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References from Chromatin accessibility trajectories reveal pre-cancerous epigenetic priming and an acid-driven immunotherapy-resistant gastric cancer subtype. Local targets link to admitted publications; unresolved targets remain external evidence.
Chromatin accessibility and the regulatory epigenome
10.1038/s41576-018-0089-8 · 2019 · External reference
The chromatin accessibility landscape of primary human cancers
10.1126/science.aav1898 · 2018 · External reference
Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets
10.1126/science.abe1505 · 2022 · External reference
Epigenetic regulation during cancer transitions across 11 tumour types
10.1038/s41586-023-06682-5 · 2023 · External reference
Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers
10.1126/science.adk9217 · 2024 · External reference
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
10.1038/s41588-022-01088-x · 2022 · External reference
Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
10.1158/2159-8290.cd-23-1445 · 2024 · External reference
Evolution and progression of Barrett's oesophagus to oesophageal cancer
10.1038/s41568-021-00400-x · 2021 · External reference
Genomic and Epigenomic Profiling of High-Risk Intestinal Metaplasia Reveals Molecular Determinants of Progression to Gastric Cancer
10.1016/j.ccell.2017.11.018 · 2018 · External reference
The somatic mutation landscape of normal gastric epithelium
10.1038/s41586-025-08708-6 · 2025 · External reference
Genomic Analyses Reveal the Evolving Characteristics of Intestinal Metaplasia and Gastric Cancer
10.1158/0008-5472.can-24-4065 · 2025 · External reference
Defining precancer: a grand challenge for the cancer community
10.1038/s41568-024-00744-0 · 2024 · External reference
A gene-environment-induced epigenetic program initiates tumorigenesis
10.1038/s41586-020-03147-x · 2021 · External reference
Transient loss of Polycomb components induces an epigenetic cancer fate
10.1038/s41586-024-07328-w · 2024 · External reference
Chromatin Remodeling in Patient-Derived Colorectal Cancer Models
10.1002/advs.202303379 · 2024 · External reference
Neoadjuvant checkpoint blockade for cancer immunotherapy
10.1126/science.aax0182 · 2020 · External reference
Neoadjuvant immune checkpoint blockade: A window of opportunity to advance cancer immunotherapy
10.1016/j.ccell.2023.07.011 · 2023 · External reference
Neoadjuvant immune checkpoint therapy: Enabling insights into fundamental human immunology and clinical benefit
10.1016/j.ccell.2025.03.005 · 2025 · External reference
Defining clinically useful biomarkers of immune checkpoint inhibitors in solid tumours
10.1038/s41568-024-00705-7 · 2024 · External reference
Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer
10.1038/s41591-018-0101-z · 2018 · External reference
Comprehensive molecular characterization of gastric adenocarcinoma
10.1038/nature13480 · 2014 · External reference
Perioperative toripalimab and chemotherapy in locally advanced gastric or gastro-esophageal junction cancer: a randomized phase 2 trial
10.1038/s41591-023-02721-w · 2024 · External reference
Intestinal Subtype as a Biomarker of Response to Neoadjuvant Immunochemotherapy in Locally Advanced Gastric Adenocarcinoma: Insights from a Prospective Phase II Trial
10.1158/1078-0432.ccr-24-2436 · 2025 · External reference
Neoadjuvant atezolizumab plus chemotherapy in gastric and gastroesophageal junction adenocarcinoma: the phase 2 PANDA trial
10.1038/s41591-023-02758-x · 2024 · External reference
Reduced intestinal-to-diffuse conversion and immunosuppressive responses underlie superiority of neoadjuvant immunochemotherapy in gastric adenocarcinoma
10.1002/mco2.762 · 2024 · External reference
Epigenetic driver mutations in ARID1A shape cancer immune phenotype and immunotherapy
10.1172/jci134402 · 2020 · External reference
Beyond the Barrier: Unraveling the Mechanisms of Immunotherapy Resistance
10.1146/annurev-immunol-101819-024752 · 2024 · External reference
Early stage gastric adenocarcinoma: clinical and molecular landscapes
10.1038/s41571-023-00767-w · 2023 · External reference
Expanded encyclopaedias of DNA elements in the human and mouse genomes
10.1038/s41586-020-2493-4 · 2020 · External reference
Integrative analysis of 111 reference human epigenomes
10.1038/nature14248 · 2015 · External reference
Precancerous nature of intestinal metaplasia with increased chance of conversion and accelerated DNA methylation
10.1136/gutjnl-2023-329492 · 2024 · External reference
A single-cell atlas of chromatin accessibility in the human genome
10.1016/j.cell.2021.10.024 · 2021 · External reference
GATA4 Controls Epithelial Morphogenesis in the Developing Stomach to Promote Establishment of Glandular Columnar Epithelium
10.1016/j.jcmgh.2021.05.021 · 2021 · External reference
ETS transcription factors: Multifaceted players from cancer progression to tumor immunity
10.1016/j.bbcan.2023.188872 · 2023 · External reference
Specificity Proteins (Sp) and Cancer
10.3390/ijms24065164 · 2023 · External reference
A mechanism for adaptive genome regulation in cancer
10.1038/s41586-026-10269-1 · 2026 · External reference
Histologic Subtyping of Gastric Intestinal Metaplasia: Overview and Considerations for Clinical Practice
10.1053/j.gastro.2019.12.004 · 2020 · External reference
Development of gastric carcinoma from intestinal metaplasia in Cdx2-transgenic mice
10.1158/0008-5472.can-04-1617 · 2004 · External reference
HNF4α pathway mapping identifies wild-type IDH1 as a targetable metabolic node in gastric cancer
10.1136/gutjnl-2018-318025 · 2020 · External reference
Regulatory crosstalk between lineage-survival oncogenes KLF5, GATA4 and GATA6 cooperatively promotes gastric cancer development
10.1136/gutjnl-2013-306596 · 2015 · External reference
Expression of Activated Ras in Gastric Chief Cells of Mice Leads to the Full Spectrum of Metaplastic Lineage Transitions
10.1053/j.gastro.2015.11.049 · 2016 · External reference
Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression
10.1016/j.ccell.2023.10.004 · 2023 · External reference
Role of Sp proteins in regulation of vascular endothelial growth factor expression and proliferation of pancreatic cancer cells
10.1158/0008-5472.can-04-0713 · 2004 · External reference
ZIC5 Drives Melanoma Aggressiveness by PDGFD-Mediated Activation of FAK and STAT3
10.1158/0008-5472.can-16-0991 · 2017 · External reference
Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase inhibitors and 5-fluorouracil
10.1053/j.gastro.2013.05.010 · 2013 · External reference
Nearest template prediction: a single-sample-based flexible class prediction with confidence assessment
10.1371/journal.pone.0015543 · 2010 · External reference
Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes
10.1038/nm.3850 · 2015 · External reference
Epigenetic regulation of tumor immunity
10.1172/jci178540 · 2024 · External reference
Mechanisms driving the immunoregulatory function of cancer cells
10.1038/s41568-022-00544-4 · 2023 · External reference
Biological and clinical significance of tumour-infiltrating lymphocytes in the era of immunotherapy: a multidimensional approach
10.1038/s41571-024-00984-x · 2025 · External reference
Tumor Immunophenotyping-Derived Signature Identifies Prognosis and Neoadjuvant Immunotherapeutic Responsiveness in Gastric Cancer
2023 · External reference
Human gastric cancer modelling using organoids
10.1136/gutjnl-2017-314549 · 2019 · External reference
The Physiology of the Gastric Parietal Cell
10.1152/physrev.00016.2019 · 2020 · External reference
How protons pave the way to aggressive cancers
10.1038/s41568-023-00628-9 · 2023 · External reference
KDM6A Loss Triggers an Epigenetic Switch That Disrupts Urothelial Differentiation and Drives Cell Proliferation in Bladder Cancer
10.1158/0008-5472.can-22-1444 · 2023 · External reference
Role of Fra-2 in cancer
10.1038/s41418-023-01248-4 · 2024 · External reference
Evidence-based clinical practice guidelines for gastroesophageal reflux disease 2021
10.1007/s00535-022-01861-z · 2022 · External reference
Clinical implications of T cell exhaustion for cancer immunotherapy
10.1038/s41571-022-00689-z · 2022 · External reference
Harnessing chimeric antigen receptor macrophages against solid tumors
10.1002/cac2.70053 · 2025 · External reference
Pharmacological activation of WASp potentiates macrophage phagocytosis and enhances ibrutinib efficacy against mouse models of brain tumors
10.1126/scitranslmed.aed1155 · 2026 · External reference
Lactate modulation of immune responses in inflammatory versus tumour microenvironments
10.1038/s41577-020-0406-2 · 2021 · External reference
PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments
2021 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
Unresolved reference
External reference
Fast gapped-read alignment with Bowtie 2
10.1038/nmeth.1923 · 2012 · External reference
The Sequence Alignment/Map format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
Unresolved reference
External reference
Model-based analysis of ChIP-Seq (MACS)
10.1186/gb-2008-9-9-r137 · 2008 · External reference
Unresolved reference
External reference
BEDTools: a flexible suite of utilities for comparing genomic features
10.1093/bioinformatics/btq033 · 2010 · External reference
MAnorm2 for quantitatively comparing groups of ChIP-seq samples
10.1101/gr.262675.120 · 2021 · External reference
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
10.1093/bioinformatics/bts034 · 2012 · External reference
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
10.1093/bioinformatics/btp616 · 2010 · External reference
Unresolved reference
External reference
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
10.1186/s13059-014-0550-8 · 2014 · External reference
Unresolved reference
2016 · External reference
Unresolved reference
External reference
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis
10.1093/bioinformatics/btt737 · 2014 · External reference
deepTools: a flexible platform for exploring deep-sequencing data
10.1093/nar/gku365 · 2014 · External reference
GSVA: gene set variation analysis for microarray and RNA-seq data
10.1186/1471-2105-14-7 · 2013 · External reference
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
10.1093/bioinformatics/btv145 · 2015 · External reference
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data
2021 · External reference
Unresolved reference
External reference
TFBSTools: an R/bioconductor package for transcription factor binding site analysis
10.1093/bioinformatics/btw024 · 2016 · External reference
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
10.1093/nar/gkab1113 · 2022 · External reference
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
10.1038/nmeth.4401 · 2017 · External reference
Functional inference of gene regulation using single-cell multi-omics
2022 · External reference
Unresolved reference
External reference
Orchestrating high-throughput genomic analysis with Bioconductor
10.1038/nmeth.3252 · 2015 · External reference
Identification of transcription factor binding sites using ATAC-seq
10.1186/s13059-019-1642-2 · 2019 · External reference
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
10.1016/j.molcel.2010.05.004 · 2010 · External reference
Inferring regulatory networks from expression data using tree-based methods
10.1371/journal.pone.0012776 · 2010 · External reference
ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking
10.1093/bioinformatics/btq170 · 2010 · External reference
fastp: an ultra-fast all-in-one FASTQ preprocessor
10.1093/bioinformatics/bty560 · 2018 · External reference
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
10.1093/bioinformatics/bts611 · 2012 · External reference
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
10.1038/s41587-019-0201-4 · 2019 · External reference
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
10.1093/bioinformatics/btt656 · 2014 · External reference
Unresolved reference
External reference
Mfuzz: a software package for soft clustering of microarray data
10.6026/97320630002005 · 2007 · External reference
Complex heatmaps reveal patterns and correlations in multidimensional genomic data
10.1093/bioinformatics/btw313 · 2016 · External reference
Unresolved reference
2000 · External reference
Unresolved reference
External reference
xCell: digitally portraying the tissue cellular heterogeneity landscape
10.1186/s13059-017-1349-1 · 2017 · External reference
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
10.1038/s41588-021-00790-6 · 2021 · External reference
Integrated analysis of multimodal single-cell data
10.1016/j.cell.2021.04.048 · 2021 · External reference
Fast, sensitive and accurate integration of single-cell data with Harmony
10.1038/s41592-019-0619-0 · 2019 · External reference
Cutadapt removes adapter sequences from high-throughput sequencing reads
10.14806/ej.17.1.200 · 2011 · External reference
A Metformin-Responsive Metabolic Pathway Controls Distinct Steps in Gastric Progenitor Fate Decisions and Maturation
10.1016/j.stem.2020.03.006 · 2020 · External reference
AQP5 enriches for stem cells and cancer origins in the distal stomach
10.1038/s41586-020-1973-x · 2020 · External reference
Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
10.1186/s13059-022-02828-2 · 2022 · External reference
Epigenetic restriction of Hippo signaling by MORC2 underlies stemness of hepatocellular carcinoma cells
10.1038/s41418-018-0095-6 · 2018 · External reference
TRIM49 Deficiency Stabilizes a Galectin-3/EGR1 Transcriptional Complex That Drives Invasiveness of Gastric Adenocarcinoma
10.1158/0008-5472.can-25-0252 · 2026 · External reference
Cancer SLC43A2 alters T cell methionine metabolism and histone methylation
10.1038/s41586-020-2682-1 · 2020 · External reference
Aberrant amino acid-sensing promotes immunotherapy resistance via the inflammatory cytokine-ZBTB5-mTORC1 axis
10.1038/s41556-026-01926-8 · 2026 · External reference
Inhibition of PCSK9 potentiates immune checkpoint therapy for cancer
10.1038/s41586-020-2911-7 · 2020 · External reference
Generation of Tumor-Reactive T Cells by Co-culture of Peripheral Blood Lymphocytes and Tumor Organoids
10.1016/j.cell.2018.07.009 · 2018 · External reference
Cyclin D-CDK4 kinase destabilizes PD-L1 via cullin 3-SPOP to control cancer immune surveillance
10.1038/nature25015 · 2018 · External reference