CoChat
Sign Up
Cited by 264

The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.

Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells

Murata, Kazutaka, Jadhav, Unmesh, Madha, Shariq, van Es, Johan, Dean, Justin, Cavazza, Alessia, Wucherpfennig, Kai, Michor, Franziska, Clevers, Hans, Shivdasani, Ramesh A.·2020·Cell Stem Cell
DOI 10.1016/j.stem.2019.12.011PMC PMC7147146
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.stem.2019.12.011

Cites

13 of 13 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Show all 13 references

Research works printed but not linked: 67

  1. Ayyaz, 2019, Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell, Nature, 569, 121, 10.1038/s41586-019-1154-y · DOI
  2. Bamba, 2003, Regulation of IL-11 expression in intestinal myofibroblasts: role of c-Jun AP-1- and MAPK-dependent pathways, Am. J. Physiol. Gastrointest. Liver Physiol., 285, G529, 10.1152/ajpgi.00050.2003 · DOI
  3. Banerjee, 2018, Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development, Genes Dev., 32, 1430, 10.1101/gad.318832.118 · DOI
  4. Bankaitis, 2018, Reserve stem cells in intestinal homeostasis and injury, Gastroenterology, 155, 1348, 10.1053/j.gastro.2018.08.016 · DOI
  5. Barker, 2012, Identifying the stem cell of the intestinal crypt: strategies and pitfalls, Cell Stem Cell, 11, 452, 10.1016/j.stem.2012.09.009 · DOI
  6. Batts, 2006, Bmp signaling is required for intestinal growth and morphogenesis, Dev. Dyn., 235, 1563, 10.1002/dvdy.20741 · DOI
  7. Biton, 2018, T helper cell cytokines modulate intestinal stem cell renewal and differentiation, Cell, 175, 1307, 10.1016/j.cell.2018.10.008 · DOI
  8. Castillo-Azofeifa, 2019, Atoh1+ secretory progenitors possess renewal capacity independent of Lgr5+ cells during colonic regeneration, EMBO J., 38, e99984, 10.15252/embj.201899984 · DOI
  9. Chaves-Perez, 2019, URI is required to maintain intestinal architecture during ionizing radiation, Science, 364, eaaq1165, 10.1126/science.aaq1165 · DOI
  10. Cheng, 1985, Whole population cell kinetics and postnatal development of the mouse intestinal epithelium, Anat. Rec., 211, 420, 10.1002/ar.1092110408 · DOI
  11. Corces, 2017, An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues, Nat. Methods, 14, 959, 10.1038/nmeth.4396 · DOI · Paper page
  12. Cornwell, 2018, VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis, BMC Bioinformatics, 19, 135, 10.1186/s12859-018-2139-9 · DOI
  13. de Sousa e Melo, 2019, Cellular plasticity in intestinal homeostasis and disease, Cell Stem Cell, 24, 54, 10.1016/j.stem.2018.11.019 · DOI
  14. Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 · DOI · Paper page
  15. Du, 1994, A bone marrow stromal-derived growth factor, interleukin-11, stimulates recovery of small intestinal mucosal cells after cytoablative therapy, Blood, 83, 33, 10.1182/blood.V83.1.33.33 · DOI
  16. el Marjou, 2004, Tissue-specific and inducible Cre-mediated recombination in the gut epithelium, Genesis, 39, 186, 10.1002/gene.20042 · DOI
  17. Fordham, 2013, Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury, Cell Stem Cell, 13, 734, 10.1016/j.stem.2013.09.015 · DOI
  18. Gregorieff, 2015, Yap-dependent reprogramming of Lgr5(+) stem cells drives intestinal regeneration and cancer, Nature, 526, 715, 10.1038/nature15382 · DOI
  19. Han, 2002, Inducible gene knockout of transcription factor recombination signal binding protein-J reveals its essential role in T versus B lineage decision, Int. Immunol., 14, 637, 10.1093/intimm/dxf030 · DOI
  20. Haramis, 2004, De novo crypt formation and juvenile polyposis on BMP inhibition in mouse intestine, Science, 303, 1684, 10.1126/science.1093587 · DOI
  21. Hulsen, 2008, BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams, BMC Genomics, 9, 488, 10.1186/1471-2164-9-488 · DOI
  22. Ishibashi, 2018, Contribution of ATOH1+ cells to the homeostasis, repair, and tumorigenesis of the colonic epithelium, Stem Cell Reports, 10, 27, 10.1016/j.stemcr.2017.11.006 · DOI
  23. Itzkovitz, 2011, Single-molecule transcript counting of stem-cell markers in the mouse intestine, Nat. Cell Biol., 14, 106, 10.1038/ncb2384 · DOI
  24. Jadhav, 2017, Dynamic reorganization of chromatin accessibility signatures during dedifferentiation of secretory precursors into Lgr5+ intestinal stem cells, Cell Stem Cell, 21, 65, 10.1016/j.stem.2017.05.001 · DOI
  25. Jenkins, 2007, Pathologic consequences of STAT3 hyperactivation by IL-6 and IL-11 during hematopoiesis and lymphopoiesis, Blood, 109, 2380, 10.1182/blood-2006-08-040352 · DOI
  26. Jones, 2019, Cellular plasticity of Defa4(Cre)-expressing Paneth cells in response to Notch activation and intestinal injury, Cell. Mol. Gastroenterol. Hepatol., 7, 533, 10.1016/j.jcmgh.2018.11.004 · DOI
  27. Jubb, 2006, Achaete-scute like 2 (ascl2) is a target of Wnt signalling and is upregulated in intestinal neoplasia, Oncogene, 25, 3445, 10.1038/sj.onc.1209382 · DOI
  28. Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 · DOI · Paper page
  29. Li, 2010, Coexistence of quiescent and active adult stem cells in mammals, Science, 327, 542, 10.1126/science.1180794 · DOI · Paper page
  30. Liu, 1996, Trophic effects of interleukin-11 in rats with experimental short bowel syndrome, J. Pediatr. Surg., 31, 1047, 10.1016/S0022-3468(96)90084-6 · DOI
  31. Lopez-Garcia, 2010, Intestinal stem cell replacement follows a pattern of neutral drift, Science, 330, 822, 10.1126/science.1196236 · DOI
  32. Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 · DOI · Paper page
  33. Madisen, 2010, A robust and high-throughput Cre reporting and characterization system for the whole mouse brain, Nat. Neurosci., 13, 133, 10.1038/nn.2467 · DOI · Paper page
  34. Metcalfe, 2014, Lgr5+ stem cells are indispensable for radiation-induced intestinal regeneration, Cell Stem Cell, 14, 149, 10.1016/j.stem.2013.11.008 · DOI · Paper page
  35. Montgomery, 2011, Mouse telomerase reverse transcriptase (mTert) expression marks slowly cycling intestinal stem cells, Proc. Natl. Acad. Sci. U S A, 108, 179, 10.1073/pnas.1013004108 · DOI
  36. Muñoz, 2012, The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4′ cell markers, EMBO J., 31, 3079, 10.1038/emboj.2012.166 · DOI
  37. Mustata, 2013, Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium, Cell Rep., 5, 421, 10.1016/j.celrep.2013.09.005 · DOI
  38. Nusse, 2018, Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche, Nature, 559, 109, 10.1038/s41586-018-0257-1 · DOI
  39. Ootani, 2009, Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche, Nat. Med., 15, 701, 10.1038/nm.1951 · DOI · Paper page
  40. Pinello, 2014, Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns, Proc. Natl. Acad. Sci. U S A, 111, E344, 10.1073/pnas.1322570111 · DOI
  41. Potten, 1996, Protection of the small intestinal clonogenic stem cells from radiation-induced damage by pretreatment with interleukin 11 also increases murine survival time, Stem Cells, 14, 452, 10.1002/stem.140452 · DOI
  42. Potten, 1998, Stem cells in gastrointestinal epithelium: numbers, characteristics and death, Philos. Trans. R. Soc. Lond. B Biol. Sci., 353, 821, 10.1098/rstb.1998.0246 · DOI
  43. Ramírez, 2016, deepTools2: a next generation web server for deep-sequencing data analysis, Nucleic Acids Res., 44, W160, 10.1093/nar/gkw257 · DOI · Paper page
  44. Robinson, 2011, Integrative genomics viewer, Nat. Biotechnol., 29, 24, 10.1038/nbt.1754 · DOI · Paper page
  45. San Roman, 2015, Distinct processes and transcriptional targets underlie CDX2 requirements in intestinal stem cells and differentiated villus cells, Stem Cell Reports, 5, 673, 10.1016/j.stemcr.2015.09.006 · DOI
  46. Sangiorgi, 2008, Bmi1 is expressed in vivo in intestinal stem cells, Nat. Genet., 40, 915, 10.1038/ng.165 · DOI
  47. Santos, 2018, The intestinal stem cell niche: Homeostasis and adaptations, Trends Cell Biol., 28, 1062, 10.1016/j.tcb.2018.08.001 · DOI
  48. Sasaki, 2016, Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon, Proc. Natl. Acad. Sci. U S A, 113, E5399, 10.1073/pnas.1607327113 · DOI · Paper page
  49. Schmitt, 2018, Paneth cells respond to inflammation and contribute to tissue regeneration by acquiring stem-like features through SCF/c-Kit signaling, Cell Rep., 24, 2312, 10.1016/j.celrep.2018.07.085 · DOI
  50. Shen, 2013, diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates, PLoS ONE, 8, e65598, 10.1371/journal.pone.0065598 · DOI
  51. Shroyer, 2007, Intestine-specific ablation of mouse atonal homolog 1 (Math1) reveals a role in cellular homeostasis, Gastroenterology, 132, 2478, 10.1053/j.gastro.2007.03.047 · DOI
  52. Snippert, 2010, Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells, Cell, 143, 134, 10.1016/j.cell.2010.09.016 · DOI · Paper page
  53. Snippert, 2014, Biased competition between Lgr5 intestinal stem cells driven by oncogenic mutation induces clonal expansion, EMBO Rep., 15, 62, 10.1002/embr.201337799 · DOI
  54. Takeda, 2011, Interconversion between intestinal stem cell populations in distinct niches, Science, 334, 1420, 10.1126/science.1213214 · DOI · Paper page
  55. Tetteh, 2016, Replacement of lost Lgr5-positive stem cells through plasticity of their enterocyte-lineage daughters, Cell Stem Cell, 18, 203, 10.1016/j.stem.2016.01.001 · DOI · Paper page
  56. Tian, 2011, A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable, Nature, 478, 255, 10.1038/nature10408 · DOI
  57. Tomic, 2018, Phospho-regulation of ATOH1 is required for plasticity of secretory progenitors and tissue regeneration, Cell Stem Cell, 23, 436, 10.1016/j.stem.2018.07.002 · DOI
  58. van der Flier, 2009, Transcription factor achaete scute-like 2 controls intestinal stem cell fate, Cell, 136, 903, 10.1016/j.cell.2009.01.031 · DOI
  59. van Es, 2012, Dll1+ secretory progenitor cells revert to stem cells upon crypt damage, Nat. Cell Biol., 14, 1099, 10.1038/ncb2581 · DOI
  60. Vermeulen, 2013, Defining stem cell dynamics in models of intestinal tumor initiation, Science, 342, 995, 10.1126/science.1243148 · DOI
  61. Yan, 2012, The intestinal stem cell markers Bmi1 and Lgr5 identify two functionally distinct populations, Proc. Natl. Acad. Sci. U S A, 109, 466, 10.1073/pnas.1118857109 · DOI
  62. Yan, 2017, Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity, Cell Stem Cell, 21, 78, 10.1016/j.stem.2017.06.014 · DOI
  63. Yousefi, 2017, Hierarchy and plasticity in the intestinal stem cell compartment, Trends Cell Biol., 27, 753, 10.1016/j.tcb.2017.06.006 · DOI
  64. Yu, 2018, Paneth cell multipotency induced by Notch activation following injury, Cell Stem Cell, 23, 46, 10.1016/j.stem.2018.05.002 · DOI
  65. Yui, 2018, YAP/TAZ-dependent reprogramming of colonic epithelium links ECM remodeling to tissue regeneration, Cell Stem Cell, 22, 35, 10.1016/j.stem.2017.11.001 · DOI
  66. Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137 · DOI · Paper page
  67. Zhou, 2013, Induction of intestinal stem cells by R-spondin 1 and Slit2 augments chemoradioprotection, Nature, 501, 107, 10.1038/nature12416 · DOI

Cited by

Sorted by citations

See all 264

Metadata

Authors
Murata, K., Jadhav, U., Madha, S., van Es, J., Dean, J., Cavazza, A., Wucherpfennig, K., Michor, F., Clevers, H., & Shivdasani, R. A.
ORCID
Shivdasani, Ramesh A.
Venue
Cell Stem Cell
Publisher
Elsevier BV
Published
2020-03
Volume
26
Issue
3
Pages
377-390.e6
ISSN
1934-5909
DOI
10.1016/j.stem.2019.12.011
PMC
PMC7147146
Cited by
264
References
13
Language
en
Licence
Funders
  • National Institute of Diabetes and Digestive and Kidney Diseases
  • National Cancer Institute

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review