using secondary ion mass spectrometry (SIMS): microanalytical analysis of extant and ancient microbial processes. Geobiology, 7: 360-372.
Orphan, V.J., Turk, K.A., Green, A.M., House, C.H. (2009). Patterns of 15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS. Environmental Microbiology, 11: 1777-1791.
Peek K. M. G., Johnson J. A., Fischer D. A., Marcy G. W., Henry G. W., Howard A. W., Wright J. T., Lowe T. B., Reffert S., Schwab C., Williams P. K. G., Isaacson H., Giguere M. J. (2009) Old, Rich, and Eccentric: Two Jovian Planets Orbiting Evolved Metal-Rich Stars. Publications of the Astronomical Society of the Pacific 121, 613-620.
Polissar P. J., Freeman K. H., Rowley D. B., Smith F. A. and B. Currie (2009). Paleoaltimetry of the Tibetan Plateau from D/H Ratios of Lipid Biomarkers. Earth and Planetary Science Letters 287 (1), p.64-76.
Polissar, P. J., Fulton J., Turich C. H. and K. H. Freeman (2009) Measurement of 13C and 15N isotopic compositions on nanomolar quantities of organic materials. Analytical Chemistry 81, 755-763.
Rambaut, A., Drummond, A.J., Ho, S.Y.W., Shapiro, B. (2009). Acommodating the effect of ancient DNA damage on inferences of demographic histories. Mol. Biol. Evol. 26: 245-248.
Rijsdijk, K.F., Hume, J.P., Bunnik, F., Florens, V., Baider, C., Shapiro, B., et al. (2009). A Middle-Holocene Concentration-Lagerstatten on Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus). Quat. Sci. Rev. 28: 14-24.
Schopf, J.W. (2009). Emergence of Precambrian paleobiology: a new field of science. In: D. Sepkoski and M. Ruse (Editors), The Paleobiological Revolution, Essays on the Growth of Modern Paleontology (University of Chicago Press, Chicago. IL), pp. 88-110.
Schopf, J.W. (2009). Organismal evolution and radiation before the Cambrian. In: M. Ruse, J. Travis, and J. Zinser (Editors), Evolution: The First 4 Billion Years (Harvard University Press, Cambridge, MA), pp. 775-786.
Schopf, J.W. (2009). Paleontology, Microbial. In: J. Lederberg and M. Schaechter (Editors), Encyclopedia of Microbiology, 3rd Edition (Amsterdam: Elsevier), pp. 390-400.
Schopf, J.W. (2009). The Hunt for Precambrian Fossils: An Abbreviated Genealogy of the Science. Precambrian Research 173: 4-9.
Schopf, J.W. and Bottjer, D.J. (2009). World Summit on Ancient Microscopic Fossils: Preface. Precambrian Research 173: 1-3.
Schopf, J.W. and Kudryavtsev, A.B. (2009). Confocal laser scanning microscopy and Raman imagery of ancient microscopic fossils. Precambrian Research 173: 39-49.
Schouten S. and 28 others (2009) An interlaboratory study of TEX86 and BIT analysis using high-performance liquid chromatography-mass spectrometry. Geochem. Geophys. Geosys. 10, Art. No. Q03012Mar2012009.
Thomas, R. B., Freeman K. H. and Arthur M.A. (2009) Intramolecular carbon isotopic analysis of acetic acid by direct injection of aqueous solution. Organic Geochemistry 40, 195-200.
Tian, F., Kasting, J.F., and Solomon, S.C. (2009). Fast thermal escape of carbon and oxygen from a dense, CO2-rich early martian atmosphere, Geophys. Res. Lett., 36, L02205, doi:10.1029/2008GL036513
Valenti, J.A., Fischer, D., Marcy, G.W., Johnson, J.A., Henry, G.W., Wright, J.T., Howard, A.W., Giguere, M., Isaacson, H. (2009). Two Exoplanets Discovered at Keck Observatory. Astrophysical Journal 702, 989-997.
Vidal, N., Rage, J.-C., Couloux, A., Hedges, S. B. (2009). Snakes (Serpentes). Pp. 390-397 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York.
Vidal, N., Rage, J.-C., Couloux, A., Hedges, S. B. (2009). Snakes (Serpentes). Pp. 390-397 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York.
Watanabe, Y., Farquhar, J., and Ohmoto, H. (2009). Anomalous fractionations of sulfur Isotopes during thermochemical sulfate reduction. Science, 324, 370-373.
Weinstock, J., Shapiro, B., Prieto, A., Martin, J.C., Gonzales, B.A., Gilbert, M.P.T., Willerslev, E. (2009). The Late Pleistocene distribution of vicunas (Vicugna vicugna) and the “extinction” of the gracile Ilama (Lama gracilis): new molecular data. Quat. Sci. Rev. 28: 15-16.
Wright J. T., Fischer D. A., Ford E. B., Veras D., Wang J., Henry G. W., Marcy G. W., Howard A. W., Johnson J. A. (2009) A Third Giant Planet Orbiting HIP 14810. The Astrophysical Journal 699, L97-L101.
Wright J. T., Howard A. W. (2009) Efficient Fitting of Multiplanet Keplerian Models to Radial Velocity and Astrometry Data. The Astrophysical Journal Supplement Series 182, 205-215.
Wright J. T., Upadhyay S., Marcy G. W., Fischer D. A., Ford E. B., Johnson J. A. (2009) Ten New and Updated Multiplanet Systems and a Survey of Exoplanetary Systems. The Astrophysical Journal 693, 1084-1099.
Young, S. A., Saltzman, M. R., Foland, K. A., Linder, J. S., and Kump, L. R. (2009). A major drop in seawater 87Sr/86Sr during the Middle Ordovician (Darriwilian): Links to volcanism and climate. Geology 37: 951-954.
Zazula, G.D., MacKay, G., Andrews, T.D., Shapiro, B., Letts, B., Brock, F. (2009). A Late Pleistocene steppe bison (Bison priscus) partial carcass from Tsiigehtchic, Northwest Territories, Canada. Quat. Sci. Rev. 28: 2734-2742.

2008

Biddle, J.F., Fitz-Gibbon, S.T., Schuster, S.C., Brenchley, J.E., House, C.H., 2008. Metagenomic signatures of the subseafloor biosphere. PNAS 105: 10583-10588.
Domagal-Goldman, S,D., Kasting, J. F., Johnson, D.T., and Farquhar, J. (2008). Organic haze, glaciations and multiple sulfur isotopes in the Mid-Archean era. In Earth and Planetary Science Letters: http://dx.doi.org/10.1016/j.epsl.2008.01.040.
Eigenbrode J. L., Freeman K. H. and Summons R. E. (2008) Methylhopane biomarker hydrocarbons in Hamersley Province sediments provide evidence for Neoarchean aerobiosis. Earth and Planetary Science Letters 273, 323-331.
Ewing, S., Yang, W., DePaolo, D.J., Michalski, G., Kendall, C., Stewart, B.W., Thiemens, M. and Amundson, R. (2008). Non-biological fractionation of stable Ca isotopes in soils of the Atacama Desert, Chile. Geochimica et Cosmochimica Acta 72, 1096-1110.
Haqq-Misra, J.D., Domagal-Goldman, S.D., Kasting, P.J., and Kasting, J.F. (2008). A revised hazy methane greenhouse for the early Earth, Astrobiol., 1127-1137.
Hausrath, E.M., Navarre-Sitchler, A.K., Sak, P.B., Steefel, C.I., and Brantley S.L. (2008). Basalt weathering rates on Earth and the duration of water on Mars. Geology 36:1, 67-70.
Hausrath, E.M., Treiman, A.H., Vicenzi, E., Bish, D.L., Blake, D., Sarrazin, P. et al. (2008). Short- and long-term olivine weathering in Svalbard: Implications for Mars. Astrobiology 8: 1079-1092.
Hayashi, K-I., Naraoka, H., and Ohmoto, H. (2008). Oxygen isotope study of paleoproterozoic banded iron formation, Hamersley Basin, Western Australia. Resources Geology 58, 43-51.
Hydutsky, D.P., Bianco, N.J., Castleman Jr., A.W. (2008). The photodissociation of SO2 between 200 and 197 nm. Chemical Physics 350, 212-219.
Junium C.K., Mawson D.H., Arthur M.A., Freeman K.H and B.J. Keely (2008) Unexpected occurrence and significance of zinc alkyl porphyrins in Cenomanian-Turonian black shales of the Demerara Rise. Organic Geochemistry 39, 1081-1087.
Kasting J.F. (2008). Chapter 8: The primitive Earth, in Prebiotic Evolution and Astrobiology, J. T.-F. Wong and A. Lazcano, eds., Landes Bioscience, Austin, TX
Kasting, J.F. (2008). Habitable planets around the Sun and other stars, in Extrasolar Planets: XVI Canary Islands Winter School of Astrophysics, H. Deeg, J.A. Belmonte, and A. Aparicio, eds., Cambridge Univ. Press Cambridge, 217-244.
Kump, L.R., (2008). The rise of atmospheric oxygen. Nature v. 451:27-278.
Kump, L.R. and Pollard, D. (2008). Brevia: Amplification of Cretaceous warmth by biological cloud feedbacks. Science, 320: 195.
Lammer, H., Kasting, J. F., Chassefiere, E., Johnson, R.E., Kulikov, Y.N., and F. Tian (2008). Atmospheric escape and evolution of terrestrial planets and satellites, Space Science Rev. 139, 399-436.
Lasaga, A.C., Otake, T., Watanabe, Y., Ohmoto, H. (2008). Anomalous fractionation of sulfur isotopes during heterogeneous reactons. Earth. Planet. Sci. Letts., 268, 225-238.
Lunine, J.I., Fischer, D., Hammel, H.B., Henning, T., Hillenbrand, L., Kasting, J., Laughlin, G., Macintosh, B., Marley, M., Melnick, G., Monet, D., Noecker, C., Peale, S., Quirrenbach, A., Seager, S., Winn, J.N. (2008). Worlds beyond: A strategy for the detection and characterization of exoplanets: Executive Summary of a report of the ExoPlanet Task Force, Astronomy and Astrophysics Advisory Committee Washington, DC June 23, 2008, Astrobiol. 8, 875-881.
Lyons, J.R., Bergin, E., Ciesla, F., Davis, A., Desch, S., Hashizume, K., Lee, J.-E. (2008). Timescales of oxygen isotope evolution in the solar nebula. Geochim Cosmochim. Acta 73, 4998-5017.
Macalady, J.L., Dattagupta, S., Schaperdoth, I., Druschel, G.K., Eastman, D. (2008). Niche differentiation among sulfur-oxidizing bacterial populations in cave waters . ISME Journal 2: 590-601, doi:10.1038/ismej.2008.25.
Meyer, K.J. and Kump, L.R. (2008). Oceanic euxinia in Earth history: Causes and Consequences. Annual Reviews of Earth and Planetary Sciences 36:251-88.
Miteva, V. (2008). in Psychrochrophiles: from biodiversity to biotechnology. (eds. Margesin, R., Schinner, F., Marx, J.-C. & Gerday, C.) 31-50 (Springer-Verlad Berlin Heidelberg.
Miteva, V.I., Lantz, S. & Brenchley, J.E. (2008). Characterization of a cryptic plasmid from a Greenland ice core Arthrobacter isolate and construction of a shuttle vector that replicates in psychrophilic high G+C Gram-positive recipients. Extremophiles 12, 441-449.
Moran, J J., Beal, E.J., Vrentas, J.M., Orphan, V.J., Freeman, K.H., House, C.H. (2008). Methyl sulfides as intermediates in the anaerobic oxidation of methane. Environmental Microbiology 10: 162 (Featured in Microbe, a magazine of the ASM).
Moran, J.J., House, C.H., Vrentas, J.M., Freeman, K.H. (2008). Methyl Sulfide Production by a Novel Carbon Monoxide Metabolism in Methanosarcina acetivorans, Applied and Environmental Microbiology. 74: 540-542.
Ohmoto, H., Runnegar, B., Kump, L.R., Fogel, M.L., Kamber, B., Anbar, A.D., Knauth, P.L., Lowe, D.R., Sumner, D.Y., and Watanabe, Y. (2008). Biosignatures in ancient rocks: a summary of discussions at a field workshop on biosignatures in ancient rocks. Astrobiology 8, 883-907.
Otake, T., Lasaga, A.C., and Ohmoto, H. (2008). Ab initio calculations for equilibrium fractionations in multiple sulfur isotope system. Chemical Geology 249, 357-376.
Panchuk, K.M., Ridgwell, A., and Kump, L.R. (2008). Sedimentary response to Paleocene-Eocene Thermal Maximum carbon release: A model-data comparison. Geology 36: 315-318.
Strapoc, D., Picardal, F., Turich, C., Schaperdoth, I., Macalady, J.L., Lipp, J., Lin, Y.-S., Mohr, T., Schuboltz, F., Hinrich, K.-U., Mastalerz, M., Schimmelmann, A. (2008). Coalbed methane-producing microbial community in the Illinois Basin. Applied and Environmental Microbiology 74(8): 2424-2432.
Tian, F., Kasting, J.F., Liu, H. and Roble, R.G. (2008). Hydrodynamic planetary thermosphere model. I: The response of the Earth’s thermosphere to extreme solar EUV conditions and the significance of adiabatic colling, J. Geophys. Res. – Planets. 113, E5 (May), E05008.
Turich, C.H., Freeman, K.H., Jones, A.D. , Bruns, M.A., Conte, M. and S.G. Wakeham (2008) Reply to the Comment by S. Schouten, M. van der Meer, E. Hopmans, and J.S. Sinninghe Damsté on “Lipids of marine Archaea: Patterns and provenance in the water column” Geochimica et Cosmochimica Acta 72, 21, 1 November 2008, Pages 5347-5349.
Wander, M.C.F., Kubicki, J.D., and Schoonen, M.A.A. (2008). Reduction of N2 by Fevia Homogeneous and Heterogeneous Reactions Part 2L The Role of Metal Binding in Activating N2 for Reduction; a Requirement for Both Pre-biotic and Biological Mechanisms. Orig. Life Biosph 38: 195-209.
Wander, M.C.F., and Schoonen, M.A.A. 2008). Reduction of N2 by Fevia Homogeneous and Heterogeneous Reactions Part I: Evaluation of Aqueous Photochemical, Prebiotic pathways. Orig Life Evol Biosph 38: 127-137
Zahnle, K.J., Haberle, R.M., Catling, D.C., and Kasting, J.F. (2008). Photochemical instability of the ancient martian atmosphere, J. Geophys. Res–Planets. 113, E11, DOI: 10.1029/2008JE003160.
Zerkle, A.L., C.K. Junium, D.E. Canfield, and House, C.H. (2008). Production of 15N-depleted biomass during cyanobacterial N2-fixation at high Fe concentrations, J. Geophys., J. Geophys. Res., 113: G03014.

2007

Biddle, J.F., House, C. Fitz-Gibbon, S. Schuster, S. & Brenchley, J.E. (2007). Metagenomics of deeply buried marine sediments. Geochimica et Cosmochimica Acta 71, A90.
Buss, H.L., Luttge, A., and Brantley, S.L. (2007). Etch pit formation on iron silicate surfaces during siderophore-promoted dissolution. Chemical Geology 240: 326-342.
Catling, D., Kasting, J.F. (2007). Planetary atmospheres and life, in Planets and Life: The Emerging Science of Astrobiology, W.T. Sullivan, III, and J.A. Baross, eds., Cambridge University Press, Cambridge, pp. 91-116.
Debes, J., Sigurdsson, S., Hansen, B., (2007). Cool Customers in the Stellar Graveyard. IV. Spitzer Searach for Mid-IR excesses Around Five DAs. Astronomical Journal, 134, 1662-1670.
Ewing, S. A., Michalski, G., Thiemens, M. H. Quinn, R. C. Macalady, J. L., Kohl, S. Wankel, S. D., Kendall, C. McKay, C. P., and Amundson, R. (2007). The Rainfall Limit of the Nitrogen Cycle on Earth. Global Biogeochem. Cycles, doi:10.1029/2006GB002734.
Hausrath, E.M., Liermann, L.J., House, C.H., Ferry, J.G. & Brantley, S.L. (2007). The effect of methanogen growth on mineral substrates: will Ni markers of methanogen-based communities be detectable in the rock record? Geobiology, 5(1):49-61.
Heinicke, M.P., Duellman, W.E. & Hedges, S.B. (2007). Major Caribbean and Central American frog faunas originated by oceanic dispersal. Proceedings of the National Academy of Sciences (USA), 104:10092-10097.
Holland, S. M., and Patzkowsky, M. E. (2007). Gradient ecology of a biotic invasion: biofacies of the type Cincinnatian series (Upper Ordovician), Cincinnati, Ohio region, USA: Palaios, v. 22, p. 392-407.
House, K. Z., House C. H., Schrag, D.P., and Aziz, M.J. (2007). Electrochemical Acceleration of Chemical Weathering as an Energetically Feasible Approach to Mitigating Anthropogenic Climate Change, Environ. Sci. Technol., 41, 24:8464-8470 (featured as a ACS most downloaded paper).
House, C.H. (2007). Linking taxonomy with environmental geochemistry and why it matters to the field of geobiology. Geobiology, 5:1-3.
Kump, L.R. and Barley, M.E. (2007). Continental tectonics, increased subaerial volanism and the rise of atmospheric oxygen. Nature 448: 1033-1036.
Krug, A. Z., and Patzkowsky, M. E . (2007) Geographic variation in turnover and recovery from the Late Ordovician mass extinction: Paleobiology, v. 33, 435-454.
Liermann, L.J., Hausrath, E.M., Anbar, A.D. & Brantley, S.L. (2007). Assimilatory and dissimilatory processes of microorganisms affecting metals in the environment. J. Anal. At. Spectrom., 22:867-877.
Macalady, J.L., Jones, D.S. & Lyon, E.H. (2007). Extremely acidic, pendulous microbial biofilms from the Frasassi cave system, Italy. Environmental Microbiology, 9(6):1402-1414.
Mandell, A., Raymond, S., Sigurdsson, S. (2007). Formation of Earth-like Planets During and After Giant Planet Migration. Astrophysical Journal, 660, 823-844.
Miteva, V.I., Sowers, T.A. & Brenchley, J.E. (2007). Production of N2O by ammonia oxidizing bacteria at subfreezing temperatures as a model for assessing the N2O anomalies in the Vostok ice core. Geomicrobiology Journal, 24(5).
Moran, J.J., House, C.H., Thomas, B. & Freeman, K.H. (2007). Products of trace methane oxidation during nonmethyltrophic growth by Methanosarcina. Journal of Geophysical Research, 112: G02011.
Otake, T., Wesolowski, D. J., Lawrence, M. A., Lawrence, F. A. & Ohmoto, H. (2007). Experimental evidence for non-redox transformations between magnetite and hematite under H2-rich hydrothermal conditions. Earth and Planetary Science Letters, 257, 60-70.
Payne, J. L. and Kump, L. R. (2007). Evidence for recurrent Early Triassic massive volcanism from quantitative interpreation of carbon isotope fluctuations. Earth and Planetary Science Letters 256: 264-277.
Payne, J.L., Lehrmann, D.J., Follet, D., Seibel, M., Kump, L.R., Riccardi, A., Altiner, D., Sano, H., Wei, J. (2007). Erosional truncation of uppermost Permian shallow-marine carbonates and implications for Permian-Triassic bundary events. Bulletin of the Geological Society of America 119: 771-784.
Patzkowsky, M. E., and Holland, S. M. (2007). Diversity partitioning of a Late Ordovician marine biotic invasion: controls on diversity in regional ecosystems: Paleobiology, v. 33, p. 295-309.
Riccardi, A.L., Kump, L.R., Arthur, M.A. & D’Hondt, S. (2007). Carbon isotopic evidence for chemocline upward excursions during the end-Permian event. Palaeogeograpy Palaeoclimatology Paleoecology, 248:73-81.
Ross, D. E., Ruebush, S., Brantley, S., Hartshorne, R. S., Clarke, T. A., Richardson, D. J., and Tien, M. (2007). Characterization of Protein-Protein Interactions Involved in iron reduction by Shewanella oneidensis MR-1. Appiied and Environmental Microbiology, 73:18, 5797-5808.
Scalo, J., Kaltenegger, L., Segura, A., Fridlund, M., Ribas, I., Kulikov, Y.N., Grenfell, J.L., Rauer, H., Odert, P., Leitzinger, M., Selsis, F., Khodachenko, M.L., Eiora, C., Kasting, J., & Lammer H. (2007). M stars as targets for terrestrial exoplanet searches and biosignature detection, Astrobiol. 7, 85-166.
Schaperdoth, I., Liermann, L.J. & Brantley, S.L. (2007). The effect of polymeric substances on apatite reactivity in the presence of a freshwater cyanobacterium. Geomicrobiology J., 24:79-91.
Segura, A., Kasting J.F., Meadows, V.S., Cohen, M., Scalo, J. (2007). Abiotic formation of O2 and O3 in high-CO2 terrestrial atmospheres, Astron. & Astrophys. 472, 665-679.
Selsis, F., Chazelas, B., Borde, P., Bouchy, F., Griessmeier, J-M., Lammer, H., Sotin, C., Grasset, O., Ehrenreich, D., Moutou, C., Barge, P., Deleuil, M., Mawet, D., Despois, D., Ollivier, M., Brachet, F., Decaudin, M., Kasting J., & Leger, A. (2007). Could we identify hot ocean-planets with CoRoT, Keper, and Doppler velocimetry? Icarus 191, 453-468.
Selsis, F., Kasting J.F., Paillet, J., & Delfosse, X. (2007). Habitable planets around the star G1581? Astron. & Astrophys. 476, 1373-1387.
Shields, .A., Kasting J.F. (2007). Evidence for hot early oceans? Nature 446-. doi:10.1038/nature05830.
Smith, F. A., Wing, S. and Freeman, K. H. (2007). Carbon and hydrogen isotope compositions of plant lipids during the PETM as evidence for the response of terrestrial ecosystems to rapid climate change. Earth Planet. Sci. Let 262 (1-2):50-65.
Trueude, T., Orphan, V., Knittel, K., Gieseke, A., House, C. H., Boetinus, A. (2007). Consumption of methane and CO2 by methanotrophic microbial mats from gas seeps of the anoxic Black Sea. Applied and Environmental Microbiology.
Turich C. H., Freeman, K. H., Bruns, M.A., Conte, M., Jones A. D. and S. G. Wakeham (2007). Marine Archea lipid distributions: Patterns and provenance in the water column. Geochem. Cosmochim Acta., 71, 3272-3291.
Wakeham S. G., Amann R., Freeman K. H., Hopmans E. C., Jorgensen B. B., Putnam I. F., Schouten S., Sinninghe Damste J. S., Talbot H. M.and D. Woebken (2007) Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study. Organic Geochemistry 39, 2070-2097.
Wasylenki, L.E., Anbar, A.D., Liermann, L.J., Mathur, R., Gordon, G.W. & Brantley, S.L. (2007). Isotope fractionation during microbial metal uptake measured by MC-ICP-MS. J. Anal. At. Spectrom., 22:905-910.
Wasylenki, L.E., Liermann, L.J., Mathur, R., Gordon, G.W., Brantley, S.L., and Anbar, A.D. (2007). Metallomics and MC-ICP-MS: Isotope fractionation during metal uptake. JAAS Metallomics II Special Issue. 22, 905-910.
Wolfe, A.L., Liu, R., Stewart, B.W., Capo, R.C. and Dzombak, D.A. (2007). A method for generating uniform size-segregated pyrite particle fractions.
Geochemical Transactions 8:9 oi:10.1186/1467-4866-8-9; 8p.
Yamaguchi, K.E., Johnson, C.M., Beard, B.L., Beukes, N.J., Gutzmer, J., and Ohmoto, H. (2007). Isotopic evidence for iron mobilization during Paleoproterozoic
laterization of the Hekpoort paleosol profile from Gaborone, Botzwana. Earth & Planetary Science Letters, 256, 577-587.

2006

Altinok, E. & Ohmoto, H. (2006). Preliminary Stratigraphic and Mineralogic Investigation of the ABDP #8 Core from the Pilbara Craton, Australia. Astrobiology, 6:203.
Biddle, J.F., House, C.H. & Brenchley, J.E. (2006). Microbial stratificaion of deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology, 3:287-295.
Biddle, J.F., Lipp, J.S., Lever, M., Lloyd, K., Soerensen, K., Anderson, R., Fredricks, H.F., Elvert, M., Kelly, T.J., Schrag, D.P., Sogin, M.L., Brenchley, J.E., Teske, A., House, C.H. & Hinrich, K.-U. (2006). Novel heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proceedings of the National Academy of Sciences, 103:3846-3851.
Bowen, G.J., Bralower, T.J., Dickens, G.R., Delaney, M., Kelly, D.C., Koch, P.L., Kump, L.R., Meng, J., Sloan, L.C., Thomas, B., Wing, S.L. & Zachos, J.C. (2006). Eocene hyperthermal event offers insight into greenhouse warning. EOS, 87:165-169..
Coker, J. & Brenchley, J.E. (2006). Protein engineering of a cold-active b-galactosidase from Arthrobacter sp. SB to increase lactose hydrolysis reveals new sites affecting low temperature activity. Extremophiles, 10:515-524.
Debes, J.H. & Sigurdsson, S. (2006). The origins of the substellar companion to GQ Lupi. Astronomy & Astrophysics, 451:351.
Eigenbrode J. L. and K. H. Freeman (2006) The rise of Late Archean aerobic microbial ecosystems. Proc. Nat. Acad. Sci. 103, 15759-15764.
Ewing, S.A., Southard, R.J., Macalady, J.L., Hartshorn, A.S., and Johnson, M.J. (2006). Localization of soil microbial community fingerprints, carbon, and nitrogen in a Mojave Desert creosote bush ecosystem. Soil Science Society of America Journal 71 (2): 469-475.
Ferry, J.G. & House, C.H. (2006). The stepwise evolution of early life driven by energy conservation. Molecular Biology and Evolution, 23:1286-1292.
Fry, B.G., N. Vidal, J.A. Norman, F.J. Vonk, H. Scheib, R. Ramjan, S. Kuruppu, K. Fung, S.B. Hedges, M.K. Richardson, W.C. Hodgson, V. Ignjatovic, R. Summerhayes, and E. Kochva (2006). Early evolution of the venom system in lizards and snakes. Nature 439:584-588.
Hausrath, E.M., Liermann, L.J., Brantley, S.L., House, C.H. & Ferry, J.G. (2006). The effect of methanogen growth on mineral substrates: Will Ni markers of methanogen-based communities be detectable in the rock record? Astrobiology.
Hedges, S.B., Battistuzzi, F.U. & Blair, J.E. (2006). Molecular timescale of evolution in the Proterozoic. In: S. Xiao & A.J. Kaufman (Eds.). Neoproterozoic geobiology and paleobiology (pp. 199-229). New York: Springer.
Hedges, S.B., Dudley, J. & Kumar, S. (2006). TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics, 22(23):2971-2972.
Hedges, S.B., Kumar, S. & M. van Tuinen (2006). Constraining fossil calibrations for molecular clocks. Bioessays, 28:770-771.
Hedges, S.B. (2006). Singularities: landmarks on the pathways of life. Quarterly Review of Biology, 81:164.
Hose, L.D. & Macalady, J. (2006). Observations from active sulfidic karst systems: Is the present the key to understanding Guadalupe Mountain speleogenesis?. 57th Annual Field Conference Guidebook. Socorro, NM: New Mexico Geological Society.
House, C.H. & Schuster, S.C. (2006). Box 1. IODP Microbiology Through Massively Parallel DNA Sequencing. Oceanography, 19:68.
Ishihara, S., Ohmoto, H., Anhaeusser, C.R., Imai, A. & Robb, L.J. (2006). Discovery of the oldest oxidized granitoids in the Kaapvaal Craton and its implications for the redox evolution of early Earth. In Kesler, S. adn Ohmoto, H. eds. Evolution of the Atmosphere, Hydrosphere, and Biosphere on Early Earth: Constraints from Ore Deposits, Geological Society of America Monograph 198, 67-80.
Kasting, J.F., Howard, M.T. (2006). Atmospheric composition and climate on the early Earth, Phil. Trans. Royal Soc. Lond. B 361, 1733-1742.
Kasting, J.F., Howard, M.T., Wallman, K., Veizer, J., Shields, G., & Jeffries, J. (2006). Paleoclimates, ocean depth, and the oxygen isotopic composition of seawater, Earth Planet. Sci. Lett. 252, 82-93.
Kasting, J.F. & Ono, S. (2006). Paleoclimates: the first two billion years. Phil. Trans. Royal Soc. Lond. B., 361:917-929.
Kasting, J.F. (2006). Runaway greenhouses and runaway glaciation: How stable is Earth’s climate? In Frontiers of Climate Modeling, J.T. Kiehl and V. Ramanathan, Eds., Cambridge Univ. Press, Cambridge, pp. 349-366.
Kasting J.F. (2006). Earth Sciences – Ups and downs of ancient oxygen, Nature 443, 643.
Kato, Y., Yamaguchi, K., and Ohmoto, H. (2006). Rare earth elements in Precambrian banded iron formations: Secular changes of Ce and Eu anomalies and evolution of atmospheric oxygen. In Kesler, S. and Ohmoto, H. eds. Evolution of the Atmosphere, Hydrosphere, and Biosphere on Early Earth: Constraints from Ore Deposits, Geological Society of America Monograph 198, 269-289.
Levine, M., Shaklan, S., & Kasting, J.F. (2006). Terrestrial Planet Finder Coronagraph: Science and Technology Definition Team (STDT) Report, JPL Document D-34923, 360 pp.
Liermann, L., Hausrath, L. & Brantley, S. (2006). Assimilatory and Dissimilatory Processes of Microorganisms Affecting Metals in the Environment. In: C. Douthitt (Ed.). Not provided. Elsevier.
Macalady, J.L., Lyon, E.H., Koffman, B., Albertson, L.K., Meyer, K., Galdenzi, S. and Mariani, S. (2006). Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy. Applied and Environmental Microbiology 72 (8): 5596-5609.
Ohmoto H., Watanabe, Y., Ikemi, H., Poulson, S.R. & Taylor, B.E. (2006). Sulphur isotope evidence for an oxic Archaean atmosphere. Nature, 442, 908-911.
Ohmoto, H., Watanabe, Y., Yamaguchi, K.E., Naraoka, H., Kakegawa, T., Haruna, M., Hayashi, K., and Kato, Y. (2006). Chemical and biological evolution of early Earth: Constraints from banded iron-formations. In Kesler, S. and Ohmoto, H. eds. Evolution of the Atmosphere, Hydrosphere, and Biosphere on Early Earth: Constraints from Ore Deposits, Geological Society of America Monograph 198, 291-331.
Ohmoto, H. (2006). Linking the MIF-S record of sedimentary rocks to thermal and biological evolutions of the Earth. AGU Joint Assembly. Baltimore, MD.
Pedenchouk N., Freeman K. H. and N. B. Harris. (2006) Hydrogen isotopic composition of organic matter from the Lower Cretaceous Lacustrine Gabon Basin. Geochimica et Cosmochimica Acta 70(8): 2063-2072.
Pollard, D., Kasting J.F. (2006). Reply to comment by Steven G. Warren and Richard E. Brandt on “Snowball Earth–a Thin-Ice Model with Flowing Sea Glaciers,” J. Geophys. Res. 111, C09017, doi10.1029/2006JC003488.
Ruebush, S.S., Icopini, G.A., Brantley, S.L. & Tien, M. (2006). In vitro enzymatic reduction kinetics of mineral oxides by membrane fractions from Shewanella oneidensis MR-1. Geochim. Cosmochim Acta, 70:56 – 70.
Smith F. A. and K. H. Freeman (2006) Influence of physiology and climate on δD of leaf wax n-alkanes from C3 and C4 grasses. Geochimica et Cosmochimica Acta. 70(5): 1172-1187.
van Rheede, T., Bastiaans, T. & t al., e. (2006). The platypus is in its place: nuclear genes and indels confirm the sister group relation of monoremes and Therians. Molecular Biology and Evolution, 23:587-597.
Yamaguchi, K.E. & Ohmoto, H. (2006). Comment on “Iron isotope constraints on the Archean and Paleoproterozoic ocean redox state”. Science, 311:175.
Yamaguchi, K.E. and Ohmoto, H. (2006). Evidence from sulfur isotope and trace elements in pyrites for their multiple post-depositional processes in uranium ores at the Stanleigh Mine, Elliot Lake, Ontario, Canada. In Kesler, S. and Ohmoto, H. eds. Evolution of the Atmosphere, Hydrosphere, and Biosphere on Early Earth: Constraints from Ore Deposits, Geological Society of America Monograph 198, 143-156.
Yamaguchi, K.E. and Ohmoto, H. (2006). Geochemical and isotopic constraints on the origin of Paleoproterozoic red shales of the Garagara/Mapedi Formation, Postmasburg Group, South Africa. South African J. of Geology, 109, 123-138.
Zimmerman, S.A. & Ferry, J.G. (2006). Proposal for a hydrogen bond network in the active site of the prototypic gamma-class carbonic anhydrase. Biochemistry, 45:5149.
Zerkle, A.J., House, C.H., Cox, R.P. & Canfield, D.E. (2006). Metal limitation of cyanobacterial N2 fixation and implications for the Precambrian nitrogen cycle. Geobiology, 4:285-297.

2005

Arthur, M.A. & Sageman, B.B. (2005). Sea Level Control on Source Rock Development: Perspectives from the Holocene Black Sea, the Mid-Cretaceous Western Interior of North America, and the Late Devonian Appalachian Basin. In: N. Harris & B. Pradier (Eds.). The Deposition of Organic Carbon-rich Sediments: Models, Mechanisms and Consequences. Society for Sedimentary Geology (SEPM) Special Publication (pp. 35-59).
Biddle, J.F., House, C.H., Brenchley, J.E., 2005. Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane geochemistry. Geobiology, 3: 287-295
. Biddle, J.F., House, C.H., Brenchley, J.E., 2005. Enrichment cultivation of microorganisms from sediment from the slope of the Peru Trench (ODP Site 1230). Proceedings of the Ocean Drilling Program, Scientific Results, 201.
Blair, J.E. & Hedges, S.B. (2005). Molecular clocks do not support the Cambrian explosion. Mol Biol Evol, 22(3):387-90.
Blair, J.E. & Hedges, S.B. (2005). Molecular phylogeny and divergence times of deuterostome animals. Molecular Biology and Evolution, 22:2275-2284.
Blair, J.E., Shah, P. & Hedges, S.B. (2005). Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics, 6(1):53.
Cordes, E.E., Arthur, M.A., Shea, K., Arvidson, R. & Fisher, C.R. (2005). Modeling the mutualistic interactions between tubeworms and microbial consortia. PLoS Biology, 3(3):e77.
Debes, J.H., Sigurdsson, S. & Woodgate, B.E. (2005). Cool Customers in the Stellar Graveyard. I. Limits to Extrasolar Planets Around the White Dwarf G29-38. Astrophysical Journal, 633:1168.
Felipe M.A., Kubicki J. D. and K. H. Freeman (2005) A mechanism for carbon isotope exchange between aqueous acetic acid and CO2/HCO3-: an Ab Initio study. Organic Geochemistry 36, 835-850.
House, C.H., Cragg, B. & Teske, A. (2005). Drilling Contamination Tests on ODP Leg 201 Using Chemical and Particulate Tracers. Proceedings of the Ocean Drilling Program, Initial Reports.
Hurtgen, M.T., Arthur, M.A. & Halverson, G. (2005). Neoproterozoic sulfur isotopes, the evolution of microbial sulfur species, and the burial efficiency of sulfide as sedimentary pyrite. Geology, 33:41-44.
Kasting, J.F. (2005). Methane and climate during the Precambrian Era. Precambrian Res., 137(119-129).
Kharecha, P., Kasting, J.F. & Siefert, J.L. (2005). A coupled atmosphere-ecosystem model of the early Archean Earth. Geobiology, 3:53-76.
Knappenberger, K.L.J. & A. W. Castleman, J. (2005). Photodissociation of (SO2)m(H2O)n clusters. Journal of Chemical Physics, 122:154306.
Kumar, S. & Filipski, A. (2005). Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proceedings of the National Academy of Sciences of the United States of America, 102:18842-18847.
Kumar, S. & Hedges, S.B. (2005). Pushing back the expansion of introns in animal genomes. Cell, 123:1182-1184.
Kump, L.R. & Seyfried, W.E. (2005). Hydrothermal Fe fluxes during the Precambrian: Effect of low oceanic sulfate concentrations and low hydrostatic pressure on the composition of black smokers. Earth and Planetary Science Letters, 235:654-662.
Kump, L.R. (2005). Ironing out the oxidation of the biosphere. Science (Perspectives), 307:1058-1059.
Kump, L.R., Pavlov, A. & Arthur, M.A. (2005). Massive release of hydrogen sulfide to the surface ocean and atmosphere during intervals of oceanic anoxia. Geology, 33:397-400.
Liermann, L.J., Guynn, R.L., Anbar, A. & Brantley, S.L. (2005). Production of a molybdophore during metal-targeted dissolution of silicates by soil bacteria. Chem Geol, 220:285-302.
Mathur, R., Ruiz, J., Titley, S., Liermann, L., Buss, H. & Brantley, S. (2005). Cuisotopic fractionation in the supergene environment with and without bacteria. Geochim. Cosmochim Acta, 69(22):5233 – 5246.
Moran, J.J., House, C.H., Freeman, K.H. & Ferry, J.G. (2005). Trace methane oxidation studied in several Euryarchaeota under diverse conditions. Archaea, 1:293.301.
Neaman, A., Chorover, J. & Brantley, S.L. (2005). Element mobility patterns record organic ligands in soils on early Earth. Geology, 33(2):117-120.
Neaman, A., Chorover, J. & Brantley, S.L. (2005). Implications of the evolution of organic acid moieties for basalt weathering over geological time. American Journal of Science, 305:147-185.
Nedachi, Y., Nedachi, M., Bennet, G. & Ohmoto, H. (2005). Geochemistry and mineralogy of the 2.45 Ga Pronto paleosols, Ontario, Canada. Chemical geology, 214(1-2):21.
Ohmoto, H., Watanabe, Y. & Ikemi, H. (2005). The absence of mass independent fractionation of sulfur isotopes in Archean sedimentary rocks; an insignificant phenomenon?. Geochimica et Cosmochimica Acta, 69(10):450.
Pagani M., Zachos J. C., Freeman K. H., Tipple B. and S. Bohaty (2005) Marked Decline in Atmospheric Carbon Dioxide Concentrations During the Paleogene Science, 309: 600-603.
Pollard, D. and Kasting, J.F. (2005). Snowball Earth: A thin-ice model with flowing sea glaciers, J. Geophys. Res. 110, C07010, doi:10.1029/2004JC002525.
Segura, A., Kasting, J.F., Meadows, V., Cohen, M., Scalo, J., Crisp, D., Butler, R.A.H., Tinetti, G. (2005). Biosignatures from Earth-like planets around M dwarfs, Astrobiology 5, 706-725.
Vidal, N. & Hedges, S.B. (2005). The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. Comptes Rendus Biologies, 328:1000-1008.
Walden, K.M. (2005). Neodymium and strontium isotope investigation of the Precambrian Kalkkloof paleosol, South Africa. Geology & Planetary Science (pp. 45). Pittsburgh: University of Pittsburgh.
Wing S. L., Harrington G. J., Smith F. A., Bloch, J. I., Boyer D. M. and K. H. Freeman (2005) Transient floral change and rapid global warming at the Paleocene-Eocene boundary. Science 310, 993-996.
Yamaguchi, K.E., Johnson, C.M., Beard, B.L. & Ohmoto, H. (2005). Biogeochemical cycling of iron in the Archean-Paleoproterozoic Earth; constraints from iron isotope variations in sedimentary rocks from the Kaapvaal and Pilbara cratons. Chemical geology, 218(1-2):135.
Zerkle, A.L., House, C.H. & Brantley, S.L. (2005). Genomic Study of Biogeochemical Signatures for Microbial Metabolisms through Time. American Journal of Science, 305(Oct., Sept., Nov.):467-502.

2004

Battistuzzi, F.U., Feijao, A. & Hedges, S.B. (2004). A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol, 4(1):44.
Buss, H.L., Brantley, S.L., Sak, P.B. & White, A.F. (2004). Mineral dissolution at the granite-saprolite interface. In: R. Wanty and R. Seal (Eds.). Proceedings of the 11th International Symposium on Water-Rock Interaction, Saratoga Springs, New York.
D’Hondt, S. & 34 others, 2004. Distributions of Microbial Activities in Deep Subseafloor Sediments. Science, 306:2216-2221.
Dermota, T.E., Hydutsky, D.P., Bianco, N.J. & Castleman, J. (2004). Cluster size effects on bound excited states of SO2. In: M.M. Martin & J.T. Hynes (Eds.). Femtochemistry and Femtobiology: Ultrafast Events in Molecular Science. Elsevier.
Dermota, T.E., Zhong, Q. & A. W. Castleman, J. (2004). Ultrafast dynamics in cluster systems. Chemical Reviews, 104:1861-1886.
Ding, Y.H. & Ferry, J.G. (2004). A FMN-binding flavoprotein family in the Archaea domain. Journal of Bacteriology, 186: 90-97.
Doran, P.T., Clifford, S.M., Forman, S.L., Nyquist, L., Papanastassiou, D.A., Stewart, B.W., Sturchio, N.C., Swindle, T.D., Cerling, T.E., Kargel, J., McDonald, G., Nishiizumi, K., Poreda, R., Rice, J.W. & Tanaka, K. (2004). Mars chronology: assessing techniques for quantifying surficial processes. Earth-Science Reviews, 67:313-337.
Harris N.B., Freeman K.H., Pancost R. D., White T.S. and G.D. Mitchell (2004) The character and origin of lacustrine source rocks in the Lower Cretaceous synrift section, Congo Basin, west Africa. AAPG Bulletin 88, 1163-1184.
Hedges, S.B. & Kumar, S. (2004). Precision of molecular time estimates. Trends in Genetics, 20(5): 242-247.
Hedges, S.B., Blair, J.E., Venturi, M.L. & Shoe, J.L. (2004). A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evolutionary Biology, 4(2): 1-9.
Herrmann, A.D., Patzkowsky, M.E. & Pollard, D. (2004). The impact of paleogeography, pCO2, poleward ocean heat transport, and sea level change on global cooling during the late Ordovician: A climate model analysis. Palaeogeography, Palaeoclimatology, Palaeoecology, 206: 59-74.
Hotinski, R.M., Kump, L.R. & Arthur, M.A. (2004). A d13C gradient from platform carbonates of the Pethei Group (Great Slave Lake Supergroup, N.W.T.) Bulletin of the Geological Society of America, 116: 539-554.
Hotinski, R.M., Kump, L.R., & Arthur, M.A. (2004). The effectiveness of the Paleoproterozoic biological pump: d13C gradients from platform carbonates of the Pethei Group (Great Slave Lake Supergroup, N.W.T.). Bulletin of the Geological Society of America, 116(5/6): 539-554.
Hurtgen, M.T., Arthur, M.A. & Prave, A.R. (2004). The sulfur isotope composition of carbonate-associated sulfate in Mesoproterozoic to Neoproterozoic carbonates from Death Valley, California. In: J.P. Amend et al. (Eds.). Sulfur Biogeochemistry — Past and Present. Geological Society of America Special Paper (pp. 177-194).
Icopini, G.A., Anbar, A.D., Ruebush, S.S., Tien, M. & Brantley, S.L. (2004). Iron isotope fractionation during microbial reduction of iron: The importance of adsorption. Geology, 32(3): 205-208.
Jiménez-López, C., Romanek, C.S., Huertas, F.J., Ohmoto, H. & Caballero, E. (2004). Oxygen isotope fractionation in synthetic magnesian calcite. Geochimica et Cosmochimica Acta, 68:3367-3377.
Kasting, J.F. (2004). When methane made climate. Scientific American, 291(1, July): 78-85.
Kasting J.F.,(2004). Comment on “Evidence from massive siderite beds for a CO2-rich atmosphere before ~1.8 billion years ago” by H. Ohmoto, Y. Watanabe, and K. Kumazawa, published as “Archean atmosphere and climate” Nature 429, doi:10.1038/nature03166.
Krug, A. Z., and Patzkowsky, M. E. (2004). Rapid recovery from the Late Ordovician mass extinction: Proceedings of the National Academy of Sciences, v. 101. P. 17605-17610.
Knappenberger, K.L. & A. W. Castleman, J. (2004). Photodissociation of sulfur dioxide: The E state revisited. Journal of Physical Chemistry A., 108:9-14.
Knappenberger, K.L.J. & A. W. Castleman, J. (2004). The Influence of Cluster Formation on the Photodissociation of Sulfur Dioxide: Excitation to the E State. J. Chem. Phys., 121:3540-3549.
Miteva, V.I., Sheridan P., & Brenchley J. (2004). Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core. Applied and Environmental Microbiology, 70: 202-213.
Moran, J.J., House, C.H., Freeman, K.H. & Ferry, J.G. (2004). Trace methane oxidation studied in several Euryarchaeota under diverse conditions. Archaea, 1.
Ohmoto, H. (2004). Archean atmosphere, hydrosphere, and biosphere. In: P. Ericksson et al. (Eds.). The Precambrian Earth: Tempos in Precambrian Development. Developments in Precambrian Geology Series, Vol. 12. (pp. 361-368). Amsterdam, The Netherlands: Elsevier.
Ohmoto, H. (2004). Reply to “Archaean atmosphere and climate” by Kasting, J. and “Archaean paleosols and Archaean air” by Sleep, M.H. Nature, 25:1-2.
Ohmoto, H., Spangler, K.R., Watanabe, Y. & Kamei, G. (2004). Smectite dissolution kinetics in high-alkaline conditions. In: V.M. Oversby & L.O. Werme (Eds.). Scientific Basis for Nuclear Waste Management XXVII (pp. 723-728). Materials Research Society, Symposium Proceedings Vol. 807. Warrendale, PA: Materials Research Society.
Ohmoto, H., Watanabe, Y. & Kumazawa, K. (2004). Evidence from massive siderite beds for a CO2-rich atmosphere before ~1.8 billion years ago. Nature, 429: 395-399.
Ohmoto, H. and Watanabe, Y. (2004). Reply to “Archaean atmosphere and climate” by Kasting, J. and “Archaeanpaleosols and Archaean air” by Sleep, M.H., Nature, 25 November 204, 1-2.
Orphan, V.J., Ussler, W. III, N_hr, T., House, C.H., Hinrichs, K.-U., & Paull, C.K. (2004). Geological, Geochemical, and Microbiological Heterogeneity of the Seafloor Around Methane Vents in the Eel River Basin, offshore California. Chemical Geology, 205: 265-289.
Pearson A., Huang Z., Ingalls A.E., Romanek C.S., Wiegel J., Freeman K. H., Smittenberg R.H. and C.L. Zhang (2004) Nonmarine crenarchaeol in Nevada hot springs Applied and Environmental Microbiology 70, 5229-5237.
Pedentchouk, N., Freeman K.H., Harris, N.B., Clifford D.J. & Grice K. (2004). Sources of alkylbenzenes in Lower Cretaceous lacustrine source rocks, West African rift basins. Organic Geochemistry, 35: 33-45.
Pisani, D., Poling, L.L., Lyons-Weiler, M. & Hedges, S.B. (2004). The colonization of land by animals: Molecular phylogeny and divergence times among arthropods. BMC Biology, 2(1): 1-10.
Pollard, D., Kasting, J.F. (2004). Climate-ice sheet simulations of Neoproterozoic glaciation before and after collapse to Snowball Earth, in Geophysical Monograph Series 146, “The Extreme Proterozoic: Geology, Geochemistry, and Climate,” G.S. Jenkins, M.A.S. McMenamin, C.P. McKay, and L. Sohl, eds., Amer. Geophys. Union, Washington, DC, pp. 91-105.
Schoonen, M., Smirnov, A. & Cohn, C.A. (2004). A perspective on the role of minerals in prebiotic synthesis. Ambio, 33(8):539-551.
Tripp, B.C., Bell III, C.B., Cruz, F., Krebs, C. & Ferry, J.G. (2004). A role for iron in an ancient carbonic anhydrase. Journal of Biological Chemistry, 279: 6683-6687.
Vidal, N. & Hedges, S.B. (2004). Molecular evidence for a terrestrial origin of snakes. Proceedings of the Royal Society: Biological Sciences, Biology Letters, 271(S4, May 7): 226-229.
Wantey, R. & Seal, R. (Eds.). (2004). Proceedings of the Eleventh International Symposium on Water Rock Interaction (WRI-II), 27 June-2 July, 2004, Saratoga Springs, New York, USA.
Watanabe, Y., Stewart, B.W. & Ohmoto, H. (2004). Organic- and carbonate-rich soil formation ~2.6 billion years ago at Schagen, East Transvaal district, South Africa. Geochimica et Cosmochimica Acta, 68: 2129-2151.

2003

Des Marais, D.J., Allamandola, L.J., Benner, S.A., Boss, A.P., Cronin, J.R., Deamer, D., Falkowski, P.G., Farmer, J.D., Hedges, S.B., Jakosky, B.M., Knoll, A.H., Liskowsky, D.R., Meadows, V.J., Meyer, M.A., Pilcher, C.B., Nealson, K.H., Spormann, A.M., Trent, J.D., Turner, W.W., Woolf, N.J., & Yorke, H.W. (2003). The NASA astrobiology roadmap. Astrobiology, 3: 219-235.
Glazko, G. & Nei, M. (2003). Estimation of divergence times for major lineages of primate species. Molecular Biology and Evolution, 20: 424-434.
Haruna, M., Hanamuro, T., Uyeda, K., Fujimaki, H. & Ohmoto, H. (2003). Chemical, isotopic, and fluid inclusion evidence for the hydrothermal alteration of the footwall rocks of the BIF-hosted iron ore deposits in the Hamersley district, Western Australia. Resource Geology, 53: 75-88.
Hedges, S.B. & Kumar, S. (2003). Genomic clocks and evolutionary timescales. Trends in Genetics, 19: 200-206.
Hedges, S.B. & Shah, P. (2003). Comparison of mode estimation methods and application in molecular clock analysis. BMC Bioinformatics, 4(31): 1-11.
Hedges, S.B. (2003). Molecular clocks and a biological trigger for the Neoproterozoic snowball Earths and Cambrian explosion. In: P. Donoghue & P. Smith (Eds.). Telling Evolutionary Time: Molecular Clocks and the Fossil Record (pp. 27-40). London: CRC Press.
Hedges, S.B. (2003). The coelacanth of frogs. Nature, 425: 669-670.
Herrmann, A.D., Patzkowsky, M.E. & Pollard, D. (2003). Obliquity forcing with 8-12x pre-industrial levels of atmospheric pCO2. Geology, 31(6): 485-488.
House, C.H., Cragg, B.A. Teske, A. & Ocean Drilling Program Leg 201 Shipboard Scientific Party. (2003). Drilling Contamination Tests on ODP Leg 201 using Chemical and Particulate Tracers. Proceedings of the Ocean Drilling Program, Initial Reports, 201: Ch.2. 1-19.
House, C.H., Runnegar, B. & Fitz-Gibbon, S.T. (2003). Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea, and Eukarya. Geobiology, 1: 15-26.
House, C.H., Schopf, J.W. & Stetter, K.O. (2003). Carbon isotopic fractionation by Archaeans and other thermophilic Prokaryotes. Organic Geochemistry, 34: 345-356.
House, C.H. (2003). To build a pre-RNA. Astrobiology, 3: 245-247.
Kasting, J. F., Catling, D. (2003) Evolution of a habitble planet. Ann. Rev. Astron. Astrophys. 41, 429-463.
Kasting, J.F. (2003). The origins of water on Earth. Scientific American, Special Edition, 13(3): 28-33.
Kasting, J.F. (2003). [Review of the book “Snowball Earth: The Story of the Great Global Catastrophe that Spawned Life as We Know It,” by Gabrielle Walker]. Bulletin of the American Meteorological Society, 84: 1581-1584.
Kurtz, A.C., Kump, L.R., Arthur, M.A., Zachos, J.C. & Paytan, A. (2003). Early Cenozoic decoupling of the global carbon and sulfur cycles. Paleoceanography, 18(4): 1090, doi:10.1029/2003PA000908.
Lunine J.I. et al. (2003). Life in the Universe, An Assessment of U.S. and International Programs in Astrobiology. A Report to the Space Studies Board, National Research Council. Washington, DC: National Academies Press.
Mandell, A. & Sigurdsson, S. (2003). Survival of terrestrial planets in the presence of giant planet migration. Astrophysical Journal Letters, 599: L111-L114.
Nei, M. (2003). Genome evolution: Let’s stick together. Heredity, 90: 411-412.
Ohmoto, H. (2003). Non-redox transformation of magnetite – hematite in hydrothermal systems. Economic Geology, 98: 157-161.
Ohmoto, H. (2003). Reply to comments by H. D. Holland on “The oxygen geochemical cycle: Dynamics and stability,” Geochimica et Cosmochimica Acta, 66: 361-381, 2002. Geochimica et Cosmochimica Acta, 67(4): 791-795.
Ono, S., Eigenbrode, J.L., Pavlov, A.A., Kharecha, P., Rumble, D., Kasting, J.F. & Freeman K.H. (Accepted, 2003). Sulfur isotopic constraints on the Archean atmosphere and ocean. Earth and Planetary Science Letters.
Patzkowsky, M.E. & Holland, S.M. (2003). Lack of community of saturation at the beginning of the Paleozoic Plateau: The dominance of regional over local processes. Paleobiology, 29(4): 545-560.
Pavlov, A.A., Hurtgen, M., Kasting, J.F. & Arthur, M.A. (2003). Methane-rich Proterozoic atmosphere? Geology, 31(1): 87-90.
Pedentchouk, N., Freeman K.H., Harris, N.B., Clifford, D.J. & Grice, K. (Accepted, 2003). Sources of alkylbenzenes in Lower Cretaceous lacustrine source rocks, West African rift basins. Organic Geochemistry.
Segura, A, Krelove, K., Kasting, J.F., Sommerlatt, D., Meadows, V., Crisp, D., Cohen, M., Mlawer, E. (2003). Ozone concentrations and ultraviolet fluxes on Earth-like planets around other stars. Astrobiology 3, 689-708.
Sheridan P.P., Freeman K.H. & Brenchley J.E. (2003). Estimated minimal divergence times of the major bacterial and archeaeal phyla. Geomicrobiology Journal, 20: 1-14.
Sheridan, P.. Miteva, V. & Brenchley, J. (2003). Phylogenetic analysis of 16S rDNA of anaerobic psychrophilic enrichment cultures obtained from a Greenland Glacier Ice Core. Applied and Environmental Microbiology, 69: 2153-2160.
Sheridan, P.P., Freeman, K.H. & Brenchley, J.E. (2003). Estimated minimal divergence times of the major bacterial and archaeal phyla. Geomicrobiology Journal, 20: 1-14.
Sigurdsson, S., Richer, H.B., Hansen, B.M., Stairs, I.H. & Thorsett, S.E. (2003). A young white dwarf companion to Pulsar B1620-26: Evidence for early planet formation. Science, 301: 193-195.
Smirnov, A. & Schoonen, M.A. (2003). Evaluating experimental artifacts in hydrothermal prebiotic synthesis experiments. Origins of Life and Evolution of the Biosphere, 33(2): 117-127
Zhang, B. & Sigurdsson, S. (2003). Electromagnetic signals from planetary collisions. Astrophysical Journal (Letters), 596: L95-L99.