Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates (Q40575939)

21 September 2017

Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates (English)

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21 September 2017

1

Chen X

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21 September 2017

2

Jung S

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21 September 2017

3

Beh LY

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21 September 2017

4

Eddy SR

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21 September 2017

5

Landweber LF

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21 September 2017

language of work or name

English

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publication date

2 September 2015

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Genome Biology and Evolution

21 September 2017

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21 September 2017

7

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21 September 2017

10

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21 September 2017

2859-2870

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describes a project that uses

21 September 2017

DESeq2

object named as

DESeq

1 reference

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

cites work

Analyses of alternatively processed genes in ciliates provide insights into the origins of scrambled genomes and may provide a mechanism for speciation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

The draft assembly of the radically organized Stylonychia lemnae macronuclear genome

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Genome structure drives patterns of gene family evolution in ciliates, a case study using Chilodonella uncinata (Protista, Ciliophora, Phyllopharyngea)

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

InterProScan 5: genome-scale protein function classification

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

New gene evolution: little did we know

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

CD-HIT: accelerated for clustering the next-generation sequencing data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

The Pfam protein families database

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

A chimeric chromosome in the ciliate oxytricha resulting from duplication

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

HMMER web server: interactive sequence similarity searching

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Full-length transcriptome assembly from RNA-Seq data without a reference genome

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Differential expression analysis for sequence count data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Alternative processing of scrambled genes generates protein diversity in the ciliate Chilodonella uncinata

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Origins, evolution, and phenotypic impact of new genes.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Alternative splicing and evolution: diversification, exon definition and function

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

BLAST+: architecture and applications

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Turning a hobby into a job: how duplicated genes find new functions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

RNA-mediated epigenetic programming of a genome-rearrangement pathway

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

PAML 4: phylogenetic analysis by maximum likelihood

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Fast rate of evolution in alternatively spliced coding regions of mammalian genes.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

The evolutionary origin of a complex scrambled gene

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Protein domains correlate strongly with exons in multiple eukaryotic genomes--evidence of exon shuffling?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

The origin of new genes: glimpses from the young and old

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Modular assembly of genes and the evolution of new functions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Common exon duplication in animals and its role in alternative splicing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

BLAT—The BLAST-Like Alignment Tool

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

MRBAYES: Bayesian inference of phylogenetic trees

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Genome evolution and the evolution of exon-shuffling--a review

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

CAP3: A DNA sequence assembly program

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

The evolutionary scrambling and developmental unscrambling of germline genes in hypotrichous ciliates

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

The DNA of ciliated protozoa

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Interconversion of germline-limited and somatic DNA in a scrambled gene

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Alternatively and constitutively spliced exons are subject to different evolutionary forces

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4684698

Polytene chromosomes of Oxytricha: biochemical and morphological changes during macronuclear development in a ciliated protozoan

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26338187

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of Oxytricha

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26338187

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/GBE/EVV172

1 reference

release_sqpyvqs6lzbebg6mbuaadd2go4

21 September 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/sqpyvqs6lzbebg6mbuaadd2go4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

21 September 2017

PubMed publication ID

26338187

1 reference