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Refereed Journal Articles





Boysen A.1, Heal K.R.1, Carlson L.T. Ingalls A.E. 2018. Best-matched internal standard normalization in liquid chromatography-mass spectrometry environmental metabolomics. Analytical Chemistry.

Fassbender A.J., Palevsky H.I., Martz T.D., Ingalls A.E., Gledhill M., Fawecett S.E., Brandes J., Aluwihare L.I., and participants of COME ABOARD and DISCO XXV. 2017. Perspectives on Chemical Oceanography in a changing environment: Participants of the COME ABOARD Meeting examine the field in the context of 40 years of DISCO. Marine Chemistry.

Qin W., Amin S.A., Lundeen R.A., Heal K.R., Martens-Habbena W., Turkarslan S., Urakawa H., Costa K.C., Hendrickson E.L. Wang T., Beck D.A.C., Tequia S.M., Taub F., Holmes A.D., Lowe T.M., Moffett J.W., Devol A.H., Baliga N.S., Arp D.J., Sayavedra-Soto L.A., Hackett M., Armbrust E.V., Ingalls A.E., Stahl D.A. 2017. Transcriptional response of a marine ammonia-oxidizing archaeon to varying ammonia and copper availability in relation to it’s global proteome. ISME Journal.

Horak R.E.A., Qin W., Bertagnolli A., Nelson A., Heal K.R., Han H., Heller M., Schauer A., Jeffrey W., Armbrust E.V., Moffett J.W., Ingalls A.E., Stahl D.A., Devol A.H. Accepted 2017. Relative impacts of light, temperature and reactive oxygen on thaumarchaeal ammonia oxidation in the North Pacific Ocean. Limnology and Oceanography. 

Ingalls A.E., 2016. Paleoceanography: Signal from the subsurface. News and Views. Nature Geosciences.

Heal K.R., Qin W., Ribalet F., Bertagnolli A.D., Coyote-Maestas W., Hmelo L.R., Moffett J. W., Devol A.H., Armbrust E.V., Stahl D.A., Ingalls A.E. 2016. Two distinct pools of B12 analogs reveal community interdependencies in the ocean.  Proceedings of the National Academy of Sciences.

French D.W., Huguet C., Turich C., Wakeham S.G., Carlson L.T. Ingalls A.E. 2015. Spatial distribution of core and intact glycerol diaslkyl glycerol tetraethers (GDGTs) in the Columbia River basin and Willapa Bay, Washington: Insights into origin and implications for the BIT index. Organic Geochemistry.

Qin W. Carlson L.T., Armbrust E.V., Devol A.H., Moffett J.W., Stahl D.A., Ingalls A.E. 2015. Confounding effects of oxygen and temperature on the TEX86 signature of marine Thaumarchaea.  Proceedings of the National Academy of Sciences. doi/10.1073/pnas.1501568112.

Amin, S.S., Hmelo L.R., van Tol H., Durham B., Truxal L., Heal K., Morales R., Berthiaume C., Djunaedi B., Ingalls A.E., Parsek M., Moran MA., Armbrust E.V.  2015. Auxin-based signaling prevalent in the marine environment. Nature. 522:98-101. doi:10.1038/nature14488.

Bridoux M. C., Neibauer J., Nunn B., Ingalls A.E., Keil R. G. 2015. Suspended marine particulate proteins in coastal and oligotrophic waters. J. Mar. Systems. 1443: 39-48. doi:10.1016/j.jmarsys.2014.10.014.

Martens-Habbena W., Qin W., Horak R.E.A., Urakawa H., Schauer A.J., Moffett J.W., Armbrust E.V., Ingalls A.E., Devol A.H., Stahl D.A.  2015. Nitric oxide metabolism in ammonia-oxidizing archaea and its significance to marine nitrification.  Environmetnal Microbiology. doi: 10.10.1111/1462-2920.12677.

Heal, K., Carlson L.T., Devol A. H., Armbrust E.V., Moffett J.W., Stahl, D.A., Ingalls A.E. 2014. Determination of four forms of vitamin B12 and other B vitamins in seawater by liquid chromatography tandem mass spectrometry.  Rapid Comm. Mass. Spec.

Qin, W., Amin S.A., Martens-Habbena,W., Walker C.B., Urakawa H., Devol A.H , Ingalls A.E., Moffett J.W., Armbrust E.V. and D.A., Stahl. 2014. Adaptive radiation of marine ammonia-oxidizing archaea. PNAS.

Urakawa H, Martens-Habbena W, Huguet C, de la Torre J, Ingalls AE, Devol A.H. and Stahl D.A. 2014.  Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary. 59(4) Limnology and Oceanography. Doi: 10.4319/lo.2014.59.4.0000.

Jacquot J.E., Horak R.E.A., Amin S.A., Devol A.H., Ingalls A.E., Armbrust E.V., Stahl D.A., Moffett J.W. 2014.  Assessment of potential for copper limitation of ammonia oxidation by Archaea in a dynamic estuary.  Mar. Chem.

Schouten S. and 56 other authors. 2013. An interlaboratory study of TEX86 and BIT analyses of sediments, extracts and standard mixtures. G-Cubed.

Ellis, E.E., A.E. Ingalls, J.E. Richey, R.G. Keil, L.T. Truxal, G.M. Santos, S.R. Alin, and E.R.M. Druffel. 2013. Young plant-derived organic matter is consistently exported from sediments of the Mekong River Basin despite high variability in the age of the bulk sediments. Geophysical Res. Lett. doi:10.1002/2013GL057450.

Amin S.A., Moffett J.W., Martens-Habbena W., Jacquot J., Devol A, Ingalls AE, Stahl D.A., Armbrust E.V.  2013. Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications for nitrification in the marine environment.  L&O. 58: 2037-2045. Doi: 10.4319/l0.2013.58.6.2037.

Hilary G. Close, Sunita R. Shah, Anitra E. Ingalls, Aaron F. Diefendorf, Eoin L. Brodie, Roberta L. Hansman, Katherine H. Freeman, Lihini I. Aluwihare, Ann Pearson.  2013.  Export of submicron particulate organic matter to mesopelagic depths in an oligotrophic gyre.  PNAS. 110:31, 12565-12570. DOI/10.1073/pnas.1217514110.

Horak R.E.A, Qin W., Schauer A.J., Armbrust E.V., Ingalls A.E., Moffett J.W., Stahl D.A., Devol A.H. 2013.  Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea.  The ISME Journal. DOI:10.1038/ismej.2013.75

Pearson, A. and Ingalls A.E. 2013.  Assessing the use of archaeal lipids as marine environmental proxies. Annual Reviews in Earth and Planetary Sciences. Invited review article.

Bridoux, M.C., and A.E. Ingalls. 2013. Diatom Microfossils from Cretaceous and Eocene Sediments Contain Native Silica Precipitating Long Chain Polyamines. Geobiology.

Bridoux, M.C., V.V. Annenkov, R.G. Keil, and A.E. Ingalls. 2012a. Widespread distribution and molecular diverstiy of diatom frustule bound aliphatic long chain polyamines (LCPAs) in marine sediments. Org. Geochem. 48:9-20. DOI 10.1016/j.orggeochem.2012.04.002

Bridoux, M.C., R.G. Keil, and A.E. Ingalls. 2012b. Analysis of natural diatom communities reveals novel insights into the diversity of long chain polyamine (LCPA) structures involved in silica precipitation. Org. Geochem. 47:9-21.

Ellis, E.E., R.G. Keil, A.E. Ingalls, J.E. Richey, and S.R. Alin. 2012. Seasonal variability in the sources of particulate organic matter of the Mekong River as discerned by elemental and lignin analyses. Journal of Geophysical Research-Biogeosciences. 117. DOI 10.1029/2011JG001816

Ingalls, A.E., C. Huguet, and L.T. Truxal. 2012. Distribution of Intact and Core Membrane Lipids of Archaeal Glycerol Dialkyl Glycerol Tetraethers among Size-Fractionated Particulate Organic Matter in Hood Canal, Puget Sound. Applied and Environmental Microbiology. 78:1480-1490.

Bridoux M., Annenko V., Menzel H., Keil R., and Ingalls A.E. 2011. A new liquid chromatography/electrospray ionization mass spectrometry method for the analysis of underivitized aliphatic long chain polyamines.  Rapid Communications in Mass Spectrometry.  25: 877-888. DOI: 10.1002/rcm.4931.

Shevenell A., Ingalls A.E., Domack E.W., Kelly C.,  2011. Holocene Southern Ocean surface temperature variability west of the Antarctic Peninsula. Nature. 470: 250-254. DOI:10.1038/nature09751.

Ingalls AE, Ellis E, McDuffee K, Keil R, dos Santos Guaciara, Druffel ERM. 2011. HPLC Purification of higher plant-derived lignin phenols for compound specific radiocarbon analysis. Analytical Chemistry. 82: 8931-8938.

Huguet C, Martens-Habbena W, Urakawa H, Truxal L, Stahl DA, Ingalls AE. 2010.  Changes in intact membrane lipid content of archaeal cells may indicate metabolic status. Organic Geochemistry. DOI: 0.1016/j.orggeochem.2010.04.012.

Bridoux M and Ingalls AE, 2010. The occurrence and application of long chain polyamines in sedimentary diatom frustules, a major component of diatom –bound organic matter. Geochim. Cosmochim Acta. 10.1016/j.gca.2010.04.010.

Huguet C, Martens-Habbena W, Urakawa H, Stahl DA, Ingalls AE. 2010. Optimization of extraction methods for intact and core glycerol dialkyl glycerol tetraethers (GDGTs). Limnology and Oceanography Methods. 8: 127-145, DOI 10.4319/lom.2010.8.127.

Ingalls AE, Whitehead KI, Bridoux, M.  2009.  Tinted windows: the presence and identification of the UV-absorbing compounds, mycosporine-like amino acids, in the frustules of marine diatoms. Geochimica Cosmochimica Acta.  doi 10.1016/j.gca.2009.09.012.

Hansman RL, Griffin S, Watson JT, Druffel ERM, Ingalls AE, Pearson A, Aluwihare LI. 2009. The radiocarbon signature of microbial organisms in the mesopelagic ocean. PNAS, 106(16) 6513-6518.


Schouten, S, Hopmans EC, van der Meer J, Mets A, Bard E, Bianchi TS, Diefendorf A, Escala M, Freeman KH, Furukawa Y, Huguet C, Ingalls AE, Ménot-Combes G, Nederbragt AJ, Oba M, Pearson A, Pearson EJ, Rosell-Melé A, Schaeffer P, Shah SR, Shanahan TM, Smith RW, Smittenberg R, Suzuki M, Talbot HM, Uchida M, Van Mooy BAS, Yamamoto M, Zhang Z, Sinningh Damsté J. 2009. An interlaboratory study of TEX86 and BIT analysis using high performance liquid chromatography/mass spectrometry. G-Cubed, 10(3) doi:10.1029/2008GC002221.

de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA. 2008. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environmental Microbiology. doi 10.1111/j1462-2920.

Walsh E. Ingalls AE, Keil R. 2008. Sources and Transport of Terrestrial Organic Matter in Vancouver Island Fjords and the Vancouver- Washington Margin:  A multiproxy approach using δ13Corg, lignin phenols and the ether lipid BIT Index. Limnology and Oceanography. 53(3) 1054-1063.

Shevenell, A.E., Ingalls, A.E., and E.W. Domack, 2007. Orbital and atmospheric forcing of western Antarctic Peninsula climate in the Holocene: The TEX86 paleotemperature record of Palmer Deep. Changing World-Online Proceedings of the 10th ISAES X, A.K. Cooper and C.R. Raymond et al., eds., USGS Open-File Report, p. 131-4p, vol. 1047.

Ingalls AE, Liu ZF and Lee C. 2006. Seasonal and latitudinal trends in source and diagenesis of sinking particles in the Pacific sector of the Southern Ocean: insights from amino acids, pigments and diatom-bound organic matter. DSR I.

Ingalls AE, Shah S, Hansman RL, Aluwihare LI, Santos GM, Druffel ERM, Pearson A. 2006.  Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. 103: 6442-6447. PNAS.  

Ingalls AE and Pearson A. The Oceanography Society, Ten Years of Compound-Specific Radiocarbon Analysis.  Invited article, Oceanography.  September, 2005, 12-25.  

Ingalls AE, Anderson RF, Pearson A, 2004. Compound-specific radiocarbon dating of diatom-bound organic compounds. Marine Chemistry. 92:  91-105.  

Ingalls AE, Lee C and Aller RC. 2004.  Organic matter diagenesis in shallow water carbonate sediments. Geochimica et Cosmochimica Acta. 68: 4363-4379.

Pearson A., Huang Z., Ingalls A. E., Romanek C., Wiegel J. Freeman K. H., Smittenberg R. H. and Zhang C.L.  2004. Non-marine crenarchaeol in Nevada hot springs, Applied and Environmental Microbiology.  70: 9, 5229-5237.

Ingalls AE, Lee C and Druffel ERM. 2003.  Preservation of organic matter in mound-forming corals skeletons.  Geochimica Cosmochimica et Acta.  67: 4, 2827-2841.  

Ingalls AE, Lee C, Hedges JI and Wakeham SG. 2003.  The role of biominerals in the sinking flux and preservation of amino acids in the Southern Ocean along 170°W.  Deep-Sea Research II.  50:3-4, 709-734.

Ingalls AE, Aller RC, Lee C and Sun M-Y.  2000. The influence of macrofauna on chlorophyll-a degradation in coastal marine sediments.  Journal of Marine Research 58:4, 631-651.  



Metabolomics method paper published!
Jan 13, 2018 4:50 PM
Boysen and Heal et al., published in Analytical Chemistry.
Best-matched internal standard normal...
Outstanding Researcher Award
Jul 25, 2017 2:00 PM
Ingalls receives the Outstanding Researcher Award from the College of the Environment!
Graduate Dean's Medalist
Mar 23, 2017 1:45 PM
Congratulations​ to Katherine Heal for being awarded the College of the Environment Graduate Dean'...
News about Katherine's paper
Jan 18, 2017 11:15 AM
Congratulations​ to Katherine Heal on the publication of her latest work in PNAS!
Jan 4, 2017 1:43 PM
Heal et al., Two distinct pools of B12 analogs reveal community interdependenci​es in the ocean. P...
News and Views in Nature Geosciences
Nov 15, 2016 10:05 PM
Read a commentary by Ingalls about the TEX86 paleo sea surface temperature index​jlzV
New Instrument Arrives
Dec 18, 2015 1:06 PM
Our new QExactive HF LC-MS is here and awaiting installation in early in 2016!
First SCOPE cruise in summer 2015 was a success
Sep 17, 2015 12:16 PM
Latest news from the Ingalls Lab
Feb 11, 2011 4:21 PM
Ingalls named SCOPE Investigator​​investigators.h​tml

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