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Publications & Software

This curated record emphasizes current biology-AI work, computational genomics, and foundational molecular genetics. Publication status is stated explicitly so manuscripts, preprints, software releases, and peer-reviewed papers are not conflated.

Selected peer-reviewed and public work

  1. Ramirez P, Martinez Montoya H, Aramayo R, Mateos M. Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma strains associated with Drosophila. Microbial Genomics. 2025;11(6). Read the article.
  2. Aramayo R, Nan B. De Novo Assembly and Annotation of the Complete Genome Sequence of Myxococcus xanthus DZ2. Microbiology Resource Announcements. 2022;11(5):e0107421. Published online April 6, 2022. Article · DOI: 10.1128/mra.01074-21 · PubMed: 35384715 · Full text: PMC9119067.
  3. Bennett CJ, Aramayo R. A Re-Analysis of an Existing Drosophila melanogaster Dataset Reveals a New Set of Genes Involved in Post-Mating Response. bioRxiv preprint. 2024:2024.04.10.588867. Preprint · DOI: 10.1101/2024.04.10.588867.
  4. Galagan JE, et al., including Aramayo R. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 2003;422:859-868. Read the article.
  5. Aramayo R, Metzenberg RL. Meiotic transvection in fungi. Cell. 1996;86(1):103-113. Read the article.

Selected open software

Current biology-AI work

  • Aramayo R. MutScan: a reproducibility-aware four-paradigm voting framework for missense-pathogenicity prediction across 15 disease-associated human proteins. Manuscript in preparation, 2026. Read the methodological rationale. This is ongoing research, not a clinically validated predictor.
  • White B, Aramayo R. Proteins as Dynamic Networks: Linking Sequence, Structure, Allostery, and Molecular Motion. Manuscript in preparation, 2026. A versioned public record is available on Zenodo, v2026-03-13-1.0.0; deposition does not imply peer review.
  • White B, Aramayo R. Dynamic Allostery as a Principal Arbiter of Amino Acid Residue Substitution in Human Pancreatic RNase 1. Manuscript in preparation, 2026. Project context.
  • Evaluating the Impact of Sequence Duplications on the Measurement of Transcriptional Profiling in the Human Genome. Manuscript in preparation, 2026; related public research artifact.

Student research outputs

  • Gallucci JL, Aramayo R. Do Public Databases Need Higher Standards for Next-Generation Data Submissions? Public research poster, 2023. Poster and research record.
  • People & projects describes the contributions of current graduate and former undergraduate researchers, with links to available public records.

Complete record

NCBI My Bibliography, ORCID, and Zenodo provide public indexes for published papers, manuscripts, research artifacts, and software releases.

NCBI bibliography ORCID Zenodo