Susan P Holmes (Susan Holmes)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2015-2023
Publications (10 Years): 18

Top Venues

PLoS computational biology

Journal of immunology (Baltimore, Md. : 1950)

Proceedings of the National Academy of Sciences of the United States of America

Scientific reports

Stanford University

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Stanford University Sep 01 1998

United States

Professor :: Statistics

Publications

Laura Symul, Pratheepa Jeganathan, Elizabeth K Costello, Michael T France, Seth M Bloom, Douglas S Kwon, Jacques Ravel, David A Relman, Susan P Holmes
Sub-communities of the vaginal microbiota in pregnant and non-pregnant women. Proceedings. Biological sciences 290 (2011) (2023)
Aaron J Wilk, Alex K Shalek, Susan P Holmes, Catherine A Blish
Comparative analysis of cell-cell communication at single-cell resolution. bioRxiv : the preprint server for biology (2022)
Matthew R Olm, Dylan Dahan, Matthew M Carter, Bryan D Merrill, Feiqiao Brian Yu, Sunit Jain, Xiandong Meng, Surya Tripathi, Hannah Wastyk, Norma Neff, Susan P Holmes, Erica D Sonnenburg, Aashish R Jha, Justin L Sonnenburg
Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science (New York, N.Y.) 376 (6598) (2022)
Sonwabile Dzanibe, Katie Lennard, Agano Kiravu, Melanie S S Seabrook, Berenice Alinde, Susan P Holmes, Catherine A Blish, Heather B Jaspan, Clive M Gray
Stereotypic Expansion of T Regulatory and Th17 Cells during Infancy Is Disrupted by HIV Exposure and Gut Epithelial Damage. Journal of immunology (Baltimore, Md. : 1950) (2021)
Claire L Donnat, Susan P Holmes
Modeling the heterogeneity in COVID-19's reproductive number and its impact on predictive scenarios. Journal of applied statistics 50 (11-12) (2021)
Aaron J Wilk, Madeline J Lee, Bei Wei, Benjamin E Parks, Ruoxi Pi, Giovanny J Martínez-Colón, Thanmayi Ranganath, Nancy Q Zhao, Shalina Taylor, Winston R Becker, null null, David Jimenez-Morales, Andra L Blomkalns, Ruth O'Hara, Euan A Ashley, Kari Christine Nadeau, Samuel Yang, Susan P Holmes, Marlene Rabinovitch, Angela J Rogers, William J Greenleaf, Catherine A Blish
Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. The Journal of experimental medicine 218 (8) (2021)
Pratheepa Jeganathan, Susan P Holmes
A Statistical Perspective on the Challenges in Molecular Microbial Biology. Journal of agricultural, biological, and environmental statistics 26 (2) (2021)
Jessica A Grembi, Lan Huong Nguyen, Thomas D Haggerty, Christopher D Gardner, Susan P Holmes, Julie Parsonnet
Author Correction: Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention. Scientific reports 10 (1) (2020)
Julia L McKechnie, Davis Beltrán, Anne-Maud M Ferreira, Rosemary Vergara, Lisseth Saenz, Ofelina Vergara, Dora Estripeaut, Ana B Araúz, Laura J Simpson, Susan P Holmes, Sandra López-Vergès, Catherine A Blish
Mass Cytometry Analysis of the NK Cell Receptor-Ligand Repertoire Reveals Unique Differences between Dengue-Infected Children and Adults. ImmunoHorizons 4 (10) (2020)
Rotem Botvinik-Nezer, Felix Holzmeister, Colin F Camerer, Anna Dreber, Juergen Huber, Magnus Johannesson, Michael Kirchler, Roni Iwanir, Jeanette A Mumford, R Alison Adcock, Paolo Avesani, Blazej M Baczkowski, Aahana Bajracharya, Leah Bakst, Sheryl Ball, Marco Barilari, Nadège Bault, Derek Beaton, Julia Beitner, Roland G Benoit, Ruud M W J Berkers, Jamil P Bhanji, Bharat B Biswal, Sebastian Bobadilla-Suarez, Tiago Bortolini, Katherine L Bottenhorn, Alexander Bowring, Senne Braem, Hayley R Brooks, Emily G Brudner, Cristian B Calderon, Julia A Camilleri, Jaime J Castrellon, Luca Cecchetti, Edna C Cieslik, Zachary J Cole, Olivier Collignon, Robert W Cox, William Andrew Cunningham, Stefan Czoschke, Kamalaker Dadi, Charles P Davis, Alberto De Luca, Mauricio R Delgado, Lysia Demetriou, Jeffrey B Dennison, Xin Di, Erin W Dickie, Ekaterina Dobryakova, Claire L Donnat, Juergen Dukart, Niall W Duncan, Joke Durnez, Amr Eed, Simon B Eickhoff, Andrew Erhart, Laura Fontanesi, G Matthew Fricke, Shiguang Fu, Adriana Galván, Rémi Gau, Sarah Genon, Tristan Glatard, Enrico Glerean, Jelle J Goeman, Sergej A E Golowin, Carlos González-García, Krzysztof J Gorgolewski, Cheryl L Grady, Mikella A Green, João F Guassi Moreira, Olivia Guest, Shabnam Hakimi, Paul J Hamilton, Roeland Hancock, Giacomo Handjaras, Bronson B Harry, Colin Hawco, Peer Herholz, Gabrielle Herman, Stephan Heunis, Felix Hoffstaedter, Jeremy Hogeveen, Susan P Holmes, Chuan-Peng Hu, Scott A Huettel, Matthew E Hughes, Vittorio Iacovella, Alexandru D Iordan, Peder Mortvedt Isager, Ayse Ilkay Isik, Andrew Jahn, Matthew R Johnson, Tom Johnstone, Michael J E Joseph, Anthony C Juliano, Joseph W Kable, Michalis Kassinopoulos, Cemal Koba, Xiang-Zhen Kong, Timothy R Koscik, Nuri Erkut Kucukboyaci, Brice A Kuhl, Sebastian Kupek, Angela R Laird, Claus Lamm, Robert Langner, Nina Lauharatanahirun, Hongmi Lee, Sangil Lee, Alexander Leemans, Andrea Leo, Elise Lesage, Flora Li, Monica Y C Li, Phui Cheng Lim, Evan N Lintz, Schuyler W Liphardt, Annabel B Losecaat-Vermeer, Bradley C Love, Michael L Mack, Norberto Malpica, Theo F Marins, Camille Maumet, Kelsey R McDonald, Joseph T McGuire, Helena Melero, Adriana S Méndez Leal, Benjamin Meyer, Kristin N Meyer, Paul Glad Mihai, Georgios D Mitsis, Jorge Moll, Dylan M Nielson, Gustav Nilsonne, Michael P Notter, Emanuele Olivetti, Adrian I Onicas, Paolo Papale, Kaustubh R Patil, Jonathan E Peelle, Alexandre Pérez, Doris Pischedda, Jean-Baptiste Poline, Yanina Prystauka, Shruti Ray, Patricia A Reuter-Lorenz, Richard C Reynolds, Emiliano Ricciardi, Jenny R Rieck, Anais M Rodriguez-Thompson, Anthony Romyn, Taylor Salo, Gregory R Samanez-Larkin, Emilio Sanz-Morales, Margaret L Schlichting, Douglas H Schultz, Qiang Shen, Margaret A Sheridan, Jennifer A Silvers, Kenny Skagerlund, Alec Smith, David V Smith, Peter Sokol-Hessner, Simon R Steinkamp, Sarah M Tashjian, Bertrand Thirion, John N Thorp, Gustav Tinghög, Loreen Tisdall, Steven H Tompson, Claudio Toro-Serey, Juan Jesus Torre Tresols, Leonardo Tozzi, Vuong Hung Truong, Luca Turella, Anna E van 't Veer, Tom Verguts, Jean M Vettel, Sagana Vijayarajah, Khoi Vo, Matthew B Wall, Wouter D Weeda, Susanne Weis, David J White, David Wisniewski, Alba Xifra-Porxas, Emily A Yearling, Sangsuk Yoon, Rui Yuan, Kenneth S L Yuen, Lei Zhang, Xu Zhang, Joshua E Zosky, Thomas E Nichols, Russell A Poldrack, Tom Schonberg
Variability in the analysis of a single neuroimaging dataset by many teams. Nature 582 (7810) (2020)
Jessica A Grembi, Lan Huong Nguyen, Thomas D Haggerty, Christopher D Gardner, Susan P Holmes, Julie Parsonnet
Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention. Scientific reports 10 (1) (2020)
Lan Huong Nguyen, Susan P Holmes
Ten quick tips for effective dimensionality reduction. PLoS computational biology 15 (6) (2019)
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric John Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodriguez, John Chase, Emily K Cope, Ricardo Da Silva, Christian Diener, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Sean M Gibbons, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan P Holmes, Hannes Holste, Curtis Huttenhower, Gavin A Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin D Kaehler, Kyo-Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G I Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine A Lozupone, Massoud Maher, Clarisse A Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie T Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima R Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam R Rivers, Michael Scott Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin Johan Jozias van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Charles H D Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology 37 (8) (2019)
Diana M Proctor, Julia A Fukuyama, Peter M Loomer, Gary C Armitage, Stacey A Lee, Nicole M Davis, Mark I Ryder, Susan P Holmes, David A Relman
A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow. Nature communications 9 (1) (2018)
Lisa M Kronstad, Christof Seiler, Rosemary Vergara, Susan P Holmes, Catherine A Blish
Differential Induction of IFN-α and Modulation of CD112 and CD54 Expression Govern the Magnitude of NK Cell IFN-γ Response to Influenza A Viruses. Journal of immunology (Baltimore, Md. : 1950) 201 (7) (2018)
Benjamin J Callahan, Daniel B DiGiulio, Daniela S Aliaga Goltsman, Christine L Sun, Elizabeth K Costello, Pratheepa Jeganathan, Joseph R Biggio, Ronald J Wong, Maurice L Druzin, Gary M Shaw, David K Stevenson, Susan P Holmes, David A Relman
Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women. Proceedings of the National Academy of Sciences of the United States of America 114 (37) (2017)
Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A Relman, Susan P Holmes
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. PLoS computational biology 13 (8) (2017)
Anastassia Gorvitovskaia, Susan P Holmes, Susan M Huse
Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome 4 (2016)
Daniel B DiGiulio, Benjamin J Callahan, Paul J McMurdie, Elizabeth K Costello, Deirdre J Lyell, Anna Robaczewska, Christine L Sun, Daniela S A Goltsman, Ronald J Wong, Gary Shaw, David K Stevenson, Susan P Holmes, David A Relman
Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences of the United States of America 112 (35) (2015)

Susan P Holmes.css-eqlu8i{font-size:small;padding-left:4px;} (Susan Holmes)

Publication Activity (10 Years)

Top Topics

Top Venues

Susan P Holmes (Susan Holmes)