Author

Daniel McDonald

University of California San Diego

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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Microbiology· 2 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Assay:metagenomics· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

Rob D. KnightiD· 3 shared Antonio Gonzalez· 2 shared Lucas PateliD· 2 shared Adwoa Agyei Nkansah· 1 shared Aïda Sadikh BadianeiD· 1 shared Ainara SistiagaiD· 1 shared Alain Fezeu· 1 shared Alain FromentiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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3 shared papersMicrobiology

Rob D. KnightORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

M. Omar Din, Caitriona Brennan, Jianshu Zhao, Renee E. Oles, Lucas Patel, Amanda Birmingham, Dilara M. Sevilir, Lauren Hansen, Gillian M. Wright, Madison Ambre, Meika Tomita, Tara Boyer, Antonio Gonzalez, Gail L. Ackermann, Daniel McDonald, , Rob D. Knight

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

bioRxiv · Sep 29, 2026 · PreprintMicrobiology

Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma

Caitlin Guccione, I. Sfiligoi, Antonio Gonzalez, Justin P. Shaffer, Mariya Kazachkova, Yuhan Weng, Daniel McDonald, Shailja C. Shah, Samuel S. Minot, Thomas G. Paulson, William M. Grady, Ludmil B. Alexandrov, Rob D. Knight, Kit Curtius

The paper models microbial community assembly dynamics in Barrett's esophagus and esophageal adenocarcinoma, finding neutral dynamics in normal tissue and BE but not EAC, with H. pylori showing non-neutral behavior in BE non-cancer outcomes.

BMC Genomics · Feb 10, 2026Peer-reviewedCancer Biology

Industrialization drives convergent microbial and physiological shifts in the human metaorganism

Mathilde Poyet, Malte Christoph Rühlemann, Ana Paula Schaan, Yue Ma, Lucas Moitinho‐Silva, Eike Matthias Wacker, Hannah Jebens, Lucas Patel, Le Thanh Tu Nguyen, Alexis Zimmer, Damian Rafal Plichta, Daniel McDonald, Christine R. Stevens, Adwoa Agyei Nkansah, Mary Afihene, , Mathieu Groussin

The paper investigates how industrialization affects microbial and physiological traits in the human gut across diverse populations, finding homogenized microbiomes, reduced diversity, and impaired disease prediction accuracy in less industrialized groups.

bioRxiv · Oct 20, 2025 · PreprintMicrobiology