(Q47132879)

8 January 2018

title

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

1 reference

8 January 2018

author

Vladimir B. Bajic

9

1 reference

8 January 2018

Arturo Magana-Mora

Arturo Magana-Mora

8

0 references

Vsevolod Makeev

Vsevolod J Makeev

12

0 references

Ilya E. Vorontsov

Ilya E. Vorontsov

2

0 references

Ivan Kulakovskiy

1

Ivan V Kulakovskiy

1 reference

8 January 2018

Ruslan Sharipov

4

Ruslan N Sharipov

1 reference

8 January 2018

Alla D Fedorova

5

Alla D Fedorova

1 reference

8 January 2018

Fedor Kolpakov

11

Fedor A Kolpakov

1 reference

8 January 2018

author name string

Ivan S Yevshin

3

1 reference

8 January 2018

Eugene I Rumynskiy

6

1 reference

8 January 2018

Yulia A Medvedeva

7

1 reference

8 January 2018

Dmitry A Papatsenko

10

1 reference

8 January 2018

language of work or name

English

0 references

publication date

11 November 2017

1 reference

8 January 2018

published in

Nucleic Acids Research

1 reference

8 January 2018

Creative Commons Attribution-NonCommercial 4.0 International

copyright license

start time

11 November 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

The Genetics of Transcription Factor DNA Binding Variation

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B cells.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Negative selection maintains transcription factor binding motifs in human cancer.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Sp7/Osterix Is Restricted to Bone-Forming Vertebrates where It Acts as a Dlx Co-factor in Osteoblast Specification

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

iRegulon and i-cisTarget: Reconstructing Regulatory Networks Using Motif and Track Enrichment

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

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

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

RSAT 2015: Regulatory Sequence Analysis Tools.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

TFClass: a classification of human transcription factors and their rodent orthologs

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Determination and inference of eukaryotic transcription factor sequence specificity

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

A promoter-level mammalian expression atlas

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Effects of cytosine methylation on transcription factor binding sites

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

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

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

The next generation of transcription factor binding site prediction

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

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

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

TFClass: an expandable hierarchical classification of human transcription factors

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

The transcription factor encyclopedia

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Reorganizing the protein space at the Universal Protein Resource (UniProt)

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Theoretical and empirical quality assessment of transcription factor-binding motifs

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

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

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Model-based analysis of ChIP-Seq (MACS)

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

YB-1 (YBX1) does not bind to Y/CCAAT boxes in vivo

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

PICS: probabilistic inference for ChIP-seq.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

Efficient and accurate P-value computation for Position Weight Matrices

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5753240

15 August 2018

Identifiers

DOI

10.1093/NAR/GKX1106

1 reference

8 January 2018

journals/nar/KulakovskiyVYSF18

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

8 January 2018

PubMed publication ID

29140464

1 reference

8 January 2018