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GimmeMotifs: an analysis framework for transcription factor motif analysis

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What this work says

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

inferredcites →https://doi.org/10.1002/0471250953.bi0211s47openalex-snapshot

Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences

inferredcites →https://doi.org/10.1007/s10994-013-5367-2openalex-snapshot

Block coordinate descent algorithms for large-scale sparse multiclass classification

inferredcites →https://doi.org/10.1007/s40484-013-0012-4openalex-snapshot

Modeling the specificity of protein‐DNA interactions

inferredcites →https://doi.org/10.1016/j.cell.2014.08.009openalex-snapshot

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

inferredcites →https://doi.org/10.1016/j.cell.2018.01.029openalex-snapshot

The Human Transcription Factors

inferredcites →https://doi.org/10.1016/j.cellimm.2015.02.009openalex-snapshot

Fatal autoimmunity results from the conditional deletion of Snai2 and Snai3

inferredcites →https://doi.org/10.1016/j.imbio.2016.01.007openalex-snapshot

Snai2 and Snai3 transcriptionally regulate cellular fitness and functionality of T cell lineages through distinct gene programs

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/10.1038/nbt1053openalex-snapshot

Assessing computational tools for the discovery of transcription factor binding sites

inferredcites →https://doi.org/10.1038/nbt1203openalex-snapshot

Gene prioritization through genomic data fusion

inferredcites →https://doi.org/10.1038/nbt717openalex-snapshot

An algorithm for finding protein–DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments

inferredcites →https://doi.org/10.1038/ng.375openalex-snapshot

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

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

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.3547openalex-snapshot

Predicting effects of noncoding variants with deep learning–based sequence model

inferredcites →https://doi.org/10.1038/nmeth1061openalex-snapshot

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation

inferredcites →https://doi.org/10.1038/s41592-018-0046-7openalex-snapshot

Bioconda: sustainable and comprehensive software distribution for the life sciences

inferredcites →https://doi.org/10.1038/sj.cr.7310125openalex-snapshot

Nanog and transcriptional networks in embryonic stem cell pluripotency

inferredcites →https://doi.org/10.1038/sj.onc.1210764openalex-snapshot

Transcriptional control of granulocyte and monocyte development

inferredcites →https://doi.org/10.1074/jbc.274.10.6567openalex-snapshot

T-cell Expression of the Human GATA-3 Gene Is Regulated by a Non-lineage-specific Silencer

inferredcites →https://doi.org/10.1089/10665270252935566openalex-snapshot

A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes

inferredcites →https://doi.org/10.1089/cmb.2008.16ttopenalex-snapshot

GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery

inferredcites →https://doi.org/10.1093/bioinformatics/19.2.212openalex-snapshot

Rank order metrics for quantifying the association of sequence features with gene regulation

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btq488openalex-snapshot

Deep and wide digging for binding motifs in ChIP-Seq data

inferredcites →https://doi.org/10.1093/bioinformatics/btq636openalex-snapshot

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments

inferredcites →https://doi.org/10.1093/bioinformatics/btr709openalex-snapshot

Robust rank aggregation for gene list integration and meta-analysis

inferredcites →https://doi.org/10.1093/bioinformatics/bts480openalex-snapshot

Snakemake—a scalable bioinformatics workflow engine

inferredcites →https://doi.org/10.1093/bioinformatics/btt230openalex-snapshot

Design of shortest double-stranded DNA sequences covering all k -mers with applications to protein-binding microarrays and synthetic enhancers

inferredcites →https://doi.org/10.1093/bioinformatics/btw689openalex-snapshot

InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites

inferredcites →https://doi.org/10.1093/bioinformatics/btx804openalex-snapshot

JASPAR RESTful API: accessing JASPAR data from any programming language

inferredcites →https://doi.org/10.1093/bioinformatics/bty575openalex-snapshot

Discovering epistatic feature interactions from neural network models of regulatory DNA sequences

inferredcites →https://doi.org/10.1093/intimm/11.10.1701openalex-snapshot

Negative regulation of CD4 expression in T cells by the transcriptional repressor ZEB

inferredcites →https://doi.org/10.1093/intimm/dxn143openalex-snapshot

The transcription repressor, ZEB1, cooperates with CtBP2 and HDAC1 to suppress IL-2 gene activation in T cells

inferredcites →https://doi.org/10.1093/nar/gki791openalex-snapshot

Limitations and potentials of current motif discovery algorithms

inferredcites →https://doi.org/10.1093/nar/gkl857openalex-snapshot

SwissRegulon: a database of genome-wide annotations of regulatory sites

inferredcites →https://doi.org/10.1093/nar/gkp1180openalex-snapshot

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

inferredcites →https://doi.org/10.1093/nar/gkr1135openalex-snapshot

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information

inferredcites →https://doi.org/10.1093/nar/gks1221openalex-snapshot

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

inferredcites →https://doi.org/10.1093/nar/gkt1249openalex-snapshot

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

inferredcites →https://doi.org/10.1093/nar/gku1045openalex-snapshot

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

inferredcites →https://doi.org/10.1093/nar/gkv577openalex-snapshot

Varying levels of complexity in transcription factor binding motifs

inferredcites →https://doi.org/10.1093/nar/gkx1092openalex-snapshot

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

inferredcites →https://doi.org/10.1093/nar/gkx1106openalex-snapshot

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

inferredcites →https://doi.org/10.1093/nar/gkx1126openalex-snapshot

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

inferredcites →https://doi.org/10.1093/nar/gkx314openalex-snapshot

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

inferredcites →https://doi.org/10.1101/gad.12.15.2403openalex-snapshot

PU.1 induces myeloid lineage commitment in multipotent hematopoietic progenitors

inferredcites →https://doi.org/10.1101/gr.100552.109openalex-snapshot

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

inferredcites →https://doi.org/10.1101/gr.139881.112openalex-snapshot

P-value-based regulatory motif discovery using positional weight matrices

inferredcites →https://doi.org/10.1101/gr.169508.113openalex-snapshot

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

inferredcites →https://doi.org/10.1101/gr.227231.117openalex-snapshot

Integrated analysis of motif activity and gene expression changes of transcription factors

inferredcites →https://doi.org/10.1101/gr.227819.117openalex-snapshot

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

inferredcites →https://doi.org/10.1142/9789814447362_0014openalex-snapshot

BIOPROSPECTOR: DISCOVERING CONSERVED DNA MOTIFS IN UPSTREAM REGULATORY REGIONS OF CO-EXPRESSED GENES

inferredcites →https://doi.org/10.1142/s0219720013400040openalex-snapshot

FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES

inferredcites →https://doi.org/10.1145/2939672.2939785openalex-snapshot

XGBoost

inferredcites →https://doi.org/10.1182/blood-2010-07-295261openalex-snapshot

NANOG induction of fetal liver kinase-1 (FLK1) transcription regulates endothelial cell proliferation and angiogenesis

inferredcites →https://doi.org/10.1186/1471-2105-6-237openalex-snapshot

Measuring similarities between transcription factor binding sites

inferredcites →https://doi.org/10.1186/1471-2164-15-752openalex-snapshot

Differential motif enrichment analysis of paired ChIP-seq experiments

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/s12859-016-1298-9openalex-snapshot

Evaluating tools for transcription factor binding site prediction

inferredcites →https://doi.org/10.1242/dev.125.1.21openalex-snapshot

δEF1, a zinc finger and homeodomain transcription factor, is required for skeleton patterning in multiple lineages

inferredcites →https://doi.org/10.1371/journal.pcbi.1003214openalex-snapshot

The Next Generation of Transcription Factor Binding Site Prediction

inferredcites →https://doi.org/10.1371/journal.pcbi.1005176openalex-snapshot

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors

inferredcites →https://doi.org/10.1371/journal.pone.0024576openalex-snapshot

AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses

inferredcites →https://doi.org/10.21105/joss.00320openalex-snapshot

genomepy: download genomes the easy way

inferredcites →https://doi.org/10.3324/haematol.2013.094243openalex-snapshot

BLUEPRINT: mapping human blood cell epigenomes

inferredcites →https://doi.org/10.5281/zenodo.592845openalex-snapshot

mwaskom/seaborn v0.11.0.rc0

inferredcites →https://doi.org/10.5281/zenodo.596029openalex-snapshot

kundajelab/atac_dnase_pipelines: 0.3.0

inferredcites →https://doi.org/10.7287/peerj.preprints.1302v1openalex-snapshot

Motif clustering with implications for transcription factor interactions

What points at this work

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

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Generation and molecular characterization of human pluripotent stem cell-derived pharyngeal foregut endoderm

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Retinoic acid signaling drives differentiation toward the absorptive lineage in colorectal cancer

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Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development

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Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment

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Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain

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Loss of PRC2 subunits primes lineage choice during exit of pluripotency

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Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development

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Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis

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Motif-based models accurately predict cell type-specific distal regulatory elements

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SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration

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Evolution of tissue-specific expression of ancestral genes across vertebrates and insects

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Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes

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Alignment-free integration of single-nucleus ATAC-seq across species with sPYce

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Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids

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Gene regulatory network inference in the era of single-cell multi-omics

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Multiomics and deep learning dissect regulatory syntax in human development

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Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq

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The transcriptional and regulatory identity of erythropoietin producing cells

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Decoding sequence determinants of gene expression in diverse cellular and disease states

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NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development

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Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers

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Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities

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ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study

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Prediction of cell states and key transcription factors of the human cornea through integrated single-cell omics analyses

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Epigenome dysregulation resulting from NSD1 mutation in head and neck squamous cell carcinoma

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Chromatin regulates genome-wide transcription factor binding affinities

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Insights into deuterostome evolution from the biphasic transcriptional programme of hemichordates

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Multi-omics analysis reveals a crucial role for Retinoic Acid in promoting epigenetic and transcriptional competence of an in vitro model of human Pharyngeal Endoderm

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Multi-omics analyses identify transcription factor interplay in corneal epithelial fate determination and disease

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Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during ESC differentiation

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Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

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Deep learning the cis-regulatory code of chromatin dynamics during cellular reprogramming

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A Bag-Of-Motif Model Captures Cell States at Distal Regulatory Sequences

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Antisense oligonucleotide depletion of CCDC146 is a broad-spectrum therapeutic strategy for ALS

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MEF2C controls segment-specific gene regulatory networks that direct heart tube morphogenesis

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Open collaborative writing with Manubot

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Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis

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Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates

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Nucleome programming is required for the foundation of totipotency in mammalian germline development

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Salmonids reveal principles of regulatory evolution following autotetraploidization

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Light-entrained chromatin priming poises rapid metamorphosis in a marine sponge

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CHAMPOLLION: Robust Multi-Omics Integration via Inverse Optimal Transport Using Paired Cells

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Parental care is a genetic capacitor

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dubTAGs enable on-demand stabilization for tunable and reversible control of endogenous protein levels

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Light-entrained chromatin priming poises rapid metamorphosis in a marine sponge

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Light-entrained chromatin priming poises rapid metamorphosis in a marine sponge

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Light-entrained chromatin priming poises rapid metamorphosis in a marine sponge

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Seq2science: an end-to-end workflow for functional genomics analysis

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