ArticleNature protocols2017
Assessment of engineered cells using CellNet and RNA-seq.
Article in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 2 of them syntheses that pooled 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.
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.
Who cites it
29 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use.Communications biology · 2022Pooled it
- Transcriptomics analysis of human iPSC-derived dopaminergic neurons reveals a novel model for sporadic Parkinson's disease.Molecular psychiatry · 2022Pooled it
- Epithelial Reprogramming and Transition during Pulmonary Bioengineering.bioRxiv : the preprint server for biology · 2026Article
- Engineered microtissues to model the effects of dynamic heterotypic cell signaling on iPSC-derived human hepatocyte maturation.Acta biomaterialia · 2025Article
- Pathway-Based Similarity Measurement to Quantify Transcriptomics Similarity Between Human Tissues and Preclinical Models.Clinical pharmacology and therapeutics · 2025Article
- The PERK Branch of the Unfolded Protein Response Safeguards Protein Homeostasis and Mesendoderm Specification of Human Pluripotent Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Article
- Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols.Stem cell reports · 2023Article
- Characterizing the composition of iPSC derived cells from bulk transcriptomics data with CellMap.Scientific reports · 2022Article
- EZH1 repression generates mature iPSC-derived CAR T cells with enhanced antitumor activity.Cell stem cell · 2022Article
- Ranking reprogramming factors for cell differentiation.Nature methods · 2022Article
- Identifying novel transcript biomarkers for hepatocellular carcinoma (HCC) using RNA-Seq datasets and machine learning.BMC cancer · 2021Article
- Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia.Scientific reports · 2021Article
- Generation and characterization of iPSC-derived renal proximal tubule-like cells with extended stability.Scientific reports · 2021Article
- Evaluating the transcriptional fidelity of cancer models.Genome medicine · 2021Article
- A comprehensive library of human transcription factors for cell fate engineering.Nature biotechnology · 2021Article
- Turning Nature's own processes into design strategies for living bone implant biomanufacturing: a decade of Developmental Engineering.Advanced drug delivery reviews · 2021Review
- Comparing in vitro human liver models to in vivo human liver using RNA-Seq.Archives of toxicology · 2021Article
- Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids.Cell systems · 2021Article
- Cellular reprogramming: Mathematics meets medicine.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
CellNet is a computational platform designed to assess cell populations engineered by either directed differentiation of pluripotent stem cells (PSCs) or direct conversion, and to suggest specific hypotheses to improve cell fate engineering protocols. CellNet takes as input gene expression data and compares them with large data sets of normal expression profiles compiled from public sources, in regard to the extent to which cell- and tissue-specific gene regulatory networks are established. CellNet was originally designed to work with human or mouse microarray expression data for 21 cell or tissue (C/T) types. Here we describe how to apply CellNet to RNA-seq data and how to build a completely new CellNet platform applicable to, for example, other species or additional cell and tissue types. Once the raw data have been preprocessed, running CellNet takes only several minutes, whereas the time required to create a completely new CellNet is several hours.
Indexed as
Identifiers
What Socratic holds
Registered trials
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 Socratic graph.