ArticlemSystems2021
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.
Abstract read
In one paragraph
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
41citing papers in PubMed, 1 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids.Biology letters · 2025Pooled it
- Host-Mediated Selection Shapes Conserved Root Bacterial Microbiomes Across Geographically SeparatedPlants (Basel, Switzerland) · 2026Article
- TreeProfiler: large-scale metadata profiling along gene and species trees.Molecular biology and evolution · 2026Article
- Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.Scientific reports · 2026Article
- Evaluating differences in uterine microbiome and inflammatory status at 1 month postpartum associated with metritis and antibiotic treatment.Journal of dairy science · 2025Article
- Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.Microbiology spectrum · 2025Article
- Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics.Research square · 2025Article
- The microbiome of the human facial skin is unique compared to that of other hominids.mSystems · 2025Article
- Article
- Effects of Baobab fruit powder on gut and cardiometabolic health in obesity-Protocol for a randomised placebo-controlled trial.PloS one · 2025Article
- Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat.ISME communications · 2025Article
- Multi-omics decodes host-specific and environmental microbiome interactions in sepsis.Frontiers in microbiology · 2025Review
- The effect ofJournal of oral microbiology · 2025Article
- Article
- MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification.Environmental microbiome · 2024Article
- Characterization of the Hoof Bacterial Communities of Active Digital Dermatitis Lesions in Feedlot Cattle.Microorganisms · 2024Article
- Greengenes2 unifies microbial data in a single reference tree.Nature biotechnology · 2024Article
- Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy.Life science alliance · 2024Article
- Systemic antibiotic treatment of cows with metritis early postpartum does not change the progression of uterine disease or the uterine microbiome at 1 month postpartum.Research square · 2024Article
- A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables.Nature microbiology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
30 authors.
Kalen Cantrell *Department of Computer Science, Jacobs School of Engineering, University of California, San Diego, California, USA.
Marcus W Fedarko *Department of Computer Science, Jacobs School of Engineering, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0002-6718-6925
Gibraan RahmanBioinformatics and Systems Biology Program, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0002-8843-0229
Daniel McDonaldDepartment of Pediatrics, School of Medicine, University of California, San Diego, California, USA.
Yimeng YangCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.
Thant ZawCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.
Antonio GonzalezDepartment of Pediatrics, School of Medicine, University of California, San Diego, California, USA.
Stefan JanssenAlgorithmic Bioinformatics, Justus Liebig University, Giessen, Germany.ORCID https://orcid.org/0000-0003-0955-0589
Mehrbod EstakiDepartment of Pediatrics, School of Medicine, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0003-4556-8444
Niina HaiminenIBM T. J. Watson Research Center, Yorktown Heights, New York, USA.ORCID https://orcid.org/0000-0002-8663-1019
Kristen L BeckIBM Almaden Research Center, San Jose, California, USA.ORCID https://orcid.org/0000-0002-4603-0235
Qiyun ZhuDepartment of Pediatrics, School of Medicine, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0002-3568-6271
Erfan SayyariCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.
James T MortonCenter for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA.
George ArmstrongCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0002-1061-3295
Anupriya TripathiDepartment of Pediatrics, School of Medicine, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0001-8912-9684
Julia M GauglitzCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0003-3146-2489
Clarisse MarotzDepartment of Pediatrics, School of Medicine, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0002-1520-8854
Nathaniel L MattesonScripps Research Institute, San Diego, California, USA.
Cameron MartinoCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.
Jon G SandersCornell Institute for Host-Microbe Interaction and Disease, Cornell University, Ithaca, New York, USA.ORCID https://orcid.org/0000-0001-6077-4014
Anna Paola CarrieriIBM Research, The Hartree Centre, Daresbury, United Kingdom.ORCID https://orcid.org/0000-0003-2349-1896
Se Jin SongCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.
Austin D SwaffordCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0001-5655-8300
Pieter C DorresteinCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.
Kristian G AndersenScripps Research Institute, San Diego, California, USA.
Laxmi ParidaIBM T. J. Watson Research Center, Yorktown Heights, New York, USA.ORCID https://orcid.org/0000-0002-7872-5074
Ho-Cheol KimIBM Almaden Research Center, San Jose, California, USA.ORCID https://orcid.org/0000-0003-0464-4340
Yoshiki Vázquez-BaezaCenter for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA.ORCID https://orcid.org/0000-0001-6014-2009
Rob KnightDepartment of Computer Science, Jacobs School of Engineering, University of California, San Diego, California, USA robknight@ucsd.edu.ORCID https://orcid.org/0000-0002-0975-9019
Funding
Project 4 - Mechanistic studies on the role of the gut microbiome in models for Alzheimer's diseaseU19AG063744 · NIA · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI ROB KNIGHT, Rima F Kaddurah-Daouk · 2019 to 2026
$54.1MTechnology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Bryan Briney · 2018 to 2026
$32.0MNIAID NIH HHS U19 AI135995NIA NIH HHS U19 AG063744
Abstract
Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality-including ordination integration and animations-alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of 'omic data.
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bioinformaticsmicrobial ecology
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LicenceCC BY
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.