Journal Publications and Preprints
2024
Noble P.A., Pozhitkov A., Singh K., Parnia S., Woods E., Liu C., King G., Levin M., Javan G., Wan J., Abouhashem A.S., Mathew-Steiner S.S., C.K. Sen. (2024) Unraveling the enigma of organismal death: insights, implications, and unexplored frontiers. ACS Physiology [in press]
Noble P.A., Hamilton BD, Gerber G.(2024) Stone Decision Engine accurately predicts stone removal and treatment complications for shock wave lithotripsy and laser ureterorenoscopy patients. PlosOne [in press] [pdf] [Supplementary data][web app]]
2019
Noble P.A. (2019) How to use AI to circumvent hospital readmissions and improve patient and business outcomes. Healthcare Business Today [web]
Noble P.A., Pasupuleti H., Poudel G., and Subramanian K. (2019) Predicting hospital readmissions using AI. Prokarma White Paper [pdf]
2018
Noble P.A., Pozhitkov A.E. (2018) Cryptic sequence features in the active postmortem transcriptome. BMC Genomics 19:675 [web] [pdf]
Noble P.A., Pozhitkov A.E. (2018) Distinct sequence patterns in the active postmortem transcriptome. Bioxriv [web] [pdf]
Bagwell C.E., Noble P.A., Milliken C.E., Li D., and Kaplan D.I. (2018) Amplicon sequencing reveals microbiological signatures in spent nuclear fuel storage basins. Frontiers of Microbiology 9:377 [pdf]
2017
Pozhitkov A.E., Neme R., Domazet-Loo T., Leroux B.G., Soni S., Tautz D, and Noble P.A. (2017) Tracing the dynamics of gene transcripts after organismal death. Royal Society Open BIology 7:160267 [pdf] [Supplementary data]
Hunter M.C., Pozhitkov A.E. and Noble P.A. (2017) Accurate predictions of postmortem interval using linear regression analyses of Gene Meter expression data. Forensic Science International 275:90–101 [web] [pdf]
Noble P.A. and Pozhitkov A.E. (2017) What happens to our genes in the twilight of death? TheScienceBreaker [web] [pdf]
Noble PA, Pozhitkov A. (2017) The postmortem microbiome and gene expression in vertebrates. The Biochemist 39:14-17 [pdf]
Noble P.A. and Pozhitkov A.E. (2017) Gene Meter: accurate abundance calculations of gene expression. Communicative and Integrative Biology, 10(4): e1329785 [web] [pdf][Supplementary data][youtube]
Pozhitkov A.E. and Noble P.A. (2017) Gene expression in the twilight of death. BioEssays, 39 (9): 1700066 [web] [pdf] [youtube]
2016
Hunter M.C., Pozhitkov A.E. and Noble P.A. (2016) Datasets used to discover the microbial signatures of oral dysbiosis, periodontitis and edentulism in humans. Data Brief 10:30–32 [pdf]
Hunter M.C., Pozhitkov A.E. and Noble P.A. (2016) Microbial signatures of oral dysbiosis, periodontitis and edentulism revealed by Gene Meter methodology. Journal of Microbiological Methods 131:85–101 [web] [pub]
Pozhitkov A.E., Neme R., Domazet-Loo T., Leroux B.G., Soni S., Tautz D, and Noble P.A. Thanatotranscriptome: genes actively expressed after organismal death. Biorxiv, June 11, 2016 [web]
Hunter M.C., Pozhitkov A.E. and Noble P.A. (2016) Accurate predictions of postmortem interval using linear regression analyses of Gene Meter expression data. Biorxiv, June 11, 2016 [web]
Noble P.A., Park H.-D., Olson B.H., Asvapathanagul P., Hunter M.C., Garrido-Baserba M., Lee S.-H., and Rosso D. (2016) A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and incubation time. Applied Microbiology and Biotechnology 100:6361-73 [pdf]
Bagwell C.E., Abernathy A., Barnwell R., Milliken C.E., Noble P.A., Dale T., Beauchesne K.R., and Moeller P.D.R. (2016) Discovery of bioactive metabolites in biofuel microalgae that offer protection against predatory bacteria. Frontiers in Microbiology 7:516 [pdf]
2015
Pozhitkov A.E., Daubert D., Brochwicz-Donimirski A., Goodigion D., Leroux B, Flemmig T.F., Hunter MC, Noble P.A., and Bryers JD. (2015) Interruption of electrical conductivity of titanium dental implants suggest a path towards elimination of the implant's corrosion PlosOne 10:e0140393 [pdf]
Pozhitkov A.E., Leroux B., Randolph T.W., Beikler T., Flemmig T.F., and Noble P.A. (2015) Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism BMC Oral Health 15:125 [pdf]
2014
Can, I., G.T. Javan, A.E. Pozhitkov and P.A. Noble (2014) Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans. Journal of Microbiological Methods 106: 1-7. [pdf]
YOUTUBE RELEASE on article below (June 2, 2014): Breathing new life into DNA microarrays. Presentation at the University of California Irvine [web].
Pozhitkov A.E., P.A. Noble, J. Bryk, D. Tautz (2014) A revised design for microarray experiments to account for experimental noise and the uncertainty of probe response. PlosOne 9: e91295 [pdf]
2013
Harrison, A., Binder, H. Buhot, A., Burden, C.J., Carlon, E., Gibas, C., Gamble, L.J. Halperin, A., Hooyberghs, J., Kreil, D.P., Levicky, R., Noble, P.A., Ott, A., Pettitt, B.M., Tautz, D., Pozhitkov, AE. (2013) Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Research 41:2779-96. [pdf]
2012
Kang, H-Y., R.A. Rule, P.A. Noble. (2012) Artificial neural network modeling of phytoplankton blooms using long term ecological research data sets and its application to sampling sites within the same estuary. Treatise on Coastal and Estuarine Science 9.09:161-171 [pdf]
2011
Noble, P.A. (2011) Metagenomic analysis of hydrocarbon-utilizing microbes from the Gulf of Mexico Science@ASU 6:32-33 [pdf]
Pozhitkov A.E., T. Beikler, T. Flemmig, P.A. Noble (2011) High-throughput methods for the analysis of human oral microbiome. Periodontology 2000 55:70-86. [pdf]
2010
Pozhitkov, A.E., I. Boubeb, M.H. Brouwer, and P.A. Noble. (2010) Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities. Nucleic Acids Research 38:e28. [pdf] [pdf_supp]
Noble, P.A. (2010) Exploration of the human oral microbiome using next generation sequencing -- a great time to be a microbiologist! Science@ASU article. Science@ASU 5: 14-16. [pdf]
2009
Rule, R.A., A.E. Pozhitkov, and P.A. Noble (2009) Use of hidden correlations in short oligonucleotide array data are insufficient for accurate quantification of nucleic acid targets in complex target mixtures. Journal of Microbiological Methods 76:188–195. [pdf] [pdf_supp]
2008
Gough, H.L., A.L. Dahl, E. Tribou, P.A. Noble, J.-F. Gaillard, and D.A. Stahl. (2008). Elevated sulfate reduction in metal contaminated freshwater lake sediments. Journal of Geophysical Research - Biosciences 113:G04037 [pdf]
Pozhitkov, A. E, G. Nies, B. Kleinhenz, D. Tautz, and P.A. Noble. (2008). Simultaneous quantification of multiple nucleic acids in target mixtures using high density microarrays. Journal of Microbiological Methods 75:92-102. [pdf] [pdf_supp]
Pozhitkov, A., R.A. Rule, R.G. Stedtfeld, S.A. Hashsham and P.A. Noble. (2008) Concentration-dependency of nonequilibrium thermal dissociation curves in complex target samples. Journal of Microbiological Methods. 74:82-88. [pdf]
2007
Pozhitkov, A., D.Tautz., and P.A. Noble. (2007) Oligonucleotide arrays: widely applied -- poorly understood. Briefings in Functional Genomics and Proteomics 6:141-148. [pdf]
Pozhitkov, A., K. D. Bailey, and P.A. Noble. (2007) Development of a statistically robust quantification method for microorganisms in mixtures using oligonucleotide microarrays. Journal of Microbiological Methods 70:292-300. [pdf] Math Supplement [doc]
Pozhitkov, A., R.G. Stedtfeld, S.A. Hashsham and P.A. Noble. (2007) Revision of the nonequilibrium dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays. Nucleic Acids Research 35:e70. [pdf]
Pozhitkov, A., and P.A. Noble. (2007) High variability in melting profiles from gel pad arrays. Environmental Microbiology 9:1865. [pdf]
Pozhitkov, A., and P.A. Noble. (2007) Comment on discrimination of shifts in soil microbial communities using nonequilibrium thermal dissociation and gel pad array technology. Environmental Science and Technology 41:1797-1798. [pdf] [pdf]
Noble, P.A. and E. Tribou. (2007) Neuroet: an easy-to-use artificial neural network for ecological and biological modelling. Ecological Modelling 203:87-98. [pdf]
2006
Pozhitkov, A., P.A. Noble, T. Domazet-Loso, A. Nolte, R. Sonnenberg, P. Staehler, M. Beier and D.Tautz. (2006) Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research 34:e66. [pdf]
2005
Pozhitkov, A., B. Chernov, G. Yershov, and P.A. Noble. (2005) Evaluation of gel-pad oligonucleotide microarray technology using artificial neural networks. Applied and Environmental Microbiology 71:8663-8676. [pdf]
Morris, J., D. Porter, M. Neet, P.A. Noble, L. Schmidt, L. A. Lapine, and J. Jensen. (2005) Integrating LIDAR elevation data, multi-spectral imagery and neural network modelling for marsh characterization. International Journal of Remote Sensing 26:5221-5234. [pdf]
Kelly, J.J., S. Siripong, J. McCormack, L.R. Janus, H. Urakawa, S. ElFantroussi, P.A. Noble, L. Sappelsa, B.E. Rittmann, and D.A. Stahl. (2005) DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Research 39:3229-3238. [pdf]
Lewitus, A.J., D. L. White, R.G. Tymowski, M.E. Geesey, S.N. Hymel and P.A. Noble. (2005) Adapting the CHEMTAX method for assessing phytoplankton taxonomic composition in southeastern U.S. estuaries. Estuaries 28:160-172. [pdf]
Noble, P.A., R.G. Tymowski, J.T. Morris, M. Fletcher, and A.J. Lewitus. (2003) Contrasting patterns of phytoplankton community pigment composition in two salt marsh estuaries in Southeastern United States.Applied and Environmental Microbiology 69:4129-4143. [pdf]
2003
El Fantroussi, S., H. Urakawa, A.E. Bernhard, J.J. Kelly, P.A. Noble, H. Smidt, G.M. Yershov, and D.A. Stahl. (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native ribosomal rRNAs hybridized to oligonucleotide microarrays.Applied and Environmental Microbiology 69:2377-2382. [pdf]
Urakawa, H., S. El Fantroussi, H. Smidt, J.C. Smoot. E. Tribou, J.J. Kelly, P.A. Noble, and D.A. Stahl. (2003) Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Applied and Environmental Microbiology 69:2848-2856. [pdf]
2002
Ogunseitan, O. A., J. LeBlanc, and P. Noble. (2002) Ecological dimensions of microbial proteomics. Recent Research Developments in Microbiology 6:487-501.
Urakawa, H., P. A. Noble, S. ElFantroussi, J.J. Kelly and D.A. Stahl. (2002) Single-base pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Applied and Environmental Microbiology 68:235-244. [pdf]
2001
Almeida J.S., J.A. Carrico, A. Maretzek A, P.A. Noble, and M. Fletcher. (2001) Analysis of genomic sequences by chaos game representation. Bioinformatics 17:429-437. [pdf]
1990 to 2000
Almeida, J.S. and P.A. Noble. (2000) Neural computing in microbiology. Journal of Microbiological Methods 43:1-2. [pdf]
Noble, P.A. , J.S. Almeida, and C.R. Lovell. (2000) Application of neural computing methods for interpreting phospholipid fatty acid profiles from natural microbial communities. Applied and Environmental Microbiology 66:694-699. [pdf]
Piceno, Y.M., Noble, P.A., and C.R. Lovell. (1999) Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis analysis. Microbial Ecology 38:157-167. [pdf]
Noble, P.A. (1999) Minireview: a hypothetical model for monitoring microbial growth by using capacitance measurements. Journal of Microbiological Methods 37:45-49. [pdf]
Noble, P.A., M. Dziuba, D.J. Harrison, and W.L. Albritton. (1999) Factors influencing capacitance-based monitoring of microbial growth. Journal of Microbiological Methods 37:51-64. [pdf]
Noble, P.A., R.W. Citek, and D.A. Ogunseitan. (1998) Tetranucleotide frequencies in microbial genomes. Electrophoresis 19:528-535. [pdf]
Noble, P.A., K.D. Bidle, and M. Fletcher (1997) Natural microbial community compositions compared by a back- propagating neural network and cluster analysis of 5S rRNA. Applied and Environmental Microbiology 63:1762-1770. [pdf]
Noble, P.A., D.L. Clark, and B.H. Olson (1996) Biological stability of ground water treated for organic carbon removal by conventional and membrane filtration methods. Journal of the American Water Works Association 88:87-96. [pdf]
Albritton, W.L., P.A. Noble, and K.D. Webster (1994) Clarification of the plasmid RSF0885 in Haemophilus influenzae serotype b. Canadian Journal of Microbiology 40:154-157. [pdf]
Dasgupta, M. K., K. Ward, P.A. Noble, M. Larabie, and J.W. Costerton (1994) Development of bacterial biofilms on silastic catheter materials in peritoneal dialysis fluids American Journal of Kidney Diseases 23:709-716.[pdf]
Dziuba, M., P.A. Noble, and W.L. Albritton (1993) A study of the nutritional requirements of a selected Haemophilus ducreyi strain by impedance and conventional methods. Current Microbiology 27:109-113. [pdf]
Noble, P.A., E. Ashton, C.A. Davidson, and W.L. Albritton (1991) Heterotrophic plate counts of surface water samples by using impedance methods, Applied and Environmental Microbiology 57:3287-3291. [pdf]
Noble, P.A., P.E. Dabinett, J.A. Gow (1990) Numerical taxonomic study of pelagic and benthic surface-layer bacteria in seasonally-cold coastal waters. Systematic and Applied Microbiology 13:77-85. [pdf]