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Paper · 37980571

Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing.

Craig AJ and 23 others. Cell Rep, 2023. Cited by 28 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing. Papers, record 37980571. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/37980571

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title
Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing.
PubMed
Journal
Cell Rep
PubMed
Year
2023
PubMed
Publication types
Journal Article, Research Support, N.I.H., Extramural, Research Support, N.I.H., Intramural
PubMed
Citations, by iCite
28
iCite
Relative citation ratio, by iCite
1.96
iCite
Revised in PubMed
2025-05-30
PubMed

Authors24

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

OrderAuthorForenameKindORCID iD
1Craig AJAmanda J
2Silveira MADMaruhen A Datsch
3Ma LLichun
4Revsine MMahler
5Wang LLimin
6Heinrich SSophia
7Rae ZZachary
8Ruchinskas AAllison
9Dadkhah KKimia
10Do WWhitney

1 to 10 of 24Source PubMed

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Topics9

NLM's MeSH indexing of the paper, its major topics first.

MeSH termMajor
Carcinoma, HepatocellularMajor topic
Liver NeoplasmsMajor topic
CholangiocarcinomaMajor topic
Bile Duct NeoplasmsMajor topic
Humans
Transcription Factors
Bile Ducts, Intrahepatic
Chromatin
Tumor Microenvironment

Source PubMed

Grants9

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

Grant, as the record writes itAgencyCountryNIH projectStated bySource
75N91019D00024NCI NIH HHSUnited StatesPubMedPubMed
ZIA BC010876Intramural NIH HHSUnited StatesZIABC010876PubMedNIH RePORTER
Z01 BC010877Intramural NIH HHSUnited StatesZ01BC010877PubMedNIH RePORTER
ZIA BC010313Intramural NIH HHSUnited StatesZIABC010313PubMedNIH RePORTER
Z01 BC010313Intramural NIH HHSUnited StatesZ01BC010313PubMedNIH RePORTER
ZIA BC011870Intramural NIH HHSUnited StatesZIABC011870PubMedNIH RePORTER
Z01 BC010876Intramural NIH HHSUnited StatesZ01BC010876PubMedNIH RePORTER
ZIA BC010877Intramural NIH HHSUnited StatesZIABC010877PubMedNIH RePORTER
F22CA000024NIHNIH RePORTER

Trials0

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

None in this release.

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References45

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

OrderPMIDTitleJournalYearIn PapersSource
134,725,479Single-cell chromatin state analysis with Signac.Nat Methods2021https://conductscience.org/library/papers/34725479PubMed
231,015,418Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM.Nat Commun2019https://conductscience.org/library/papers/31015418PubMed
318,701,503Focal gains of VEGFA and molecular classification of hepatocellular carcinoma.Cancer Res2008https://conductscience.org/library/papers/18701503PubMed
430,970,190Hepatocellular Carcinoma.N Engl J Med2019https://conductscience.org/library/papers/30970190PubMed
531,588,021Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer.Cancer Cell2019https://conductscience.org/library/papers/31588021PubMed
636,692,965Top advances of the year: Hepatobiliary cancers.Cancer2023https://conductscience.org/library/papers/36692965PubMed
723,635,789Cancer stem cells in the development of liver cancer.J Clin Invest2013https://conductscience.org/library/papers/23635789PubMed
829,087,512TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions.Nucleic Acids Res2018https://conductscience.org/library/papers/29087512PubMed
931,178,118Comprehensive Integration of Single-Cell Data.Cell2019https://conductscience.org/library/papers/31178118PubMed
1037,041,032Dynamically regulated transcription factors are encoded by highly unstable mRNAs in the Drosophila larval brain.RNA2023https://conductscience.org/library/papers/37041032PubMed

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Cited by25

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 28 citations.

PMIDTitleJournalYearIn PapersSource
42,900,287Construction of a liver hepatocellular carcinoma risk model based on fumarate metabolism-associated genes to predict prognosis and immunological landscape.Clin Exp Med2026https://conductscience.org/library/papers/42900287PubMed
42,880,979Neuro-associated SEMA3C+ tumour cells promote gastric cancer peritoneal metastasis via EBF2-FGF7-FGFR2-mediated tumour-endothelial crosstalk.Clin Transl Med2026https://conductscience.org/library/papers/42880979PubMed
42,697,859Multi-Omics Biomarker Signatures for Precision Diagnosis and Prognosis in Primary Liver Cancer: A Literature Review.Biofactors2026https://conductscience.org/library/papers/42697859PubMed
42,620,997AI-integrated single-cell multi-omics decodes the hepatocellular carcinoma metabolism-immune axis: a new strategy for precision therapeutic targeting.Front Oncol2026https://conductscience.org/library/papers/42620997PubMed
42,302,326Inhibition of PERK signaling suppresses tumor progression and blocks GP73-GRP78-dependent stromal activation in hepatocellular carcinoma.Neoplasia2026https://conductscience.org/library/papers/42302326PubMed
42,253,501Functional Interpretation of Recurrent Genetic Variants in Hepatocellular Carcinoma: Molecular Consequences and Clinical Relevance.Hum Mutat2026https://conductscience.org/library/papers/42253501PubMed
42,078,198How to efficiently establish animal models of cholangiocarcinoma: challenges and inspiration.Med Rev (2021)2026https://conductscience.org/library/papers/42078198PubMed
41,663,439A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.Nat Commun2026https://conductscience.org/library/papers/41663439PubMed
41,530,870Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.Genome Med2026https://conductscience.org/library/papers/41530870PubMed
41,152,549FOXP1-transcriptionally regulated AEG-1 enhances tumor cell stemness to promote hepatocellular carcinoma radioresistance.Mol Cell Biochem2026https://conductscience.org/library/papers/41152549PubMed

1 to 10 of 25

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Genes45

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

GeneNCBI Gene IDLinked byIn GenesSource
AFP174PubTator's text mininghttps://conductscience.org/library/genes/174NCBI Gene
ALB213PubTator's text mininghttps://conductscience.org/library/genes/213NCBI Gene
CCL4L29,560PubTator's text mininghttps://conductscience.org/library/genes/9560NCBI Gene
CD16011,126PubTator's text mininghttps://conductscience.org/library/genes/11126NCBI Gene
CD4920PubTator's text mininghttps://conductscience.org/library/genes/920NCBI Gene
CD69969PubTator's text mininghttps://conductscience.org/library/genes/969NCBI Gene
CD8A925PubTator's text mininghttps://conductscience.org/library/genes/925NCBI Gene
CEBPA1,050PubTator's text mininghttps://conductscience.org/library/genes/1050NCBI Gene
CTNNB11,499PubTator's text mininghttps://conductscience.org/library/genes/1499NCBI Gene
CXCL103,627PubTator's text mininghttps://conductscience.org/library/genes/3627NCBI Gene

1 to 10 of 45

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Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed
2026-11-06
PubMed
iCite
2026-11-05
iCite
PMC's ID file
2026-11-05
PMC's ID file
NIH RePORTER's grant and paper links
2026-11-01
NIH RePORTER's grant and paper links
Trials
2026-11-12
Gene search
2026-11-11
Pipelines
2026-09-18

Sources 11

  • ChEMBL, through Open TargetsCC BY-SA 3.0
  • ClinicalTrials.govNo license stated
  • HGNCCC0
  • iCiteCC BY 4.0
  • NCBI GenePublic domain (US government)
  • NIH RePORTER's grant and paper linksPublic domain
  • Open TargetsCC0 1.0
  • PMC's ID filePublic domain (US government)
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0
Each source's terms
  • ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • ClinicalTrials.govnone stated
  • HGNCCC0: https://www.genenames.org/about/license/
  • iCiteCC BY 4.0
  • NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
  • Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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