# Publications that cite or use PEPkit tools. # # Rendered into docs/statistics.md at build time by hooks/publications.py. # Machine-readable copy published at # https://pep.databio.org/data/publications.yaml # # Mostly maintained by .github/workflows/scheduled-publications-update.yml. # Hand edits are fine; keep entries sorted by year descending. publications: - doi: 10.1038/s41467-026-75287-z title: ERG preserves endothelial identity to limit atherosclerosis authors: Botts et al. year: 2026 journal: Nature Communications tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1093/bioinformatics/btag053 title: Using semantic search to find publicly available gene-expression datasets authors: Brown et al. year: 2026 journal: Bioinformatics preprint_doi: 10.1101/2025.03.13.643153 tools: [] evidence: cites:10.1093/bioinformatics/btad069 added: 2026-08-27 - doi: 10.1093/gigascience/giag029 title: 'SCSEQ: A web tool for analyzing single-cell RNA-seq data' authors: Du et al. year: 2026 journal: GigaScience tools: [] evidence: cites:10.1093/gigascience/giae033 added: 2026-08-27 - doi: 10.1186/s12859-026-06382-7 title: >- ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species authors: Hossain et al. year: 2026 journal: BMC Bioinformatics tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.3389/fpls.2025.1687700 title: >- Chromatin accessibility directly governs flavonoid biosynthesis and indirectly orchestrates cannabinoid production in Cannabis authors: Ma et al. year: 2026 journal: Frontiers in Plant Science tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.5772/intechopen.1013230 title: >- Perspectives Chapter: Data-Centric Strategies for Machine Learning-Driven Therapeutic Peptide Design – Challenges and Perspectives authors: Medina-Ortiz et al. year: 2026 journal: Data Quality Matters - Best Practices for Integrity and Assurance tools: [] evidence: cites:10.1093/gigascience/giae033 added: 2026-08-27 - doi: 10.64898/2026.05.13.724835 title: >- ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition authors: Mueller et al. year: 2026 tools: [] evidence: cites:10.1093/gigascience/giab077 added: 2026-08-27 - doi: 10.1093/nar/gkag128 title: >- Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate authors: Mukherjee and Guertin year: 2026 journal: Nucleic Acids Research tools: [] evidence: cites:10.1186/s13059-021-02349-4 added: 2026-08-27 - doi: 10.3390/cells15030221 title: >- Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T Cells authors: Pastor et al. year: 2026 journal: Cells tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1016/j.omton.2026.201229 title: >- Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition authors: Radic-Sarikas et al. year: 2026 journal: Molecular Therapy Oncology preprint_doi: 10.1101/2025.11.20.689456 tools: [] evidence: cites:10.1093/gigascience/giab077 added: 2026-08-27 - doi: 10.1038/s42003-025-09457-y title: >- Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells authors: Shtolz et al. year: 2026 journal: Communications Biology tools: [] evidence: cites:10.1186/s13059-021-02349-4 added: 2026-08-27 - doi: 10.64898/2026.08.03.742578 title: >- BCL11B targeting in tumor CD8+ T cells amplifies anti-tumor response by blocking exhaustion while promoting stemness and cytotoxicity authors: Silvane et al. year: 2026 tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1093/gigascience/giag039 title: >- GEfetch2R: fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools authors: Song et al. year: 2026 journal: GigaScience tools: [] evidence: cites:10.1093/bioinformatics/btad069 added: 2026-08-27 - doi: 10.1016/j.xgen.2025.101040 title: Predictive prioritization of enhancers associated with pancreatic disease risk authors: Wang et al. year: 2026 journal: Cell Genomics tools: [] evidence: cites:10.1101/2020.10.21.347054 added: 2026-08-27 - doi: 10.1186/s40168-025-02223-6 title: >- Cervicovaginal microbiome alters transcriptomic and chromatin accessibility signatures across cervicovaginal epithelial barriers authors: Anton et al. year: 2025 journal: Microbiome preprint_doi: 10.21203/rs.3.rs-6171614/v1 tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1093/nar/gkaf952 title: 'OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis' authors: Cho et al. year: 2025 journal: Nucleic Acids Research tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1002/advs.202505214 title: >- Targeting eRNA‐Producing Super‐Enhancers Regulates TNFα Expression and Mitigates Chronic Inflammation in Mice and Patient‐Derived Immune Cells authors: Cho et al. year: 2025 journal: Advanced Science tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1016/j.molcel.2025.06.029 title: Enhancing transcriptome mapping with rapid PRO-seq profiling of nascent RNA authors: Cingaram et al. year: 2025 journal: Molecular Cell tools: [] evidence: cites:10.1186/s13059-021-02349-4 added: 2026-08-27 - doi: 10.1016/j.synbio.2025.04.001 title: >- MTD: A cloud-based omics database and interactive platform for Myceliophthora thermophila authors: Dong et al. year: 2025 journal: Synthetic and Systems Biotechnology tools: [] evidence: cites:10.1093/bioinformatics/btad069 added: 2026-08-27 - doi: 10.1093/bib/bbaf560 title: >- How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO authors: Escobedo-Muñoz et al. year: 2025 journal: Briefings in Bioinformatics tools: [] evidence: cites:10.1093/bioinformatics/btad069 added: 2026-08-27 - doi: 10.1016/j.celrep.2025.115913 title: >- Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming authors: Favaro et al. year: 2025 journal: Cell Reports tools: [] evidence: cites:10.1101/2020.10.21.347054 added: 2026-08-27 - doi: 10.1126/sciadv.adu3346 title: >- Spinal motor neuron development and metabolism are transcriptionally regulated by nuclear factor IA authors: Gauberg et al. year: 2025 journal: Science Advances tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1093/bioadv/vbaf039 title: >- Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes authors: Kananen et al. year: 2025 journal: Bioinformatics Advances tools: [peppy, eido, looper] evidence: fulltext:PMC11964587 added: 2026-08-27 - doi: 10.1038/s41698-025-00932-7 title: >- Epigenomic profiling of papillary thyroid carcinoma reveals distinct subtypes with clinical implications authors: Lee et al. year: 2025 journal: npj Precision Oncology tools: [pepatac] evidence: fulltext:PMC12065858 added: 2026-08-27 - doi: 10.1101/2025.11.03.685753 title: >- Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data authors: LeRoy et al. year: 2025 tools: [] evidence: cites:10.1093/bioinformatics/btad069 added: 2026-08-27 - doi: 10.1186/s13072-025-00579-5 title: >- Integrative analysis of gene expression and chromatin dynamics multi-omics data in mouse models of bleomycin-induced lung fibrosis authors: Li et al. year: 2025 journal: Epigenetics & Chromatin tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1016/j.critrevonc.2025.104677 title: >- Heterogeneity of the tumor immune cell microenvironment revealed by single-cell sequencing in head and neck cancer authors: Li et al. year: 2025 journal: Critical Reviews in Oncology/Hematology tools: [] evidence: cites:10.1186/s13059-021-02349-4 added: 2026-08-27 - doi: 10.1101/2025.03.03.638093 title: >- Zinc-finger proteins with a co-opted capsid domain anchor nucleosomes over transposon sequences authors: Matsushima et al. year: 2025 tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1101/2025.10.09.681187 title: >- Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity authors: Mehta et al. year: 2025 tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1016/j.celrep.2025.115381 title: >- YAP1 is a key regulator of EWS::FLI1-dependent malignant transformation upon IGF-1-mediated reprogramming of bone mesenchymal stem cells authors: Noorizadeh et al. year: 2025 journal: Cell Reports tools: [] evidence: cites:10.1101/2020.10.21.347054 added: 2026-08-27 - doi: 10.1016/j.celrep.2025.115767 title: Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements authors: Patty et al. year: 2025 journal: Cell Reports tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1016/j.molcel.2025.03.001 title: >- Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma authors: Pulice and Meyerson year: 2025 journal: Molecular Cell tools: [] evidence: cites:10.1101/2020.10.21.347054 added: 2026-08-27 - doi: 10.1101/2025.07.03.663002 title: PRMT5 activity sustains histone production to maintain genome integrity authors: Roth et al. year: 2025 tools: [] evidence: cites:10.1186/s13059-021-02349-4 added: 2026-08-27 - doi: 10.1186/s12864-025-11568-z title: Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages authors: Sigauke et al. year: 2025 journal: BMC Genomics tools: [] evidence: cites:10.1186/s13059-021-02349-4 added: 2026-08-27 - doi: 10.1093/nar/gkaf816 title: >- A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes authors: Tripplehorn et al. year: 2025 journal: Nucleic Acids Research tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1038/s43018-025-01059-1 title: >- MEF2D-expressing cancer precursors reprogram tissue-resident macrophages to support liver tumorigenesis authors: Xiang et al. year: 2025 journal: Nature Cancer tools: [] evidence: cites:10.1093/nargab/lqab101 added: 2026-08-27 - doi: 10.1016/j.csbj.2025.11.026 title: >- EAP: A versatile cloud-based platform for efficient quantitative analysis of large-scale ChIP/ATAC-seq datasets authors: Zheng et al. year: 2025 journal: Computational and Structural Biotechnology Journal tools: [] evidence: fulltext:PMC12670574 added: 2026-08-27 - doi: 10.21203/rs.3.rs-2679520/v1 title: 'Evolution of promoter-proximal pausing enabled a new layer of transcription control' authors: Danko et al. year: 2023 tools: [] evidence: legacy added: 2023-01-01 - doi: 10.1016/j.celrep.2023.112021 title: >- Epiblast-like stem cells established by Wnt/β-catenin signaling manifest distinct features of formative pluripotency and germline competence authors: Luo et al. year: 2023 journal: Cell Reports tools: [] evidence: legacy added: 2023-01-01 - doi: 10.1016/j.celrep.2023.112393 title: >- Maternal diet alters long-term innate immune cell memory in fetal and juvenile hematopoietic stem and progenitor cells in nonhuman primate offspring authors: Nash et al. year: 2023 journal: Cell Reports tools: [] evidence: legacy added: 2023-01-01 - doi: 10.1126/sciadv.ade3876 title: Cohesin regulates alternative splicing authors: Singh et al. year: 2023 journal: Science Advances tools: [] evidence: legacy added: 2023-01-01 - doi: 10.1101/2022.12.31.521782 title: 'Flexible and scalable control of T cell memory by a reversible epigenetic switch' authors: Abadie et al. year: 2022 tools: [] evidence: legacy added: 2022-01-01 - doi: 10.3389/fcell.2022.936168 title: >- High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma authors: Callahan et al. year: 2022 journal: Frontiers in Cell and Developmental Biology tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1073/pnas.2201267119 title: >- Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development authors: Duvall et al. year: 2022 journal: Proceedings of the National Academy of Sciences tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1038/s41596-022-00692-9 title: Chromatin accessibility profiling by ATAC-seq authors: Grandi et al. year: 2022 journal: Nature Protocols tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1016/j.celrep.2022.110697 title: HNF4A modulates glucocorticoid action in the liver authors: Hunter et al. year: 2022 journal: Cell Reports tools: [] evidence: legacy added: 2022-01-01 - doi: 10.3389/fimmu.2022.856966 title: >- BET Protein Inhibition Regulates Macrophage Chromatin Accessibility and Microbiota-Dependent Colitis authors: O'Connor et al. year: 2022 journal: Frontiers in Immunology tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1038/s41588-022-01211-y title: >- Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features authors: Robbe et al. year: 2022 journal: Nature Genetics tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1101/2022.10.07.511310 title: >- The methyltransferases METTL7A and METTL7B confer resistance to thiol-based histone deacetylase inhibitors authors: Robey et al. year: 2022 tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1038/s41598-022-14675-z title: >- Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy authors: Taklifi et al. year: 2022 journal: Scientific Reports tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1038/s41588-022-01026-x title: >- Prediction of histone post-translational modification patterns based on nascent transcription data authors: Wang et al. year: 2022 journal: Nature Genetics tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1101/2022.12.08.519600 title: 'Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling' authors: Wolpe et al. year: 2022 tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1186/s12864-021-08266-x title: 'Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei' authors: Zhang et al. year: 2022 journal: BMC Genomics tools: [] evidence: legacy added: 2022-01-01 - doi: 10.1038/s41590-021-00928-y title: >- Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation authors: Cheung et al. year: 2021 tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1093/bioinformatics/btab439 title: 'Embeddings of genomic region sets capture rich biological associations in low dimensions' authors: Gharavi et al. year: 2021 journal: Bioinformatics tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1038/s41588-021-00790-6 title: >- ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis authors: Granja et al. year: 2021 journal: Nature Genetics tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1186/s13059-021-02440-w title: 'Bedshift: perturbation of genomic interval sets' authors: Gu et al. year: 2021 journal: Genome Biology tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1101/2021.04.28.441728 title: 'Clonal inactivation of telomerase promotes accelerated stem cell differentiation' authors: Hasegawa et al. year: 2021 journal: bioRxiv tools: [] evidence: legacy added: 2021-01-01 - doi: 10.12688/f1000research.29032.2 title: Sustainable data analysis with Snakemake authors: Mölder et al. year: 2021 journal: F1000Research tools: [] evidence: legacy added: 2021-01-01 - doi: 10.26508/lsa.202000976 title: >- Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection authors: Ram-Mohan et al. year: 2021 journal: Life Science Alliance tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1038/s41588-021-00880-5 title: >- Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes authors: Robertson et al. year: 2021 journal: Nature Genetics tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1126/sciimmunol.abe3981 title: >- Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity authors: Shahin et al. year: 2021 journal: Science Immunology tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1186/s13059-021-02349-4 title: 'PEPPRO: quality control and processing of nascent RNA profiling data' authors: Smith et al. year: 2021 journal: Genome Biology tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1101/2021.01.29.428733 title: >- Integrative phenotypic and genomic analyses reveal strain-dependent responses to acute ozone exposure and their associations with airway macrophage transcriptional activity authors: Tovar et al. year: 2021 journal: bioRxiv tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1126/science.aba1786 title: >- Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling authors: Weber et al. year: 2021 journal: Science tools: [] evidence: legacy added: 2021-01-01 - doi: 10.1186/s12920-020-0695-0 title: >- Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain authors: Cai et al. year: 2020 tools: [] evidence: legacy added: 2020-01-01 - doi: 10.1016/j.celrep.2020.108473 title: >- Epigenomic Reprogramming toward Mesenchymal-Epithelial Transition in Ovarian-Cancer-Associated Mesenchymal Stem Cells Drives Metastasis authors: Fan et al. year: 2020 journal: Cell Reports tools: [] evidence: legacy added: 2020-01-01 - doi: 10.1038/s41419-020-2303-9 title: >- Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia authors: Li et al. year: 2020 journal: Cell Death & Disease tools: [] evidence: legacy added: 2020-01-01 - doi: 10.18632/oncotarget.27584 title: Clinical implications of chromatin accessibility in human cancers authors: Liu year: 2020 tools: [] evidence: legacy added: 2020-01-01 - doi: 10.2337/db20-112-or title: >- 112-OR: Integrative Analysis of Chromatin Accessibility and Genetic Risk in T1D Patients and Controls authors: ROBERTSON et al. year: 2020 journal: Diabetes tools: [] evidence: legacy added: 2020-01-01 - doi: 10.1002/cphg.101 title: Analytical Approaches for ATAC-seq Data Analysis authors: Smith and Sheffield year: 2020 journal: Current Protocols in Human Genetics tools: [] evidence: legacy added: 2020-01-01 - doi: 10.1093/gigascience/giz149 title: 'Refgenie: a reference genome resource manager' authors: Stolarczyk et al. year: 2020 journal: GigaScience tools: [] evidence: legacy added: 2020-01-01 - doi: 10.1101/2020.04.08.032730 title: Interdependence between histone marks and steps in Pol II transcription authors: Wang et al. year: 2020 tools: [] evidence: legacy added: 2020-01-01 - doi: 10.1101/2020.05.16.099325 title: 'CATA: a comprehensive chromatin accessibility database for cancer' authors: Zhou et al. year: 2020 journal: bioRxiv tools: [] evidence: legacy added: 2020-01-01 - doi: 10.1002/1873-3468.13549 title: >- Global changes in chromatin accessibility and transcription following ATRX inactivation in human cancer cells authors: Liang et al. year: 2019 tools: [] evidence: legacy added: 2019-01-01 - doi: 10.1126/science.aav1898 title: The chromatin accessibility landscape of primary human cancers authors: Corces et al. year: 2018 journal: Science tools: [] evidence: legacy added: 2018-01-01 - doi: 10.1038/nmeth.4177 title: Pooled CRISPR screening with single-cell transcriptome readout authors: Datlinger et al. year: 2017 journal: Nat. Methods tools: [] evidence: legacy added: 2017-01-01 - doi: 10.1038/nm.4273 title: DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma authors: Sheffield et al. year: 2017 journal: Nature Medicine tools: [] evidence: legacy added: 2017-01-01