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List of works by Claude W dePamphilis

"Stealth dissemination" of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma

scientific article published on 28 September 2017

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

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach

scientific article published on 9 February 2006

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

scientific article

Ancestral chloroplast polymorphism and historical secondary contact in a broad hybrid zone ofAesculus(Sapindaceae) ⬇️

scientific article published on March 1, 2006

Ancestral polyploidy in seed plants and angiosperms

scientific article (publication date: 5 May 2011)

Antiquity and evolution of the MADS-box gene family controlling flower development in plants

scientific article (publication date: September 2003)

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

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella

scientific article published in December 2013

Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies.

scientific article

Chasing the hare - evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae).

scientific article

ChloroplastDB: the Chloroplast Genome Database

scientific article

Comparative Metabolomics of Early Development of the Parasitic Plants Phelipanche aegyptiaca and Triphysaria versicolor

scientific article published on 13 June 2019

Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty.

scientific article

Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies ⬇️

scientific article published on October 15, 2010

Comparison of next generation sequencing technologies for transcriptome characterization

scientific article

Compensatory sequence variation between -species small RNAs and their target sites

scientific article published on 17 December 2019

Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids

scientific article

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower

scientific article (publication date: 28 December 2010)

Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events

scientific article

Conservation and divergence of microRNAs in Populus

scientific article

Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants

scientific article published on 22 July 2019

Data access for the 1,000 Plants (1KP) project

scientific article

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum

scientific article

Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae)

scientific article

Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae

scientific article published on 15 December 2013

Dissecting the contributions of dispersal and host properties to the local abundance of a tropical mistletoe

scientific article published in 2017

ELECTROPHORETIC CONFIRMATION OF INTERSPECIFIC HYBRIDIZATION IN AESCULUS (HIPPOCASTANACEAE) AND THE GENETIC STRUCTURE OF A BROAD HYBRID ZONE.

scientific article published on August 1990

EST clustering error evaluation and correction

scientific article published on 9 June 2004

EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot

scientific article published on 17 August 2006

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

scientific article

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species

scientific article

Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis

scientific article published on 09 November 2005

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

article

Functional genomics of a generalist parasitic plant: laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression.

scientific article

Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao

scientific article published on 01 January 2020

Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries

scientific article

Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat.

scientific article

Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism

scientific article published on 12 September 2019

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

scientific article

Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

article by Vikram A Misra et al published 14 May 2019 in BMC Plant Biology

Genomics of sorghum local adaptation to a parasitic plant

scientific article published on 11 February 2020

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

scientific article published on 10 September 2020

Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications

scientific article published on 31 October 2003

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation.

scientific article

Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella.

scientific article

Hybridization and Introgression in Buckeyes (Aesculus: Hippocastanaceae): A Review of the Evidence and a Hypothesis to Explain Long-Distance Gene Flow

article published in 1989

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

scientific article

In silico identification and structure function analysis of a putative coclaurine N-methyltransferase from Aristolochia fimbriata

scientific article published on 11 January 2020

Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome

scientific article published on 02 September 2021

Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants

scientific article

Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum

scientific article (publication date: August 2016)

Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants.

scientific article

Methods for obtaining and analyzing whole chloroplast genome sequences.

scientific article

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs

scientific article published in January 2018

Missing links: the genetic architecture of flowers [correction of flower] and floral diversification

scientific article

Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants

scientific article

Molecular Phylogenetic And Evolutionary Studies Of Parasitic Plants

scientific article

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots

scientific article published in 2018

Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora

scientific article published on 31 December 2018

Parallel loss of plastid introns and their maturase in the genus Cuscuta

scientific article

Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth

scientific article published on 23 April 2007

Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae)

scientific article published on 01 January 2022

Phylogenetic analysis of pectin-related gene families in Physcomitrella patens and nine other plant species yields evolutionary insights into cell walls

scientific article

Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families.

scientific article published in August 2008

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

scientific article

Phylotranscriptomic analysis of the origin and early diversification of land plants

scientific article

Plant science. Genomic-scale exchange of mRNA between a parasitic plant and its hosts

scientific article

Plant-based FRET biosensor discriminates environmental zinc levels

scientific article

PlantTribes: a gene and gene family resource for comparative genomics in plants

scientific article

Poplar maintains zinc homeostasis with heavy metal genes HMA4 and PCS1.

scientific article published on 19 April 2011

RNA viruses in hymenopteran pollinators: evidence of inter-Taxa virus transmission via pollen and potential impact on non-Apis hymenopteran species

scientific article

Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function

scientific article

Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor

scientific article published on 01 August 2019

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

scientific article published on 5 January 2016

Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages

scientific article

Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae).

scientific article

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

scientific article

The Amborella genome: an evolutionary reference for plant biology

scientific article

The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats

scientific article published in November 2002

The Evolution of Parasitism in Scrophulariaceae/Orobanchaceae: Plastid Gene Sequences Refute an Evolutionary Transition Series

scientific article (publication date: 1999)

The Hemiparasitic Plant Phtheirospermum (Orobanchaceae) Is Polyphyletic and Contains Cryptic Species in the Hengduan Mountains of Southwest China.

scientific article published on 9 February 2018

The Parasitic Plant Genome Project: New Tools for Understanding the Biology of Orobanche and Striga

article

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants

scientific article

The TvPirin gene is necessary for haustorium development in the parasitic plant Triphysaria versicolor

scientific article published on 29 November 2011

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

scientific article

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

scientific article

The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral populus diploid

scientific article published in January 2008

The evolution of parasitism in plants

scientific article

The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history

scientific article

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

scientific article published on 22 March 2011

The evolutionary history of ferns inferred from 25 low-copy nuclear genes

scientific article

The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression

scientific article (publication date: August 2007)

The impact of multiple protein sequence alignment on phylogenetic estimation

scientific article

The minimum information about a genome sequence (MIGS) specification

scientific article

Towards improved reconstruction of ancestral gene order in angiosperm phylogeny

scientific article published in October 2009

Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata

scientific article published on 28 July 2014

Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis ⬇️

scientific article published on December 8, 2011

Transcriptomics of Differential Ripening in ‘d’Anjou’ Pear (Pyrus communis L.)

scientific article

Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (<i>Striga hermonthica</i>)

scientific article published on 10 June 2019

Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family

article

Utility of Amborella trichopoda and Nuphar advena Expressed Sequence Tags for Comparative Sequence Analysis

scientific article published on November 2008

Widespread genome duplications throughout the history of flowering plants

scientific article

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