ArticleBioinformatics (Oxford, England)2018
Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Multiomic analyses delineate human neuroendocrine tumor cell states in relation to normal enteroendocrine cell ontogeny.The Journal of clinical investigation · 2026Article
- Dynamics and master transcription factors dependence of intestinal super-enhancers during differentiation and oncogenesis.Nucleic acids research · 2026Article
- Sustained MYC overexpression drives myeloid differentiation block and acquisition of leukemic phenotypes.Experimental hematology · 2026Article
- Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4.Cell reports · 2024Article
- Dynamic RNA Polymerase II Recruitment Drives Differentiation of the Intestine under the direction of HNF4.bioRxiv : the preprint server for biology · 2023Article
- TGFB1 induces fetal reprogramming and enhances intestinal regeneration.Cell stem cell · 2023Article
- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- TGFB1 Induces Fetal Reprogramming and Enhances Intestinal Regeneration.bioRxiv : the preprint server for biology · 2023Article
- Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators.Bioinformatics (Oxford, England) · 2021Article
- The nuclear receptor HNF4 drives a brush border gene program conserved across murine intestine, kidney, and embryonic yolk sac.Nature communications · 2021Article
- Epigenetic Alterations in Keratinocyte Carcinoma.The Journal of investigative dermatology · 2021Article
- Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4.Cell reports · 2021Article
- Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.Nature methods · 2020Article
- HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine.Development (Cambridge, England) · 2019Article
- A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity.Nature genetics · 2019Article
- The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development.Development (Cambridge, England) · 2019Article
- Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability.Nature neuroscience · 2019Article
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Authors and funding
3 authors.
Funding
Abstract
Motivation: With the increasing amount of genomic and epigenomic data in the public domain, a pressing challenge is to integrate these data to investigate the role of epigenetic mechanisms in regulating gene expression and maintenance of cell-identity. To this end, we have implemented a computational pipeline to systematically study epigenetic variability and uncover regulatory DNA sequences. Results: Haystack is a bioinformatics pipeline to identify hotspots of epigenetic variability across different cell-types, cell-type specific cis-regulatory elements, and associated transcription factors. Haystack is generally applicable to any epigenetic mark and provides an important tool to investigate the mechanisms underlying epigenetic switches during development. This software is accompanied by a set of precomputed tracks, which may be used as a valuable resource for functional annotation of the human genome. Availability and implementation: The Haystack pipeline is implemented as an open-source, multiplatform, Python package called haystack_bio freely available at https://github.com/pinellolab/haystack_bio. Contact: lpinello@mgh.harvard.edu or gcyuan@jimmy.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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