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Susan Holmes

Stanford University

80H-index
393Paper Count
11.6WCitation Count
Published Papers 89
Publication Date
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Vaginal microbiota impacts of a Lactobacillus crispatus live biotherapeutic and predictors of colonization in randomized controlled trial
errCell Host & Microbe
IF18.7
err2026-03-27
err0
PREAI
errSeth M. Bloom; Laura Symul; Joseph Elsherbini; Jiawu Xu; Salina Hussain; Johnathan Shih; Ashley Sango; Caroline M. Mitchell; Anke Hemmerling; Thomas P. Parks; Aditi Kannan; Fatima A. Hussain; Craig R. Cohen; Susan P. Holmes; Douglas S. Kwon
errShare
errSave
NKp30 and NKG2D contribute to natural killer cell-mediated recognition of HIV-infected cells
erriScience
IF4.1
err2025-09-12
err0
errOAAI
errRuoxi Pi; Nancy Q. Zhao; Allison J. Bien; Thanmayi Ranganath; Christof Seiler; Susan Holmes; Alexander Marson; David N. Nguyen; Catherine A. Blish
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errSave
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)
errCONTEMPORARY CLINICAL TRIALS COMMUNICATIONS
IF1.4
err2025-09-01
err1
errOAAI
errChetty, Callin; Mafunda, Nomfuneko; Happel, Anna-Ursula; Khan, Anam; Demidkina, Briah Cooley; Yende-Zuma, Nonhlanhla; Saidi, Yusra; Polliah, Asthu Mahabeer; Lewis, Lara; Osman, Farzana; Radebe, Precious; Passmore, Jo-Ann S.; Kwon, Doug; Ravel, Jacques; Ngcapu, Sinaye; Liebenberg, Lenine; Symul, Laura; Holmes, Susan; Mitchell, Caroline M.; Potloane, Disebo
errShare
errSave
Guidelines for preventing and reporting contamination in low-biomass microbiome studies
errNature Microbiology
IF19.4
err2025-06-20
err0
PREAI
errNoah Fierer; Pok Man Leung; Rachael Lappan; Raphael Eisenhofer; Francesco Ricci; Sophie I. Holland; Nicholas Dragone; Linda L. Blackall; Xiyang Dong; Cristina Dorador; Belinda C. Ferrari; Jacqueline Goordial; Susan P. Holmes; Fumio Inagaki; Tal Korem; Simone S. Li; Thulani P. Makhalanyane; Jessica L. Metcalf; Niranjan Nagarajan; William D. Orsi; Erin R. Shanahan; Alan W. Walker; Laura S. Weyrich; Jack A. Gilbert; Amy D. Willis; Benjamin J. Callahan; Ashley Shade; Julian Parkhill; Jillian F. Banfield; Chris Greening
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errSave
Sex differences and immune correlates of Long Covid development, symptom persistence, and resolution
errSCIENCE TRANSLATIONAL MEDICINE
IF14.6
err2024-11-13
err0
errOAAI
errHamlin, Rebecca E.; Pienkos, Shaun M.; Chan, Leslie; Stabile, Mikayla A.; Pinedo, Kassandra; Rao, Mallika; Grant, Philip; Bonilla, Hector; Holubar, Marisa; Singh, Upinder; Jacobson, Karen B.; Jagannathan, Prasanna; Maldonado, Yvonne; Holmes, Susan P.; Subramanian, Aruna; Blish, Catherine A.
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errSave
Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants
errNATURE COMMUNICATIONS
IF15.7
err2024-05-14
err0
errOAAI
errDzanibe, Sonwabile; Wilk, Aaron J.; Canny, Susan; Ranganath, Thanmayi; Alinde, Berenice; Rubelt, Florian; Huang, Huang; Davis, Mark M.; Holmes, Susan P.; Jaspan, Heather B.; Blish, Catherine A.; Gray, Clive M.
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errSave
Abrupt perturbation and delayed recovery of the vaginal ecosystem following childbirth (vol 14, 4141 ,2023)
errNATURE COMMUNICATIONS
IF15.7
err2024-02-26
err0
errOAAI
errCostello, Elizabeth K.; DiGiulio, Daniel B.; Robaczewska, Anna; Symul, Laura; Wong, Ronald J.; Shaw, Gary M.; Stevenson, David K.; Holmes, Susan P.; Kwon, Douglas S.; Relman, David A.
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errSave
Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses
errMICROBIOLOGY SPECTRUM
IF3.8
err2024-02-06
err1
errOAAI
errIwase, Saori C.; Osawe, Sophia; Happel, Anna-Ursula; Gray, Clive M.; Holmes, Susan P.; Blackburn, Jonathan M.; Abimiku, Alash'le; Jaspan, Heather B.
errShare
errSave
Pro-inflammatory feedback loops define immune responses to pathogenic Lentivirus infection
errGENOME MEDICINE
IF11.2
err2024-02-05
err0
errOAAI
errWilk, Aaron J.; Marceau, Joshua O.; Kazer, Samuel W.; Fleming, Ira; Miao, Vincent N.; Galvez-Reyes, Jennyfer; Kimata, Jason T.; Shalek, Alex K.; Holmes, Susan; Overbaugh, Julie; Blish, Catherine A.
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errSave
Sub-communities of the vaginal microbiota in pregnant and non-pregnant women
errPROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
IF3.5
err2023-11-29
err7
errOAAI
errSymul, Laura; Jeganathan, Pratheepa; Costello, Elizabeth K.; France, Michael; Bloom, Seth M.; Kwon, Douglas S.; Ravel, Jacques; Relman, David A.; Holmes, Susan
errShare
errSave
Abrupt perturbation and delayed recovery of the vaginal ecosystem following childbirth
errNATURE COMMUNICATIONS
IF15.7
err2023-07-12
err9
errOAAI
errCostello, Elizabeth K. K.; DiGiulio, Daniel B. B.; Robaczewska, Anna; Symul, Laura; Wong, Ronald J. J.; Shaw, Gary M. M.; Stevenson, David K. K.; Holmes, Susan P. P.; Kwon, Douglas S. S.; Relman, David A. A.
errShare
errSave
Comparative analysis of cell-cell communication at single-cell resolution
errNATURE BIOTECHNOLOGY
IF41.7
err2023-05-11
err32
errOAAI
errWilk, Aaron J.; Shalek, Alex K.; Holmes, Susan; Blish, Catherine A.
errShare
errSave
HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing
errVIRUSES-BASEL
IF3.5
err2023-04-18
err2
errOAAI
errTao, Kaiming; Rhee, Soo-Yon; Tzou, Philip L.; Osman, Zachary A.; Pond, Sergei L. Kosakovsky; Holmes, Susan P.; Shafer, Robert W.
errShare
errSave
Generative Models: An Interdisciplinary Perspective
errANNUAL REVIEW OF STATISTICS AND ITS APPLICATION
IF8.7
err2023-03-10
err2
errOAAI
errSankaran, Kris; Holmes, Susan P.
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errSave
SARS-CoV-2 escapes direct NK cell killing through Nsp1-mediated downregulation of ligands for NKG2D
errCELL REPORTS
IF6.9
err2022-12-01
err20
errOAAI
errLee, Madeline J.; Leong, Michelle W.; Rustagi, Arjun; Beck, Aimee; Zeng, Leiping; Holmes, Susan; Qi, Lei S.; Blish, Catherine A.
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errSave
Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos
errCELL REPORTS
IF6.9
err2022-08-01
err4
errOAAI
errRoodgar, Morteza; Suchy, Fabian P.; Nguyen, Lan H.; Bajpai, Vivek K.; Sinha, Rahul; Vilches-Moure, Jose G.; Van Bortle, Kevin; Bhadury, Joydeep; Metwally, Ahmed; Jiang, Lihua; Jian, Ruiqi; Chiang, Rosaria; Oikonomopoulos, Angelos; Wu, Joseph C.; Weissman, Irving L.; Mankowski, Joseph L.; Holmes, Susan; Loh, Kyle M.; Nakauchi, Hiromitsu; VandeVoort, Catherine A.; Snyder, Michael P.
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errSave
Statistical Modeling for Practical Pooled Testing During the COVID-19 Pandemic
errSTATISTICAL SCIENCE
IF3.4
err2022-05-01
err8
errOAAI
errComess, Saskia; Wang, Hannah; Holmes, Susan; Donnat, Claire
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errSave
Labeling Self-Tracked Menstrual Health Records With Hidden Semi-Markov Models
errIEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
IF6.8
err2022-03-01
err1
errOAAI
errSymul, Laura; Holmes, Susan
errShare
errSave
Stereotypic Expansion of T Regulatory and Th17 Cells during Infancy Is Disrupted by HIV Exposure and Gut Epithelial Damage
errJOURNAL OF IMMUNOLOGY
IF3.4
err2022-01-01
err6
errOAAI
errDzanibe, Sonwabile; Lennard, Katie; Kiravu, Agano; Seabrook, Melanie S. S.; Alinde, Berenice; Holmes, Susan P.; Blish, Catherine A.; Jaspan, Heather B.; Gray, Clive M.
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errSave
Reporting guidelines for human microbiome research: the STORMS checklist
errNATURE MEDICINE
IF50
err2021-11-17
err212
errOAAI
errMirzayi, Chloe; Renson, Audrey; Zohra, Fatima; Elsafoury, Shaimaa; Geistlinger, Ludwig; Kasselman, Lora J.; Eckenrode, Kelly; van de Wijgert, Janneke; Loughman, Amy; Marques, Francine Z.; MacIntyre, David A.; Arumugam, Manimozhiyan; Azhar, Rimsha; Beghini, Francesco; Bergstrom, Kirk; Bhatt, Ami; Bisanz, Jordan E.; Braun, Jonathan; Bravo, Hector Corrada; Buck, Gregory A.; Bushman, Frederic; Casero, David; Clarke, Gerard; Carmen Collado, Maria; Cotter, Paul D.; Cryan, John F.; Demmer, Ryan T.; Devkota, Suzanne; Elinav, Eran; Escobar, Juan S.; Fettweis, Jennifer; Finn, Robert D.; Fodor, Anthony A.; Forslund, Sofia; Franke, Andre; Furlanello, Cesare; Gilbert, Jack; Grice, Elizabeth; Haibe-Kains, Benjamin; Handley, Scott; Herd, Pamela; Holmes, Susan; Jacobs, Jonathan P.; Karstens, Lisa; Knight, Rob; Knights, Dan; Koren, Omry; Kwon, Douglas S.; Langille, Morgan; Lindsay, Brianna; McGovern, Dermot; McHardy, Alice C.; McWeeney, Shannon; Mueller, Noel T.; Nezi, Luigi; Olm, Matthew; Palm, Noah; Pasolli, Edoardo; Raes, Jeroen; Redinbo, Matthew R.; Ruhlemann, Malte; Sartor, R. Balfour; Schloss, Patrick D.; Schriml, Lynn; Segal, Eran; Shardell, Michelle; Sharpton, Thomas; Smirnova, Ekaterina; Sokol, Harry; Sonnenburg, Justin L.; Srinivasan, Sujatha; Thingholm, Louise B.; Turnbaugh, Peter J.; Upadhyay, Vaibhav; Walls, Ramona L.; Wilmes, Paul; Yamada, Takuji; Zeller, Georg; Zhang, Mingyu; Zhao, Ni; Zhao, Liping; Bao, Wenjun; Culhane, Aedin; Devanarayan, Viswanath; Dopazo, Joaquin; Fan, Xiaohui; Fischer, Matthias; Jones, Wendell; Kusko, Rebecca; Mason, Christopher E.; Mercer, Tim R.; Sansone, Susanna-Assunta; Scherer, Andreas; Shi, Leming; Thakkar, Shraddha; Tong, Weida; Wolfinger, Russ; Hunter, Christopher; Segata, Nicola; Huttenhower, Curtis; Dowd, Jennifer B.; Jones, Heidi E.; Waldron, Levi
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Research Directions

No research directions
Co-authors
Cooperation Journals
R
Rob Knight
H-index: 255 · Papers: 1.8K
I
Irving L. Weissman
H-index: 215 · Papers: 1.3K
M
M Snyder
H-index: 210 · Papers: 3.3K
J
Julian Parkhill
H-index: 177 · Papers: 1.1K
M
Mark M. Davis
H-index: 173 · Papers: 988
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