Susan Holmes

115.7k citations

189 papers · 52.9k indexed · 9 hit papers · h-index 60

Impact in

Ecology top 0.02%
- Microbial Community Ecology and Physiology
- Environmental DNA in Biodiversity Studies
Molecular Biology top 0.05%
- Gut microbiota and health
- Genomics and Phylogenetic Studies

Papers in

Virology 21
- HIV Research and Treatment 21
Statistics and Probability 15

Co-authors: Paul J. McMurdie Benjamin J. Callahan Michael Rosen Andrew Han David A. Relman Diana M. Proctor Nicole M. Davis Elizabeth Halloran
Journals: Proceedings of the National Academy of Sciences (9 papers)PLoS ONE (6 papers)PLoS Computational Biology (5 papers)Nature Communications (5 papers)Behavioral Ecology (4 papers)
Partner nations: United States France Canada

In The Last Decade

Susan Holmes

179 papers receiving 52.3k citations

Hit Papers

9 papers align trajectories log scale

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data 2018 · 1.9k citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2018 Microbiome
2017 Proceedings of the National Academy of Sciences
2017 The ISME Journal
2016 Nature Methods
2015 Proceedings of the National Academy of Sciences
2014 PLoS Computational Biology
2013 PLoS ONE
2013 Methods in enzymology on CD-ROM/Methods in enzymology
1996 Proceedings of the National Academy of Sciences

Peers

Countries citing papers authored by Susan Holmes

Since Specialization

Citations

This map shows the geographic impact of Susan Holmes'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 Susan Holmes with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Susan Holmes more than expected).

Fields of papers citing papers by Susan Holmes

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Susan Holmes. 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 Susan Holmes. The network helps show where Susan Holmes may publish in the future.

Co-authors

The 25 scholars most cited alongside Susan Holmes, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Susan Holmes Line = papers co-authored together Susan Holmes links everyone, so they are left out of the graph.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work
1	Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial) Contemporary Clinical Trials Communications ·Melese Niguse Robele, Y Leblais, Anna‐Ursula Happel, Melvin O. Steen, A. Anand Babu Christus, Nonhlanhla Yende‐Zuma, Y Saïdi, Mutsumi Oishi, Lara Lewis, Farzana Osman, Tze-Chun Chang, Allen Kim, Irina Skorobogatyh, 良道宮沢, Sinaye Ngcapu, Lenine J. P. Liebenberg, Laura Symul, Susan Holmes, Caroline M. Mitchell, Disebo Potloane	2025	1
2	Sex differences and immune correlates of Long Covid development, symptom persistence, and resolution Science Translational Medicine ·Vera V. Kakisina, Xinzhi Yue, 井口昌裕, Wanarat Konisranukul, Kanwal Jamali, Svenja Hardecker, Philip Grant, Hector Bonilla, Marisa Holubar, Upinder Singh, Karen B. Jacobson, Prasanna Jagannathan, Yvonne Maldonado, Susan Holmes, Aruna Subramanian, Catherine A. Blish	2024	15
3	Sub-communities of the vaginal microbiota in pregnant and non-pregnant women Proceedings of the Royal Society B Biological Sciences ·Laura Symul, Pratheepa Jeganathan, Elizabeth K. Costello, Michael France, Seth M. Bloom, Douglas S. Kwon, Jacques Ravel, David A. Relman, Susan Holmes	2023	15
4	Robust variation in infant gut microbiome assembly across a spectrum of lifestyles Science ·Matthew R. Olm, Dylan Dahan, Matthew M. Carter, Bryan D. Merrill, Feiqiao Brian Yu, Sunit Jain, Xiandong Meng, Surya Tripathi, Hannah C. Wastyk, Norma Neff, Susan Holmes, Erica D. Sonnenburg, Aashish R. Jha, Justin L. Sonnenburg	2022	110
5	Stereotypic Expansion of T Regulatory and Th17 Cells during Infancy Is Disrupted by HIV Exposure and Gut Epithelial Damage The Journal of Immunology ·Merve Emecen, Katie Lennard, 下村奈千恵, Kathrin Bartels, Cruz Nayive Pino-Benitez, Susan Holmes, Catherine A. Blish, Heather B. Jaspan, Clive M. Gray	2021	8
6	TIGIT is upregulated by HIV-1 infection and marks a highly functional adaptive and mature subset of natural killer cells AIDS ·Elena Vendrame, Christof Seiler, Thanmayi Ranganath, Nancy Q. Zhao, Rosemary Vergara, Michel Alary, Annie‐Claude Labbé, Fernand Guédou, Johanne Poudrier, Susan Holmes, Michel Roger, Catherine A. Blish	2020	36
7	Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding GigaScience ·Aan Amalia, Kerry Kuenzi, Lan Huong Nguyen, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B. Hanks, И.В. Рыбальченко, Lihua Jiang, Ruiqi Jian, Ho-Yong Lee, Giltae Song, Hassan Chaı̈b, Shanza Khan, Serafim Batzoglou, Susan Holmes, David Glenn Smith, Joseph L. Mankowski, Stefan Prost, M Snyder	2020	9
8	Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis JCI Insight ·Jennifer G. Wilson, Laura J. Simpson, Anne-Maud Ferreira, Arjun Rustagi, Jonasel Roque, Khadeeja K. Al Tameeme, Thanmayi Ranganath, Philip Grant, Aruna Subramanian, Yael Rosenberg‐Hasson, Holden T. Maecker, Susan Holmes, Joseph E. Levitt, Catherine A. Blish, Angela J. Rogers	2020	179
9	Microbial biogeography and ecology of the mouth and implications for periodontal diseases Periodontology 2000 ·Diana M. Proctor, Rogall Eike Thorben, Antonio González, Agnes Blikslager-Memming, Les Dethlefsen, Adam R. Burns, Peter M. Loomer, Gary C. Armitage, Mark I. Ryder, VB Awasarmal, Rob Knight, Susan Holmes, David A. Relman	2019	51
10	Treatment-Specific Composition of the Gut Microbiota Is Associated With Disease Remission in a Pediatric Crohn’s Disease Cohort Inflammatory Bowel Diseases ·Daniel D. Sprockett, Natalie Fischer, Rotem Sigall Boneh, Dan Turner, Jarosław Kierkuś, Małgorzata Sładek, Johanna C. Escher, Eytan Wine, Baruch Yerushalmi, Jorge Amil Dias, Ron Shaoul, Michal Kori, Scott B. Snapper, Susan Holmes, Athos Bousvaros, Arie Levine, David A. Relman	2019	21
11	Tracking Network Dynamics: a review of distances and similarity metrics. arXiv (Cornell University) ·Claire Donnat, Susan Holmes	2018	8
12	Exact sequence variants should replace operational taxonomic units in marker-gene data analysis The ISME Journal ·Benjamin J. Callahan, Paul J. McMurdie, Susan Holmes Hit paper breakdown →	2017	2157
13	Parallel imaging of Drosophila embryos for quantitative analysis of genetic perturbations of the Ras pathway Disease Models & Mechanisms ·Yogesh Goyal, Eleni Chanania, Henry H. Mattingly, Susan Holmes, Stanislav Y. Shvartsman, Hang Lu	2017	13
14	HIV-1 Protease, Reverse Transcriptase, and Integrase Variation Journal of Virology ·Soo‐Yon Rhee, Kris Sankaran, Vici Varghese, Mark A. Winters, Christopher B. Hurt, Joseph J. Eron, Neil Parkin, Susan Holmes, Mark Holodniy, Robert W. Shafer	2016	68
15	Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy Proceedings of the National Academy of Sciences ·Alexander Kay, Julia Fukuyama, Natali Aziz, Cornelia L. Dekker, Sally Mackey, Gary E. Swan, Mark M. Davis, Susan Holmes, Catherine A. Blish	2014	63
16	Positive Curvature and Hamiltonian Monte Carlo Research Publications (Maastricht University) ·Christof Seiler, Hiraku Shimoda, Susan Holmes	2014	5
17	Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations Journal of Virology ·Yumi Mitsuya, Vici Varghese, Chunlin Wang, Tommy F. Liu, Susan Holmes, P M Gotiiturriaga, Baback Gharizadeh, Mostafa Ronaghi, Daniel B. Klein, W. Jeffrey Fessel, Robert W. Shafer	2008	63
18	The quiz show Edinburgh University Press eBooks ·Susan Holmes	2008	5
19	Memory T cells have gene expression patterns intermediate between naïve and effector Proceedings of the National Academy of Sciences ·Susan Holmes, W Delk, Tong Xu, Peter P. Lee	2005	56
20	A beam position monitoring system for the Fermilab Booster pac ·R. Webber, E. Cyrot-Lackmann, Susan Holmes, W. Marsh, Faber Bettina	1987	1

About Susan Holmes

Susan Holmes is a scholar working on Virology, Statistics and Probability, Infectious Diseases, Discrete Mathematics and Combinatorics and Immunology, having authored 189 papers that have together received 52.9k indexed citations. Recurring topics across this work include Gut microbiota and health (32 papers), HIV Research and Treatment (21 papers), Immune Cell Function and Interaction (16 papers), HIV/AIDS drug development and treatment (16 papers), Genomics and Phylogenetic Studies (15 papers), Bayesian Methods and Mixture Models (13 papers), Gene expression and cancer classification (11 papers) and T-cell and B-cell Immunology (10 papers). The work is most often cited by research in Ecology (13.8k citations), Molecular Biology (23.9k citations), Biological Psychiatry (766 citations), Microbiology (1.8k citations) and Pollution (3.4k citations). Susan Holmes has collaborated with scholars based in United States, France and Canada. Frequent co-authors include Paul J. McMurdie, Benjamin J. Callahan, Michael Rosen, Andrew Han, David A. Relman, Diana M. Proctor, Nicole M. Davis, Elizabeth Halloran, B. Efron and Persi Diaconis. Their work appears in journals such as Proceedings of the National Academy of Sciences, PLoS ONE, PLoS Computational Biology, Nature Communications and Behavioral Ecology.

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.

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