Publications

2021

Jagilinki, B. P., Paluy, I., Tyryshkin, A.M., Nanda, V. & Noy,D. (2021). Biophysical Characterization of Iron-Sulfur Proteins, Bio-protocol , 11(20, e4202. DOI: 10.21769/BioProtoc.4202 

Jagilinki, B. P., Paluy, I., Nanda, V., & Noy, D. (2021). Anaerobic Expression and Purification of Holo-CCIS, an Artificial Iron-sulfur Protein. Bio-protocol, 11(18), e4169-e4169. DOI: 10.21769/BioProtoc.4169 

James, J. K., & Nanda, V. (2021). A folding insulator defines cryptic domains in tropomyosin. Journal of Molecular Biology, 167281. DOI: 10.1016/j.jmb.2021.167281

Boujibar, A., Howell, S., Zhang, S., Hystad, G., Prabhu, A., Liu, N., … & Nittler, L. R. (2021). Cluster analysis of presolar silicon carbide grains: evaluation of their classification and astrophysical implications. The Astrophysical Journal Letters, 907(2), L39. DOI: 10.3847/2041-8213/abd102

Freiberger, M. I., Wolynes, P. G., Ferreiro, D. U., & Fuxreiter, M. (2021). Frustration in fuzzy protein complexes leads to interaction versatility. The Journal of Physical Chemistry B. DOI: 10.1021/acs.jpcb.0c11068

Tang, M., Chu, X., Hao, J., & Shen, B. (2021). Orogenic quiescence in Earth’s middle age. Science, 371(6530), 728. DOI: 10.1126/science.abf1876

Cleland, C. E., Hazen, R. M., & Morrison, S. M. (2021). Historical natural kinds and mineralogy: Systematizing contingency in the context of necessity. Proceedings of the National Academy of Sciences, 118(1). DOI: 10.1073/pnas.2015370118

2020

Srivastava, N., Spielman, S. J., Morrison, S. M., & Moore, E. K. (2020). Geological factors impacted cadmium availability and use as an alternative cofactor for zinc in the carbon fixation pathways of marine diatoms. Journal of Geophysical Research: Biogeosciences, e2020JG005966. DOI: 10.1029/2020JG005966

Boujibar, A., Zhang, S., Howell, S., Prabhu, A., Narkar, S., Hystad, G., Morrison S.M., Hazen R.M., et al. (2020). Cluster analysis and classification of presolar silicon carbide grains. in LPSC, 2070. Bibcode: 2020LPI….51.2070B

Chiama, K., Rutledge, R., Gabor, M., Lupini, I., Hazen, R. M., Zhang, S., et al. (2020). Garnet: a comprehensive, standardized, geochemical database incorporating locations and paragenesis. in Geological Society of America Abstracts with Programs DOI:10.1130/abs/2020se-344505.

Spielman, S. J., and Moore, E. K. (2020). dragon: A New Tool for Exploring Redox Evolution Preserved in the Mineral Record. Front. Earth Sci. 8. DOI:10.3389/feart.2020.585087.

Hoarfrost, A., Aptekmann, A., Farfanuk, G., & Bromberg, Y. (2020). Shedding light on microbial dark matter with a universal language of life. bioRxiv. DOI: 10.1101/2020.12.23.424215 

LaRowe, D. E., Arndt, S., Bradley, J. A., Estes, E. R., Hoarfrost, A., Lang, S. Q., Lloyd, K., Mahmoudi, N., Orsi, W., Shah Walter, S., Steen, A. & Zhao, L. (2020). The fate of organic carbon in marine sediments-New insights from recent data and analysis. Earth-Science Reviews, 204, 103146. DOI: 10.1016/j.earscirev.2020.103146

Morrison, S. M., & Hazen, R. M. (2020). An evolutionary system of mineralogy. Part II: Interstellar and solar nebula primary condensation mineralogy (> 4.565 Ga). American Mineralogist, 105(10), 1508-1535. DOI: 10.2138/am-2020-7447

Hazen, R.M., Morrison, S.M., and Prabhu, A. (2020) An evolutionary system of mineralogy, Part III: Primary chondrule mineralogy (4.566 to 4.561 Ga). American Mineralogist. DOI:10.2138/am-2020-7564

Morrison, S.M. and Hazen, R.M. (2020) An evolutionary system of mineralogy, Part IV: Planetesimal differentiation and impact mineralization (4.566 to 4.560 Ga). American Mineralogist. DOI: 10.2138/am-2021-7632

Hazen, R.M., and Morrison, S.M. (2020) An evolutionary system of mineralogy, Part V: Planetesimal Aqueous and thermal alteration of planetesimals (4.565 to 4.550 Ga). American Mineralogist. DOI:  10.2138/am-2021-7760

Prabhu, A., Morrison, S., Eleish, A., Zhong, H., Huang, F., Golden, J., Perry, S., Hummer, D., Runyon, S., Fontaine, K., Krivovichev, S., Downs, R., Hazen, R., & Fox, P. (2020) Global Earth mineral inventory: A data legacy. Geoscience Data Journal. DOI:  10.1002/gdj3.106

Hazen, R.M. (2020) Reply to “Comment on ‘An evolutionary system of mineralogy: Proposal for a classification based on natural kind clustering’.” American Mineralogist. DOI: 10.2138/am-2021-7773

Poudel, S., Pike, D. H., Raanan, H., Mancini, J. A., Nanda, V., Rickaby, R. E., & Falkowski, P. G. (2020). Biophysical analysis of the structural evolution of substrate specificity in RuBisCO. Proceedings of the National Academy of Sciences, 117(48), 30451-30457. DOI: 10.1073/pnas.2018939117

Jagilinki, B.P., Ilic, S., Trncik, C., Tyryshkin, A.M., Pike, D.H., Lubitz, W., Bill, E., Einsle, O., Birrell, J.A., Akabayov, B. & Noy, D.(2020). In Vivo Biogenesis of a De Novo Designed Iron–Sulfur Protein. ACS Synthetic Biology. DOI: 10.1021/acssynbio.0c00514

Kakkis, A., Gagnon, D., Esselborn, J., Britt, R. D., & Tezcan, F. A. (2020). Metal‐Templated Design of Chemically Switchable Protein Assemblies with High‐Affinity Coordination Sites. Angewandte Chemie. DOI: 10.1002/anie.202009226

Murphy, A. E., Wieman, S. T., Gross, J., Stern, J. C., Steele, A., & Glamoclija, M. (2020). Preservation of organic carbon in dolomitized cambrian stromatolites and implications for microbial biosignatures in diagenetically replaced carbonate rock. Sedimentary Geology, 105777. DOI: 10.1016/j.sedgeo.2020.105777

Fornaro, T., Brucato, J., Poggiali, G., Corazzi, M. A., Biczysko, M., Jaber, M., Foustoukos, D., Hazen, R.M.,   & Steele, A. (2020). UV Irradiation and Near Infrared Characterization of Laboratory Mars Soil Analog Samples: the case of Phthalic Acid, Adenosine 5’-Monophosphate, L-Glutamic Acid and L-Phenylalanine Adsorbed onto the Clay Mineral Montmorillonite in the presence of Magnesium Perchlorate. DOI: 10.20944/preprints202003.0172.v1

Hao, J., Knoll, A. H., Huang, F., Hazen, R. M., & Daniel, I. (2020). Cycling phosphorus on the Archean Earth: Part I. Continental weathering and riverine transport of phosphorus. Geochimica et Cosmochimica Acta, 273, 70-84. DOI: 10.1016/j.gca.2020.01.027

Hazen, R. M., & Morrison, S. M. (2020). An evolutionary system of mineralogy. Part I: Stellar mineralogy (> 13 to 4.6 Ga). American Mineralogist: Journal of Earth and Planetary Materials, 105(5), 627-651. DOI: 10.2138/am-2019-7173

Johnson, S. S., Graham, H. V., Des Marais, D. J., Hazen, R. M., Meadows, V., Arney, G. N., Schmidt, B.E, & Des Marais, D. J. (2020). Detecting life on Earth and the limits of analogy. Planetary Astrobiology, 121-150.  ISBN: 9780816540068

Liu, W., Hao, J., Elzinga, E. J., Piotrowiak, P., Nanda, V., Yee, N., & Falkowski, P. G. (2020). Anoxic photogeochemical oxidation of manganese carbonate yields manganese oxide. Proceedings of the National Academy of Sciences, 117(37), 22698-22704. DOI: 10.1073/pnas.2002175117

Mancini, J. A., Pike, D. H., Tyryshkin, A. M., Haramaty, L., Wang, M. S., Poudel, S., Hecht, M., & Nanda, V. (2020). Design of a Fe (4) S (4) cluster into the core of ade novofour-helix bundle. Biotechnology and Applied Biochemistry. DOI: 10.1002/bab.2003

Morrison, S. M., Buongiorno, J., Downs, R. T., Eleish, A., Fox, P., Giovannelli, D., Golden, J.J., Hummer, D.R., Hystad, G., Kellogg, L.H. & Kreylos, O. (2020). Exploring carbon mineral systems: Recent advances in C mineral evolution, mineral ecology, and network analysis. Frontiers in Earth Science, 8, 208. DOI: 10.3389/feart.2020.00208

Campbell, I.J., Olmos, J.L., Xu, W., Kahanda, D., Atkinson, J.T., Sparks, O.N., Miller, M.D., Phillips, G.N., Bennett, G.N. and Silberg, J.J., (2020). Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases. Journal of Biological Chemistry, pp.jbc-RA120. DOI: 10.1074/jbc.RA120.013501

ElAbd, H., Bromberg, Y., Hoarfrost, A. et al.(2020). Amino acid encoding for deep learning applications. BMC Bioinformatics 21, 235. DOI: 10.1186/s12859-020-03546-x

Raanan, H., Poudel, S., Pike, D. H., Nanda, V., & Falkowski, P. G. (2020). Small protein folds at the root of an ancient metabolic network. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1914982117

Moore, E. K., Hao, J., Spielman, S. J., & Yee, N. (2020). The evolving redox chemistry and bioavailability of vanadium in deep time. Geobiology. DOI: 10.1111/gbi.12375

2019

Buongiorno, J., Fullerton, K., Rogers, T., Giovannelli, D., DeMoor, M., Barry, P., Morrison S.M., Hazen R.M et al. (2019a). Interactions between microbial communities and their geologic environment at the Costa Rica active margin. in Goldschmidt Annual Meeting.

Buongiorno, J., Herbert, L. C., Wehrmann, L. M., Michaud, A., Laufer, K., Røy, H., et al. (2019b). Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments. Appl. Environ. Microbiol., AEM.00949-19. doi:10.1128/AEM.00949-19.

Zhang, S., Morrison, S. M., Prabhu, A., Ma, C., Huang, F., Gregory, D., … & Hazen, R. (2019, December). Natural clustering of pyrite with implications for its formational environment. In AGU Fall Meeting Abstracts (Vol. 2019, pp. EP23D-2284). Bibcode: 2019AGUFMEP23D2284Z

Campbell, I. J., Bennett, G. N., & Silberg, J. J. (2019). Evolutionary relationships between low potential ferredoxin and flavodoxin electron carriers. Frontiers in Energy Research, 7, 79.DOI: 10.3389/fenrg.2019.00079

Hazen, R.M., Bromberg, Y., Downs, R.T., Eleish, A., Falkowski, P.G., Fox, P., Giovannelli, D., Hummer, D.R., Hystad, G., Golden, J.J., Knoll, A.H., Li, C., Liu, C., Moore, E.K., Morrison, S.M., Muscente, A.D., Prabhu, A., Ralph, J., Rucker, M.Y., Runyon, S.E., Warden, L.A., Zhong, H. (2019) Deep carbon through deep time: Data-driven insights. In: B. Orcutt, I. Danielle, R. Dasgupta [eds], Deep Carbon: Past to Present. Cambridge, UK: Cambridge University Press, pp.320-352. DOI: 1017/9781108677950.020

Hazen, R.M., Downs, R.T., Elesish, A., Fox, P., Gagné, O., Golden, J.J., Grew, E.S., Hummer, D.R., Hystad, G., Krivovichev, S.V., Li, C., Liu, C., ma, X., Morrison, S.M., Pan, F., Pires, A.J., Prabhu, A., Ralph, J., Runyon, S.E., & Zhong, H. (2019) Data-driven discovery in mineralogy: Recent advances in data resources, analysis, and visualization. DOI: 10.1016/j.eng.2019.03.006

Hystad, G., Eleish, A., Hazen, R. M., Morrison, S. M., & Downs, R. T. (2019). Bayesian estimation of Earth’s undiscovered mineralogical diversity using noninformative priors. Mathematical Geosciences, 51(4), 401-417. DOI: 1007/s11004-019-09795-8

Hazen, R.M. (2019) Symphony in C: Carbon and the Emergence of (Almost) Everything. New York: W.W. Norton. British edition (London: HarperCollins, 2019). ISBN: 978-0-393-60943-1

Grew, E. S., Hystad, G., Toapanta, M. P., Eleish, A., Ostroverkhova, A., Golden, J., & Hazen, R. M. (2019). Lithium mineral evolution and ecology: comparison with boron and beryllium. European Journal of Mineralogy, 31(4), 755-774. DOI: 10.1127/ejm/2019/0031-2862

Hystad, G., Morrison, S. M., & Hazen, R. M. (2019). Statistical analysis of mineral evolution and mineral ecology: The current state and a vision for the future. Applied Computing and Geosciences, 1, 100005. DOI: 10.1016/j.acags.2019.100005

Miller, M., Vitale, D., Kahn, P.C., Rost, B., & Bromberg, Y. (2019). fuNTRp: Identifying protein positions for variation driven functional tuning. Nucleic Acids Research, , gkz818, DOI:10.1093/nar/gkz818

Chan, M.A., Hinman, N.W., Potter-McIntyre, S.L., Schubert, K.E., Gillams, R.J., Awramik, S.M., Boston, P.J., Bower, D.M., Des Marais, D.J., Farmer, J.D., Jia, T.Z., King, P.L., Hazen, R.M., Leveille, R.J., Papineau, D., Rempfert, K.R., Sanchez-Roman, M., Spear, J.R., Southam, G., Stern, J.C., and Cleaves, H.J. II (2019) Deciphering biosignatures in planetary contexts. Astrobiology, 19, 28 p.   DOI:10.1089/ast.2018.1903

Hazen, R.M. (2019) An evolutionary system of mineralogy: Proposal for a classification based on natural kind clustering. American Mineralogist, 104, 810-816. DOI:10.2138/am-2019-6709CCBYNCND

Andrew C. Mutter, Alexei M. Tyryshkin, Ian J. Campbell, Saroj Poudel, George N. Bennett, Jonathan J. Silberg, Vikas Nanda, and Paul G. Falkowski. 2019. De novo design of symmetric ferredoxins that shuttle electrons in vivo. Proceedings of the National Academy of Sciences, 116(29), pp.14557-14562.  DOI:10.1073/pnas.1905643116

Price R. E. and Giovannelli D. (2019). Marine Shallow-Water Hydrothermal Vents: Geochemistry, in Encyclopedia of Ocean Sciences (Third Edition), eds. J. K. Cochran, H. J. Bokuniewicz, and P. L. Yager (Oxford: Academic Press), 346–352. DOI:10.1016/B978-0-12-409548-9.11015-2

Freiberger, M. I., Guzovsky, A. B., Wolynes, P. G., Parra, R. G., & Ferreiro, D. U. (2019). Local frustration around enzyme active sites. Proceedings of the National Academy of Sciences, 116(10), 4037-4043. DOI:10.1073/pnas.1819859116

Hazen, R. M. (2019). Earth in five reactions: Grappling with meaning and value in science. American Mineralogist, 104(4), 468-470. DOI:10.2138/am-2019-6745

Merino, N., Aronson, H. S., Bojanova, D. P., Feyhl-Buska, J., Wong, M. L., Zhang, S., Giovannelli, D. (2019). Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context. Frontiers in Microbiology, 10, 780. DOI:10.3389/fmicb.2019.00780

Estrada, C., Sverjensky, D. A., and Hazen, R. M. (2019). Selective Adsorption of Aspartate Facilitated by Calcium on Brucite [Mg(OH)2]. ACS Earth Space Chem, 3(1), 1-7. DOI:10.1021/acsearthspacechem.8b00081

2018

Morrison, S., Runyon, S., and Hazen, R. (2018). The Paleomineralogy of the Hadean Eon Revisited. Life, 8(4), 64. DOI:10.3390/life8040064

Loell, K. and Nanda, V. (2018). Marginal protein stability drives subcellular proteome isoelectric point. Proceedings of the National Academy of Sciences, 115(46), 11778-11783. DOI:10.1073/pnas.1809098115

Turjanski, P. and Ferreiro, D. U. (2018). On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences. The Journal of Physical Chemistry B, 122(49), 11295-11301. DOI:10.1021/acs.jpcb.8b07206

Kim, J. D., Pike, D. H., Tyryshkin, A. M., Swapna, G. V. T., Raanan, H., Montelione, G. T., … and Falkowski, P. G. (2018). Minimal Heterochiral de Novo Designed 4Fe–4S Binding Peptide Capable of Robust Electron Transfer. Journal of the American Chemical Society, 140(36), 11210-11213. DOI:10.1021/jacs.8b07553