Selected Publications

Academic Article

Year Title Altmetric
2018 Cryptic sequence features in the active postmortem transcriptome 06 Biological Sciences 0604 GeneticsBMC Genomics.  19. 2018
2018 Amplicon sequencing reveals microbiological signatures in spent nuclear fuel storage basinsFrontiers in Microbiology.  9. 2018
2017 Gene expression in the twilight of death: The increase of thousands of transcripts has implications to transplantation, cancer, and forensic researchBioEssays.  39. 2017
2017 Accurate predictions of postmortem interval using linear regression analyses of gene meter expression dataForensic Science International.  275:90-101. 2017
2017 Datasets used to discover the microbial signatures of oral dysbiosis, periodontitis and edentulism in humansData in Brief.  10:30-32. 2017
2017 Gene Meter: Accurate abundance calculations of gene expressionCommunicative and Integrative Biology.  10. 2017
2017 The postmortem microbiome and gene expression in vertebratesBiochemist.  39:14-17. 2017
2017 Tracing the dynamics of gene transcripts after organismal deathOpen Biology.  7. 2017
2016 Microbial signatures of oral dysbiosis, periodontitis and edentulism revealed by Gene Meter methodologyJournal of Microbiological Methods.  131:85-101. 2016
2016 Microbial Signatures of Oral Dysbiosis, Periodontitis and Edentulism Revealed by Gene Meter Methodology 2016
2016 A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and timeApplied Microbiology and Biotechnology.  100:6361-6373. 2016
2016 Accurate Predictions of Postmortem Interval Using Linear Regression Analyses of Gene Meter Expression Data 2016
2016 Thanatotranscriptome: genes actively expressed after organismal death 2016
2016 Discovery of bioactive metabolites in biofuel microalgae that offer protection against predatory bacteriaFrontiers in Microbiology.  7. 2016
2015 Towards microbiome transplant as a therapy for periodontitis: An exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulismBMC Oral Health.  15. 2015
2015 Interruption of electrical conductivity of titanium dental implants suggests a path towards elimination of corrosionPLoS ONE.  10. 2015
2014 A revised design for microarray experiments to account for experimental noise and uncertainty of probe responsePLoS ONE.  9. 2014
2014 Distinctive thanatomicrobiome signatures found in the blood and internal organs of humansJournal of Microbiological Methods.  106:1-7. 2014
2013 Physico-chemical foundations underpinning microarray and next-generation sequencing experimentsNucleic Acids Research.  41:2779-2796. 2013
2011 High-throughput methods for analysis of the human oral microbiomePeriodontology 2000.  55:70-86. 2011
2009 Beyond Affymetrix arrays: Expanding the set of known hybridization isotherms and observing pre-wash signal intensitiesNucleic Acids Research.  38. 2009
2009 Use of hidden correlations in short oligonucleotide array data are insufficient for accurate quantification of nucleic acid targets in complex target mixturesJournal of Microbiological Methods.  76:188-195. 2009
2008 Elevated sulfate reduction in metal-contaminated freshwater lake sedimentsJournal of Geophysical Research.  113. 2008
2008 Simultaneous quantification of multiple nucleic acid targets in complex rRNA mixtures using high density microarrays and nonspecific hybridization as a source of informationJournal of Microbiological Methods.  75:92-102. 2008
2008 Concentration dependency of nonequilibrium thermal dissociation curves in complex target samplesJournal of Microbiological Methods.  74:82-88. 2008
2007 Development of a statistically robust quantification method for microorganisms in mixtures using oligonucleotide microarraysJournal of Microbiological Methods.  70:292-300. 2007
2007 High variability in melting profiles from gel pad arrays [1]Environmental Microbiology.  9:1865. 2007
2007 Oligonucleotide microarrays: Widely applied - Poorly understoodBriefings in Functional Genomics.  6:141-148. 2007
2007 Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarraysNucleic Acids Research.  35. 2007
2007 Neuroet: An easy-to-use artificial neural network for ecological and biological modelingEcological Modelling.  203:87-98. 2007
2007 Comment on "discrimination of shifts in a soil microbial community associated with TNT-contamination using a functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays" 2007
2007 Neuroet: An easy-to-use artificial neural network for ecological and biological modeling 2007
2006 Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predictedNucleic Acids Research.  34. 2006
2005 Integrating LIDAR elevation data, multi-spectral imagery and neural network modelling for marsh characterizationInternational Journal of Remote Sensing.  26:5221-5234. 2005
2005 Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networksApplied and Environmental Microbiology.  71:8663-8676. 2005
2005 Adapting the CHEMTAX method for assessing phytoplankton taxonomic composition in southeastern U.S. estuaries 2005
2005 DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samplesWater Research.  39:3229-3238. 2005
2005 DNA microarrays as salivary diagnostic tools for characterizing the oral cavity's microbial community.Advances in Dental Research.  18:6-11. 2005
2003 Contrasting patterns of phytoplankton community pigment composition in two salt marsh estuaries in southeastern United StatesApplied and Environmental Microbiology.  69:4129-4143. 2003
2003 Optimization of single-base-pair mismatch discrimination in oligonucleotide microarraysApplied and Environmental Microbiology.  69:2848-2856. 2003
2003 Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarraysApplied and Environmental Microbiology.  69:2377-2382. 2003
2002 Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analysesApplied and Environmental Microbiology.  68:235-244. 2002
2001 Analysis of genomic sequences by Chaos Game RepresentationBioinformatics.  17:429-437. 2001
2000 Neural computing in microbiologyJournal of Microbiological Methods.  43:1-2. 2000
2000 Application of neural computing methods for interpreting phospholipid fatty acid profiles of natural microbial communitiesApplied and Environmental Microbiology.  66:694-699. 2000
1999 Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis analysis 1999
1999 Factors influencing capacitance-based monitoring of microbial growthJournal of Microbiological Methods.  37:51-64. 1999
1999 Hypothetical model for monitoring microbial growth by using capacitance measurements - A minireviewJournal of Microbiological Methods.  37:45-49. 1999
1998 Tetranucleotide frequencies in microbial genomesELECTROPHORESIS.  19:528-535. 1998
1997 Natural microbial community compositions compared by a back-propagating neural network and cluster analysis of 5S rRNAApplied and Environmental Microbiology.  63:1762-1770. 1997
1996 Biological stability of groundwater 1996
1994 Clarification of the structure of the ampicillin-resistance plasmid RSF0885 from Haemophilus influenzae HR-885 serotype bCanadian Journal of Microbiology.  40:154-157. 1994
1994 Development of Bacterial Biofilms on Silastic Catheter Materials in Peritoneal Dialysis FluidAmerican Journal of Kidney Diseases.  23:709-716. 1994
1993 A study of the nutritional requirements of a selected Haemophilus ducreyi strain by impedance and conventional methods 1993
1991 Heterotrophic plate counts of surface water samples by using impedance methodsApplied and Environmental Microbiology.  57:3287-3291. 1991
1990 A Numerical Taxonomic Study of Pelagic and Benthic Surface-layer Bacteria in Seasonally-cold Coastal WatersSystematic and Applied Microbiology.  13:77-85. 1990


Year Title Altmetric
2012 Artificial Neural Network Modeling of Phytoplankton Blooms and its Application to Sampling Sites within the Same Estuary.  161-172. 2012

Research Overview

  • I am interested in basic and interdisciplinary research in molecular biology, microbial ecology, and bioinformatics.

    My research studies depend on high throughput devices such as DNA microarrays and next-generation sequencing instruments. To improve their accuracy and precision, my team developed calibrated DNA microarrays (Gene Meters) and we are currently trying to calibrate next-generation instruments in the same way. Output from these instruments can then be used to model biological systems and understand how they work.

    Research has a way of dragging you down different paths from where you started -- whether you like it or not. One path I traveled was fixing the “noise” problem in DNA microarray output. My team produced a large body of research on the physicochemistry of DNA microarrays and with this newfound knowledge, developed a way to quantify genes and transcripts in biological samples. Another path was human oral microbiome research in patients with periodontitis and caries. Our focus was finding a way to return an unhealthy microbiome to a healthy one. A third path was investigating how vertebrates respond to stress in terms of their genetic regulatory networks. Microorganisms exploit stressful situations in vertebrates and therefore understanding how vertebrates respond to stress will shed light on how microbial populations interact with them in both health and disease. Lastly, a fortuitous outcome of my travels is the discovery that I have a talent for C++ programming, statistics (e.g., Machine Learning) and scientific writing. I use these tools to investigate challenging problems and provide solutions.
  • Education And Training

  • Doctor of Philosophy Level Degree in Microbiology, 1994
  • Master's Level Degree in Microbiology, 1984
  • Bachelor's Level Degree in Biology, 1982
  • Full Name

  • Peter Noble