OOIR: Observatory of International Research

Papers

(The median citation count of Applications in Plant Sciences is 2. 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 2022-08-01 to 2026-08-01.)

Article	Citations
	160
	59
A unified framework to investigate and interpret hybrid and allopolyploid biodiversity across biological scales	44
Astragalean819: An Astragalean clade‐specific bait set to resolve phylogenetic relationships in Astragalus	43
Making sense of complexity: Advances in bioinformatics for plant biology	40
Correction to Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes	33
Optimizing efficient PCR‐amplifiable DNA extraction from herbarium specimens	30
Use of electrolyte leakage to assess floral damage after freezing	29
	29
mvh: An R tool to assemble and organize virtual herbaria from openly available specimen images	26
Garryanalyzer: A morphometric workflow and open‐source ImageJ plug‐in for quantitative morphological analysis of Pacific Northwest Quercus leaves	25
Conservation Action Tracker: A tool to identify and monitor conservation actions for tree species	21
Charting the course for new discoveries in polyploid lineages	21
Correction to “A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming”	20
Building capacity in the conservation of exceptional plant species	19
A practical and easy‐to‐scale protocol for removing chlorophylls from leaf extracts	18
Leveraging target enrichment and genome skimming (Hyb‐Seq) of herbarium collections to unlock timber DNA barcoding	17
The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques	17
Supporting long‐term sustainability of ex situ collections using a pedigree‐based population management approach	15
Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections	15
SkelPy: A graphic user interface–based approach for skeletonizing fungal networks	14
	14
Enhancing plant morphological trait identification in herbarium collections through deep learning–based segmentation	13
Experimental methods for wind tunnel studies of seed dispersal by wind	13
Acknowledgment of Reviewers	13

Data‐centric species distribution modeling: Impacts of modeler decisions in a case study of invasive European frog‐bit	12
Expression‐based machine learning models for predicting plant tissue identity	12
A machine learning algorithm for the automatic classification of Phytophthora infestans genotypes into clonal lineages	12
An automated pipeline for supervised classification of petal color from citizen science photographs	12
Non‐model plants: Challenges and solutions	11
Fully automatic extraction of morphological traits from the web: Utopia or reality?	11
	11
	11
Integrating machine learning, deep learning, and image analysis for seed species classification	11
Semi‐automated assessment for NatureServe subnational conservation status ranks for state floras	11
Advances in analyzing and engineering plant metabolic diversity	10
A novel combination of in vitro propagation and hydroponic culture for hybrid cacao (Theobroma cacao) plants	10
Issue Information	10
Are they two seeds in a pod? Comparing seed rain recovery in grasslands using artificial grass carpets versus sticky traps	9
DNA release from plant tissue using focused ultrasound extraction (FUSE)	9
	9
Just add water: A simple floral bud injection method for stable Agrobacterium ‐mediated transformation in two ecotypes of Mimulus	9
A low‐cost protocol for the optical method of vulnerability curves to calculate P₅₀	9
Modified CTAB protocols for high‐molecular‐weight DNA extractions from ferns	9
	8
Review of the cellulose acetate peel method and the physical and digital curation of coal balls	8
Issue Information	7
Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies	7
Detecting introgression from phylogenetic invariant site patterns using machine learning	7
Chromosome‐scale reference genome of Pectocarya recurvata , the species with the smallest reported genome size in Boraginaceae	7
Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species	7
HapAsmbl: A reference‐aided pipeline for assembling haplotypes in Nanopore amplicon sequence data of polymorphic populations	7
Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens	7
An open‐source LED lamp for use with the LI‐6800 photosynthesis system	7
Analysis of plant metabolomics data using identification‐free approaches	7
DNA assays for genetic discrimination of three Phragmites australis subspecies in the United States	6
A new spin on chemotaxonomy: Using non‐proteogenic amino acids as a test case	6
A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming	6
A simple and affordable protocol to assess censer seed dispersal: First confirmation of the mechanism in the genus Solanum	6
PlantSAM: An object detection‐driven segmentation pipeline for herbarium specimens	6
Applying interpretable machine learning to assess intraspecific trait divergence under landscape‐scale population differentiation	6
InDelGT: An integrated pipeline for extracting indel genotypes for genetic mapping in a hybrid population using next‐generation sequencing data	6
Using large language models to extract plant functional traits from unstructured text	6
Animal‐mediated seed dispersal: A review of study methods	6
	6
Optogenetic control of transgene expression in Marchantia polymorpha	6
Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants	6
expowo: An R package for mining global plant diversity and distribution data	5
Issue Information	5
What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol	5
Turning a new leaf: PhenoVision provides leaf phenology data at the global scale	5
A two‐photon fluorescence micro‐spectroscopy method for chemotaxonomic characterization of fossil resins	5
The Computer‐Assisted Sequence Annotation (CASA) workflow for enzyme discovery	5
Using disposable food packaging materials as printing, embedding, and sectioning media in the plant anatomy lab	5
FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes	5

Unlocking fruit dimensions: Quantification of functional traits driving plant–frugivore interactions	5
	5
Correction to GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data	5
A field‐capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring	5
BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more	5
Optimizing the lysis step in CTAB DNA extractions of silica‐dried and herbarium leaf tissues	4
Issue Information	4
infinitylists: A Shiny application and R package for rapid generation of place‐based species checklists	4
Improving computer vision for plant pathology through advanced training techniques	4
Expanded application to plant reproductive tissues of a branched DNA probe‐based in situ hybridization method	4
A simple and cost‐effective method for studying anoxia tolerance in plants	4
Variant calling in polyploids for population and quantitative genetics	4
florabr: An R package to explore and spatialize species distribution using Flora e Funga do Brasil	4
Issue Information	4
Embryo excision in Compositae, with implications for combating biodiversity loss	4
Whole‐genomic DNA amplifications from individually isolated sweet sorghum microspores	4
Evaluation of floral volatile patterns in the genus Narcissus using gas chromatography–coupled ion mobility spectrometry	4
	4
Novel method for the quantification of rosette area from images of Arabidopsis seedlings grown on agar plates	4
Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales	4
Procrustean pseudo‐landmark methods in Python to measure massive quantities of leaf shape data	4
Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans	4
Issue Information	4
From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?	4
HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees	3
	3
Issue Information	3
Ensemble automated approaches for producing high‐quality herbarium digital records	3
A comparison of methods for excluding light from stems to evaluate stem photosynthesis	3
Computer vision species identification of lichens and bryophytes from biocrusts in Australian drylands	3
Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems	3
Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos	3
	3
The sensitivity of reconstructed carbon dioxide concentrations to stomatal preparation methods using a leaf gas exchange model	3
Using photogrammetry to create virtual permanent plots in rare and threatened plant communities	3
Correction to “Conservation applications of niche modeling: Native and naturalized ferns may compete for limited Hawaiian dryland habitat”	3
Issue Information	3
Developing Asparagaceae1726: An Asparagaceae‐specific probe set targeting 1726 loci for Hyb‐Seq and phylogenomics in the family	3
Acclimation and hardening of a slow‐growing woody species emblematic to western North America from in vitro plantlets	3
Efficient homology‐based annotation of transposable elements using minimizers	3
The impact of extraction method and pollen concentration on community composition for pollen metabarcoding	3
Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data	2
Rapid character scoring and tabulation of large leaf‐image libraries using Adobe Bridge	2
	2
A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae	2
Issue Information	2
Tailoring convolutional neural networks for custom botanical data	2
An assessment of methods to combine evolutionary history and conservation: A case study in the Brazilian campo rupestre	2
RootBot: High‐throughput root stress phenotyping robot	2
An artificial neural network–based deep learning model to predict combined stress impact and interaction in plants	2
Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference	2
Creation of a Pseudotsuga menziesii nucellus cell suspension culture system to produce proteins involved in reproduction	2
Calceolariaceae809: A bait set for targeted sequencing of nuclear loci	2
tanggle: An R package for the visualization of phylogenetic networks	2
Looking to the past to inform the future: What eDNA from herbarium specimens can tell us about plant–animal interactions	2
hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution	2
Issue Information	2
Raspberry Pi–powered temperature monitoring of growth chamber microclimates	2