(Q36434887)

14 August 2017

HGTree: database of horizontally transferred genes determined by tree reconciliation (English)

1 reference

phylogenetic reconciliation

14 August 2017

0 references

1 reference

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

Arshan Nasir

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

Heebal Kim

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

author name string

Hyeonsoo Jeong

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

Samsun Sung

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

Taehyung Kwon

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

Minseok Seo

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

Kelsey Caetano-Anollés

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

Seoae Cho

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

language of work or name

English

0 references

publication date

17 November 2015

1 reference

14 August 2017

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

volume

44

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

issue

D1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

page(s)

D610-9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

7 June 2020

copyright license

start time

15 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Inferring horizontal gene transfer

1 reference

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Expanded microbial genome coverage and improved protein family annotation in the COG database

30 September 2017

1 reference

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Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

30 September 2017

1 reference

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Global patterns of protein domain gain and loss in superkingdoms

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss

30 September 2017

1 reference

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'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era

30 September 2017

1 reference

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Structure, function and diversity of the healthy human microbiome

30 September 2017

1 reference

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Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

The Pfam protein families database

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

D³: Data-Driven Documents

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Rapid evolutionary innovation during an Archaean genetic expansion.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

30 September 2017

1 reference

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FastTree 2--approximately maximum-likelihood trees for large alignments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Jane: a new tool for the cophylogeny reconstruction problem

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

BLAST+: architecture and applications

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Estimating maximum likelihood phylogenies with PhyML.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

An approach of orthology detection from homologous sequences under minimum evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

RNAmmer: consistent and rapid annotation of ribosomal RNA genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

TreeFam: a curated database of phylogenetic trees of animal gene families

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Human intestinal bacteria as reservoirs for antibiotic resistance genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Are viruses driving microbial diversification and diversity?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes

30 September 2017

1 reference

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Horizontal gene transfer in prokaryotes: quantification and classification

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

On surrogate methods for detecting lateral gene transfer

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Lateral gene transfer and the nature of bacterial innovation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Phylogenetic classification and the universal tree

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Analysis of genomic G + C content, codon usage, initiator codon context and translation termination sites in Tetrahymena thermophila

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Jungles: a new solution to the host/parasite phylogeny reconciliation problem

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Correlation of GC content with replication timing and repair mechanisms in weakly expressed E.coli genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

The guanine and cytosine content of genomic DNA and bacterial evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Reconciling the many faces of lateral gene transfer.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

The closest BLAST hit is often not the nearest neighbor.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702880

21 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1245

Refining transcriptional regulatory networks using network evolutionary models and gene histories

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1245

Maps between Trees and Cladistic Analysis of Historical Associations Among Genes, Organisms, and Areas

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1245

Database resources of the National Center for Biotechnology Information

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1245

21 January 2018

Identifiers

DOI

10.1093/NAR/GKV1245

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json

journals/nar/JeongSKSCCCNK16

7 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:26578597%20AND%20SRC:MED&resulttype=core&format=json

7 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26578597%20AND%20SRC:MED&resulttype=core&format=json