Evidence map›Paper›PMID 40894616›Full record

ArticlebioRxiv : the preprint server for biology2025

IsoPairFinder: A tool for biochemical pathway discovery using stable isotope tracing metabolomics.

Zhiwei Zhou, Yuanyuan Liu, Mingxun Wang, Dylan Dodd

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

4 authors.

Zhiwei ZhouDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-1249-6870
Yuanyuan LiuDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Mingxun WangDepartment of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.ORCID 0000-0001-7647-6097
Dylan DoddDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-6210-6239

Funding

Collaborative Microbial Metabolite CenterU24DK133658 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2022 to 2026
$2.9M
Microbiota-based probiotics to treat inborn errors in metabolismR01AT011396 · NCCIH · STANFORD UNIVERSITY · PI Dylan Dodd · 2022 to 2026
$2.9M
Physiology of bacterial metabolism in the human gut microbiomeR35GM142873 · NIGMS · STANFORD UNIVERSITY · PI DODD, DYLAN · 2021 to 2025
$2.0M
NCCIH NIH HHS R01 AT011396NIDDK NIH HHS U24 DK133658NIGMS NIH HHS R35 GM142873
6 · The paper itself

Abstract

The functional annotation of microbial genes lags far behind genome sequencing, leaving critical gaps in our knowledge of metabolic pathways. While integrating genetic manipulation with stable isotope tracing (SIT) metabolomics holds promise for pathway discovery, existing tools lack specialized capabilities for gene perturbation experiments. To address this need, we developed IsoPairFinder, a computational tool that identifies pathway intermediates by analyzing paired unlabeled (

Identifiers

PMID40894616
PMCPMC12393393

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.