Daniel McDonald

108.2k total citations · 12 hit papers
116 papers, 22.8k citations indexed

About

Daniel McDonald is a scholar working on Molecular Biology, Physiology and Ecology. According to data from OpenAlex, Daniel McDonald has authored 116 papers receiving a total of 22.8k indexed citations (citations by other indexed papers that have themselves been cited), including 77 papers in Molecular Biology, 22 papers in Physiology and 19 papers in Ecology. Recurrent topics in Daniel McDonald's work include Gut microbiota and health (59 papers), Genomics and Phylogenetic Studies (25 papers) and Diet and metabolism studies (17 papers). Daniel McDonald is often cited by papers focused on Gut microbiota and health (59 papers), Genomics and Phylogenetic Studies (25 papers) and Diet and metabolism studies (17 papers). Daniel McDonald collaborates with scholars based in United States, Australia and Netherlands. Daniel McDonald's co-authors include Rob Knight, J. Gregory Caporaso, José C. Clemente, Curtis Huttenhower, Dan Knights, Jesse Zaneveld, Rebecca L. Vega Thurber, Robert G. Beiko, Morgan G. I. Langille and Deron E. Burkepile and has published in prestigious journals such as Nature, Science and Proceedings of the National Academy of Sciences.

In The Last Decade

Daniel McDonald

113 papers receiving 22.5k citations

Hit Papers

Predictive functional profiling of microbial communities ... 2011 2026 2016 2021 2013 2011 2017 2017 2017 2.0k 4.0k 6.0k
What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

  1. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
    2013 7.1k citations Jesse Zaneveld, Daniel McDonald et al. profile →
  2. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    2011 4.0k citations Daniel McDonald, Rob Knight et al. profile →
  3. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
    2017 1.3k citations Amnon Amir, Daniel McDonald et al. mSystems profile →
  4. Dynamics of the human gut microbiome in inflammatory bowel disease
    2017 839 citations Daniel McDonald, Rob Knight et al. Nature Microbiology profile →
  5. Strains, functions and dynamics in the expanded Human Microbiome Project
    2017 804 citations Daniel McDonald, Rob Knight et al. profile →
  6. GABA-modulating bacteria of the human gut microbiota
    2018 794 citations Daniel McDonald, Karsten Zengler et al. Nature Microbiology profile →
  7. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
    2012 590 citations Daniel McDonald, Jesse Stombaugh et al. profile →
  8. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
    2014 421 citations Luke K. Ursell, Daniel McDonald et al. profile →
  9. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
    2018 356 citations Stefan Janssen, Daniel McDonald et al. mSystems profile →
  10. QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data
    2020 318 citations Lingjing Jiang, Daniel McDonald et al. profile →
  11. Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults
    2019 270 citations Jacobo de la Cuesta‐Zuluaga, Scott T. Kelley et al. mSystems profile →
  12. High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
    2021 221 citations Søren Michael Karst, Ryan Ziels et al. Nature Methods profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name h Career Trend Papers Cites
Daniel McDonald United States 47 13.3k 4.6k 3.0k 2.4k 2.2k 116 22.8k
William A. Walters United States 24 11.6k 0.9× 4.1k 0.9× 3.3k 1.1× 2.3k 0.9× 1.8k 0.8× 30 19.8k
Todd Z. DeSantis United States 29 11.5k 0.9× 6.3k 1.4× 2.1k 0.7× 1.9k 0.8× 2.0k 0.9× 52 21.6k
Levi Waldron United States 37 13.3k 1.0× 2.6k 0.6× 2.7k 0.9× 2.3k 0.9× 1.8k 0.8× 90 21.7k
Jacques Izard United States 29 11.7k 0.9× 2.8k 0.6× 3.3k 1.1× 2.3k 1.0× 1.9k 0.9× 61 20.7k
Benjamin J. Callahan United States 22 13.4k 1.0× 8.7k 1.9× 2.1k 0.7× 2.0k 0.8× 2.3k 1.1× 42 28.9k
Jeroen Raes Belgium 75 18.9k 1.4× 4.8k 1.0× 4.3k 1.4× 3.2k 1.3× 2.6k 1.2× 224 27.8k
Lars Hestbjerg Hansen Denmark 64 9.1k 0.7× 3.8k 0.8× 1.6k 0.5× 1.6k 0.7× 1.6k 0.7× 331 16.9k
Andrew Han United States 13 10.4k 0.8× 6.9k 1.5× 1.8k 0.6× 1.6k 0.6× 1.8k 0.9× 18 22.7k
Robert G. Beiko Canada 40 9.4k 0.7× 4.2k 0.9× 1.6k 0.5× 1.4k 0.6× 1.5k 0.7× 107 16.5k
Scot E. Dowd United States 83 10.9k 0.8× 2.6k 0.6× 2.0k 0.7× 3.5k 1.4× 2.6k 1.2× 289 23.3k

Countries citing papers authored by Daniel McDonald

Since Specialization
Citations

This map shows the geographic impact of Daniel McDonald's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Daniel McDonald with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Daniel McDonald more than expected).

Fields of papers citing papers by Daniel McDonald

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Daniel McDonald. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Daniel McDonald. The network helps show where Daniel McDonald may publish in the future.

Co-authorship network of co-authors of Daniel McDonald

This figure shows the co-authorship network connecting the top 25 collaborators of Daniel McDonald. A scholar is included among the top collaborators of Daniel McDonald based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Daniel McDonald. Daniel McDonald is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
1.
McDonald, Daniel, Pekka Jousilahti, Guillaume Méric, et al.. (2025). Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort. European Journal of Nutrition. 64(4). 153–153. 3 indexed citations
2.
Song, Se Jin, Britta De Pessemier, Daniel McDonald, et al.. (2025). Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis. Communications Biology. 8(1). 1159–1159.
3.
Nonejuie, Poochit, Alisa Wilantho, Daniel McDonald, et al.. (2024). Differential gut microbiota composition in β-Thalassemia patients and its correlation with iron overload. Scientific Reports. 14(1). 23858–23858. 2 indexed citations
4.
Lukacz, Emily S., Cynthia S. Fok, MacKenzie Bryant, et al.. (2024). Feasibility of Home Collection for Urogenital Microbiome Samples. Urogynecology. 30(11). 896–905. 2 indexed citations
5.
Harris, Grant, David R. Stewart, Matthew J. Butler, et al.. (2024). N-mixture models with camera trap imagery produce accurate abundance estimates of ungulates. Scientific Reports. 14(1). 31421–31421.
6.
Tap, Julien, Franck Lejzerowicz, Aurélie Cotillard, et al.. (2023). Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nature Communications. 14(1). 3310–3310. 20 indexed citations
7.
Minich, Jeremiah J., Andreas Härer, Benjamin W. Frable, et al.. (2022). Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nature Communications. 13(1). 6978–6978. 47 indexed citations
8.
Karst, Søren Michael, Ryan Ziels, Rasmus Hansen Kirkegaard, et al.. (2021). High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nature Methods. 18(2). 165–169. 221 indexed citations breakdown →
9.
Mu, Andre, Daniel McDonald, Alan K. Jarmusch, et al.. (2021). Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection. Microbiome. 9(1). 92–92. 54 indexed citations
10.
Cotillard, Aurélie, Nicole S. Litwin, Franck Lejzerowicz, et al.. (2021). A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. American Journal of Clinical Nutrition. 115(2). 432–443. 52 indexed citations
11.
Huey, Samantha L, Lingjing Jiang, Marcus W. Fedarko, et al.. (2020). Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India. mSphere. 5(5). 23 indexed citations
12.
Bouslimani, Amina, Ricardo Silva, Tomasz Kościółek, et al.. (2019). The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biology. 17(1). 121 indexed citations
13.
Cuesta‐Zuluaga, Jacobo de la, Scott T. Kelley, Yingfeng Chen, et al.. (2019). Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems. 4(4). 270 indexed citations breakdown →
14.
Washburne, Alex D., James T. Morton, Jon G. Sanders, et al.. (2018). Methods for phylogenetic analysis of microbiome data. Nature Microbiology. 3(6). 652–661. 60 indexed citations
15.
Knights, Dan, Tonya Ward, Hannah Miller, et al.. (2014). Rethinking “Enterotypes”. Cell Host & Microbe. 16(4). 433–437. 261 indexed citations
16.
Ursell, Luke K., Manjula Gunawardana, John A. Moss, et al.. (2013). Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings. Antiviral Research. 102. 87–94. 20 indexed citations
17.
Widmann, Jeremy, Jesse Stombaugh, Daniel McDonald, et al.. (2012). RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA. 18(7). 1319–1327. 20 indexed citations
18.
Almodóvar, Sharilyn, Rob Knight, Amanda A. Allshouse, et al.. (2011). Human Immunodeficiency Virus nef Signature Sequences Are Associated with Pulmonary Hypertension. AIDS Research and Human Retroviruses. 28(6). 607–618. 42 indexed citations
19.
McDonald, Daniel, et al.. (2003). Foot and Mouth Disease: Implications of Adopting Tests that Differentiate Vaccinated Animals. 10(1). 141. 1 indexed citations
20.
McDonald, Daniel & David A. Norton. (1992). LIGHT ENVIRONMENTS IN TEMPERATE NEW ZEALAND PODOCARP RAINFORESTS. New Zealand Journal of Ecology. 16(1). 15–22. 27 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

Explore authors with similar magnitude of impact

Breakdown of academic impact, for papers by William A. Walters Breakdown of academic impact, for papers by Todd Z. DeSantis Breakdown of academic impact, for papers by Levi Waldron Breakdown of academic impact, for papers by Jacques Izard Breakdown of academic impact, for papers by Benjamin J. Callahan Breakdown of academic impact, for papers by Jeroen Raes Breakdown of academic impact, for papers by Lars Hestbjerg Hansen Breakdown of academic impact, for papers by Andrew Han Breakdown of academic impact, for papers by Robert G. Beiko Breakdown of academic impact, for papers by Scot E. Dowd
Rankless by CCL
2026