Evidence map›Paper›PMID 39187941›Full record

ArticleBioinformatics (Oxford, England)2024

Eliater: a Python package for estimating outcomes of perturbations in biomolecular networks.

Sara Mohammad-Taheri, Pruthvi Prakash Navada, Charles Tapley Hoyt, Jeremy Zucker, Karen Sachs, Benjamin M Gyori, Olga Vitek

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2024. 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

7 authors.

Sara Mohammad-TaheriBarnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, United States.ORCID 0000-0002-6554-9083
Pruthvi Prakash NavadaKhoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, United States.
Charles Tapley HoytKhoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, United States.ORCID 0000-0003-4423-4370
Jeremy ZuckerPacific Northwest National Laboratory, Richland, WA, 99354, United States.
Karen SachsNext Generation Analytics, Palo Alto, CA, United States.
Benjamin M GyoriBarnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, United States.
Olga VitekBarnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, United States.

Funding

Implementing a coupled system of integrative ML modeling and data validation for elucidating microglial therapeutic targets in neurodegenerative diseaseR44MH135465 · NIMH · MODULO BIO, INC. · PI SACHS, KAREN · 2023 to 2024
$2.9M
NIMH NIH HHS 1R44MH135465NIMH NIH HHS R44 MH135465
6 · The paper itself

Abstract

summaryWe introduce Eliater, a Python package for estimating the effect of perturbation of an upstream molecule on a downstream molecule in a biomolecular network. The estimation takes as input a biomolecular network, observational biomolecular data, and a perturbation of interest, and outputs an estimated quantitative effect of the perturbation. We showcase the functionalities of Eliater in a case study of Escherichia coli transcriptional regulatory network. AVAILABILITY AND IMPLEMENTATION: The code, the documentation, and several case studies are available open source at https://github.com/y0-causal-inference/eliater.

Indexed as

Escherichia coliGene Regulatory NetworksSoftwareComputational Biology

Identifiers

PMID39187941
PMCPMC11410922

What OpenQuestion holds

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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.