Evidence map›Paper›PMID 41881704›Full record

ReviewTrends in plant science2026

Modeling of gene regulatory networks: an annotated glossary.

Avilash Singh Yadav, Nicholas J Russell, Adriana I Hernández, Alaina R Petlewski, Arielle R Johnson, Ayress D Grinage, Barituziga Banuna, Clarice J Guan, Elizabeth H Mahood, Gordon C Younkin and 10 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Trends in plant science, 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

20 authors.

Avilash Singh YadavWeill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA. Electronic address: as2977@cornell.edu.
Nicholas J RussellDepartment of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany; Polyploidy Integration and Innovation Institute.
Adriana I HernándezSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Alaina R PetlewskiSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Arielle R JohnsonSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Ayress D GrinageSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Barituziga BanunaSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Clarice J GuanSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Elizabeth H MahoodSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Gordon C YounkinSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Hannah R ThomasSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Heather R PhillipsSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Kate HarlineSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Madison FlascoSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Michael B MillerSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Nathan J Scinto-MadonichSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Nicole M SzelugaSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Patrick N MendozaSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
Pau Formosa-JordanDepartment of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany; Polyploidy Integration and Innovation Institute.
Adrienne H K RoederWeill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA; Polyploidy Integration and Innovation Institute. Electronic address: ahr75@cornell.edu.

Funding

Mechanisms of robustness in organogenesisR35GM158190 · NIGMS · CORNELL UNIVERSITY · PI ADRIENNE HK ROEDER · 2025 to 2026
$856k
NIGMS NIH HHS R35 GM158190
6 · The paper itself

Abstract

Biological processes are complex. Their behavior cannot be understood from the sum of their parts. Modeling, which allows for articulating hypotheses as equations and rules, has become indispensable for studying biological complexities. When written as computer code, mathematical models can be evaluated to test multiple potential outcomes. Modeling is useful for identifying essential system components and revealing new interactions. However, implementing models in biological research requires a solid understanding of computational and mathematical vocabulary, which typically requires formal training. Furthermore, communication barriers often hinder collaborations with computational modelers. To address this, we present an annotated glossary of terms associated with modeling gene regulatory networks. Aimed at biologists, we explain common computational modeling terms and frameworks using examples from published studies.

Indexed as

Gene Regulatory NetworksModels, GeneticComputer SimulationModels, Biologicalcomputation modelingdeterministic modelsgene regulatory networkssimulationstochastic models

Identifiers

PMID41881704
PMCPMC13025759

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.