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Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self-Organizing Maps

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What this work says

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

inferredcites →https://doi.org/10.1007/bf00337288openalex-snapshot

Self-organized formation of topologically correct feature maps

inferredcites →https://doi.org/10.1016/j.bpj.2018.07.003openalex-snapshot

Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics

inferredcites →https://doi.org/10.1016/j.cell.2012.04.040openalex-snapshot

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

inferredcites →https://doi.org/10.1016/j.cell.2018.03.074openalex-snapshot

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

inferredcites →https://doi.org/10.1016/j.cell.2018.05.057openalex-snapshot

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

inferredcites →https://doi.org/10.1016/j.cels.2015.07.011openalex-snapshot

Taking Stock of Regulatory Variation

inferredcites →https://doi.org/10.1016/j.cels.2017.03.005openalex-snapshot

Dynamic Gene Regulatory Networks of Human Myeloid Differentiation

inferredcites →https://doi.org/10.1016/j.exphem.2014.07.171openalex-snapshot

PAX5 loss imposes a reversible differentiation block in b-progenitor acute lymphoblastic leukemia

inferredcites →https://doi.org/10.1016/j.tcb.2018.05.004openalex-snapshot

Analyzing Circulating Tumor Cells One at a Time

inferredcites →https://doi.org/10.1038/cr.2016.23openalex-snapshot

Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas

inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot

An integrated encyclopedia of DNA elements in the human genome

inferredcites →https://doi.org/10.1038/nature13985openalex-snapshot

Principles of regulatory information conservation between mouse and human

inferredcites →https://doi.org/10.1038/nature13992openalex-snapshot

A comparative encyclopedia of DNA elements in the mouse genome

inferredcites →https://doi.org/10.1038/nature14590openalex-snapshot

Single-cell chromatin accessibility reveals principles of regulatory variation

inferredcites →https://doi.org/10.1038/nature15740openalex-snapshot

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

inferredcites →https://doi.org/10.1038/nbt.1630openalex-snapshot

GREAT improves functional interpretation of cis-regulatory regions

inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

inferredcites →https://doi.org/10.1038/nbt.3701openalex-snapshot

Single-cell sequencing of the small-RNA transcriptome

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.3370openalex-snapshot

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

inferredcites →https://doi.org/10.1038/nmeth.3728openalex-snapshot

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

inferredcites →https://doi.org/10.1038/s41467-018-04629-3openalex-snapshot

Unsupervised clustering and epigenetic classification of single cells

inferredcites →https://doi.org/10.1073/pnas.1610617114openalex-snapshot

Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network

inferredcites →https://doi.org/10.1073/pnas.1711335115openalex-snapshot

Foxp1 controls mature B cell survival and the development of follicular and B-1 B cells

inferredcites →https://doi.org/10.1074/jbc.m109.074856openalex-snapshot

The Tumor Suppressor Protein HBP1 Is a Novel c-Myc-binding Protein That Negatively Regulates c-Myc Transcriptional Activity

inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot

TopHat: discovering splice junctions with RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/btr064openalex-snapshot

FIMO: scanning for occurrences of a given motif

inferredcites →https://doi.org/10.1093/database/baw100openalex-snapshot

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

inferredcites →https://doi.org/10.1093/nar/gkv1249openalex-snapshot

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

inferredcites →https://doi.org/10.1093/nar/gkx796openalex-snapshot

dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals

inferredcites →https://doi.org/10.1101/155473openalex-snapshot

Chromatin accessibility dynamics of myogenesis at single cell resolution

inferredcites →https://doi.org/10.1101/gr.158261.113openalex-snapshot

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

inferredcites →https://doi.org/10.1126/science.aab1601openalex-snapshot

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

inferredcites →https://doi.org/10.1128/mcb.00163-12openalex-snapshot

GATA-1 Utilizes Ikaros and Polycomb Repressive Complex 2 To Suppress Hes1 and To Promote Erythropoiesis

inferredcites →https://doi.org/10.1146/annurev-genom-091416-035324openalex-snapshot

Single-Cell (Multi)omics Technologies

inferredcites →https://doi.org/10.1146/annurev.cellbio.20.010403.095114openalex-snapshot

FUNDAMENTALS OF PLANARIAN REGENERATION

inferredcites →https://doi.org/10.1182/blood-2002-06-1797openalex-snapshot

Oscillation between B-lymphoid and myeloid lineages in Myc-induced hematopoietic tumors following spontaneous silencing/reactivation of the EBF/Pax5 pathway

inferredcites →https://doi.org/10.1182/blood-2012-08-450114openalex-snapshot

Genome-wide identification of Ikaros targets elucidates its contribution to mouse B-cell lineage specification and pre-B–cell differentiation

inferredcites →https://doi.org/10.1182/blood-2013-01-474916openalex-snapshot

Transcriptional regulation of the Ikzf1 locus

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1186/s12859-016-1042-5openalex-snapshot

Identifying peaks in *-seq data using shape information

inferredcites →https://doi.org/10.1186/s13059-015-0737-7openalex-snapshot

Single-cell ATAC-seq: strength in numbers

inferredcites →https://doi.org/10.1186/s13059-016-1045-6openalex-snapshot

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

inferredcites →https://doi.org/10.1242/dev.147256openalex-snapshot

Hes5 regulates the transition timing of neurogenesis and gliogenesis in mammalian neocortical development

inferredcites →https://doi.org/10.1371/journal.pone.0020319openalex-snapshot

High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells

inferredcites →https://doi.org/10.21105/joss.00861openalex-snapshot

UMAP: Uniform Manifold Approximation and Projection

inferredcites →https://doi.org/10.3324/haematol.2017.185603openalex-snapshot

The many faces of IKZF1 in B-cell precursor acute lymphoblastic leukemia

inferredcites →https://doi.org/10.3389/fimmu.2018.01553openalex-snapshot

Single Cell RNA Sequencing of Rare Immune Cell Populations

inferredcites →https://doi.org/10.4331/wjbc.v2.i6.132openalex-snapshot

Ikaros in B cell development and function

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.celrep.2022.110333openalex-snapshot

Network inference with Granger causality ensembles on single-cell transcriptomics

inferred← citeshttps://doi.org/10.1038/s41597-019-0202-7openalex-snapshot

STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse

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