% ---------------------------------------------------------------------------
% Canonical publication list — Michael Whiteside (ORCID 0009-0000-0643-5791)
% https://par2discovery.com/publications.bib
%
% Maintained by hand. Every DOI below was resolved against Crossref or DataCite
% on 2026-08-14. Prefer this file over automatically generated exports: those
% duplicate works, truncate titles, collide on keys and have in the past carried
% a journal reference and an ORCID that were not correct.
%
% Conventions
%   * One entry per work. Where a work exists both as a Research Square preprint
%     and as a Zenodo deposit, the preprint is the primary entry and the Zenodo
%     concept DOI is given in a note.
%   * Zenodo entries use the *concept* DOI, which always resolves to the latest
%     version, rather than a version DOI that freezes on one upload.
%   * Entry types follow the deposit's own resource type.
%   * @misc is used in place of biblatex's @software and @dataset so the file
%     compiles under classic BibTeX as well.
%
% Not by this author: 10.7282/t3-gh0y-zj49 ("Genetics of shell shape and color
% in the eastern oyster", 2021) is a different Michael Whiteside and appears in
% some DataCite creator-name searches. It is listed here only so it is not
% mistakenly attributed.
% ---------------------------------------------------------------------------


% ===== Journal ==============================================================

@article{whiteside2026fibonacci,
  author  = {Whiteside, Michael},
  title   = {A Time-Domain Analogue to Fibonacci Structure via Phase-Gated
             {AR(2)} Dynamics: Reply to {Boman} on Tissue {Fibonacci} Patterns
             and Colonic Crypt Renewal},
  journal = {The Fibonacci Quarterly},
  year    = {2026},
  pages   = {1--8},
  doi     = {10.1080/00150517.2026.2716122},
  url     = {https://doi.org/10.1080/00150517.2026.2716122},
  note    = {Published online 6 October 2026; volume and issue not yet assigned},
}


% ===== Preprints under review ==============================================

@misc{whiteside2026modulus,
  author       = {Whiteside, Michael},
  title        = {{AR(2)} eigenvalue modulus as a measure of temporal persistence
                  in gene expression: circadian hierarchy emerges from two
                  coefficients},
  year         = {2026},
  howpublished = {Research Square},
  doi          = {10.21203/rs.3.rs-9283100/v1},
  url          = {https://doi.org/10.21203/rs.3.rs-9283100/v1},
  note         = {Preprint. Also deposited on Zenodo,
                  concept DOI 10.5281/zenodo.19070875},
}

@misc{whiteside2026phasegated,
  author       = {Whiteside, Michael},
  title        = {A Phase-Gated Autoregressive Framework Reveals Tissue-Specific
                  Circadian Gating of Cancer-Relevant Genes Across Mammalian
                  Tissues},
  year         = {2026},
  howpublished = {Research Square},
  doi          = {10.21203/rs.3.rs-9214347/v1},
  url          = {https://doi.org/10.21203/rs.3.rs-9214347/v1},
  note         = {Preprint},
}

@misc{whiteside2026halflife,
  author       = {Whiteside, Michael},
  title        = {Context-Dependent Expression Persistence: {AR(2)} Eigenvalue
                  $|\lambda|$ Is Independent of Intrinsic {mRNA} Half-Life},
  year         = {2026},
  howpublished = {Research Square},
  doi          = {10.21203/rs.3.rs-9385465/v1},
  url          = {https://doi.org/10.21203/rs.3.rs-9385465/v1},
  note         = {Preprint},
}


% ===== Zenodo preprints and working papers =================================

@misc{whiteside2026gating,
  author    = {Whiteside, Michael},
  title     = {Phase-dependent autoregressive modelling maps tissue-specific
               clock-target gating architectures},
  year      = {2026},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17920427},
  url       = {https://doi.org/10.5281/zenodo.17920427},
  note      = {Preprint. Concept DOI; earlier versions of this concept were
               deposited under the title ``A Stability-Constrained
               Phase-Dependent AR(2) Framework for Discovering Cross-Tissue
               Circadian Gating Architectures''},
}

@misc{whiteside2025oscillatorhypothesis,
  author    = {Whiteside, Michael},
  title     = {Integrated Temporal-Spatial Oscillator Hypothesis for Crypt
               Renewal},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17366926},
  url       = {https://doi.org/10.5281/zenodo.17366926},
  note      = {Preprint. A second concept, 10.5281/zenodo.17334256, holds an
               earlier deposit of the same text and should be treated as
               superseded},
}

@misc{whiteside2025oscillatorrules,
  author    = {Whiteside, Michael},
  title     = {The Oscillator--Rules Hypothesis: Temporal--Spatial Regulation of
               Cell Cycle Dynamics and Boman's Five Rules for Colonic Crypt
               Renewal},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17170556},
  url       = {https://doi.org/10.5281/zenodo.17170556},
  note      = {Preprint},
}

@misc{whiteside2025stochastictemporal,
  author    = {Whiteside, Michael},
  title     = {Phase-Gated Order-2 Autoregressive Dynamics Resolve the
               Stochastic-Temporal Paradox in Colonic Crypt Renewal},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17449517},
  url       = {https://doi.org/10.5281/zenodo.17449517},
  note      = {Working paper},
}

@misc{whiteside2025cryptrenewal,
  author    = {Whiteside, Michael},
  title     = {A Phase-Gated {AR(2)} Framework for Colonic Crypt Renewal: A
               Temporal Analogue to Fibonacci Tissue Codes with Tuft Cell
               Readouts},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17637477},
  url       = {https://doi.org/10.5281/zenodo.17637477},
  note      = {Earlier deposit of the work later accepted by The Fibonacci
               Quarterly; see \texttt{whiteside2026fibonacci}. This record is
               typed \emph{JournalArticle} at DataCite, which overstates it},
}

@misc{whiteside2025tuftcells,
  author    = {Whiteside, Michael},
  title     = {Extension to Cell-Type-Specific Dynamics: Tuft Cells as {PAR(2)}
               Readout},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17550624},
  url       = {https://doi.org/10.5281/zenodo.17550624},
  note      = {A second concept, 10.5281/zenodo.17545169, holds the same text
               and should be treated as superseded},
}

@misc{whiteside2025tissuesystems,
  author    = {Whiteside, Michael},
  title     = {{PAR2} Framework for Phase-Gated Renewal: Applications Across
               Tissue Systems},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17556529},
  url       = {https://doi.org/10.5281/zenodo.17556529},
  note      = {Preprint},
}


% ===== Software =============================================================

@misc{par2circadian,
  author    = {Whiteside, Michael},
  title     = {{par2-circadian}: {AR(2)} eigenvalue analysis for gene
               expression time series},
  year      = {2026},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.21963192},
  url       = {https://doi.org/10.5281/zenodo.21963192},
  note      = {Software, version 1.2.0. Concept DOI, resolving to the latest
               release. Distributed on PyPI as
               https://pypi.org/project/par2-circadian/, source
               https://github.com/mickwh2764/par2discovery.
               Licensed under Apache-2.0 from version 1.2.0; earlier releases
               under PolyForm Noncommercial 1.0.0},
}

@misc{par2reproducibility,
  author    = {Whiteside, Michael},
  title     = {{PAR(2)} reproducibility: analysis code and expected results},
  year      = {2026},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.21963088},
  url       = {https://doi.org/10.5281/zenodo.21963088},
  note      = {Software. Concept DOI; v1.0.0 is 10.5281/zenodo.21963103.
               Source: https://github.com/mickwh2764/par2-reproducibility},
}

@misc{par2engine,
  author    = {Whiteside, Michael},
  title     = {{PAR(2)} Discovery Engine: Circadian Clock-Target Dynamics
               Analysis Platform},
  year      = {2026},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.18730680},
  url       = {https://doi.org/10.5281/zenodo.18730680},
  note      = {Software. Authoritative concept DOI, currently resolving to the
               clean v2.5.2 release (version DOI 10.5281/zenodo.22084312).
               The superseded v2.5.0 upload is not authoritative},
}


% ===== Datasets and supplementary material =================================

@misc{whiteside2026supplementary,
  author    = {Whiteside, Michael},
  title     = {Supplementary Data: {PAR(2)} --- Circadian gene expression
               hierarchy via {AR(2)} eigenvalue modulus ({GSE54650}, 12 mouse
               tissues)},
  year      = {2026},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.21341986},
  url       = {https://doi.org/10.5281/zenodo.21341986},
  note      = {Dataset},
}

@misc{whiteside2025cryptreproducible,
  author    = {Whiteside, Michael},
  title     = {A Phase-Gated {AR(2)} Framework for Colonic Crypt Renewal ---
               Reproducible Analysis},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17628997},
  url       = {https://doi.org/10.5281/zenodo.17628997},
  note      = {Dataset and analysis code accompanying
               \texttt{whiteside2025cryptrenewal}},
}

@misc{whiteside2025crypthomeostasis,
  author    = {Whiteside, Michael},
  title     = {{PAR(2)} Framework for Crypt Homeostasis},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17710891},
  url       = {https://doi.org/10.5281/zenodo.17710891},
  note      = {Dataset},
}


% ===== Figure deposits ======================================================
% Deposited separately from the manuscripts they belong to. Listed for
% completeness; cite the parent work rather than these.

@misc{whiteside2025figs111,
  author    = {Whiteside, Michael},
  title     = {Figures 1--11},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17342357},
  url       = {https://doi.org/10.5281/zenodo.17342357},
}

@misc{whiteside2025figs1b4b,
  author    = {Whiteside, Michael},
  title     = {Figures 1b--4b},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.17389928},
  url       = {https://doi.org/10.5281/zenodo.17389928},
}