Publications

Reichardt, T.A., Timlin, J.A., Collins, A.M., Jones, H.D.T., & Jones, H.D.T. (2013). Spectroradiometric Monitoring of Algal Cultures:Translating Technology from the Benchtop to the Raceway [Presentation]. https://www.osti.gov/biblio/1658211

Jones, H.D.T. (2013). Advanced 3D-hyperspectral confocal fluorescence software [Presentation]. 10.2172/1087298

la Bauve, E., Jones, H.D.T., Sinclair, M.B., Williams, K.P., Solberg, O.D., Timlin, J.A., Hatch, A., Carson, B., & Carson, B. (2013). A novel approach to unknown pathogen detection in clinical samples [Presentation]. https://www.osti.gov/biblio/1299038

Jones, H.D.T. (2013). Test Image Sample from Nestle-Purina [Presentation]. https://www.osti.gov/biblio/1649693

Timlin, J.A., Jones, H.D.T., Collins, A.M., Carson, B., la Bauve, E., & la Bauve, E. (2013). QUANTIFICATION OF MULTIPLE FLUOROPHORES AT THE SINGLE CELL AND SUBCELLULAR LEVEL? [Presentation]. https://www.osti.gov/biblio/1649852

Timlin, J.A., Collins, A.M., Jones, H.D.T., Beechem, T., Davis, R.W., & Davis, R.W. (2013). Spatial-Temporal Dynamics of Carotenoids in Living Cells with Hyperspectral Confocal Raman Microscopy [Conference]. https://www.osti.gov/biblio/1063424

Ruffing, A.M., Jones, H.D.T., & Jones, H.D.T. (2012). Genetic engineering of cyanobacteria as biodiesel feedstock. 10.2172/1088046

Jones, H.D.T., Collins, A.M., & Collins, A.M. (2012). Integrating Sphere Data [Presentation]. https://www.osti.gov/biblio/1649713

Jones, H.D.T. (2012). Nile Red Staining of Acid Pretreated Algae [Conference]. https://www.osti.gov/biblio/1062284

Jones, H.D.T., Thomas, E.V., Harper, J.C., & Harper, J.C. (2012). Detectability of Neuronal Currents in Human Brain with Magnetic Resonance Spectroscopy. 10.2172/1113876

Timlin, J.A., Dwyer, B.P., Trahan, C.A., Garcia, O.F., Parchert, K.J., Ruffing, A.M., Jones, H.D.T., Reichardt, T.A., Powell, A.J., Collins, A.M., Gharagozloo, P.E., & Gharagozloo, P.E. (2012). From benchtop to raceway : spectroscopic signatures of dynamic biological processes in algal communities. 10.2172/1055623

Jones, H.D.T., Collins, A.M., Timlin, J.A., & Timlin, J.A. (2012). Chytrid infections of algal cells [Presentation]. https://www.osti.gov/biblio/1648002

Jones, H.D.T., Sinclair, M.B., Timlin, J.A., & Timlin, J.A. (2012). Cellular Characterization of Algal Biomass Acid-Catalyzed Conversion using Hyperspectral Imaging [Presentation]. https://www.osti.gov/biblio/1648000

Timlin, J.A., Reichardt, T.A., Collins, A.M., Jones, H.D.T., Gharagozloo, P.E., & Gharagozloo, P.E. (2012). Sandia/ Sapphire Collaboration [Conference]. https://www.osti.gov/biblio/1061117

Singh, S., Jones, H.D.T., & Jones, H.D.T. (2012). Multidimensional signatures of photo-osmotic adaptation in Dunaliella salina [Conference]. https://www.osti.gov/biblio/1073357

Timlin, J.A., Collins, A.M., Jones, H.D.T., & Jones, H.D.T. (2012). The Pyrenoid Paradox [Presentation]. https://www.osti.gov/biblio/1647962

Timlin, J.A., Carson, B., Jones, H.D.T., & Jones, H.D.T. (2012). Progress Towards Multiplexed Super-Resolution Microscopy [Presentation]. https://www.osti.gov/biblio/1732205

Ruffing, A.M., Jones, H.D.T., & Jones, H.D.T. (2012). Physiological effects of free fatty acid production in genetically engineered Synechococcus elongatus PCC 7942. Biotechnology and Bioengineering, 109(9), pp. 2190-2199. 10.1002/bit.24509

Jones, H.D.T., Sinclair, M.B., Melgaard, D.K., Collins, A.M., Timlin, J.A., & Timlin, J.A. (2012). Preprocessing strategies to improve MCR analyses of hyperspectral images. Chemometrics and Intelligent Laboratory Systems, 117, pp. 149-158. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84864307807&origin=inward

Jones, H.D.T., Timlin, J.A., Collins, A.M., Hadi, M., Dibble, D.C., Kessler, M.K., Davis, R.W., Sinclair, M.B., Reichardt, T.A., Yu, E., & Yu, E. (2012). Cellular Characterization of Algal Biomass using Fluorescence Hyperspectral Imaging [Conference]. https://www.osti.gov/biblio/1064231

Timlin, J.A., Collins, A.M., Jones, H.D.T., Garcia, O.F., & Garcia, O.F. (2012). Cyanobacteria Remodel Thylakoid Membrane Architecture [Presentation]. https://www.osti.gov/biblio/1649972

Kessler, M.K., Jones, H.D.T., Carney, L.T., Lane, T., Timlin, J.A., & Timlin, J.A. (2012). Tracking Early Infection Events of Paramecium bursaria Chlorella Virus with Confocal Fluorescence Microscopy [Conference]. https://www.osti.gov/biblio/1106410

Reichardt, T.A., Collins, A.M., Ruffing, A.M., Jones, H.D.T., Dwyer, B.P., Timlin, J.A., & Timlin, J.A. (2012). Remote spectroradiometric monitoring of Nannochloropsis salina in a fluidically mixed pond [Conference]. https://www.osti.gov/biblio/1067567

Timlin, J.A., Parchert, K.J., Hughes, L., Collins, A.M., Reichardt, T.A., Jones, H.D.T., Powell, A.J., Dwyer, B.P., Ruffing, A.M., & Ruffing, A.M. (2012). Optimizing Algal Cultivation: An Innovative Multidiscipline and Multiscale Approach [Conference]. https://www.osti.gov/biblio/1141076

Ruffing, A.M., Trahan, C.A., Jones, H.D.T., & Jones, H.D.T. (2012). Blue-Green Biofuels: Engineering Cyanobacteria for Fuel Production [Presentation]. https://www.osti.gov/biblio/1650271

Jones, H.D.T., Timlin, J.A., & Timlin, J.A. (2012). Research Overview [Presentation]. https://www.osti.gov/biblio/1659025

Jones, H.D.T., Sinclair, M.B., Timlin, J.A., & Timlin, J.A. (2012). Light-Harvesting Pigment Distribution in Living Photosynthetic Organisms Determined by Hyperspectral Confocal Fluorescence Microscopy [Conference]. https://www.osti.gov/biblio/1078682

Jones, H.D.T., Timlin, J.A., Sinclair, M.B., & Sinclair, M.B. (2012). Advanced Spectroscopic Imaging Techniques in Support of the Biomass Conversion Team [Presentation]. https://www.osti.gov/biblio/1658060

Collins, A.M., Liberton, M., Jones, H.D.T., Garcia, O.F., Pakrasi, H.B., Timlin, J.A., & Timlin, J.A. (2012). Photosynthetic pigment localization and thylakoid membrane morphology are altered in Synechocystis 6803 phycobilisome mutants. Plant Physiology, 158(4), pp. 1600-1609. https://doi.org/10.1104/pp.111.192849

Altman, S.J., Hibbs, M., Jones, H.D.T., Branda, S., Kirk, M.F., Marry, C., & Marry, C. (2011). Linking Ceragenins to Water-Treatment Membranes to Minimize Biofouling. 10.2172/1034896

Jones, H.D.T., Collins, A.M., Garcia, O.F., Timlin, J.A., & Timlin, J.A. (2011). Does the algal CO2 concentrating mechanism affect lipid production? [Conference]. https://www.osti.gov/biblio/1113274

Jones, H.D.T., Hughes, L., Parchert, K.J., & Parchert, K.J. (2011). Algal biomass constituent analysis: method uncertainties and investigation of the underlying measuring chemistries. Analytical Chemistry. https://www.osti.gov/biblio/1106817

Collins, A.M., Jones, H.D.T., Han, D., Hu, Q., Beechem, T., Timlin, J.A., & Timlin, J.A. (2011). Carotenoid distribution in living cells of haematococcus pluvialis (chlorophyceae). PLoS ONE, 6(9). https://doi.org/10.1371/journal.pone.0024302

Jones, H.D.T., Garcia, O.F., Thomas, E.V., & Thomas, E.V. (2011). Applying Multivariate Analysis Approaches to 1H-MRS Data to Detect Neuronal Currents [Conference]. https://www.osti.gov/biblio/1143482

Ruffing, A.M., Aragon, M., Garcia, O.F., Jones, H.D.T., & Jones, H.D.T. (2011). Genetic Engineering of Cyanobacteria as Biodiesel Feedstock [Presentation]. https://www.osti.gov/biblio/1662112

Timlin, J.A., Collins, A.M., Garcia, O.F., Jones, H.D.T., & Jones, H.D.T. (2011). Structure and Function of Photosynthetic Complexes in Cyanobacteria Revealed by Hyperspectral Confocal Fluorescence & Electron Microscopy [Conference]. https://www.osti.gov/biblio/1106294

Reichardt, T.A., Garcia, O.F., Collins, A.M., Ruffing, A.M., Jones, H.D.T., Aragon, M., Dwyer, B.P., Trahan, C.A., Timlin, J.A., & Timlin, J.A. (2011). Remote spectraradiometric monitoring of Nannochloropsis salina growth [Conference]. https://www.osti.gov/biblio/1289796

Ruffing, A.M., Collins, A.M., Garcia, O.F., Parchert, K.J., Jones, H.D.T., Timlin, J.A., Powell, A.J., & Powell, A.J. (2011). Programmed cell death-like responses in Chlamydomonas reinhardtii [Conference]. https://www.osti.gov/biblio/1289697

Ruffing, A.M., Aragon, M., Garcia, O.F., Jones, H.D.T., & Jones, H.D.T. (2011). Characterization of genetically engineered Synechococcus elongatus PCC 7942 for biofuel production [Conference]. https://www.osti.gov/biblio/1288484

Carvalho, B.J., Jones, H.D.T., Singh, S., & Singh, S. (2011). Multidimensional Signatures of Photo-Osmotic Adaptation in Dunaliella salina [Conference]. https://www.osti.gov/biblio/1107561

Ruffing, A.M., Aragon, M., Garcia, O.F., Jones, H.D.T., & Jones, H.D.T. (2011). Genetic Engineering and Characterization of Cyanobacteria for Biodiesel Production [Conference]. https://www.osti.gov/biblio/1108247

Timlin, J.A., Jones, H.D.T., Garcia, O.F., Sinclair, M.B., & Sinclair, M.B. (2011). Light-harvesting pigment distribution in algae and cyanobacteria determined by hyperspectral confocal fluorescence microscopy [Conference]. https://www.osti.gov/biblio/1288863

Collins, A.M., Reichardt, T.A., Ruffing, A.M., Trahan, C.A., Dwyer, B.P., Garcia, O.F., Hughes, L., Jones, H.D.T., Lane, T., Carney, L.T., Powell, A.J., & Powell, A.J. (2011). Pond-Scale Diagnostics in Algae Production [Conference]. https://www.osti.gov/biblio/1109317

Timlin, J.A., Jones, H.D.T., Beechem, T., & Beechem, T. (2011). Resolving carotenoid distribution in living cells of Haematococcus pluvialis with hyperspectral confocal Raman microscopy [Conference]. https://www.osti.gov/biblio/1108272

Timlin, J.A., Jones, H.D.T., Beechem, T., Sinclair, M.B., Collins, A.M., & Collins, A.M. (2011). Hyperspectral raman and fluorescence microscopy of individual algal cells for biochemical analysis [Conference]. https://www.osti.gov/biblio/1288765

Rempe, S., Kozina, C.L., Singh, S., Branda, S., Jones, H.D.T., Sinclair, M.B., & Sinclair, M.B. (2011). Environmental perturbations to fluorescent proteins allow unambiguous discrimination of constructs with identical sequence. Physical Biology. https://www.osti.gov/biblio/1109408

Jones, H.D.T., Sinclair, M.B., & Sinclair, M.B. (2010). Cellular characterization goes hyperspectral [Conference]. https://www.osti.gov/biblio/1035639

Ruffing, A.M., Aragon, M., Jones, H.D.T., & Jones, H.D.T. (2010). Metabolic engineering of synechococcus elongatus PCC 7942 for free fatty acid production [Conference]. https://www.osti.gov/biblio/1030278

Jones, H.D.T., Sinclair, M.B., Luk, T.S., Collins, A.M., Garcia, O.F., Melgaard, D.K., Timlin, J.A., Reichardt, T.A., & Reichardt, T.A. (2010). Hyperspectral imaging of microalgae using two-photon excitation [Conference]. https://www.osti.gov/biblio/1030351

Timlin, J.A., Dwyer, B.P., Jones, H.D.T., Collins, A.M., Ruffing, A.M., Reichardt, T.A., Garcia, O.F., Ricken, B., Powell, A.J., Trahan, C.A., & Trahan, C.A. (2010). Optimizing Algal Cultivation & Productivity: An Innovative Multidiscipline and Multiscale Approach [Presentation]. https://www.osti.gov/biblio/1732236

Jones, H.D.T., Beechem, T., Davis, R.W., McDonald, A., Timlin, J.A., & Timlin, J.A. (2010). Hyperspectral raman and fluorescence microscopy of individual algal cells for biochemical analysis [Conference]. https://www.osti.gov/biblio/1028364

Reichardt, T.A., Schmitt, R.L., Sickafoose, S., Jones, H.D.T., Timlin, J.A., & Timlin, J.A. (2010). Fluorescence measurements for evaluating the application of multivariate analysis techniques to optically thick environments. 10.2172/1008131

Altman, S.J., Jones, H.D.T., & Jones, H.D.T. (2010). Preparation of biofouling-resistant RO membranes by the attachment of ceragenins [Conference]. https://www.osti.gov/biblio/1022984

Timlin, J.A., Garcia, O.F., Aragon, M., Powell, A.J., Jones, H.D.T., Reichardt, T.A., Ricken, B., Trahan, C.A., Ruffing, A.M., Collins, A.M., Dwyer, B.P., & Dwyer, B.P. (2010). From benchtop to raceway : spectroscopic signatures of dynamic biological processes in algal communities [Conference]. https://www.osti.gov/biblio/1028414

Jones, H.D.T. (2010). Volumetric Measurement of Lipid [Presentation]. https://www.osti.gov/biblio/1677577

Jones, H.D.T., Sinclair, M.B., & Sinclair, M.B. (2010). Hyperspectral Confocal Fluorescence Microscope: A New Look into the Cell. Microscopy Today. https://www.osti.gov/biblio/1123415

Altman, S.J., Jones, H.D.T., Kirk, M.F., & Kirk, M.F. (2010). Use of ceregenins to create novel biofouling resistant water water-treatment membranes [Conference]. https://www.osti.gov/biblio/1014626

Altman, S.J., Jones, H.D.T., Clem, P., Ho, C.K., Ho, C.K., & Ho, C.K. (2010). Novel approaches to mitigate biofouling on water-treatment membranes [Conference]. https://www.osti.gov/biblio/1011684

Altman, S.J., Jones, H.D.T., & Jones, H.D.T. (2010). Novel approaches to mitigate biofouling on polyamide water treatment membranes [Conference]. https://www.osti.gov/biblio/1011642

Timlin, J.A., Jones, H.D.T., Ricken, B., Murton, J.K., Dwyer, B.P., Ruffing, A.M., Powell, A.J., Reichardt, T.A., & Reichardt, T.A. (2010). Optimizing algal cultivation & productivity : an innovative, multidiscipline, and multiscale approach [Conference]. https://www.osti.gov/biblio/1000993

Wu, H., Singh, S., Jones, H.D.T., Ricken, B., & Ricken, B. (2010). SNL's unique label-free single cell methods of alga interrogation [Presentation]. https://www.osti.gov/biblio/1682557

Altman, S.J., Clem, P., Cook, A., Hart, W.E., Hibbs, M., Ho, C.K., Jones, H.D.T., Sun, A., Webb, S.W., & Webb, S.W. (2009). Analysis of micromixers and biocidal coatings on water-treatment membranes to minimize biofouling. 10.2172/972867

Sinclair, M.B., Jones, H.D.T., Melgaard, D.K., Stork, C.L., Timlin, J.A., Davis, R.W., van Benthem, M.H., & van Benthem, M.H. (2009). Hyperspectral Confocal Fluorescence Microscope System [Presentation]. https://www.osti.gov/biblio/1692288

Timlin, J.A., Noek, R.M., Kaiser, J.N., Sinclair, M.B., Jones, H.D.T., Davis, R.W., Lane, T., & Lane, T. (2008). Accurate measurement of cellular autofluorescence is critical for imaging of host-pathogen interactions [Conference]. Progress in Biomedical Optics and Imaging - Proceedings of SPIE. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=66749101743&origin=inward

Altman, S.J., Hibbs, M., Jones, H.D.T., Fellows, B.D., & Fellows, B.D. (2008). Use of ceragenins to create novel biofouling resistant water-treatment membranes. 10.2172/946575

Hayes, D.C., Jones, H.D.T., van Benthem, M.H., Brozik, S.M., Sinclair, M.B., & Sinclair, M.B. (2008). Antimicrobial peptide interactions with supported bilayer cells and E. coli : buforin II, magainin II, and arenicin. Proposed for publication in Langmuir.. https://www.osti.gov/biblio/951549

Singh, A.K., Poschet, J.F., Carson, B., Branda, C., Manginell, R., Renzi, R.F., Perroud, T., Patel, K., Moorman, M.W., Jones, H.D.T., Srivastava, N., Joo, J., & Joo, J. (2008). An Automated Microfluidic Platform for Systems-Level Elucidation of Host-Pathogen Interactions [Conference]. https://www.osti.gov/biblio/1142841

Ho, C.K., Altman, S.J., Jones, H.D.T., Khalsa, S.S., Clem, P., & Clem, P. (2008). Analysis of micromixers to reduce biofouling on reverse-osmosis membranes. Environmental Progress, 27(2), pp. 195-203. 10.1002/ep.10274

Altman, S.J., Jones, H.D.T., Sinclair, M.B., & Sinclair, M.B. (2008). Imaging of Biofilms [Presentation]. https://www.osti.gov/biblio/1710250

Jones, H.D.T., Haaland, D.M., Sinclair, M.B., Melgaard, D.K., & Melgaard, D.K. (2008). Copy of Fluorescent Hyperspectral Imaging of Biological Samples: Evaluating the sensitivity of our quantitative measurement [Conference]. https://www.osti.gov/biblio/1145997

Haaland, D.M., Jones, H.D.T., van Benthem, M.H., Sinclair, M.B., & Sinclair, M.B. (2008). Advanced Approaches to Multivariate Curve Resolution Analysis of Hyperspectral Fluorescence Images [Conference]. https://www.osti.gov/biblio/1146315

Haaland, D.M., Jones, H.D.T., van Benthem, M.H., Sinclair, M.B., Melgaard, D.K., Stork, C.L., & Stork, C.L. (2008). Hyperspectral Confocal Fluorescence Imaging: Exploring Alternative Multivariate Curve Resolution Approaches. Journal of Applied Spectroscopy. https://www.osti.gov/biblio/1146246

Van Benthem, M.H., Keenan, M.R., Davis, R.W., Liu, P., Jones, H.D.T., Haaland, D.M., Sinclair, M.B., Brasier, A.R., & Brasier, A.R. (2008). Trilinear analysis of images obtained with a hyperspectral imaging confocal microscope. Journal of Chemometrics, 22(9), pp. 491-499. https://doi.org/10.1002/cem.1165

Jones, H.D.T., Timlin, J.A., Altman, S.J., Ho, C.K., Clem, P., Sinclair, M.B., Melgaard, D.K., Haaland, D.M., Rebeil, R., Carson, B., & Carson, B. (2008). Fluorescence Hyperspectral Imaging of Biofilms [Conference]. https://www.osti.gov/biblio/1146116

Jones, H.D.T., Haaland, D.M., Sinclair, M.B., Melgaard, D.K., van Benthem, M.H., Pedroso, M.C., & Pedroso, M.C. (2008). Weighting hyperspectral image data for improved multivariate curve resolution results. Journal of Chemometrics, 22(9), pp. 482-490. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=55449096038&origin=inward

Meyer, L.A., van Benthem, M.H., Jones, H.D.T., Brozik, S.M., Haaland, D.M., Sinclair, M.B., & Sinclair, M.B. (2007). ANTIMICROBIAL PEPTIDE INTERACTIONS WITH SUPPORTED BIOMIMETIC MEMBRANES ON MESOPOROUS SILICA [Conference]. https://www.osti.gov/biblio/1146718

Altman, S.J., Jones, H.D.T., Ho, C.K., Cornelius, C., Hibbs, M., Haaland, D.M., Sinclair, M.B., & Sinclair, M.B. (2007). Testing of RO Membrane Biofouling Using Fluorescent Hyperspectral Imaging [Conference]. https://www.osti.gov/biblio/1147989

Jones, H.D.T., Altman, S.J., Ho, C.K., Haaland, D.M., Sinclair, M.B., Melgaard, D.K., Clem, P., & Clem, P. (2007). Fluorescent hyperspectral imaging of biofilms on water treatment membranes [Conference]. https://www.osti.gov/biblio/909915

Haaland, D.M., Sinclair, M.B., Burns, A.R., Jones, H.D.T., & Jones, H.D.T. (2007). Exploring membrane protein dynamics by multicolor single Exploring membrane protein dynamics by multicolor single quantum dot imaging using wide field TIRF and hyperspectral microscopy [Conference]. https://www.osti.gov/biblio/1143313

Haaland, D.M., Sinclair, M.B., Jones, H.D.T., Timlin, J.A., Bachand, G.D., Sasaki, D.Y., Davidson, G.S., van Benthem, M.H., & van Benthem, M.H. (2007). 3D optical sectioning with a new hyperspectral confocal fluorescence imaging system. 10.2172/902877

Sinclair, M.B., Haaland, D.M., Timlin, J.A., Jones, H.D.T., & Jones, H.D.T. (2006). Hyperspectral confocal microscope. Applied Optics, 45(24), pp. 6283-6291. 10.1364/AO.45.006283

Timlin, J.A., Nieman, L.T., Jones, H.D.T., Sinclair, M.B., Haaland, D.M., Guzowski, J.F., & Guzowski, J.F. (2006). Imaging multiple endogenous and exogenous fluorescent species in cells and tissues [Conference]. Progress in Biomedical Optics and Imaging - Proceedings of SPIE. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=33646189842&origin=inward

Jones, H.D.T., Thomas, E.V., Haaland, D.M., Melgaard, D.K., Sinclair, M.B., Timlin, J.A., & Timlin, J.A. (2006). Improving multivariate curve resolution analysis performance when applied to fluorescence hyperspectral biological imaging [Conference]. https://www.osti.gov/biblio/900028

Altman, S.J., Souza, C.A., Jones, H.D.T., Sinclair, M.B., & Sinclair, M.B. (2005). Preliminary assessment of the interaction of introduced biological agents with biofilms in water distribution systems. 10.2172/876521

Nieman, L.T., Sinclair, M.B., Jones, H.D.T., Timlin, J.A., Haaland, D.M., & Haaland, D.M. (2005). HYPERSPECTRAL IMAGING SYSTEM FOR QUANTITATIVE IDENTIFICATION AND DISCRIMINATION OF FLUORESCENT LABELS IN THE PRESENCE OF AUTOFLUORESCENCE [Conference]. 10.1109/ISBI.2006.1625161

Jones, H.D.T., Timlin, J.A., Haaland, D.M., & Haaland, D.M. (2005). Understanding and correcting for the effects of instrumental artifacts in fluorescence hyperspectral images [Conference]. https://www.osti.gov/biblio/950926