StemID statistics

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Citations per year

Number of citations per year for the bioinformatics software tool StemID

Tool usage distribution map

This map represents all the scientific publications referring to StemID per scientific context
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Associated diseases


Popular tool citations

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StemID specifications


Unique identifier OMICS_17165
Name StemID
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Alexander van Oudenaarden

Publication for StemID

StemID citations


Expansion of Adult Human Pancreatic Tissue Yields Organoids Harboring Progenitor Cells with Endocrine Differentiation Potential

Stem Cell Reports
PMCID: 5918840
PMID: 29539434
DOI: 10.1016/j.stemcr.2018.02.005

[…] cells can be generated from cultured human pancreatic ductal tissue (, , , ). We recently showed that in silico analysis of single-cell transcriptome profiles of human adult pancreatic cells using a StemID algorithm predicts a distinct subpopulation of ductal cells with multipotential differentiation potential (). In mice, the existence of postnatal endocrine progenitors within the pancreatic duc […]


Using Smart Technology to Improve Outcomes in Myocardial Infarction Patients: Rationale and Design of a Protocol for a Randomized Controlled Trial, The Box

PMCID: 5630694
PMID: 28939546
DOI: 10.2196/resprot.8038

[…] care visit, or admission for any reason. This factor will be measured via questionnaires and verified by EMR data.Major Adverse Cardiac Events (MACEs)a. Death of any causeb. Cardiac deathc. Recurrent STEMId. Recurrent NST-ACSe. Revascularizationf. Hospitalization for heart failureg. Transient Ischemic Attackh. Ischemic strokePropensity of medication adherence, measured by the 8-item Morisky Medica […]


Systematic single cell analysis provides new insights into heterogeneity and plasticity of the pancreas

PMCID: 5605721
PMID: 28951822
DOI: 10.1016/j.molmet.2017.06.021

[…] l pancreatic lineages as well as neural lineages . In agreement, Grün et al. identified two ductal cell clusters with a high multipotency score in the adult human pancreas using their newly developed StemID algorithm to detect potential stem cell populations within heterogeneous cell populations . The inferred pancreatic lineage tree implies that distinct subtypes of ductal cells give rise to diff […]


Single cell entropy for accurate estimation of differentiation potency from a cell's transcriptome

Nat Commun
PMCID: 5461595
PMID: 28569836
DOI: 10.1038/ncomms15599

[…] it is worth emphasizing in this context that signalling entropy provided a more accurate and robust measure of differentiation potency than other transcriptomic entropy-based measures (those used in StemID and SLICE) which do not use network information.To conclude, signalling entropy and the SCENT algorithm provide a computational framework to advance our understanding of single-cell biology. We […]


Discovering sparse transcription factor codes for cell states and state transitions during development

PMCID: 5352226
PMID: 28296636
DOI: 10.7554/eLife.20488.034

[…] lineage or distance relationship among the putative types is immediately apparent from this clustering. Analysis of this data with other recent methods such as Monocle and Monocle2 (), TSCAN (), and StemID () did not clearly reconstruct lineage or infer key genes regulating transitions ( – Bottom, ). Monocle2 () produces a tree with complex branching, but SOX2+ progenitors and DCX+ differentiated […]


A Single Cell Transcriptome Atlas of the Human Pancreas

Cell Syst
PMCID: 5092539
PMID: 27693023
DOI: 10.1016/j.cels.2016.09.002

[…] en adjusted to the expected number of molecules based on counts, 256 possible UMI’s and poissonian counting statistics.Samples were normalized by downsampling to a minimum number of 6000 transcripts. StemID was used to cluster cells and to perform outlier analysis. Differentially expressed genes between two subgroups of cells were identified similar to a previously published method (). First, a ne […]

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StemID institution(s)
Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, Utrecht, Netherlands; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Department of Medicine, Section of Nephrology and Section of Endocrinology, Leiden University Medical Center, Leiden, Netherlands; Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
StemID funding source(s)
Supported by European Research Council Advanced Grant ERC-AdG 294325-GeneNoiseControl, a Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) Vici award, the DON Foundation, and the Dutch Research Foundation.

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