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D-Index & Metrics

Biology and Biochemistry

D-Index
77
Citations
114585
World Ranking
4662
National Ranking
2257

Overview

Susan Holmes is affiliated with Stanford University in the United States. Their research spans multiple disciplines primarily within medicine, immunology, and microbiology, with additional focus areas in biochemistry, genetics, and molecular biology.

Their work covers a range of subfields including molecular biology, immunology, infectious diseases, virology, and artificial intelligence. These areas align with their main topics of study, which include gut microbiota and health, immune cell function and interaction, HIV research and treatment, reproductive system and pregnancy, COVID-19 clinical research studies, single-cell and spatial transcriptomics, and reproductive tract infections research.

Their recent publications have appeared in prominent scientific venues, reflecting the diversity and interdisciplinary nature of their research. Frequent publication venues include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • arXiv (Cornell University)
  • Nature Communications
  • Nature
  • Frontiers in Immunology

Some notable recent papers authored by or associated with Susan Holmes include:

  • "Variability in the analysis of a single neuroimaging dataset by many teams," 2020, Nature
  • "Reporting guidelines for human microbiome research: the STORMS checklist," 2021, Nature Medicine
  • "Profiling the human intestinal environment under physiological conditions," 2023, Nature
  • "Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis," 2020, JCI Insight
  • "Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19," 2021, The Journal of Experimental Medicine

Throughout their career, Susan Holmes has collaborated frequently with a number of researchers, indicating a collaborative approach within their scientific community. Their prominent coauthors include:

  • Catherine A. Blish
  • Thanmayi Ranganath
  • Nancy Q. Zhao
  • Laura Symul
  • David A. Relman

Best Publications

  • Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

    Evan Bolyen;Jai Ram Rideout;Matthew R. Dillon;Nicholas A. Bokulich

  • phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

    Paul J. McMurdie;Susan Holmes

  • Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

    Evan Bolyen;Jai Ram Rideout;Matthew R. Dillon;Nicholas A. Bokulich

  • Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.

    Nicole M. Davis;Diana M. Proctor;Diana M. Proctor;Susan P. Holmes;David A. Relman;David A. Relman

  • Exact sequence variants should replace operational taxonomic units in marker-gene data analysis.

    Benjamin J Callahan;Paul J McMurdie;Susan P Holmes

  • Waste not, want not: why rarefying microbiome data is inadmissible.

    Paul J. McMurdie;Susan P. Holmes

  • Temporal and spatial variation of the human microbiota during pregnancy

    Daniel B. DiGiulio;Benjamin J. Callahan;Paul J. McMurdie;Elizabeth K. Costello

  • Bootstrap confidence levels for phylogenetic trees.

    Bradley Efron;Elizabeth Halloran;Susan Holmes

  • QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

    Evan Bolyen;Jai Ram Rideout;Matthew R Dillon;Nicholas A Bokulich

  • Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

    Ben J. Callahan;Kris Sankaran;Julia A. Fukuyama;Paul J. McMurdie

  • Bioconductor workflow for microbiome data analysis: From raw reads to community analyses [version 1; referees: 3 approved]

    Ben J. Callahan;Kris Sankaran;Julia A. Fukuyama;Paul J. McMurdie

  • Geometry of the space of phylogenetic trees

    Louis J. Billera;Susan P. Holmes;Karen Vogtmann

  • Advancing our understanding of the human microbiome using QIIME

    José A. Navas-Molina;Juan M. Peralta-Sánchez;Antonio González;Paul J. McMurdie

  • A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes.

    Fulvio Cruciani;Piero Santolamazza;Peidong Shen;Vincent Macaulay

  • Colonic Contribution to Uremic Solutes

    Pavel A. Aronov;Frank J.-G. Luo;Natalie S. Plummer;Zhe Quan

  • Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

    Anastassia Gorvitovskaia;Susan P. Holmes;Susan M. Huse

  • Nasal Microenvironments and Interspecific Interactions Influence Nasal Microbiota Complexity and S. aureus Carriage

    Miling Yan;Sünje Johanna Pamp;Julia Fukuyama;Peter H. Hwang

  • Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women

    Benjamin J Callahan;Daniel B DiGiulio;Daniel B DiGiulio;Daniela S Aliaga Goltsman;Christine L Sun

  • Impaired interferon signaling is a common immune defect in human cancer

    Rebecca J. Critchley-Thorne;Diana L. Simons;Ning Yan;Andrea K. Miyahira

  • Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology

    Susan P. Holmes;Dan Gusfield

Frequent Co-Authors

David A. Relman
David A. Relman Stanford University
Catherine A. Blish
Catherine A. Blish Stanford University
Persi Diaconis
Persi Diaconis Stanford University
Robert W. Shafer
Robert W. Shafer Stanford University
Peter P. Lee
Peter P. Lee City Of Hope National Medical Center
Soo-Yon Rhee
Soo-Yon Rhee Stanford University
Rob Knight
Rob Knight University of California, San Diego
Xavier Pennec
Xavier Pennec French Institute for Research in Computer Science and Automation - INRIA
Alfred M. Spormann
Alfred M. Spormann Stanford University
Curtis Huttenhower
Curtis Huttenhower Harvard University

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