Susan Holmes

Also affiliated with Stanford University

Biochemistry, Genetics and Molecular BiologyImmunology and MicrobiologyComputer Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 4%percentile

0.702Author DataRank

Indexed papers

1in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 1 indexed paper attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

GigaScience(2020)10.1093/gigascience/giaa069

Top 28%

0.702DataRank

Top 28%17 citations

Afshin Babveyh, Lan Huong Nguyen, Wenyu Zhou, Rahul Sinha, Hayan Lee +15 more

Papers

Driven by 52 papers — median percentile 72. Top paper: “Variability in the analysis of a single neuroimaging dataset by many teams”.

Variability in the analysis of a single neuroimaging dataset by many teams

Nature(2020)10.1038/s41586-020-2314-9

N/A

9.7DataRank · unranked

1209 citations

Felix Holzmeister, Colin F. Camerer, Anna Dreber, Jürgen Huber, Magnus Johannesson +95 more

Profiling the human intestinal environment under physiological conditions

Nature(2023)10.1038/s41586-023-05989-7

N/A

6.9DataRank · unranked

463 citations

Rebecca N. Culver, Jessica A. Grembi, Jacob Folz, Peter V. Treit, Handuo Shi +16 more

Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19

The Journal of Experimental Medicine(2021)10.1084/jem.20210582

N/A

5.6DataRank · unranked

230 citations

Madeline J. Lee, Bei Wei, Benjamin Parks, Ruoxi Pi, Giovanny J. Martínez-Colón +52 more

DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods(2016)10.1038/nmeth.3869

N/A

1.6DataRank · unranked

35281 citations

Paul J. McMurdie, Michael J. Rosen, Andrew W Han, Amy Jo A Johnson, Michael Rosen +3 more

Reporting guidelines for human microbiome research: the STORMS checklist

Nature Medicine(2021)10.1038/s41591-021-01552-x

N/A

0.918DataRank · unranked

454 citations

Audrey Renson, Genomic Standards Consortium, Cesare Furlanello, Shaimaa Elsafoury, Ludwig Geistlinger +98 more

Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis

JCI Insight(2020)10.1172/jci.insight.140289

N/A

0.841DataRank · unranked

272 citations

Laura J. Simpson, Anne-Maud Ferreira, Arjun Rustagi, Jonasel Roque, Adijat Asuni +10 more

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

GigaScience(2020)10.1093/gigascience/giaa069

Top 28%

0.702DataRank

Top 28%17 citations

Afshin Babveyh, Lan Huong Nguyen, Wenyu Zhou, Rahul Sinha, Hayan Lee +15 more

SARS-CoV-2 escapes direct NK cell killing through Nsp1-mediated downregulation of ligands for NKG2D

Cell Reports(2022)10.1016/j.celrep.2022.111892

N/A

0.568DataRank · unranked

43 citations

Michelle Leong, Arjun Rustagi, Aimee Beck, Leiping Zeng, Susan Holmes +3 more

Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences

PLoS ONE(2020)10.1371/journal.pone.0225352

N/A

0.550DataRank · unranked

38 citations

Sergei L. Kosakovsky Pond, Santiago Ávila‐Ríos, Susan Holmes, Rami Kantor, Robert W. Shafer +1 more

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.19.476920

N/A

0.545DataRank · unranked

9 citations

Rebecca N. Culver, Jessica A. Grembi, Jacob Folz, Peter V. Treit, Les Dethlefsen +13 more

Community-wide hackathons to identify central themes in single-cell multi-omics

Genome Biology(2021)10.1186/s13059-021-02433-9

N/A

0.436DataRank · unranked

15 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

Learning and teaching biological data science in the Bioconductor community

PLoS Computational Biology(2025)10.1371/journal.pcbi.1012925

N/A

0.241DataRank · unranked

4 citations

Frederick J. Tan, Fabricio Almeida‐Silva, Robert Castelo, Aedín C. Culhane, Sean Davis +13 more

Genotypic Correlates of Resistance to the HIV-1 Strand Transfer Integrase Inhibitor Cabotegravir

Research Square(2022)10.21203/rs.3.rs-2012078/v1

N/A

0.241DataRank · unranked

4 citations

Neil Parkin, P. Richard Harrigan, Susan Holmes, Robert W. Shafer, Soo‐Yon Rhee

The 15th Genomic Standards Consortium meeting

Standards in Genomic Sciences(2013)10.4056/sigs.3457

N/A

0.226DataRank · unranked

1 citations

Ilene Karsch-Mizrachi, Peter Sterk, Dawn Field, Lynette Hirschman, Tatiana Tatusova +54 more

Treated HIV Infection Alters Phenotype But Not HIV-specific Function of Peripheral Blood Natural Killer Cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.12.038604

N/A

0.208DataRank · unranked

3 citations

Anne-Maud Ferreira, Philip Grant, Susan Holmes, Catherine A. Blish, Nancy Q. Zhao

Influenza-Induced Interferon Lambda Response Is Associated With Longer Time to Delivery Among Pregnant Kenyan Women

Frontiers in Immunology(2020)10.3389/fimmu.2020.00452

N/A

0.165DataRank · unranked

2 citations

Nicholas Bayless, Rosemary Vergara, Jillian Pintye, John Kinuthia, Lusi Osborn +6 more

A short course of antibiotics selects for persistent resistance in the human gut

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.04.556257

N/A

0.165DataRank · unranked

2 citations

Les Dethlefsen, Arati V. Patankar, Gui Chen, Susan Holmes, David A. Relman +1 more

A short course of antibiotics selects for persistent resistance in the human gut

Research Square(2023)10.21203/rs.3.rs-3399159/v1

N/A

0.104DataRank · unranked

1 citations

Les Dethlefsen, Arati V. Patankar, Gui Chen, Susan Holmes, David A. Relman +1 more

Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.19.533358

N/A

0.104DataRank · unranked

1 citations

Joshua O. Marceau, Samuel W. Kazer, Ira Fleming, Vincent N. Miao, Jennyfer Galvez-Reyes +5 more

Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients

Frontiers in Cellular and Infection Microbiology(2022)10.3389/fcimb.2022.757846

N/A

0DataRank · unranked

14 citations

Elena Vendrame, Giovanny J. Martínez-Colón, Thanmayi Ranganath, Rosemary Vergara, Nancy Q. Zhao +14 more

Comparative analysis of cell-cell communication at single-cell resolution

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.04.479209

N/A

0DataRank · unranked

16 citations

Alex K. Shalek, Susan Holmes, Catherine A. Blish, Aaron J. Wilk

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.30.486467

N/A

0DataRank · unranked

11 citations

Dylan Dahan, Matthew M. Carter, Bryan D. Merrill, Brian Yu, Sunit Jain +9 more

Comparative analysis of cell–cell communication at single-cell resolution

Nature Biotechnology(2023)10.1038/s41587-023-01782-z

N/A

0DataRank · unranked

131 citations

Alex K. Shalek, Susan Holmes, Catherine A. Blish, Aaron J. Wilk

Sub-communities of the vaginal microbiota in pregnant and non-pregnant women

Proceedings of the Royal Society B Biological Sciences(2023)10.1098/rspb.2023.1461

N/A

0DataRank · unranked

26 citations

Pratheepa Jeganathan, Elizabeth K. Costello, Michael France, Seth M. Bloom, Douglas S. Kwon +4 more

Disrupted memory T cell expansion in HIV-exposed uninfected infants is preceded by premature skewing of T cell receptor clonality

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.19.540713

N/A

0DataRank · unranked

0 citations

Aaron J. Wilk, Susan Canny, Thanmayi Ranganath, Berenice Alinde, Florian Rubelt +7 more

Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses

Research Square(2023)10.21203/rs.3.rs-3112263/v1

N/A

0DataRank · unranked

0 citations

Heather B. Jaspan, Anna‐Ursula Happel, Susan Holmes, Alashʼle Abimiku, Sophia Osawe +3 more

Sex differences and immune correlates of Long Covid development, symptom persistence, and resolution

Science Translational Medicine(2024)10.1126/scitranslmed.adr1032

N/A

0DataRank · unranked

48 citations

S. Pienkos, Leslie Chan, Mikayla A. Stabile, Kassandra Pinedo, Mallika Rao +11 more

Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants

Nature Communications(2024)10.1038/s41467-024-47955-5

N/A

0DataRank · unranked

6 citations

Aaron J. Wilk, Susan Canny, Thanmayi Ranganath, Berenice Alinde, Florian Rubelt +7 more

Pro-inflammatory feedback loops define immune responses to pathogenic Lentivirus infection

Genome Medicine(2024)10.1186/s13073-024-01290-y

N/A

0DataRank · unranked

3 citations

Joshua O. Marceau, Samuel W. Kazer, Ira Fleming, Vincent N. Miao, Jennyfer Galvez-Reyes +6 more

Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses

Microbiology Spectrum(2024)10.1128/spectrum.03190-23

N/A

0DataRank · unranked

2 citations

Sophia Osawe, Anna‐Ursula Happel, Clive M. Gray, Susan Holmes, Jonathan M. Blackburn +3 more

Prior vaccination prevents overactivation of innate immune responses during COVID-19 breakthrough infection

Science Translational Medicine(2025)10.1126/scitranslmed.adq1086

N/A

0DataRank · unranked

20 citations

Kassandra Pinedo, Mikayla A. Stabile, Rebecca E. Hamlin, S. Pienkos, Kalani Ratnasiri +52 more

NKp30 and NKG2D contribute to natural killer cell-mediated recognition of HIV-infected cells

iScience(2025)10.1016/j.isci.2025.113548

N/A

0DataRank · unranked

3 citations

Nancy Q. Zhao, Allison J Bien, Thanmayi Ranganath, Christof Seiler, Susan Holmes +4 more

Community-wide hackathons to identify central themes in single-cell multi-omics

UNC Libraries(2025)10.17615/96cj-z232

N/A

0DataRank · unranked

0 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

Microbiota effects and predictors of Lactobacillus crispatu s colonization after treatment with a vaginal live biotherapeutic: results from a randomized, double-blinded, placebo-controlled trial

medRxiv(2025)10.1101/2025.08.18.25333897

N/A

0DataRank · unranked

0 citations

Laura Symul, Joseph Elsherbini, Jiawu Xu, Salina Hussain, Johnathan Shih +10 more

Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics

Genome Biology(2021)10.1186/s13059-021-02468-y

N/A

0DataRank · unranked

0 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics

UNC Libraries(2025)10.17615/vzc0-qk25

N/A

0DataRank · unranked

0 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

Effect of Water, Sanitation, Handwashing, and Nutrition Interventions on Enteropathogens in Children 14 Months Old: A Cluster-Randomized Controlled Trial in Rural Bangladesh

The Journal of Infectious Diseases(2020)10.1093/infdis/jiaa549

N/A

0DataRank · unranked

53 citations

Audrie Lin, Md Abdul Karim, Md Ohedul Islam, Rana Miah, Benjamin F. Arnold +21 more

Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon

Nature Communications(2020)10.1038/s41467-020-17541-6

N/A

0DataRank · unranked

47 citations

Mélanie Martin, Elizabeth K. Costello, Adam R. Burns, Susan Holmes, Michael Gurven +2 more

Natural killer cell phenotype is altered in HIV-exposed seronegative women

PLoS ONE(2020)10.1371/journal.pone.0238347

N/A

0DataRank · unranked

20 citations

Elena Vendrame, Anne-Maud Ferreira, Christof Seiler, Thanmayi Ranganath, Michel Alary +7 more

Treated HIV Infection Alters Phenotype but Not HIV-Specific Function of Peripheral Blood Natural Killer Cells

Frontiers in Immunology(2020)10.3389/fimmu.2020.00829

N/A

0DataRank · unranked

13 citations

Anne-Maud Ferreira, Philip Grant, Susan Holmes, Catherine A. Blish, Nancy Q. Zhao

Mass Cytometry Analysis of the NK Cell Receptor–Ligand Repertoire Reveals Unique Differences between Dengue-Infected Children and Adults

ImmunoHorizons(2020)10.4049/immunohorizons.2000074

N/A

0DataRank · unranked

12 citations

Davis Beltrán, Anne-Maud Ferreira, Rosemary Vergara, Lisseth Sáenz, Ofelina Vergara +7 more

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

Scientific Reports(2020)10.1038/s41598-020-58000-y

N/A

0DataRank · unranked

40 citations

Lan Huong Nguyen, Thomas D. Haggerty, Christopher D. Gardner, Susan Holmes, Julie Parsonnet +1 more

Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2

The Journal of Infectious Diseases(2020)10.1093/infdis/jiaa026

N/A

0DataRank · unranked

26 citations

Diane Descamps, Soo‐Yon Rhee, Dana N. Raugi, Charlotte Charpentier, Nuno Taveira +7 more

CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.09.417584

N/A

0DataRank · unranked

2 citations

Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame +3 more

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation

UNC Libraries(2020)10.17615/j3nc-yk91

N/A

0DataRank · unranked

0 citations

Vici Varghese, Soo‐Yon Rhee, Kris Sankaran, Joseph J. Eron, Susan Holmes +5 more

CytoGLMM: conditional differential analysis for flow and mass cytometry experiments

BMC Bioinformatics(2021)10.1186/s12859-021-04067-x

N/A

0DataRank · unranked

37 citations

Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame +3 more

Stereotypic Expansion of T Regulatory and Th17 Cells during Infancy Is Disrupted by HIV Exposure and Gut Epithelial Damage

The Journal of Immunology(2021)10.4049/jimmunol.2100503

N/A

0DataRank · unranked

10 citations

Katie Lennard, Agano Kiravu, Mélanie S. S. Seabrook, Berenice Alinde, Susan Holmes +4 more

Supervised topic modeling for predicting molecular substructure from mass spectrometry

F1000Research(2021)10.12688/f1000research.52549.1

N/A

0DataRank · unranked

5 citations

Adamo Young, Jaan Altosaar, Jakub Rajniak, Noémie Elhadad, Michael A. Fischbach +2 more

Spatial patterns of dental disease in patients with low salivary flow

medRxiv(2021)10.1101/2021.10.04.21264534

N/A

0DataRank · unranked

2 citations

Christof Seiler, Adam R. Burns, Samuel Walker, Tina Jung, Jonathan Weng +10 more

Stereotypic expansion of T regulatory and Th 17 cells during infancy is disrupted by HIV exposure and gut epithelial damage

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.03.442468

N/A

0DataRank · unranked

0 citations

Katie Lennard, Agano Kiravu, Mélanie S. S. Seabrook, Berenice Alinde, Susan Holmes +4 more

Genotypic correlates of resistance to the HIV-1 strand transfer integrase inhibitor cabotegravir

Antiviral Research(2022)10.1016/j.antiviral.2022.105427

N/A

0DataRank · unranked

24 citations

Neil Parkin, P. Richard Harrigan, Susan Holmes, Robert W. Shafer, Soo‐Yon Rhee

Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos

Cell Reports(2022)10.1016/j.celrep.2022.111264

N/A

0DataRank · unranked

17 citations

Fabian Suchy, Lan Huong Nguyen, Vivek K. Bajpai, Rahul Sinha, José G. Vilches-Moure +16 more

Susan Holmes

Indexed papers

Top data-sharing exemplar

Papers