ArticleNucleic acids research2019
Stemformatics: visualize and download curated stem cell data.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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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.
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Who cites it
26 citing papers in PubMed.
- Computational modelling of cell identity.The Biochemical journal · 2026Review
- The changing landscape of gene expression analysis.Briefings in bioinformatics · 2026Review
- Article
- Identifying Molecular Determinants and Therapeutic Targets in Luminal B Breast Cancer: A Systems Biology Approach.Iranian journal of pathology · 2025Article
- Guidelines for managing and using the digital phenotypes of pluripotent stem cell lines.Stem cell reports · 2024Review
- Integrated multi-omics with machine learning to uncover the intricacies of kidney disease.Briefings in bioinformatics · 2024Review
- Stemformatics data portal enables transcriptional benchmarking of lab-derived myeloid cells.Stem cell reports · 2024Article
- FcRn regulates antigen presentation in dendritic cells downstream of DEC205-targeted vaccines.NPJ vaccines · 2024Article
- Calcium influx, oxidative stress, and apoptosis induced by TRPV1 in chronic myeloid leukemia cells: Synergistic effects with imatinib.Frontiers in molecular biosciences · 2023Article
- The Human Dendritic Cell Atlas: An Integrated Transcriptional Tool to Study Human Dendritic Cell Biology.Journal of immunology (Baltimore, Md. : 1950) · 2022Article
- Bioinformatics Analysis of RNA-seq Data Reveals Genes Related to Cancer Stem Cells in Colorectal Cancerogenesis.International journal of molecular sciences · 2022Article
- Assessing and enhancing migration of human myogenic progenitors using directed iPS cell differentiation and advanced tissue modelling.EMBO molecular medicine · 2022Article
- Survivin Inhibition by Piperine Sensitizes Glioblastoma Cancer Stem Cells and Leads to Better Drug Response.International journal of molecular sciences · 2022Article
- Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references.Briefings in bioinformatics · 2022Article
- An integrated analysis of human myeloid cells identifies gaps in in vitro models of in vivo biology.Stem cell reports · 2021Article
- Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis.Cell discovery · 2021Article
- Cellular Fitness Phenotypes of Cancer Target Genes from Oncobiology to Cancer Therapeutics.Cells · 2021Article
- Ten simple rules for navigating the computational aspect of an interdisciplinary PhD.PLoS computational biology · 2021Article
- Challenges for Computational Stem Cell Biology: A Discussion for the Field.Stem cell reports · 2021Article
- Computational Stem Cell Biology: Open Questions and Guiding Principles.Cell stem cell · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Stemformatics is an established gene expression data portal containing over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focus on pluripotency, tissue stem cells, and staged differentiation. Stemformatics includes curated 'collections' of data relevant to cell reprogramming, as well as hematopoiesis and leukaemia. Rather than simply rehosting datasets as they appear in public repositories, Stemformatics uses a stringent set of quality control metrics and its own pipelines to process handpicked datasets from raw files. This means that about 30% of datasets processed by Stemformatics fail the quality control metrics and never make it to the portal, ensuring that Stemformatics data are of high quality and have been processed in a consistent manner. Stemformatics provides easy-to-use and intuitive tools for biologists to visually explore the data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. The addition of tools that facilitate cross-dataset comparisons provides users with snapshots of gene expression in multiple cell and tissues, assisting the identification of cell-type restricted genes, or potential housekeeping genes. Stemformatics is freely available at stemformatics.org.
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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 OpenQuestion graph.