HINT

Names

More detailed information about this field from each metasource. ×

HINT

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:09.074783

---

hint

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:09.074783

Close

Other names: hint

HMM-based Identification of TF Footprints

Webpage:

Licence:

Publications:

Publications

More detailed information about this field from each metasource. ×

Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications
PMID: 25086003

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:09.074783

Close

• Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications PubMed citations: 35.

  35 articles citing: Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications

  ×

  AI applications in functional genomics. PMID:34765093

  ---

  HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence. PMID:34166567

  ---

  TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. PMID:34050351

  ---

  Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq. PMID:33606259

  ---

  Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease. PMID:33294859

  ---

  ATACdb: a comprehensive human chromatin accessibility database. PMID:33125076

  ---

  Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types. PMID:32814038

  ---

  The Meningioma Enhancer Landscape Delineates Novel Subgroups and Drives Druggable Dependencies. PMID:32703768

  ---

  Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756

  ---

  Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization. PMID:32457798

  ---

  From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. PMID:32014034

  ---

  Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability. PMID:31595288

  ---

  Reproducible big data science: A case study in continuous FAIRness. PMID:30973881

  ---

  Identification of transcription factor binding sites using ATAC-seq. PMID:30808370

  ---

  Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling. PMID:30791920

  ---

  Accurate prediction of cell type-specific transcription factor binding. PMID:30630522

  ---

  Anchor: trans-cell type prediction of transcription factor binding sites. PMID:30567711

  ---

  Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. PMID:30467459

  ---

  BiFET: sequencing Bias-free transcription factor Footprint Enrichment Test. PMID:30428075

  ---

  ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference. PMID:30064353

  ---

  Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. PMID:29802342

  ---

  Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes. PMID:29363429

  ---

  Noncoding Variants Functional Prioritization Methods Based on Predicted Regulatory Factor Binding Sites. PMID:29081688

  ---

  Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. PMID:28750606

  ---

  RegulatorTrail: a web service for the identification of key transcriptional regulators. PMID:28472408

  ---

  Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. PMID:28334916

  ---

  Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers. PMID:28122501

  ---

  Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. PMID:27899623

  ---

  Most brain disease-associated and eQTL haplotypes are not located within transcription factor DNase-seq footprints in brain. PMID:27798116

  ---

  Genome-wide footprinting: ready for prime time? PMID:26914206

  ---

  Genomic footprinting. PMID:26914205

  ---

  Analysis of computational footprinting methods for DNase sequencing experiments. PMID:26901649

  ---

  Epigenetic program and transcription factor circuitry of dendritic cell development. PMID:26476451

  ---

  On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions. PMID:26442258

  ---

  MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures. PMID:26099518

Tags:

Tags

More detailed information about this field from each metasource. ×

gene regulation

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:09.074783

---

epigenomics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:09.074783

---

transcription factors and regulatory sites

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:09.074783

Close

gene regulation epigenomics transcription factors and regulatory sites