On the public citation graph

Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

https://doi.org/10.1101/130070
0 signed · 73 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cell.2013.04.053openalex-snapshot
Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment
inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2015.11.024openalex-snapshot
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
inferredcites →https://doi.org/10.1016/j.cell.2017.03.024openalex-snapshot
Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription
inferredcites →https://doi.org/10.1016/j.cell.2017.05.004openalex-snapshot
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization
inferredcites →https://doi.org/10.1016/j.celrep.2016.10.061openalex-snapshot
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
inferredcites →https://doi.org/10.1016/j.molcel.2015.02.023openalex-snapshot
Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing
inferredcites →https://doi.org/10.1016/j.molcel.2015.09.023openalex-snapshot
CTCF Binding Polarity Determines Chromatin Looping
inferredcites →https://doi.org/10.1016/j.molcel.2016.05.018openalex-snapshot
Chromatin Domains: The Unit of Chromosome Organization
inferredcites →https://doi.org/10.1016/j.stem.2014.05.017openalex-snapshot
The 3D Genome in Transcriptional Regulation and Pluripotency
inferredcites →https://doi.org/10.1016/j.tig.2015.05.007openalex-snapshot
A unified architecture of transcriptional regulatory elements
inferredcites →https://doi.org/10.1016/j.ygeno.2007.11.002openalex-snapshot
Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes
inferredcites →https://doi.org/10.1016/s0140-6736(16)31711-1openalex-snapshot
Crohn's disease
inferredcites →https://doi.org/10.1038/79896openalex-snapshot
A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression
inferredcites →https://doi.org/10.1038/nature06947openalex-snapshot
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
inferredcites →https://doi.org/10.1038/nature11049openalex-snapshot
Spatial partitioning of the regulatory landscape of the X-inactivation centre
inferredcites →https://doi.org/10.1038/nature11082openalex-snapshot
Topological domains in mammalian genomes identified by analysis of chromatin interactions
inferredcites →https://doi.org/10.1038/nature11232openalex-snapshot
The accessible chromatin landscape of the human genome
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature11279openalex-snapshot
The long-range interaction landscape of gene promoters
inferredcites →https://doi.org/10.1038/nature12787openalex-snapshot
An atlas of active enhancers across human cell types and tissues
inferredcites →https://doi.org/10.1038/nature13182openalex-snapshot
A promoter-level mammalian expression atlas
inferredcites →https://doi.org/10.1038/nature13986openalex-snapshot
Topologically associating domains are stable units of replication-timing regulation
inferredcites →https://doi.org/10.1038/nature19800openalex-snapshot
Formation of new chromatin domains determines pathogenicity of genomic duplications
inferredcites →https://doi.org/10.1038/ng.2653openalex-snapshot
The Genotype-Tissue Expression (GTEx) project
inferredcites →https://doi.org/10.1038/ng.3286openalex-snapshot
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
inferredcites →https://doi.org/10.1038/ng.3404openalex-snapshot
Partitioning heritability by functional annotation using genome-wide association summary statistics
inferredcites →https://doi.org/10.1038/ng.3539openalex-snapshot
Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin
inferredcites →https://doi.org/10.1038/ng.496openalex-snapshot
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
inferredcites →https://doi.org/10.1038/ng1423openalex-snapshot
Active genes dynamically colocalize to shared sites of ongoing transcription
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot
HISAT: a fast spliced aligner with low memory requirements
inferredcites →https://doi.org/10.1038/nrm.2016.138openalex-snapshot
Regulation of disease-associated gene expression in the 3D genome
inferredcites →https://doi.org/10.1053/j.gastro.2008.07.017openalex-snapshot
Genome-Wide Association Analysis in Sarcoidosis and Crohn's Disease Unravels a Common Susceptibility Locus on 10p12.2
inferredcites →https://doi.org/10.1053/j.gastro.2015.08.001openalex-snapshot
Genetics of Inflammatory Bowel Diseases
inferredcites →https://doi.org/10.1093/bioinformatics/bti623openalex-snapshot
ROCR: visualizing classifier performance in R
inferredcites →https://doi.org/10.1093/bioinformatics/btp328openalex-snapshot
rtracklayer: an R package for interfacing with genome browsers
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/molbev/msv053openalex-snapshot
Neighboring Genes Show Correlated Evolution in Gene Expression
inferredcites →https://doi.org/10.1093/nar/gkq1019openalex-snapshot
The Sequence Read Archive
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1093/nar/gku365openalex-snapshot
deepTools: a flexible platform for exploring deep-sequencing data
inferredcites →https://doi.org/10.1101/gad.179804.111openalex-snapshot
A decade of 3C technologies: insights into nuclear organization
inferredcites →https://doi.org/10.1101/gad.241422.114openalex-snapshot
Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation
inferredcites →https://doi.org/10.1101/gad.454008openalex-snapshot
Transcription factories are nuclear subcompartments that remain in the absence of transcription
inferredcites →https://doi.org/10.1101/gr.115469.110openalex-snapshot
Unamplified cap analysis of gene expression on a single-molecule sequencer
inferredcites →https://doi.org/10.1101/gr.176586.114openalex-snapshot
Genome-wide map of regulatory interactions in the human genome
inferredcites →https://doi.org/10.1101/gr.196006.115openalex-snapshot
Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
inferredcites →https://doi.org/10.1101/gr.229102openalex-snapshot
The Human Genome Browser at UCSC
inferredcites →https://doi.org/10.1111/j.1467-9868.2008.00700.xopenalex-snapshot
Approximate Bayesian Inference for Latent Gaussian models by using Integrated Nested Laplace Approximations
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1177/154405910408300516openalex-snapshot
Indian Hedgehog: A Mechanotransduction Mediator in Condylar Cartilage
inferredcites →https://doi.org/10.1186/1471-2105-12-77openalex-snapshot
pROC: an open-source package for R and S+ to analyze and compare ROC curves
inferredcites →https://doi.org/10.1186/1471-2164-14-553openalex-snapshot
Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes
inferredcites →https://doi.org/10.1186/1471-2164-5-4openalex-snapshot
Inter-species differences of co-expression of neighboring genes in eukaryotic genomes
inferredcites →https://doi.org/10.1186/s13059-015-0621-5openalex-snapshot
The Ensembl Regulatory Build
inferredcites →https://doi.org/10.1186/s13059-015-0866-zopenalex-snapshot
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
inferredcites →https://doi.org/10.1186/s13059-016-0992-2openalex-snapshot
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
inferredcites →https://doi.org/10.12688/f1000research.7334.1openalex-snapshot
HiCUP: pipeline for mapping and processing Hi-C data
inferredcites →https://doi.org/10.1371/journal.pbio.0040138openalex-snapshot
Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations
inferredcites →https://doi.org/10.1371/journal.pcbi.1003118openalex-snapshot
Software for Computing and Annotating Genomic Ranges
inferredcites →https://doi.org/10.1613/jair.953openalex-snapshot
SMOTE: Synthetic Minority Over-sampling Technique
inferredcites →https://doi.org/10.18637/jss.v033.i01openalex-snapshot
Regularization Paths for Generalized Linear Models via Coordinate Descent
inferredcites →https://doi.org/10.32614/cran.package.caretopenalex-snapshot
caret: Classification and Regression Training
inferredcites →https://doi.org/10.32614/cran.package.venndiagramopenalex-snapshot
VennDiagram: Generate High-Resolution Venn and Euler Plots
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.32614/rj-2009-002openalex-snapshot
EMD: A Package for Empirical Mode Decomposition and Hilbert Spectrum
inferredcites →https://doi.org/10.7554/elife.02557openalex-snapshot
Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/395822openalex-snapshot
Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genome
inferred← citeshttps://doi.org/10.1104/pp.18.00758openalex-snapshot
RNA Polymerase II Read-Through Promotes Expression of Neighboring Genes in SAL1-PAP-XRN Retrograde Signaling
inferred← citeshttps://doi.org/10.32657/10356/146910openalex-snapshot
Autonomy vs. artificial intelligence : studies on healthcare work and analytics
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.