Analytical tools and current challenges in the modern era of neuroepigenomics (Q34670822)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25349914%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

review article

1 reference

title

Analytical tools and current challenges in the modern era of neuroepigenomics (English)

1 reference

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22 February 2020

1

1 reference

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22 February 2020

Li Shen

2

1 reference

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22 February 2020

Ning-Yi Shao

5

1 reference

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22 February 2020

9

C David Allis

1 reference

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22 February 2020

author name string

Bin Zhang

3

1 reference

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22 February 2020

Benjamin A Garcia

4

1 reference

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22 February 2020

Amanda Mitchell

6

1 reference

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22 February 2020

HaoSheng Sun

7

1 reference

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22 February 2020

Schahram Akbarian

8

1 reference

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22 February 2020

Eric J Nestler

10

1 reference

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22 February 2020

language of work or name

English

0 references

publication date

28 October 2014

1 reference

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22 February 2020

1 reference

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22 February 2020

volume

17

1 reference

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22 February 2020

issue

11

1 reference

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22 February 2020

page(s)

1476-1490

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describes a project that uses

22 February 2020

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/4262187

based on heuristic

inferred from PubMed Central ID database lookup

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging

7 July 2018

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7 July 2018

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Neuronal activity modifies the DNA methylation landscape in the adult brain

7 July 2018

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7 July 2018

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7 July 2018

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Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.

7 July 2018

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Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol

7 July 2018

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Human-specific loss of regulatory DNA and the evolution of human-specific traits

7 July 2018

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Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons.

7 July 2018

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A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

7 July 2018

1 reference

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Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens

7 July 2018

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Integrative genomics viewer

7 July 2018

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lncRNAdb: a reference database for long noncoding RNAs

7 July 2018

1 reference

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Analysis and design of RNA sequencing experiments for identifying isoform regulation

7 July 2018

1 reference

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Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation

7 July 2018

1 reference

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Differential expression analysis for sequence count data

7 July 2018

1 reference

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A simple method for gene expression and chromatin profiling of individual cell types within a tissue

7 July 2018

1 reference

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Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

7 July 2018

1 reference

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Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

7 July 2018

1 reference

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ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Altered histone acetylation is associated with age-dependent memory impairment in mice.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Modern approaches for investigating epigenetic signaling pathways

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

BEDTools: a flexible suite of utilities for comparing genomic features

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Essential role of the histone methyltransferase G9a in cocaine-induced plasticity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Archiving next generation sequencing data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

High throughput characterization of combinatorial histone codes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

BSMAP: whole genome bisulfite sequence MAPping program

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

The Sequence Alignment/Map format and SAMtools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Fast and accurate short read alignment with Burrows-Wheeler transform

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Common genetic variation and human traits

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Histone modifications at human enhancers reflect global cell-type-specific gene expression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

TopHat: discovering splice junctions with RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

ChIP-seq accurately predicts tissue-specific activity of enhancers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

PTMap--a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Purification of proteins associated with specific genomic Loci

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Model-based analysis of ChIP-Seq (MACS)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Delta FosB mediates epigenetic desensitization of the c-fos gene after chronic amphetamine exposure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Mapping and quantifying mammalian transcriptomes by RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

The transcriptional landscape of the yeast genome defined by RNA sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Isolation of neuronal chromatin from brain tissue

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Discovering microRNAs from deep sequencing data using miRDeep

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

piRNABank: a web resource on classified and clustered Piwi-interacting RNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

A general framework for weighted gene co-expression network analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Initial sequence of the chimpanzee genome and comparison with the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

An integrative genomics approach to infer causal associations between gene expression and disease

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Proteomic and genomic characterization of chromatin complexes at a boundary

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Open mass spectrometry search algorithm

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Probability-based protein identification by searching sequence databases using mass spectrometry data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Evolution at two levels in humans and chimpanzees

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4262187

Morphine epigenomically regulates behavior through alterations in histone H3 lysine 9 dimethylation in the nucleus accumbens

7 July 2018

1 reference

Decoding neural transcriptomes and epigenomes via high-throughput sequencing

21 January 2018

1 reference

Cutadapt removes adapter sequences from high-throughput sequencing reads

21 January 2018

1 reference

DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing

21 January 2018

1 reference

Integrative genomics identifies APOE ε4 effectors in Alzheimer's disease

21 January 2018

1 reference

Alzheimer's disease: From big data to mechanism

21 January 2018

1 reference

Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark

21 January 2018

1 reference

Interpreting top-down mass spectra using spectral alignment.

21 January 2018

1 reference

Proteomic study and marker protein identification of Caenorhabditis elegans lipid droplets

21 January 2018

1 reference

Insertional chromatin immunoprecipitation: a method for isolating specific genomic regions

21 January 2018

1 reference

Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions

21 January 2018

1 reference

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.

21 January 2018

1 reference

Cell biology: Nondisjunction, aneuploidy and tetraploidy (Reply)

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1038/NN.3816

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25349914%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25349914%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

PubMed publication ID

25349914

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25349914%20AND%20SRC:MED&resulttype=core&format=json