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List of works by Jim Leebens-Mack

A COMBINED 18S rDNA AND rbcL PHYLOGENETIC ANALYSIS OF CHLOROMONAS AND CHLAMYDOMONAS (CHLOROPHYCEAE, VOLVOCALES) EMPHASIZING SNOW AND OTHER COLD-TEMPERATURE HABITATS1

article

A Century of Sex Determination in Flowering Plants

scientific article

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

Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach

scientific article

Altered Gene Regulatory Networks Are Associated With the Transition From C to Crassulacean Acid Metabolism in (Oncidiinae: Orchidaceae)

article

An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers

scientific article published on 23 August 2006

Ancestral polyploidy in seed plants and angiosperms

scientific article (publication date: 5 May 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

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

ChloroplastDB: the Chloroplast Genome Database

scientific article

Comparative genomic analyses in Asparagus

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

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

scientific article

Complex scaffold remodeling in plant triterpene biosynthesis

scientific article published on 26 January 2023

Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids

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)

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

article

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

scientific article

Distributed phenomics with the unPAK project reveals the effects of mutations

scientific article published on 09 July 2019

EST clustering error evaluation and correction

scientific article published on 9 June 2004

Elucidation of the pathway for biosynthesis of saponin adjuvants from the soapbark tree

scientific article published on 23 March 2023

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

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae).

scientific article

Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land

article

Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications.

scientific article

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

scientific article published on 09 November 2005

Floral gene resources from basal angiosperms for comparative genomics research

scientific article

Floral homeotic C function genes repress specific B function genes in the carpel whorl of the basal eudicot California poppy (Eschscholzia californica)

scientific article

Gas exchange and leaf anatomy of a C3-CAM hybrid, Yucca gloriosa (Asparagaceae)

scientific article published on 29 December 2015

Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants

scientific article published on 17 October 2014

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

scientific article published in Nature Communications

Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification

scientific article

HOST SPECIFICITY AND THE GENETIC STRUCTURE OF TWO YUCCA MOTH SPECIES IN A YUCCA HYBRID ZONE

scientific article published on 01 October 1998

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

Homoploid hybrid origin of Yucca gloriosa: intersectional hybrid speciation in Yucca (Agavoideae, Asparagaceae)

scientific article (publication date: September 2012)

Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, <i>Yucca gloriosa</i> (Asparagaceae)

scientific article published on 01 January 2020

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

scientific article published on 02 September 2021

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

scientific article

Insights into the Musa genome: syntenic relationships to rice and between Musa species

scientific article

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

scientific article

Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species, Yucca gloriosa

scientific article published on 13 March 2020

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

scientific article (publication date: 25 December 2010)

Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes

scientific article

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

scientific article published on 24 November 2008

Orchid phylogenomics and multiple drivers of their extraordinary diversification

scientific article

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

scientific article

Pattern and timing of diversification in Yucca (Agavaceae): specialized pollination does not escalate rates of diversification

scientific article (publication date: 7 February 2008)

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

Patterns of genetic structure among populations of an oligophagous pollinating yucca moth (Tegeticula yuccasella).

scientific article

Patterns of speciation in the Yucca moths: parallel species radiations within the Tegeticula yuccasella species complex

scientific article

PhylOnt: A domain-specific ontology for phylogeny analysis

scholarly article published October 2012

Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences.

scientific article published on 26 December 2013

Phylogenomic analyses of species relationships in the genus<i>Sabal</i>(Arecaceae) using targeted sequence capture

scientific article published on 14 May 2015

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 and genome evolution of the Cypripedioideae (Orchidaceae)

scientific article published on 02 April 2018

Phylotranscriptomic analysis of the origin and early diversification of land plants

scientific article

Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots

scientific article published on 12 July 2018

Plant Comparative and Functional Genomics

scientific article published on 31 December 2015

Plant reproductive genomics at the Plant and Animal Genome Conference

scientific article (publication date: 2005)

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

scientific article

Pollination biology in hybridizing Baptisia (Fabaceae) populations

scientific article published on 01 April 1998

Polyploidy and angiosperm diversification ⬇️

scientific article published on January 1, 2009

Power analysis of tests for loss of selective constraint in cave crayfish and nonphotosynthetic plant lineages

scientific article published in August 2002

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

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

scientific article

Representing sex chromosomes in genome assemblies

scientific article published on 04 May 2022

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

scientific article (publication date: 2014)

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

scientific article published on 24 June 2016

Reversal of Mutualism as a Mechanism for Adaptive Radiation in Yucca Moths

scientific article published on 01 October 2000

Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants

scientific article published on 18 December 2019

Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis).

scientific article

Shared expression of crassulacean acid metabolism (CAM) genes pre-dates the origin of CAM in the genus Yucca

scientific article published on 01 November 2019

Single Nucleotide Polymorphism–based Genetic Diversity in the Reference Set of Peanut ( spp.) by Developing and Applying Cost-Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays

scientific article published in 2013

Single nucleotide polymorphism isolated from a novel EST dataset in garden asparagus (Asparagus officinalis L.).

scientific article

Single nucleotide polymorphism-based parentage analysis and population structure in garden asparagus, a worldwide genetic stock classification

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

scientific article

Target‐enrichment sequencing reveals for the first time a well‐resolved phylogeny of the core Bromelioideae (family Bromeliaceae) ⬇️

scientific article published on 28 November 2022

The Amborella genome: an evolutionary reference for plant biology

scientific article

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

scientific article

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

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 banana (Musa acuminata) genome and the evolution of monocotyledonous plants

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 CHROMOMETHYLASES and gene body DNA methylation 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 evolutionary ecology of "mutual services" in the 21st century

scientific article published on 26 October 2016

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

scientific article (publication date: August 2007)

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

scientific article published in 2011

The impact of multiple protein sequence alignment on phylogenetic estimation

scientific article

The minimum information about a genome sequence (MIGS) specification

scientific article

The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage ⬇️

scientific article (publication date: 11 June 2012)

The phylogeny of yuccas

scientific article published on 31 December 2006

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

scientific article

To B or Not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms.

scientific article

Towards improved reconstruction of ancestral gene order in angiosperm phylogeny

scientific article published in October 2009

Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae)

scientific article (publication date: 2 June 2009)

Using partial genomic fosmid libraries for sequencing complete organellar genomes.

scientific article published in July 2006

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

Yucca aloifolia (Asparagaceae) opts out of an obligate pollination mutualism.

scientific article published on 26 November 2014

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