Evidence map›Paper›PMID 42156662›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

LambdaPy and LambdaR: Thermodynamics-Based Biogeochemical Reaction Modeling Packages for Integrating High-Resolution Mass Spectrometry Data.

Manokaran Veeramani, Sanjog Kharel, Hugh C McCullough, Xingyuan Chen, Jianqiu Zheng, James C Stegen, Timothy D Scheibe, Hyun-Seob Song

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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. 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

8 authors.

Manokaran VeeramaniUniversity of Nebraska-Lincoln, Lincoln, NE, USA.
Sanjog KharelUniversity of Nebraska-Lincoln, Lincoln, NE, USA.
Hugh C McCulloughUniversity of Nebraska-Lincoln, Lincoln, NE, USA.
Xingyuan ChenPacific Northwest National Laboratory, Richland, WA, USA.
Jianqiu ZhengPacific Northwest National Laboratory, Richland, WA, USA.
James C StegenPacific Northwest National Laboratory, Richland, WA, USA.
Timothy D ScheibePacific Northwest National Laboratory, Richland, WA, USA.
Hyun-Seob SongUniversity of Nebraska-Lincoln, Lincoln, NE, USA. hsong5@unl.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Microorganisms are key drivers of biogeochemical cycles in natural environments. Microbially mediated biogeochemical reactions are influenced by both biotic and abiotic factors, including microbe-microbe interactions, enzyme kinetics, and chemical traits. To address the impact of chemical substrates on biogeochemical reactions, this chapter provides guidance on substrate-explicit thermodynamic modeling (SXTM) (also known as lambda modeling). SXTM enables automatic formulation of stoichiometric and kinetic models of biogeochemistry from the chemical formulas of organic matter (OM). This approach is particularly useful for formulating biogeochemical reaction models from ultra-high-resolution mass spectrometry data that identify thousands of compounds with distinct molecular formulas. Regardless of the complexity of OM data, SXTM requires only two parameters, maximum growth rate (μ

Indexed as

Mass SpectrometrySoftwareBacteriaKineticsModels, BiologicalThermodynamicsBiogeochemical modelingFTICR-MSOrganic matterSubstrate-explicit modelingThermodynamics

Identifiers

PMID42156662

What OpenQuestion holds

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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.