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Incorporating chromatin accessibility data into sequence-to-expression modeling
scientific article
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instance of
scholarly article
1 reference
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Europe PubMed Central
PMC publication ID
4375458
retrieved
14 October 2017
title
Incorporating chromatin accessibility data into sequence-to-expression modeling
(English)
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Europe PubMed Central
PMC publication ID
4375458
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14 October 2017
author
Pei-Chen Peng
series ordinal
1
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Europe PubMed Central
PMC publication ID
4375458
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25762337%20AND%20SRC:MED&resulttype=core&format=json
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5 June 2020
Saurabh Sinha
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3
object named as
Saurabh Sinha
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Europe PubMed Central
PMC publication ID
4375458
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25762337%20AND%20SRC:MED&resulttype=core&format=json
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5 June 2020
author name string
Md Abul Hassan Samee
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2
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Europe PubMed Central
PMC publication ID
4375458
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5 June 2020
language of work or name
English
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publication date
1 March 2015
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PMC publication ID
4375458
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14 October 2017
number of pages
11
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published in
Biophysical Journal
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Europe PubMed Central
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4375458
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5 June 2020
volume
108
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Europe PubMed Central
PMC publication ID
4375458
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25762337%20AND%20SRC:MED&resulttype=core&format=json
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5 June 2020
issue
5
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Europe PubMed Central
PMC publication ID
4375458
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5 June 2020
page(s)
1257-1267
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PMC publication ID
4375458
reference URL
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5 June 2020
cites work
In pursuit of design principles of regulatory sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Transcriptional enhancers: from properties to genome-wide predictions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Quantitative modeling of a gene's expression from its intergenic sequence.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Identifying and mapping cell-type-specific chromatin programming of gene expression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
The grammar of transcriptional regulation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Chromatin modifiers and remodellers: regulators of cellular differentiation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Modification of enhancer chromatin: what, how, and why?
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Deciphering the transcriptional cis-regulatory code
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Sequence and chromatin determinants of cell-type-specific transcription factor binding
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Predicting cell-type-specific gene expression from regions of open chromatin
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
The accessible chromatin landscape of the human genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
DNase I sensitivity QTLs are a major determinant of human expression variation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Temporal coordination of gene networks by Zelda in the early Drosophila embryo.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Histone modification levels are predictive for gene expression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
From DNA sequence to transcriptional behaviour: a quantitative approach
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
The biology of chromatin remodeling complexes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
The DNA-encoded nucleosome organization of a eukaryotic genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Dual regulation by the Hunchback gradient in the Drosophila embryo
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
High-resolution mapping and characterization of open chromatin across the genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Enhancer responses to similarly distributed antagonistic gradients in development
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Transcriptional regulation by the numbers: models.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Discovery of functional noncoding elements by digital analysis of chromatin structure
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
A database for management of gene expression data in situ
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
On schemes of combinatorial transcription logic
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
DNA binding sites: representation and discovery
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Specificity, free energy and information content in protein-DNA interactions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
21 June 2018
A comparative evaluation on prediction methods of nucleosome positioning
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
25 November 2018
Predicting expression patterns from regulatory sequence in Drosophila segmentation.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
25 November 2018
Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
25 November 2018
Computational models for neurogenic gene expression in the Drosophila embryo.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
25 November 2018
REDfly: a Regulatory Element Database for Drosophila.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
25 November 2018
Going the distance: a current view of enhancer action
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4375458
retrieved
25 November 2018
The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25762337
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1016/J.BPJ.2014.12.037
1 reference
stated in
Europe PubMed Central
PMC publication ID
4375458
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25762337%20AND%20SRC:MED&resulttype=core&format=json
retrieved
5 June 2020
PMC publication ID
4375458
1 reference
stated in
Europe PubMed Central
PMC publication ID
4375458
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25762337%20AND%20SRC:MED&resulttype=core&format=json
retrieved
5 June 2020
PubMed publication ID
25762337
1 reference
stated in
Europe PubMed Central
PMC publication ID
4375458
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25762337%20AND%20SRC:MED&resulttype=core&format=json
retrieved
5 June 2020
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