(Q30358676)

20 October 2017

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning (English)

1 reference

Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

20 October 2017

0 references

1 reference

corrigendum / erratum

1 reference

10.1186/S13059-017-1233-Z

DOI

12 July 2019

http://api.crossref.org/works?select=update-to&filter=doi:10.1186/S13059-017-1233-Z

author

Oliver Stegle

series ordinal

4

1 reference

20 October 2017

5

1 reference

20 October 2017

Heather J Lee

2

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Wolf Reik

series ordinal

3

object named as

Wolf Reik

1 reference

20 October 2017

Christof Angermueller

series ordinal

1

1 reference

20 October 2017

11 April 2017

1 reference

20 October 2017

1 reference

20 October 2017

18

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20 October 2017

1

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20 October 2017

67

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PMCID

5387360

describes a project that uses

20 October 2017

scikit-learn

object named as

scikit-learn

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

1 reference

https://scigraph.springernature.com/pub.10.1186/s13059-017-1189-z

0 references

cites work

Deep learning for computational biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

IL-6 mediates differentiation disorder during spermatogenesis in obesity-associated inflammation by affecting the expression of Zfp637 through the SOCS3/STAT3 pathway

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Simultaneous profiling of transcriptome and DNA methylome from a single cell

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

A pooling-based approach to mapping genetic variants associated with DNA methylation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Predicting the human epigenome from DNA motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Determination and inference of eukaryotic transcription factor sequence specificity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Functions of DNA methylation: islands, start sites, gene bodies and beyond

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect chromatin and DNA methylation of imprinting control regions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

A functional family-wide screening of SP/KLF proteins identifies a subset of suppressors of KRAS-mediated cell growth

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

GC-rich sequence elements recruit PRC2 in mammalian ES cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

CpG islands influence chromatin structure via the CpG-binding protein Cfp1.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Principles and challenges of genomewide DNA methylation analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Dnmt3/transcription factor interactions as crucial players in targeted DNA methylation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

MEME SUITE: tools for motif discovery and searching

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Mouse development with a single E2F activator.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

DNA methylation landscapes: provocative insights from epigenomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

On counting position weight matrix matches in a sequence, with application to discriminative motif finding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

DNA methylation and human disease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Prediction of methylated CpGs in DNA sequences using a support vector machine

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Foxa2 is required for the differentiation of pancreatic alpha-cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Compensatory roles of Foxa1 and Foxa2 during lung morphogenesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

WebLogo: A Sequence Logo Generator

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

HMG20A and HMG20B map to human chromosomes 15q24 and 19p13.3 and constitute a distinct class of HMG-box genes with ubiquitous expression

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Serum response factor is essential for mesoderm formation during mouse embryogenesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

The SRF accessory protein Elk-1 contains a growth factor-regulated transcriptional activation domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites inE. coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

3 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5387360

3 June 2018

https://api.crossref.org/works/10.1186%2FS13059-017-1189-Z

iDNA-Methyl: identifying DNA methylation sites via pseudo trinucleotide composition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1189-Z

Prediction of methylation CpGs and their methylation degrees in human DNA sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1189-Z

Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival Forests

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1189-Z

Robust Locally Weighted Regression and Smoothing Scatterplots

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1189-Z

10.1186/S13059-017-1189-Z

21 January 2018

Identifiers

DOI

1 reference

PMCID

5387360

Dimensions Publication ID

20 October 2017

0 references

1 reference

20 October 2017

1 reference

PMCID

5387360