Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs? (Q36035025)

11 August 2017

Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs? (English)

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11 August 2017

Christian Rödelsperger

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2

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Christian Rödelsperger

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author name string

Neel Prabh

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1

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PMC publication ID

4888513

11 August 2017

Christian Rödelsperger

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2

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11 August 2017

31 May 2016

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11 August 2017

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11 August 2017

17

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11 August 2017

1

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11 August 2017

226

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https://scigraph.springernature.com/pub.10.1186/s12859-016-1102-x

11 August 2017

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Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis)

2 October 2017

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New genes drive the evolution of gene interaction networks in the human and mouse genomes

2 October 2017

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Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

2 October 2017

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Identification and evolution of the orphan genes in the domestic silkworm, Bombyx mori

2 October 2017

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Genome-wide identification of lineage-specific genes within Caenorhabditis elegans

2 October 2017

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Microevolution of Duplications and Deletions and Their Impact on Gene Expression in the Nematode Pristionchus pacificus

2 October 2017

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The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation

2 October 2017

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2 October 2017

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Genes from scratch--the evolutionary fate of de novo genes

2 October 2017

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Genomics of divergence along a continuum of parapatric population differentiation

2 October 2017

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Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes

2 October 2017

1 reference

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Genomics of ecological adaptation in cactophilic Drosophila.

2 October 2017

1 reference

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Extensive copy-number variation of young genes across stickleback populations

2 October 2017

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Extensive error in the number of genes inferred from draft genome assemblies

2 October 2017

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The life cycle of Drosophila orphan genes

2 October 2017

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Comparative RNAi screens in C. elegans and C. briggsae reveal the impact of developmental system drift on gene function

2 October 2017

1 reference

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Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data

2 October 2017

1 reference

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A developmental switch coupled to the evolution of plasticity acts through a sulfatase

2 October 2017

1 reference

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Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish

2 October 2017

1 reference

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Mechanisms and dynamics of orphan gene emergence in insect genomes

2 October 2017

1 reference

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System wide analysis of the evolution of innate immunity in the nematode model species Caenorhabditis elegans and Pristionchus pacificus

2 October 2017

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Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

2 October 2017

1 reference

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Genome-wide patterns of divergence during speciation: the lake whitefish case study

2 October 2017

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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

2 October 2017

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The evolutionary origin of orphan genes

2 October 2017

1 reference

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Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects

2 October 2017

1 reference

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Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover

2 October 2017

1 reference

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Genome-wide analysis of a long-term evolution experiment with Drosophila

2 October 2017

1 reference

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Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes

2 October 2017

1 reference

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Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

2 October 2017

1 reference

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More than just orphans: are taxonomically-restricted genes important in evolution?

2 October 2017

1 reference

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Functional annotations improve the predictive score of human disease-related mutations in proteins

2 October 2017

1 reference

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Lineage-specific biology revealed by a finished genome assembly of the mouse

2 October 2017

1 reference

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Comparative genomics and the study of evolution by natural selection

2 October 2017

1 reference

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Origin of primate orphan genes: a comparative genomics approach

2 October 2017

1 reference

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The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

Significant comparative characteristics between orphan and nonorphan genes in the rice (Oryza sativa L.) genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

PAML 4: phylogenetic analysis by maximum likelihood

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

Identification and characterization of insect-specific proteins by genome data analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

MUSCLE: multiple sequence alignment with high accuracy and high throughput

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

The importance of being regular: Caenorhabditis elegans and Pristionchus pacificus defecation mutants are hypersusceptible to bacterial pathogens

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

Cryptic variation in vulva development by cis-regulatory evolution of a HAIRY-binding site

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

Expressional and functional variation of horizontally acquired cellulases in the nematode Pristionchus pacificus.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4888513

10.1186/S12859-016-1102-X

23 September 2018

Identifiers

DOI

1 reference

11 August 2017

journals/bmcbi/PrabhR16

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

PMC publication ID

4888513

11 August 2017

PubMed publication ID

27245157

1 reference

PMC publication ID

4888513