List of works - Joseph Christopher Pires

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales

scientific article published on 17 March 2016

A genome triplication associated with early diversification of the core eudicots

scientific article (publication date: 26 January 2012)

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

scientific article

A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

scientific article

Affordable remote monitoring of plant growth in facilities using Raspberry Pi computers

scientific article published on 12 August 2019

Allopolyploidization lays the foundation for evolution of distinct populations: evidence from analysis of synthetic Arabidopsis allohexaploids

scientific article

Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy

scientific article published on 2 February 2012

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

scientific article published on 30 June 2013

Analysis of B-genome chromosome introgression in interspecific hybrids of Brassica napus × B. carinata

scientific article

Are all sex chromosomes created equal?

scientific article published on September 2011

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

scholarly article by Thomas J. Givnish et al published 27 December 2010 in Annals of the Missouri Botanical Garden

Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

scientific article published in Scientific Reports

Building a feral future: Open questions in crop ferality

scientific article published in 2023

Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence

scientific article published on 14 July 2009

Comparative genetics at the gene and chromosome levels between rice ( Oryza sativa) and wildrice ( Zizania palustris).

scientific article published on 5 August 2003

Complementing model species with model clades

scientific article published on 12 October 2023

Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis

scientific article

Contrasting patterns of support among plastid genes and genomes for major clades of the monocotyledons

article

Convergent evolution of polyploid genomes from across the eukaryotic tree of life

scientific article published on 01 May 2022

De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa.

scientific article published on 5 August 2011

Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence.

scientific article published on 3 January 2014

Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

scientific article

Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells

scientific article published on June 2015

Epigenetic regulation of flowering time in polyploids

scientific article published on 04 April 2011

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes

scientific article

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism

scientific article published on 12 June 2015

Functional characterization of SMN evolution in mouse models of SMA

scientific article published on 01 July 2019

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

scientific article

Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus.

scientific article

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses

scientific article published on 19 October 2017

Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype

scientific article

Genomic inferences of domestication events are corroborated by written records inBrassica rapa

Genomic insights into the origin, domestication and diversification of Brassica juncea

scientific article published on 06 September 2021

Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding

scientific article published in 2022

Getting up to speed

scientific article published on 04 April 2012

Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants.

scientific article published on 16 September 2016

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

scientific article published on 10 January 2018

Homoeologous recombination in allopolyploids: the polyploid ratchet

scientific article published on December 2009

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

scientific article (publication date: 10 May 2011)

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

scientific article

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

scientific article

Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7.

scientific article published on 13 July 2010

Long identical multispecies elements in plant and animal genomes

scientific article

Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis

scientific article published on 4 September 2012

Mitotic instability in resynthesized and natural polyploids of the genus Arabidopsis (Brassicaceae).

scientific article published on 13 August 2009

Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors.

scientific article

Nonadditive gene expression in polyploids

scientific article

Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids

scientific article published on 23 December 2005

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).

scientific article

Phylogeny and multiple independent whole-genome duplication events in the Brassicales

scientific article published on 24 August 2020

Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)

scientific article published on 02 April 2018

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

scientific article published on 21 August 2014

Polyphyly and convergent morphological evolution in Commelinales and Commelinidae: evidence from rbcL sequence data.

scientific article

Preface

scientific article published on 13 July 2010

Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods

scientific article

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

scientific article

Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae).

scientific article

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny

scientific article

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

scientific article (publication date: 3 November 2009)

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

scientific article published on 24 June 2016

Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa-B. oleracea monosomic alien addition lines.

scientific article

Selection for higher gene copy number after different types of plant gene duplications

scientific article published on 4 November 2011

Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species

scientific article

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

scientific article published on 16 August 2017

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

scientific article

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

scientific article

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

scientific article published on 2 November 2017

The butterfly plant arms-race escalated by gene and genome duplications

scientific article

The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects

scientific article

The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa

scientific article published on January 2013

The genome of the mesopolyploid crop species Brassica rapa

scientific article (publication date: 28 August 2011)

The pangenome of an agronomically important crop plant Brassica oleracea

scientific article published on 11 November 2016

The renaissance of comparative biochemistry

scientific article published on 10 January 2019

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae).

scientific article

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

scientific article

Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus

scientific article published on 28 June 2019

Understanding mechanisms of novel gene expression in polyploids

scientific article

Watching the grin fade: tracing the effects of polyploidy on different evolutionary time scales

scientific article published on March 2013

List of works by Joseph Christopher Pires

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales

A genome triplication associated with early diversification of the core eudicots

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

Affordable remote monitoring of plant growth in facilities using Raspberry Pi computers

Allopolyploidization lays the foundation for evolution of distinct populations: evidence from analysis of synthetic Arabidopsis allohexaploids

Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Analysis of B-genome chromosome introgression in interspecific hybrids of Brassica napus × B. carinata

Are all sex chromosomes created equal?

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

Building a feral future: Open questions in crop ferality

Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence

Comparative genetics at the gene and chromosome levels between rice ( Oryza sativa) and wildrice ( Zizania palustris).

Complementing model species with model clades

Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis

Contrasting patterns of support among plastid genes and genomes for major clades of the monocotyledons

Convergent evolution of polyploid genomes from across the eukaryotic tree of life

De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa.

Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence.

Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells

Epigenetic regulation of flowering time in polyploids

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism

Functional characterization of SMN evolution in mouse models of SMA

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus.

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses

Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype

Genomic inferences of domestication events are corroborated by written records inBrassica rapa

Genomic insights into the origin, domestication and diversification of Brassica juncea

Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding

Getting up to speed

Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants.

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

Homoeologous recombination in allopolyploids: the polyploid ratchet

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7.

Long identical multispecies elements in plant and animal genomes

Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis

Mitotic instability in resynthesized and natural polyploids of the genus Arabidopsis (Brassicaceae).

Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors.

Nonadditive gene expression in polyploids

Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).

Phylogeny and multiple independent whole-genome duplication events in the Brassicales

Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Polyphyly and convergent morphological evolution in Commelinales and Commelinidae: evidence from rbcL sequence data.

Preface

Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae).

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa-B. oleracea monosomic alien addition lines.

Selection for higher gene copy number after different types of plant gene duplications

Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

The butterfly plant arms-race escalated by gene and genome duplications

The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects

The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa

The genome of the mesopolyploid crop species Brassica rapa

The pangenome of an agronomically important crop plant Brassica oleracea

The renaissance of comparative biochemistry

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae).

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus

Understanding mechanisms of novel gene expression in polyploids

Watching the grin fade: tracing the effects of polyploidy on different evolutionary time scales