Author

D. P. Martin

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 2 Microbiology· 2 Bioengineering· 1 Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Organism:human· 3 Approach:experimental assay· 2 Research Focus:host-pathogen & immune response· 2 Assay:metagenomics· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

S. L. Kosakovsky Pond· 3 shared A. G. Lucaci· 2 shared A. Nekrutenko· 2 shared A. Varsani· 2 shared B. Murrell· 2 shared J. D. Zehr· 2 shared S. Weaver· 2 shared A. De Klerk· 1 shared

Activity by Year

2019-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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3 shared papersEvolutionary Biology

S. L. Kosakovsky Pond

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

S. L. Kosakovsky Pond, S. Weaver, D. Callan, J. D. Zehr, A. G. Lucaci, H. Verdonk, A. Selberg, G. Brown, M. Chikina, N. L. Clark, K. D. Makova, D. P. Martin, A. Nekrutenko

HyphAeon is a transformer model that accelerates detection of episodic diversifying selection in mammalian genomes and enables new analytical capabilities beyond traditional dN/dS methods.

bioRxiv · Sep 10, 2026 · PreprintBioinformatics

Primary Ciliary Dyskinesia patient specific hiPSC-derived airway epithelium in Air Liquid Interface culture recapitulates disease specific phenotypes in vitro

L. von Schledorn, D. P. Martin, N. Cleve, J. Zoellner, D. Roth, B. O. Staar, J. Hegermann, F. Ringshausen, J. C. Nawroth, U. Martin, R. Olmer

The paper develops an in vitro model of PCD using hiPSC-derived airway epithelium that recapitulates disease-specific phenotypes.

bioRxiv · Apr 25, 2023 · PreprintBioengineering

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

D. P. Martin, S. Lytras, A. G. Lucaci, W. Maier, B. Gruning, S. D. Shank, S. Weaver, O. S. MacLean, R. J. Orton, P. Lemey, M. F. Boni, H. Tegally, G. W. Harkins, C. Scheepers, J. N. Bhiman, , S. L. Kosakovsky Pond

The paper identifies 13 rare mutations in the Omicron S-gene that cluster in functionally important regions and likely impact Spike function, suggesting cooperative interactions that mitigate fitness costs.

bioRxiv · Jan 14, 2022 · PreprintEvolutionary Biology

Variable loss of antibody potency against SARS-CoV-2 B.1.1.529 (Omicron)

D. J. Sheward, C. Kim, R. A. Ehling, A. Pankow, X. Castro Dopico, D. P. Martin, S. T. Reddy, J. Dillner, G. B. Karlsson Hedestam, J. Albert, B. Murrell

This study assesses neutralizing antibody responses against the SARS-CoV-2 Omicron variant, showing reduced potency compared to the pandemic founder but with some cross-neutralizing capacity in vaccinated individuals.

bioRxiv · Dec 19, 2021 · PreprintImmunology

Recent zoonotic spillover and tropism shift of a Canine Coronavirus is associated with relaxed selection and putative loss of function in NTD subdomain of spike protein.

J. D. Zehr, S. L. Kosakovsky Pond, D. P. Martin, K. Ceres, G. R. Whittaker, L. B. Goodman, M. J. Stanhope

This paper analyzes the evolutionary changes in the spike protein of a Canine Coronavirus isolate, identifying relaxed selection and amino acid substitutions associated with a shift in tropism from enteric to respiratory.

bioRxiv · Nov 15, 2021Evolutionary Biology

A novel lineage of polyomaviruses identified in bark scorpions

K. Schmidlin, S. Kraberger, C. Cook, D. F. DeNardo, R. S. Fontenele, K. Van Doorslaer, D. P. Martin, C. B. Buck, A. Varsani

The paper identifies eight novel polyomaviruses in bark scorpions and shows evidence of host-virus co-evolution with arthropods and chordates.

bioRxiv · May 12, 2021Microbiology

crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyads

B. P. Brown, J. Wendoh, D. Chopera, E. Havyarimana, S. Z. Jaumdally, D. D. Nyangahu, C. Gray, D. P. Martin, A. Varsani, H. B. Jaspan

The paper investigates crAssphage transmission and genomic evolution in South African mother-infant dyads, finding evidence of vertical transmission and positive selection in phage genes correlated with bacterial abundance.

bioRxiv · Mar 19, 2019 · PreprintMicrobiology