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 2021-09-01 to 2025-09-01.)

Article	Citations
	79
	34
Correction to Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes	29
A unified framework to investigate and interpret hybrid and allopolyploid biodiversity across biological scales	27
Use of electrolyte leakage to assess floral damage after freezing	25
Optimizing efficient PCR‐amplifiable DNA extraction from herbarium specimens	24
mvh: An R tool to assemble and organize virtual herbaria from openly available specimen images	22
Making sense of complexity: Advances in bioinformatics for plant biology	21
Supporting long‐term sustainability of ex situ collections using a pedigree‐based population management approach	20
The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques	20
Building capacity in the conservation of exceptional plant species	18
A practical and easy‐to‐scale protocol for removing chlorophylls from leaf extracts	18
Correction to “A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming”	17
Conservation Action Tracker: A tool to identify and monitor conservation actions for tree species	16
Charting the course for new discoveries in polyploid lineages	14
Data‐centric species distribution modeling: Impacts of modeler decisions in a case study of invasive European frog‐bit	14
Photographic analysis of field‐monitored fern gametophyte development and response to environmental stress	14
An automated pipeline for supervised classification of petal color from citizen science photographs	13
Acknowledgment of Reviewers	12
Expression‐based machine learning models for predicting plant tissue identity	11
Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections	11
	11
Enhancing plant morphological trait identification in herbarium collections through deep learning–based segmentation	10
	9
Protocol to control the invasive alga Avrainvillea lacerata in a shallow Hawaiian reef flat	9

The future of plant science: Applications at the intersection	8
Issue Information	8
	8
Accelerating gametophytic growth in the model hornwort Anthoceros agrestis	8
Fully automatic extraction of morphological traits from the web: Utopia or reality?	8
A machine learning algorithm for the automatic classification of Phytophthora infestans genotypes into clonal lineages	8
	7
Modified CTAB protocols for high‐molecular‐weight DNA extractions from ferns	7
	7
Review of the cellulose acetate peel method and the physical and digital curation of coal balls	7
A low‐cost protocol for the optical method of vulnerability curves to calculate P₅₀	7
DNA release from plant tissue using focused ultrasound extraction (FUSE)	7
A novel combination of in vitro propagation and hydroponic culture for hybrid cacao (Theobroma cacao) plants	7
Providing the missing links in fern life history: Insights from a phenological survey of the gametophyte stage	7
Using marsh organs to test seed recruitment in tidal freshwater marshes	7
Informed cover measurement: Guidelines and error for point‐intercept approaches	7
Advances in analyzing and engineering plant metabolic diversity	7
Issue Information	7
A protocol for the generation of Arachis hypogaea composite plants: A valuable tool for the functional study of mycorrhizal symbiosis	6
	6
Analysis of plant metabolomics data using identification‐free approaches	6
Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens	6
Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies	6
Identifying cryptic fern gametophytes using DNA barcoding: A review	6
Corrigendum	5
Selection on the gametophyte: Modeling alternation of generations in plants	5
Chromosome‐scale reference genome of Pectocarya recurvata, the species with the smallest reported genome size in Boraginaceae	5
Issue Information	5
Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species	5
Using large language models to extract plant functional traits from unstructured text	5
A dormant resource for genome size estimation in ferns: C‐value inference of the Ophioglossaceae using herbarium specimen spores	5
An open‐source LED lamp for use with the LI‐6800 photosynthesis system	5
Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants	5
Issue Information	4
PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data	4
	4
	4
A new spin on chemotaxonomy: Using non‐proteogenic amino acids as a test case	4
DNA assays for genetic discrimination of threePhragmites australissubspecies in the United States	4
Using disposable food packaging materials as printing, embedding, and sectioning media in the plant anatomy lab	4
The Computer‐Assisted Sequence Annotation (CASA) workflow for enzyme discovery	4
A field‐capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring	4
Applying interpretable machine learning to assess intraspecific trait divergence under landscape‐scale population differentiation	4
Choices on sampling, sequencing, and analyzing DNA influence the estimation of community composition of plant fungal symbionts	4
A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming	4
Correction to GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data	4
What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol	4
FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes	4
Optogenetic control of transgene expression in Marchantia polymorpha	4
InDelGT: An integrated pipeline for extracting indel genotypes for genetic mapping in a hybrid population using next‐generation sequencing data	4

expowo: An R package for mining global plant diversity and distribution data	4
Issue Information	3
Issue Information	3
Variant calling in polyploids for population and quantitative genetics	3
infinitylists: A Shiny application and R package for rapid generation of place‐based species checklists	3
Embryo excision in Compositae, with implications for combating biodiversity loss	3
Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts	3
Expanded application to plant reproductive tissues of a branched DNA probe‐based in situ hybridization method	3
Stable isotope mixing models demonstrate the role of an invasive plant in wetland songbird food webs	3
Evaluation of floral volatile patterns in the genus Narcissus using gas chromatography–coupled ion mobility spectrometry	3
Digital morphometrics: Application of MorphoLeaf in shape visualization and species delimitation, using Cucurbitaceae leaves as a model	3
A simple and cost‐effective method for studying anoxia tolerance in plants	3
florabr: An R package to explore and spatialize species distribution using Flora e Funga do Brasil	3
Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?	3
Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales	3
Whole‐genomic DNA amplifications from individually isolated sweet sorghum microspores	3
Calculation of the ovule number in the genus Salix: A method for taxa differentiation	3
BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more	3
Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans	3
Improving computer vision for plant pathology through advanced training techniques	3
	3
Looking to the past to inform the future: What eDNA from herbarium specimens can tell us about plant–animal interactions	2
A comprehensive illustrated protocol for clearing, mounting, and imaging leaf venation networks	2
hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution	2
Issue Information	2
An assessment of methods to combine evolutionary history and conservation: A case study in the Brazilian campo rupestre	2
Developing Asparagaceae1726: An Asparagaceae‐specific probe set targeting 1726 loci for Hyb‐Seq and phylogenomics in the family	2
Efficient homology‐based annotation of transposable elements using minimizers	2
Using photogrammetry to create virtual permanent plots in rare and threatened plant communities	2
Optimizing the lysis step in CTAB DNA extractions of silica‐dried and herbarium leaf tissues	2
The impact of extraction method and pollen concentration on community composition for pollen metabarcoding	2
Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data	2
Issue Information	2
Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference	2
A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae	2
Rapid character scoring and tabulation of large leaf‐image libraries using Adobe Bridge	2
The sensitivity of reconstructed carbon dioxide concentrations to stomatal preparation methods using a leaf gas exchange model	2
Issue Information	2
Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems	2
Issue Information	2
From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?	2
Ensemble automated approaches for producing high‐quality herbarium digital records	2
Tailoring convolutional neural networks for custom botanical data	2
RootBot: High‐throughput root stress phenotyping robot	2
Issue Information	2
Acclimation and hardening of a slow‐growing woody species emblematic to western North America from in vitro plantlets	2
Calceolariaceae809: A bait set for targeted sequencing of nuclear loci	2
Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos	2
	2
A comparison of methods for excluding light from stems to evaluate stem photosynthesis	2
Novel method for the quantification of rosette area from images of Arabidopsis seedlings grown on agar plates	2
	2