ArticleBioinformatics (Oxford, England)2015
damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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93 citing papers in PubMed.
- HDAC1/2-mediated repression of Wnt receptor expression orients asymmetric division polarity in Caenorhabditis elegans.Development (Cambridge, England) · 2026Article
- Tailless terminates the neural stem cell temporal cascade in both the optic lobe and central brain.Development (Cambridge, England) · 2026Article
- damidBind: an R/bioconductor package for differential DamID analysis and data exploration.Bioinformatics (Oxford, England) · 2026Article
- Autoinhibitory feedback preserves intestinal stem cell maintenance and fate commitment.The EMBO journal · 2026Article
- Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male Drosophila neurons.PLoS biology · 2026Article
- MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.Nature structural & molecular biology · 2026Article
- Transcriptional repression of reaper by Stand still ensures female germline development in Drosophila.PLoS genetics · 2026Article
- Neural stem cell quiescence is actively maintained by the epigenome.Cell reports · 2026Article
- Pre-marking chromatin with H3K4 methylation is required for accurate zygotic genome activation and development.Nature communications · 2025Article
- A conserved differentiation programme facilitates inhibitory neuron production in the developing mouse and human cerebellum.Development (Cambridge, England) · 2025Article
- Local chromatin context informs transcriptional outcomes for the histone demethylase KDM5.Epigenetics & chromatin · 2025Article
- Hypoxia promotes airway differentiation in the human lung epithelium.Cell stem cell · 2025Article
- Mapping SET1B chromatin interactions with DamID using DamMapper, a comprehensive Snakemake workflow.BMC genomics · 2025Article
- SMCHD1 maintains heterochromatin, genome compartments and epigenome landscape in human myoblasts.Nature communications · 2025Article
- EFL-3/E2F7 modulates Wnt signalling by repressing the Nemo-like kinase LIT-1 during asymmetric epidermal cell division in Caenorhabditis elegans.Development (Cambridge, England) · 2025Article
- Targeted DamID detects cell-type-specific histone modifications in intact tissues or organisms.PLoS biology · 2025Article
- Cell-specific genetic expression profile of antennal glia in Drosophila reveals candidate genes in neuron-glia interactions.Scientific reports · 2025Article
- Perturbing TET2 condensation promotes aberrant genome-wide DNA methylation and curtails leukaemia cell growth.Nature cell biology · 2024Article
- Damsel: analysis and visualisation of DamID sequencing in R.Bioinformatics (Oxford, England) · 2024Article
- A human progeria-associated BAF-1 mutation modulates gene expression and accelerates aging in C. elegans.The EMBO journal · 2024Article
33 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
unlabelledDamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with normalization based on read-counts alone can lead to high background and the loss of bound signal. DamID-seq thus presents novel challenges in terms of normalization and background minimization. We describe here damidseq_pipeline, a software pipeline that performs automatic normalization and background reduction on multiple DamID-seq FASTQ datasets. AVAILABILITY AND IMPLEMENTATION: Open-source and freely available from http://owenjm.github.io/damidseq_pipeline. The damidseq_pipeline is implemented in Perl and is compatible with any Unix-based operating system (e.g. Linux, Mac OSX). CONTACT: o.marshall@gurdon.cam.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.