Add 37 publications citing PEPkit tools

[claude]

Summary

Monthly publications search (18-month lookback window: 2025-02-27 to 2026-08-27), covering all 7 seed manuscripts (Channel A: OpenAlex citations) and all 8 full-text queries (Channel B: Europe PMC).

• 37 new publications added, all DOIs verified against Crossref.
• 2 preprint/published pairs collapsed to a single entry (published version kept, preprint_doi set).
• python validate_publications.py --check-dois --only-changed passes with 0 errors.

Added publications

Authors	Year	Title	Journal	DOI	Evidence
Botts et al.	2026	ERG preserves endothelial identity to limit atherosclerosis	Nature Communications	10.1038/s41467-026-75287-z	cites:10.1093/nargab/lqab101
Brown et al.	2026	Using semantic search to find publicly available gene-expression datasets	Bioinformatics	10.1093/bioinformatics/btag053	cites:10.1093/bioinformatics/btad069
Du et al.	2026	SCSEQ: A web tool for analyzing single-cell RNA-seq data	GigaScience	10.1093/gigascience/giag029	cites:10.1093/gigascience/giae033
Hossain et al.	2026	ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species	BMC Bioinformatics	10.1186/s12859-026-06382-7	cites:10.1093/nargab/lqab101
Ma et al.	2026	Chromatin accessibility directly governs flavonoid biosynthesis and indirectly orchestrates cannabinoid production in Cannabis	Frontiers in Plant Science	10.3389/fpls.2025.1687700	cites:10.1093/nargab/lqab101
Medina-Ortiz et al.	2026	Perspectives Chapter: Data-Centric Strategies for Machine Learning-Driven Therapeutic Peptide Design – Challenges and Perspectives	Data Quality Matters - Best Practices for Integrity and Assurance	10.5772/intechopen.1013230	cites:10.1093/gigascience/giae033
Mueller et al.	2026	ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition	(preprint)	10.64898/2026.05.13.724835	cites:10.1093/gigascience/giab077
Mukherjee and Guertin	2026	Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate	Nucleic Acids Research	10.1093/nar/gkag128	cites:10.1186/s13059-021-02349-4
Pastor et al.	2026	Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T Cells	Cells	10.3390/cells15030221	cites:10.1093/nargab/lqab101
Radic-Sarikas et al.	2026	Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition	Molecular Therapy Oncology	10.1016/j.omton.2026.201229	cites:10.1093/gigascience/giab077
Shtolz et al.	2026	Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells	Communications Biology	10.1038/s42003-025-09457-y	cites:10.1186/s13059-021-02349-4
Silvane et al.	2026	BCL11B targeting in tumor CD8+ T cells amplifies anti-tumor response by blocking exhaustion while promoting stemness and cytotoxicity	(preprint)	10.64898/2026.08.03.742578	cites:10.1093/nargab/lqab101
Song et al.	2026	GEfetch2R: fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools	GigaScience	10.1093/gigascience/giag039	cites:10.1093/bioinformatics/btad069
Wang et al.	2026	Predictive prioritization of enhancers associated with pancreatic disease risk	Cell Genomics	10.1016/j.xgen.2025.101040	cites:10.1101/2020.10.21.347054
Anton et al.	2025	Cervicovaginal microbiome alters transcriptomic and chromatin accessibility signatures across cervicovaginal epithelial barriers	Microbiome	10.1186/s40168-025-02223-6	cites:10.1093/nargab/lqab101
Cho et al.	2025	OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis	Nucleic Acids Research	10.1093/nar/gkaf952	cites:10.1093/nargab/lqab101
Cho et al.	2025	Targeting eRNA‐Producing Super‐Enhancers Regulates TNFα Expression and Mitigates Chronic Inflammation in Mice and Patient‐Derived Immune Cells	Advanced Science	10.1002/advs.202505214	cites:10.1093/nargab/lqab101
Cingaram et al.	2025	Enhancing transcriptome mapping with rapid PRO-seq profiling of nascent RNA	Molecular Cell	10.1016/j.molcel.2025.06.029	cites:10.1186/s13059-021-02349-4
Dong et al.	2025	MTD: A cloud-based omics database and interactive platform for Myceliophthora thermophila	Synthetic and Systems Biotechnology	10.1016/j.synbio.2025.04.001	cites:10.1093/bioinformatics/btad069
Escobedo-Muñoz et al.	2025	How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO	Briefings in Bioinformatics	10.1093/bib/bbaf560	cites:10.1093/bioinformatics/btad069
Favaro et al.	2025	Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming	Cell Reports	10.1016/j.celrep.2025.115913	cites:10.1101/2020.10.21.347054
Gauberg et al.	2025	Spinal motor neuron development and metabolism are transcriptionally regulated by nuclear factor IA	Science Advances	10.1126/sciadv.adu3346	cites:10.1093/nargab/lqab101
Kananen et al.	2025	Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes	Bioinformatics Advances	10.1093/bioadv/vbaf039	fulltext:PMC11964587
Lee et al.	2025	Epigenomic profiling of papillary thyroid carcinoma reveals distinct subtypes with clinical implications	npj Precision Oncology	10.1038/s41698-025-00932-7	fulltext:PMC12065858
LeRoy et al.	2025	Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data	(preprint)	10.1101/2025.11.03.685753	cites:10.1093/bioinformatics/btad069
Li et al.	2025	Integrative analysis of gene expression and chromatin dynamics multi-omics data in mouse models of bleomycin-induced lung fibrosis	Epigenetics & Chromatin	10.1186/s13072-025-00579-5	cites:10.1093/nargab/lqab101
Li et al.	2025	Heterogeneity of the tumor immune cell microenvironment revealed by single-cell sequencing in head and neck cancer	Critical Reviews in Oncology/Hematology	10.1016/j.critrevonc.2025.104677	cites:10.1186/s13059-021-02349-4
Matsushima et al.	2025	Zinc-finger proteins with a co-opted capsid domain anchor nucleosomes over transposon sequences	(preprint)	10.1101/2025.03.03.638093	cites:10.1093/nargab/lqab101
Mehta et al.	2025	Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity	(preprint)	10.1101/2025.10.09.681187	cites:10.1093/nargab/lqab101
Noorizadeh et al.	2025	YAP1 is a key regulator of EWS::FLI1-dependent malignant transformation upon IGF-1-mediated reprogramming of bone mesenchymal stem cells	Cell Reports	10.1016/j.celrep.2025.115381	cites:10.1101/2020.10.21.347054
Patty et al.	2025	Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements	Cell Reports	10.1016/j.celrep.2025.115767	cites:10.1093/nargab/lqab101
Pulice and Meyerson	2025	Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma	Molecular Cell	10.1016/j.molcel.2025.03.001	cites:10.1101/2020.10.21.347054
Roth et al.	2025	PRMT5 activity sustains histone production to maintain genome integrity	(preprint)	10.1101/2025.07.03.663002	cites:10.1186/s13059-021-02349-4
Sigauke et al.	2025	Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages	BMC Genomics	10.1186/s12864-025-11568-z	cites:10.1186/s13059-021-02349-4
Tripplehorn et al.	2025	A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes	Nucleic Acids Research	10.1093/nar/gkaf816	cites:10.1093/nargab/lqab101
Xiang et al.	2025	MEF2D-expressing cancer precursors reprogram tissue-resident macrophages to support liver tumorigenesis	Nature Cancer	10.1038/s43018-025-01059-1	cites:10.1093/nargab/lqab101
Zheng et al.	2025	EAP: A versatile cloud-based platform for efficient quantitative analysis of large-scale ChIP/ATAC-seq datasets	Computational and Structural Biotechnology Journal	10.1016/j.csbj.2025.11.026	fulltext:PMC12670574

Rejected candidates

Already represented (title match against an existing entry)

• Evolution of promoter-proximal pausing enabled a new layer of transcription control (published version, 10.1038/s41594-025-01718-y, Nature Structural & Molecular Biology, cites the PEPPRO seed) — the preprint of this same paper (10.21203/rs.3.rs-2679520/v1, Danko et al. 2023) is already listed. Not upgraded in place per the "never modify an existing entry" rule; flagging here so a human can decide whether to swap it by hand.

Full-text hits judged as false positives (term collision, not real PEPkit usage)

• Analysis of IL-6 and IL-1β Gene coding and study on specific clearance using histidine-grafted PVDF membranes (10.1016/j.gmg.2025.100080) — matched the "PEPPRO" query only because the text says "IL-1 and IL-6 standard (PeproTech)", a reagent vendor name, not the PEPPRO pipeline.
• PepScorer::RMSD: An Improved Machine Learning Scoring Function for Protein-Peptide Docking (10.3390/ijms27020870) — matched "PEPPRO" only because it cites an unrelated structural-biology benchmark dataset also named "PepPro" (Xu & Zou, J. Comput. Chem.), unrelated to PEPkit.

Ambiguous / unverifiable — dropped per "when in doubt, exclude"

• A tumor-associated photoreceptor signature unifies distinct central nervous system malignancies (10.1016/j.ccell.2026.02.010) — matched "PEPATAC" in Europe PMC search, but the article is not open access, so the match context could not be confirmed as genuine tool usage rather than a passing citation.

Preprints merged into their published counterpart (not separate rejects, but not separate entries either)

• 10.1101/2025.03.13.643153 → merged into 10.1093/bioinformatics/btag053
• 10.21203/rs.3.rs-6171614/v1 → merged into 10.1186/s40168-025-02223-6
• 10.1101/2025.11.20.689456 → merged into 10.1016/j.omton.2026.201229

No candidates were dropped for exceeding max_new_per_run (37 ≤ 40 cap).