List of works - Manuel Irimia

A compendium of RNA-binding motifs for decoding gene regulation.

scientific article

The evolutionary landscape of alternative splicing in vertebrate species

scientific article

Elephant shark genome provides unique insights into gnathostome evolution

scientific article (publication date: 9 January 2014)

Widespread intron retention in mammals functionally tunes transcriptomes

scientific article

Tissue-specific alternative splicing remodels protein-protein interaction networks

scientific article published in June 2012

A highly conserved program of neuronal microexons is misregulated in autistic brains

scientific article published on December 2014

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

scientific article

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.

scientific article published on 05 June 2013

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

scientific article

5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary

scientific article

A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals

scientific article published on August 2012

Alternative splicing: decoding an expansive regulatory layer

scientific article published on 30 March 2012

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

scientific article

A global regulatory mechanism for activating an exon network required for neurogenesis

scientific article published on 11 September 2014

Origin of introns by ‘intronization’ of exonic sequences

article

Transphyletic conservation of developmental regulatory state in animal evolution

scientific article

Regulated aggregative multicellularity in a close unicellular relative of metazoa

scientific article published on 24 December 2013

Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing

scientific article

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development

scientific article

An alternative splicing event amplifies evolutionary differences between vertebrates

scientific article

Spliceosomal introns as tools for genomic and evolutionary analysis

scientific article (publication date: March 2008)

Coevolution of genomic intron number and splice sites

scientific article published on 18 April 2007

Mystery of intron gain: new data and new models

scientific article

Origin of spliceosomal introns and alternative splicing

scientific article

Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome

scientific article

Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus

scientific article published on 11 June 2008

Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates

scientific article published on 03 January 2013

Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer

scientific article published on September 2010

When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis

scientific article

Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis

scientific article published in 2007

Amphioxus functional genomics and the origins of vertebrate gene regulation

scientific article published in Nature

Distinct types of disorder in the human proteome: functional implications for alternative splicing

scientific article

Splicing in the eukaryotic ancestor: form, function and dysfunction

scientific article

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

scientific article

CpG island promoter hypermethylation of the Ras-effector gene NORE1A occurs in the context of a wild-type K-ras in lung cancer

scientific article

Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata.

scientific article published on 24 May 2007

High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae

scientific article published in February 2007

Quantitative regulation of alternative splicing in evolution and development

scientific article published on January 2009

Widespread recurrent evolution of genomic features

scientific article

Postnatal isoform switch and protein localization of LEF1 and TCF7L2 transcription factors in cortical, thalamic, and mesencephalic regions of the adult mouse brain

scientific article

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

scientific article (publication date: April 2012)

Convergent evolution of clustering of Iroquois homeobox genes across metazoans.

scientific article

Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax

scientific article (publication date: June 2008)

Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1.

scientific article published in January 2012

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians

scientific article published on 09 August 2016

Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes

scientific article published on 17 July 2006

The alternative splicing factor Nova2 regulates vascular development and lumen formation

scientific article

Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates

scientific article

Internal and external paralogy in the evolution of tropomyosin genes in metazoans

scientific article

Complex selection on 5' splice sites in intron-rich organisms

scientific article published on 10 September 2009

List of works by Manuel Irimia

A compendium of RNA-binding motifs for decoding gene regulation.

The evolutionary landscape of alternative splicing in vertebrate species

Elephant shark genome provides unique insights into gnathostome evolution

Widespread intron retention in mammals functionally tunes transcriptomes

Tissue-specific alternative splicing remodels protein-protein interaction networks

A highly conserved program of neuronal microexons is misregulated in autistic brains

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary

A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals

Alternative splicing: decoding an expansive regulatory layer

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

A global regulatory mechanism for activating an exon network required for neurogenesis

Origin of introns by ‘intronization’ of exonic sequences

Transphyletic conservation of developmental regulatory state in animal evolution

Regulated aggregative multicellularity in a close unicellular relative of metazoa

Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development

An alternative splicing event amplifies evolutionary differences between vertebrates

Spliceosomal introns as tools for genomic and evolutionary analysis

Coevolution of genomic intron number and splice sites

Mystery of intron gain: new data and new models

Origin of spliceosomal introns and alternative splicing

Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome

Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus

Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates

Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer

When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis

Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis

Amphioxus functional genomics and the origins of vertebrate gene regulation

Distinct types of disorder in the human proteome: functional implications for alternative splicing

Splicing in the eukaryotic ancestor: form, function and dysfunction

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

CpG island promoter hypermethylation of the Ras-effector gene NORE1A occurs in the context of a wild-type K-ras in lung cancer

Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata.

High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae

Quantitative regulation of alternative splicing in evolution and development

Widespread recurrent evolution of genomic features

Postnatal isoform switch and protein localization of LEF1 and TCF7L2 transcription factors in cortical, thalamic, and mesencephalic regions of the adult mouse brain

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

Convergent evolution of clustering of Iroquois homeobox genes across metazoans.

Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax

Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1.

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians

Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes

The alternative splicing factor Nova2 regulates vascular development and lumen formation

Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates

Internal and external paralogy in the evolution of tropomyosin genes in metazoans

Complex selection on 5' splice sites in intron-rich organisms