Evidence map›Paper›PMID 36778259›Full record

ArticlebioRxiv : the preprint server for biology2023

Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference.

Andreas Tjärnberg, Maggie Beheler-Amass, Christopher A Jackson, Lionel A Christiaen, David Gresham, Richard Bonneau

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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

5 · Who and what money

Authors and funding

6 authors.

Andreas TjärnbergCenter for Developmental Genetics, New York University, New York 10003 NY, USA.
Maggie Beheler-AmassCenter For Genomics and Systems Biology, NYU, New York, NY 10008, USA.
Christopher A JacksonCenter For Genomics and Systems Biology, NYU, New York, NY 10008, USA.
Lionel A ChristiaenCenter for Developmental Genetics, New York University, New York 10003 NY, USA.
David GreshamCenter For Genomics and Systems Biology, NYU, New York, NY 10008, USA.
Richard BonneauCenter For Genomics and Systems Biology, NYU, New York, NY 10008, USA.

Funding

Integrating Spatial Multi-omics and Clinical Covariates to Identify Mechanisms of Disease in ALS-FTDR01NS118183 · NINDS · NEW YORK GENOME CENTER · PI Hemali Phatnani · 2020 to 2026
$4.7M
Spatially Resolved Dynamics of Molecular Pathology and Intercellular Interactions in Amytrophic Lateral SclerosisR01NS116350 · NINDS · NEW YORK GENOME CENTER · PI Hemali Phatnani · 2020 to 2026
$3.6M
Modeling Gene Regulatory Networks for Early Cardiopharyngeal DevelopmentR01HD096770 · NICHD · NEW YORK UNIVERSITY · PI BONNEAU, RICHARD A, CHRISTIAEN, LIONEL · 2018 to 2022
$3.0M
Regulation of Quiescence in Eukaryotic CellsR01GM107466 · NIGMS · NEW YORK UNIVERSITY · PI GRESHAM, DAVID · 2013 to 2022
$3.0M
Constraints and Consequences of Copy Number VariationR01GM134066 · NIGMS · NEW YORK UNIVERSITY · PI GRESHAM, DAVID · 2020 to 2023
$1.2M
NICHD NIH HHS R01 HD096770NIGMS NIH HHS R01 GM107466NIGMS NIH HHS R01 GM134066NINDS NIH HHS R01 NS116350NINDS NIH HHS R01 NS118183
6 · The paper itself

Abstract

The modeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of regulatory features in genome-wide screens. Most GRN inference methods are therefore forced to model relationships between regulatory genes and their targets with expression as a proxy for the upstream independent features, complicating validation and predictions produced by modeling frameworks. Separating covariance and regulatory influence requires aggregation of independent and complementary sets of evidence, such as transcription factor (TF) binding and target gene expression. However, the complete regulatory state of the system,

Identifiers

PMID36778259
PMCPMC9915715

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.