seq

Peter A Noble

Journal Publications, Press Releases and Preprints

2017

PRESS RELEASES on article below: "Life Continues Within the Body After Death, Evidence Shows". Seeker, January 25, 2017 [web]; "Gene transcription found to increase after death for some cells". Phys.org, January 25, 2017 [web].; "Monitoring Post-Mortem Gene Transcription in Mice and Zebrafish". New Scientist, January 26, 2017 [web].

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 [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), http://dx.doi.org/10.1080/19420889.2017.1329785 [Supplementary data][youtube]


Pozhitkov A.E. and Noble P.A. (2017) Gene expression in the twilight of death. BioEssays, 39 (9): 1700066, August 8, 2017 http://doi.wiley.com/10.1002/bies.201700066 [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]

PRESS RELEASE on article below: "The Sleeping Monsters in your Mouth". Microbial World October 19, 2016 [web].

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]

PRESS RELEASES on two articles below: "‘Undead’ genes come alive days after life ends" Science June 22, 2016 [web], "Hundreds of genes seen sparking to life two days after death" New Scientist June 21, 2016 [web], "Zombie Genes Awaken!" GenomeWeb June 22, 2016 [web], "Your genes could be full of life, even when you die" Huffington Post June 23, 2016 [web], "Genes Expressed After Death" The Scientist June 23, 2016 [web], "Some genes remain alive for days after the body dies" Smithsonian June 24, 2016 [web], "Zombie genes come to life after animals die" BioTechniques July 6, 2016 [web], and 30+ other articles [web].

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]

PRESS RELEASE on article below: "A Tale of Three Biofilm Cities on Aeration Diffusers". Microbial World June 23, 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

PRESS RELEASE on article below: "Powerhouse in your mouth" Microbial World October 13, 2015 [web].

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]

PRESS RELEASE on article below: "Treating gum disease with oral microbiota transplants" Microbial World October 16, 2015 [web].

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

PRESS RELEASES on the article below: "Your death microbiome could catch your killer." New Scientist August 27, 2014 [pdf], "Introducing the Thanatomicrobiome" MicrobialWorld August 15, 2014[ pdf], "The microbiome of death" Forensic Anna:thropology August 28, 2014 [pdf] and "The Death Microbiome: Invasion of the Body Snatchers" BioTechniques - The International Journal of Life Science Methods September 11, 2014 [pdf]

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].

PRESS RELEASE on article below (March 13, 2014) on the article below: Researchers develop new microarray experimental design that improves data quality, reliability. GenomeWeb March 14, 2014 [pdf]

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]

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]