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Author Details

Susan Holmes
Stanford University
1996
133
49
PMIDPaper TitleJournal TitlePublished Year
37169965Comparative analysis of cell-cell communication at single-cell resolution.Nat Biotechnol2024
36515174Highly Ambiguous HIV-1 Pol Positions Encoding Multiple Amino Acids Usually Result from Antiviral or Immune Selection Pressure.AIDS Res Hum Retroviruses2023
37461449Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses.Res Sq2023
37112972HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing.Viruses2023
37438386Abrupt perturbation and delayed recovery of the vaginal ecosystem following childbirth.Nat Commun2023
37165188Profiling the human intestinal environment under physiological conditions.Nature2023
37292866Disrupted memory T cell expansion in HIV-exposed uninfected infants is preceded by premature skewing of T cell receptor clonality.bioRxiv2023
34819390Stereotypic Expansion of T Regulatory and Th17 Cells during Infancy Is Disrupted by HIV Exposure and Gut Epithelial Damage.J Immunol2022
35679413Robust variation in infant gut microbiome assembly across a spectrum of lifestyles.Science2022
36543165SARS-CoV-2 escapes direct NK cell killing through Nsp1-mediated downregulation of ligands for NKG2D.Cell Rep2022
36044843Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos.Cell Rep2022
36191692Genotypic correlates of resistance to the HIV-1 strand transfer integrase inhibitor cabotegravir.Antiviral Res2022
35223535Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients.Front Cell Infect Microbiol2022
35169794Comparative analysis of cell-cell communication at single-cell resolution.bioRxiv2022
34128959Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19.J Exp Med2021
37554662Modeling the heterogeneity in COVID-19's reproductive number and its impact on predictive scenarios.J Appl Stat2021
36398283A Statistical Perspective on the Challenges in Molecular Microbial Biology.J Agric Biol Environ Stat2021
33752595CytoGLMM: conditional differential analysis for flow and mass cytometry experiments.BMC Bioinformatics2021
34789871Reporting guidelines for human microbiome research: the STORMS checklist.Nat Med2021
34433496Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics.Genome Biol2021
34353350Community-wide hackathons to identify central themes in single-cell multi-omics.Genome Biol2021
31285547Nuclear degradation dynamics in a nonapoptotic programmed cell death.Cell Death Differ2020
32028328TIGIT is upregulated by HIV-1 infection and marks a highly functional adaptive and mature subset of natural killer cells.AIDS2020
31996717Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention.Sci Rep2020
31965175Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2.J Infect Dis2020
32102090Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences.PLoS One2020
31850642Microbial biogeography and ecology of the mouth and implications for periodontal diseases.Periodontol 20002020
33067399Mass Cytometry Analysis of the NK Cell Receptor-Ligand Repertoire Reveals Unique Differences between Dengue-Infected Children and Adults.Immunohorizons2020
32861214Effect of water, sanitation, handwashing and nutrition interventions on enteropathogens in children 14 months old: a cluster-randomized controlled trial in rural Bangladesh.J Infect Dis2020
32606436Author Correction: Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention.Sci Rep2020
32728114Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon.Nat Commun2020
32870938Natural killer cell phenotype is altered in HIV-exposed seronegative women.PLoS One2020
32391016Characterization of the Impact of Daclizumab Beta on Circulating Natural Killer Cells by Mass Cytometry.Front Immunol2020
32477342Treated HIV Infection Alters Phenotype but Not HIV-Specific Function of Peripheral Blood Natural Killer Cells.Front Immunol2020
32256497Influenza-Induced Interferon Lambda Response Is Associated With Longer Time to Delivery Among Pregnant Kenyan Women.Front Immunol2020
31220072Ten quick tips for effective dimensionality reduction.PLoS Comput Biol2019
31719220Successful strategies for human microbiome data generation, storage and analyses.J Biosci2019
31708922Pregnancy-Induced Alterations in NK Cell Phenotype and Function.Front Immunol2019
29868846Latent variable modeling for the microbiome.Biostatistics2019
31555316Multitable Methods for Microbiome Data Integration.Front Genet2019
31519210Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation.Microbiome2019
31399723Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.Nat Biotechnol2019
31341288Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.Nat Biotechnol2019
29270892Multi-Table Differential Correlation Analysis of Neuroanatomical and Cognitive Interactions in Turner Syndrome.Neuroinformatics2018
30232199Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome.Genome Res2018
30143589Differential Induction of IFN-α and Modulation of CD112 and CD54 Expression Govern the Magnitude of NK Cell IFN-γ Response to Influenza A Viruses.J Immunol2018
30416327Interactive Visualization of Hierarchically Structured Data.J Comput Graph Stat2018
30558668Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.Microbiome2018
30439937Gut microbiome transition across a lifestyle gradient in Himalaya.PLoS Biol2018
29445174A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow.Nat Commun2018
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Collaborators

Robert W Shafer
Co-authored papers 22
Kris Sankaran
University of Wisconsin - Madison, 1300 University Ave
Co-authored papers 8
Rob Knight
University of California
Co-authored papers 6
Justin L Sonnenburg
Stanford University
Co-authored papers 5
Pratheepa Jeganathan
McMaster University
Co-authored papers 5
Antonio Gonzalez
University of California San Diego School of Medicine
Co-authored papers 4
Morgan G I Langille
Dalhousie University
Co-authored papers 3
Jordan E Bisanz
University of California san francisco
Co-authored papers 3
Yoshiki V??zquez-Baeza
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Co-authored papers 3
Nicola Segata
University of Trento
Co-authored papers 3
Curtis Huttenhower
Broad Institute of MIT and Harvard
Co-authored papers 3
Aedin C Culhane
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Co-authored papers 3
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Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen
Co-authored papers 3
Dan Knights
University of Minnesota
Co-authored papers 3
Mark M Davis
Co-authored papers 3
Peter J Turnbaugh
University of California san francisco
Co-authored papers 3
Pieter C Dorrestein
Co-authored papers 2
C Titus Brown
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Luke R Thompson
Northern Gulf Institute, Mississippi State University
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Kyle Bittinger
Children's Hospital of Philadelphia
Co-authored papers 2
Kim-Anh L?? Cao
University of Melbourne
Co-authored papers 2
Austin D Swafford
Center for Microbiome Innovation, University of California San Diego
Co-authored papers 2
Daniel McDonald
University of California San Diego
Co-authored papers 2
Clarisse Marotz
University of California San Diego
Co-authored papers 2
Eric J Alm
Massachusetts Institute of Technology 21 Ames St. Cambridge
Co-authored papers 2
Ricard Argelaguet
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
Vera Pancaldi
Universite de Toulouse, Inserm, CNRS, Universite Toulouse III-Paul Sabatier
Co-authored papers 2
Alan K Jarmusch
Co-authored papers 2
Dmitri A Petrov
Stanford University
Co-authored papers 2
Alex K Shalek
Institute for Medical Engineering & Science, Massachusetts Institute of Technology
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Release 1.2