ArticleNucleic acids research2015
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
89 citing papers in PubMed, 2 syntheses or guidelines pooled it, 134 citations in OpenAlex.
- Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance.Genome medicine · 2021Pooled it
- Sex-specific DNA methylation differences in Alzheimer's disease pathology.Acta neuropathologica communications · 2021Pooled it
- Risk variants disrupting enhancers of TProceedings of the National Academy of Sciences of the United States of America · 2019Trial
- Computational identification of lineage-committed precursors in mammalian organogenesis reveals a novel hematopoietic enhancer regulating Bhlhe41 expression.Briefings in bioinformatics · 2026Article
- Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution.Nature communications · 2025Article
- Article
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- Whole genome sequence, CAZyme repertoire and sugar metabolic model of the phytopathogenic fungus Kretzschmaria zonata GFP 132.Molecular genetics and genomics : MGG · 2025Article
- 3D chromatin hubs as regulatory units of identity and survival in human acute leukemia.Molecular cell · 2025Article
- Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.Cardiovascular toxicology · 2025Article
- Transcription processes compete with loop extrusion to homogenize promoter and enhancer dynamics.Science advances · 2024Article
- The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells.PLoS genetics · 2024Article
- Genomic landscape of patients with germline RUNX1 variants and familial platelet disorder with myeloid malignancy.Blood advances · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- StemDriver: a knowledgebase of gene functions for hematopoietic stem cell fate determination.Nucleic acids research · 2024Article
- Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.Research square · 2023Article
- Esrrb guides naive pluripotent cells through the formative transcriptional programme.Nature cell biology · 2023Article
- Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.bioRxiv : the preprint server for biology · 2023Article
- Multifaceted role for p53 in pancreatic cancer suppression.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Fibroblasts - the cellular choreographers of wound healing.Frontiers in immunology · 2023Review
29 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
CODEX (http://codex.stemcells.cam.ac.uk/) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the database's cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.