iRegulon: from a gene list to a gene regulatory network using large motif and track collections (Q35212382)

25058159

7 August 2017

title

iRegulon: from a gene list to a gene regulatory network using large motif and track collections (English)

1 reference

7 August 2017

0 references

12

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13 June 2020

Delphine Potier

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Jean-Christophe Marine

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Bram Van de Sande

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Gert Hulselmans

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Marina N Sanchez

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6

Valerie Christiaens

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2

Annelien Verfaillie

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11

Dmitry Svetlichnyy

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13

Mark Fiers

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13 June 2020

author name string

Rekin's Janky

1

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13 June 2020

Koen Herten

8

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13 June 2020

publication date

24 July 2014

1 reference

25058159

PLOS Computational Biology

7 August 2017

published in

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13 June 2020

volume

10

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13 June 2020

issue

7

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13 June 2020

page(s)

e1003731

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Creative Commons Attribution 4.0 International

13 June 2020

copyright license

start time

24 July 2014

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

Cytoscape

object named as

Cytoscape

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9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

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

DESeq2

object named as

DESeq

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

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13 July 2018

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13 July 2018

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13 July 2018

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13 July 2018

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13 July 2018

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Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

13 July 2018

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13 July 2018

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13 July 2018

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13 July 2018

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13 July 2018

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Regulation of the p53 transcriptional response by structurally diverse core promoters

13 July 2018

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13 July 2018

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13 July 2018

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The expanding universe of p53 targets

13 July 2018

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ChIP-seq: advantages and challenges of a maturing technology

13 July 2018

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Blinded by the Light: The Growing Complexity of p53

13 July 2018

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TopHat: discovering splice junctions with RNA-Seq

13 July 2018

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13 July 2018

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13 July 2018

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Allegro: analyzing expression and sequence in concert to discover regulatory programs

13 July 2018

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13 July 2018

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PASTAA: identifying transcription factors associated with sets of co-regulated genes

13 July 2018

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13 July 2018

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13 July 2018

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Reactome knowledgebase of human biological pathways and processes

13 July 2018

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Model-based analysis of ChIP-Seq (MACS)

13 July 2018

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DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

13 July 2018

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DiRE: identifying distant regulatory elements of co-expressed genes

13 July 2018

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Transcriptional control of human p53-regulated genes

13 July 2018

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ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

13 July 2018

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Identification of regulatory factor X as a novel mismatch repair stimulatory factor

13 July 2018

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Systematic identification of mammalian regulatory motifs' target genes and functions

13 July 2018

1 reference

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Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

13 July 2018

1 reference

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A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response.

13 July 2018

1 reference

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Analysis of a Gibbs sampler method for model-based clustering of gene expression data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Fine-tuning enhancer models to predict transcriptional targets across multiple genomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Divergent evolution of human p53 binding sites: cell cycle versus apoptosis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Quantifying similarity between motifs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Large-scale discovery of promoter motifs in Drosophila melanogaster

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Both the basal transcriptional activity of the GADD45A gene and its enhancement after ionizing irradiation are mediated by AP-1 element

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Gene prioritization through genomic data fusion

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Concordant regulation of gene expression by hypoxia and 2-oxoglutarate-dependent dioxygenase inhibition: the role of HIF-1alpha, HIF-2alpha, and other pathways

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Profiling condition-specific, genome-wide regulation of mRNA stability in yeast

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Assessing computational tools for the discovery of transcription factor binding sites

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Genomic analysis of regulatory network dynamics reveals large topological changes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

WebLogo: A Sequence Logo Generator

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Applied bioinformatics for the identification of regulatory elements

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

A census of human cancer genes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Motif discovery in heterogeneous sequence data.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Detection of functional DNA motifs via statistical over-representation

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Computational prediction of transcription-factor binding site locations

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

In vivo activation of the p53 pathway by small-molecule antagonists of MDM2

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Combining phylogenetic data with co-regulated genes to identify regulatory motifs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Regulatory element detection using correlation with expression.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

The TRANSFAC system on gene expression regulation.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Gene ontology: tool for the unification of biology

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Activators and target genes of Rel/NF-kappaB transcription factors

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

The cyclin B2 promoter depends on NF-Y, a trimer whose CCAAT-binding activity is cell-cycle regulated

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Gibbs motif sampling: detection of bacterial outer membrane protein repeats

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

WAF1, a potential mediator of p53 tumor suppression

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Identification of consensus patterns in unaligned DNA sequences known to be functionally related.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

cisExpress: motif detection in DNA sequences

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Genome-wide discovery of cis-elements in promoter sequences using gene expression

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Module networks revisited: computational assessment and prioritization of model predictions

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Predicting transcription factor affinities to DNA from a biophysical model

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Transcriptional regulation of the mouse PNRC2 promoter by the nuclear factor Y (NFY) and E2F1.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Cdk2-dependent phosphorylation of the NF-Y transcription factor and its involvement in the p53-p21 signaling pathway

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

Algorithms for phylogenetic footprinting

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109854

An algorithm for finding signals of unknown length in DNA sequences

26 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003731

10.1371/JOURNAL.PCBI.1003731

21 January 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25058159%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/JankyVISSCHHSPSAFMA14

13 June 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25058159%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

25058159

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25058159%20AND%20SRC:MED&resulttype=core&format=json