Evidence map›Paper›PMID 39886798›Full record

ArticleAnalytical chemistry2025

iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments.

Damien Olivier-Jimenez, Rico J E Derks, Oscar Harari, Carlos Cruchaga, Muhammad Ali, Alessandro Ori, Domenico Di Fraia, Birol Cabukusta, Andy Henrie, Martin Giera and 1 more

Abstract read
In one paragraph

Article in Analytical chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

The trial behind it

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Article
  2. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Damien Olivier-JimenezCenter for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands.
Rico J E DerksCenter for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands.ORCID 0000-0002-8920-7133
Oscar HarariDepartment of Neurology, The Ohio State University, Columbus, Ohio 43210, United States of America.
Carlos CruchagaWashington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States of America.
Muhammad AliWashington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States of America.
Alessandro OriLeibniz Institute on Aging─Fritz Lipmann Institute (FLI), Jena 07745, Germany.
Domenico Di FraiaLeibniz Institute on Aging─Fritz Lipmann Institute (FLI), Jena 07745, Germany.
Birol CabukustaDepartment of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden 2333ZA, Netherlands.
Andy HenrieDataTecnica, Washington, District of Columbia 20037, United States of America.
Martin GieraCenter for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands.ORCID 0000-0003-1684-1894
Yassene MohammedCenter for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands.ORCID 0000-0003-3265-3332

Funding

MVP Data Integration into the ADSP Phenotype Harmonization ConsortiumU24AG074855 · NIA · VANDERBILT UNIVERSITY MEDICAL CENTER · PI CUCCARO, MICHAEL L, HOHMAN, TIMOTHY J · 2021 to 2025
$37.5M
Investigating the Functional Impact of AD Risk Genes on Neuro-Vascular InteractionsU01AG072464 · NIA · REGENERATIVE RESEARCH FOUNDATION · PI HARARI, OSCAR, KAMPMANN, MARTIN · 2021 to 2025
$8.7M
MENDELIAN RANDOMIZATION FOR UNBIAS BIOMARKER DISCOVERY FOR AD AND OTHER COMPLEX TRAITSR01AG057777 · NIA · WASHINGTON UNIVERSITY · PI HARARI, OSCAR · 2018 to 2022
$4.1M
Human iPSC model of Cerebro-Vascular Interactions in ADRDR61NS138655 · NINDS · REGENERATIVE RESEARCH FOUNDATION · PI TEMPLE, SALLY · 2024 to 2024
$1.9M
NIA NIH HHS R01 AG057777NIA NIH HHS U01 AG072464NIA NIH HHS U24 AG074855NINDS NIH HHS R61 NS138655
6 · The paper itself

Abstract

Thanks to the plummeting costs of continuously evolving omics analytical platforms, research centers collect multiomics data more routinely. They are, however, confronted with the lack of a versatile software solution to harmoniously analyze single-omics and interpret multiomics data. We have developed iSODA, a web-based application for the analysis of single- and multiomics data. The tool emphasizes intuitive interactive visualizations designed for user-driven data exploration. Researchers can access a variety of functions ranging from simple visualization like volcano plots and PCA to advanced functional analyses like enrichment analysis and lipid saturation analysis. For integrated multiomics, iSODA incorporates multi-omics factor analysis and similarity network fusion. The ability to adapt the data on-the-fly allows for tasks, such as the removal of outlier samples or failed features, imputation, or normalization. All results are presented through interactive plots, the modular design supports extensions, and tooltips and tutorials provide comprehensive guidance for users. iSODA is accessible under http://isoda.online/.

Identifiers

PMID39886798
PMCPMC11822744

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Registered trials

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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.