Evidence map›Paper›PMID 37292934›Full record

ArticlebioRxiv : the preprint server for biology2023

Studying stochastic systems biology of the cell with single-cell genomics data.

Gennady Gorin, John J Vastola, Lior Pachter

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
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, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors at 2 institutions in 1 country.

Gennady GorinDivision of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125.
John J VastolaDepartment of Neurobiology, Harvard Medical School, Boston, MA, 02115.
Lior PachterDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125.
California Institute of Technology · USHarvard University · US

Funding

Generation of novel cell type specific mouse genetic toolsU19MH114830 · NIMH · ALLEN INSTITUTE · PI NGAI, JOHN J. · 2017 to 2021
$64.7M
Center for Mouse Genomic Variation at Single Cell ResolutionUM1HG012077 · NHGRI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Seyed Ali Mortazavi, BARBARA J WOLD · 2021 to 2026
$13.7M
Project C: Neural basis of causal inference in continuous navigationU19NS118246 · NINDS · UNIVERSITY OF ROCHESTER · PI DRUGOWITSCH, JAN · 2020 to 2024
$12.0M
NHGRI NIH HHS UM1 HG012077NIMH NIH HHS U19 MH114830NINDS NIH HHS U19 NS118246
6 · The paper itself

Abstract

Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.

Identifiers

PMID37292934
PMCPMC10245677
OpenAlexW4377098649

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.