OOIR: Observatory of International Research

Papers

(The median citation count of Applications in Plant Sciences is 1. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-11-01 to 2024-11-01.)

Article	Citations
A target enrichment probe set for resolving the flagellate land plant tree of life	52
New targets acquired: Improving locus recovery from the Angiosperms353 probe set	49
High‐throughput methods for efficiently building massive phylogenies from natural history collections	45
HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets	34
On the potential of Angiosperms353 for population genomic studies	28
Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci	24
The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions	24
What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol	23
Composite modeling of leaf shape along shoots discriminates Vitis species better than individual leaves	21
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae	21
Toward genomic selection inPinus taeda: Integrating resources to support array design in a complex conifer genome	20
Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family	19
Algae to angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa	17
A new, simple, highly scalable, and efficient protocol for genomic DNA extraction from diverse plant taxa	17
Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics	17
The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques	16
PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data	15
The ecology and physiology of fern gametophytes: A methodological synthesis	15
Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes	14
Application of remote sensing technology to estimate productivity and assess phylogenetic heritability	14
hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution	12
Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?	12
Supporting long‐term sustainability of ex situ collections using a pedigree‐based population management approach	11
Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts	11
Methodologies for soil extraction and conservation analysis of ferns and lycophytes with belowground gametophytes	11

High‐molecular‐weight DNA extraction for long‐read sequencing of plant genomes: An optimization of standard methods	10
Polishing entire stems and roots using sandpaper under water: An alternative method for macroscopic analyses	10
Evaluation and application of tools for the identification of known microRNAs in plants	10
Identifying cryptic fern gametophytes using DNA barcoding: A review	10
Minimizing the deleterious effects of endophytes in plant shoot tip cryopreservation	10
Comparative chloroplast genomes and phylogenetic analysis of Aquilegia	10
From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2	9
A sick plot–based protocol for dry root rot disease assessment in field‐grown chickpea plants	9
Accelerating gametophytic growth in the model hornwort Anthoceros agrestis	9
Selection on the gametophyte: Modeling alternation of generations in plants	8
Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales	8
Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species	8
Harnessing the power of botanical gardens: Evaluating the costs and resources needed for exceptional plant conservation	8
Modified CTAB protocols for high‐molecular‐weight DNA extractions from ferns	7
Seed dormancy and germination of the endangered exceptional Hawaiian lobelioid Brighamia rockii	7
Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq	7
SSRgenotyper: A simple sequence repeat genotyping application for whole‐genome resequencing and reduced representational sequencing projects	7
Optimizing the lysis step in CTAB DNA extractions of silica‐dried and herbarium leaf tissues	7
Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana)	6
Target capture and genome skimming for plant diversity studies	6
Harnessing aquatic plant growth forms to apply European nutrient‐enrichment bioindicators to Canadian waters	6
Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques	6
Genotypic confirmation of a biased phenotypic sex ratio in a dryland moss using restriction fragment length polymorphisms	6
Asymbiotic in vitro seed germination, in vitro seedling development, and ex vitro acclimatization of Spiranthes	6
A field‐capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring	5
An image‐based technique for automated root disease severity assessment using PlantCV	5
A dormant resource for genome size estimation in ferns: C‐value inference of the Ophioglossaceae using herbarium specimen spores	5
Calculation of the ovule number in the genus Salix: A method for taxa differentiation	5
Providing the missing links in fern life history: Insights from a phenological survey of the gametophyte stage	5
Long‐read genotyping with SLANG (Simple Long‐read loci Assembly of Nanopore data for Genotyping)	5
Integrating tissue‐direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field	5
A metabarcoding protocol targeting two DNA regions to analyze root‐associated fungal communities in ferns and lycophytes	5
Using marsh organs to test seed recruitment in tidal freshwater marshes	5
Digital morphometrics: Application of MorphoLeaf in shape visualization and species delimitation, using Cucurbitaceae leaves as a model	5
A low‐cost high‐throughput phenotyping system for automatically quantifying foliar area and greenness	5
Photographic analysis of field‐monitored fern gametophyte development and response to environmental stress	5
Informed cover measurement: Guidelines and error for point‐intercept approaches	4
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids	4
Measuring volatile emissions from moss gametophytes: A review of methodologies and new applications	4
Using acetone for rapid PCR‐amplifiable DNA extraction from recalcitrant woody plant taxa	4
Can alpine plant species “bank” on conservation?: Using artificial aging to understand seed longevity	4
Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits	4
A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming	4
TagSeq for gene expression in non‐model plants: A pilot study at the Santa Rita Experimental Range NEON core site	4
Virus‐induced gene silencing as a tool for functional studies in Cleome violacea	4
Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos	4
An automated pipeline for supervised classification of petal color from citizen science photographs	4
Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens	4
Bringing genomics to the field: An integrative approach to seed sourcing for forest restoration	3
Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest	3

A pipeline for the rapid collection of color data from photographs	3
Techniques for locating and analyzing subterranean Lycopodium and Diphasiastrum gametophytes in the field	3
Choices on sampling, sequencing, and analyzing DNA influence the estimation of community composition of plant fungal symbionts	3
Evaluation of floral volatile patterns in the genus Narcissus using gas chromatography–coupled ion mobility spectrometry	3
Rapid character scoring and tabulation of large leaf‐image libraries using Adobe Bridge	3
Computer vision for plant pathology: A review with examples from cocoa agriculture	3
Efficient homology‐based annotation of transposable elements using minimizers	3
Evaluation of sampling effort required to assess pollen species richness on pollinators using rarefaction	3
Stable isotope mixing models demonstrate the role of an invasive plant in wetland songbird food webs	3
Rapid imaging in the field followed by photogrammetry digitally captures the otherwise lost dimensions of plant specimens	3
GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data	3
Research inequity in the plant sciences	3
Humans in the loop: Community science and machine learning synergies for overcoming herbarium digitization bottlenecks	2
Acclimation and hardening of a slow‐growing woody species emblematic to western North America from in vitro plantlets	2
FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes	2
Integrated plant conservation through the Global Conservation Consortia	2
A maceration technique for soft plant tissue without hazardous chemicals	2
An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex	2
A standardized and efficient technique to estimate seed traits in plants with numerous small propagules	2
Estimating herbarium specimen digitization rates: Accounting for human experience	2
Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology	2
Optimizing efficient PCR‐amplifiable DNA extraction from herbarium specimens	2
Sequencing vs. amplification for the estimation of allele dosages in sugarcane (Saccharum spp.)	2
DNA release from plant tissue using focused ultrasound extraction (FUSE)	2
Development of a petal protoplast transfection system for Sinningia speciosa	2
Unfurling an improved method for visualizing mitotic chromosomes in ferns	2
Using photogrammetry to create virtual permanent plots in rare and threatened plant communities	2
Thallus hydrophobicity: A low‐cost method for understanding lichen ecophysiological responses to environmental changes	2
Conservation Action Tracker: A tool to identify and monitor conservation actions for tree species	2
Does sorting by color using visible and high‐energy violet light improve classification of taxa in honey bee pollen pellets?	2
Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data	2
Reference‐free discovery of nuclear SNPs permits accurate, sensitive identification of Carya (hickory) species and hybrids	2
CuticleTrace: A toolkit for capturing cell outlines from leaf cuticle with implications for paleoecology and paleoclimatology	2
Improving culture initiation of mature oak shoots through use of silver thiosulfate	2
3D pollination biology using micro‐computed tomography and geometric morphometrics in Theobroma cacao	2
Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections	2
An efficient, high‐throughput method for the simultaneous exposure of drought stress and bacterial infection in plants	2
nQuack: An R package for predicting ploidal level from sequence data using site‐based heterozygosity	2
A protocol for the generation of Arachis hypogaea composite plants: A valuable tool for the functional study of mycorrhizal symbiosis	2
Making sense of complexity: Advances in bioinformatics for plant biology	1
A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae	1
Genome‐wide patterns of homoeologous gene flow in allotetraploid coffee	1
An assessment of methods to combine evolutionary history and conservation: A case study in the Brazilian campo rupestre	1
Seed classification with random forest models	1
Improved image processing for 3D virtual object construction from serial sections reveals tissue patterns in root tips of Zea mays	1
Using disposable food packaging materials as printing, embedding, and sectioning media in the plant anatomy lab	1
A comparison of methods for excluding light from stems to evaluate stem photosynthesis	1
High‐speed video and plant ultrastructure define mechanisms of gametophyte dispersal	1
Charting the course for new discoveries in polyploid lineages	1
Variant calling in polyploids for population and quantitative genetics	1
Simulating pollen flow and field sampling constraints helps revise seed sampling recommendations for conserving genetic diversity	1
Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies	1
Use of electrolyte leakage to assess floral damage after freezing	1
Advances, applications, and prospects in aquatic botany	1
An inexpensive moist chamber culture technique for finding microbiota on live tree bark	1
Emerging methods in botanical DNA/RNA extraction	1
Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems	1
Data‐centric species distribution modeling: Impacts of modeler decisions in a case study of invasive European frog‐bit	1
Spatially resolved detection of small molecules from press‐dried plant tissue using MALDI imaging	1
expowo: An R package for mining global plant diversity and distribution data	1
Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants	1
Efficient imaging and computer vision detection of two cell shapes in young cotton fibers	1
A roadmap of phylogenomic methods for studying polyploid plant genera	1
RootBot: High‐throughput root stress phenotyping robot	1
How dense can you be? New automatic measures of vein density in angiosperm leaves	1
florabr: An R package to explore and spatialize species distribution using Flora e Funga do Brasil	1
An updated and extended version of the Melastomataceae probe set for target capture	1
Protocol to control the invasive alga Avrainvillea lacerata in a shallow Hawaiian reef flat	1
Novel method for the quantification of rosette area from images of Arabidopsis seedlings grown on agar plates	1
An experimental assessment of competitive interactions between sexual and apomictic fern gametophytes using Easy Leaf Area	1
Advancing the science and practice of rare plant conservation with the Center for Plant Conservation Reintroduction Database	1
Building capacity in the conservation of exceptional plant species	1
Capturing and managing genetic diversity in ex situ collections of threatened tropical trees: A case study in Karomia gigas	1