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 2021-05-01 to 2025-05-01.)

Article	Citations
Issue Information	66
Issue Information	55
Optimizing efficient PCR‐amplifiable DNA extraction from herbarium specimens	46
Use of electrolyte leakage to assess floral damage after freezing	37
A unified framework to investigate and interpret hybrid and allopolyploid biodiversity across biological scales	30
	25
Correction to Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes	25
	24
Making sense of complexity: Advances in bioinformatics for plant biology	24
mvh: An R tool to assemble and organize virtual herbaria from openly available specimen images	22
Building capacity in the conservation of exceptional plant species	22
Supporting long‐term sustainability of ex situ collections using a pedigree‐based population management approach	19
The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques	19
Charting the course for new discoveries in polyploid lineages	18
Photographic analysis of field‐monitored fern gametophyte development and response to environmental stress	18
Correction to “A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming”	18
Conservation Action Tracker: A tool to identify and monitor conservation actions for tree species	18
Data‐centric species distribution modeling: Impacts of modeler decisions in a case study of invasive European frog‐bit	17
An automated pipeline for supervised classification of petal color from citizen science photographs	16
Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections	16
	15
Acknowledgment of Reviewers	15
Polishing entire stems and roots using sandpaper under water: An alternative method for macroscopic analyses	14
Expression‐based machine learning models for predicting plant tissue identity	13
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae	13

	11
Enhancing plant morphological trait identification in herbarium collections through deep learning–based segmentation	11
A machine learning algorithm for the automatic classification of Phytophthora infestans genotypes into clonal lineages	11
The future of plant science: Applications at the intersection	11
	10
Protocol to control the invasive alga Avrainvillea lacerata in a shallow Hawaiian reef flat	10
DNA release from plant tissue using focused ultrasound extraction (FUSE)	9
	9
Modified CTAB protocols for high‐molecular‐weight DNA extractions from ferns	8
	8
Informed cover measurement: Guidelines and error for point‐intercept approaches	8
Issue Information	8
Accelerating gametophytic growth in the model hornwort Anthoceros agrestis	8
HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets	7
Providing the missing links in fern life history: Insights from a phenological survey of the gametophyte stage	7
New targets acquired: Improving locus recovery from the Angiosperms353 probe set	7
	7
Using marsh organs to test seed recruitment in tidal freshwater marshes	7
A low‐cost protocol for the optical method of vulnerability curves to calculate P₅₀	7
Review of the cellulose acetate peel method and the physical and digital curation of coal balls	7
Issue Information	7
Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies	6
Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens	6
A protocol for the generation of Arachis hypogaea composite plants: A valuable tool for the functional study of mycorrhizal symbiosis	6
Analysis of plant metabolomics data using identification‐free approaches	6
	6
Identifying cryptic fern gametophytes using DNA barcoding: A review	6
Issue Information	5
Corrigendum	5
Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics	5
Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species	5
An open‐source LED lamp for use with the LI‐6800 photosynthesis system	5
Selection on the gametophyte: Modeling alternation of generations in plants	5
	5
A dormant resource for genome size estimation in ferns: C‐value inference of the Ophioglossaceae using herbarium specimen spores	5
Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants	5
Choices on sampling, sequencing, and analyzing DNA influence the estimation of community composition of plant fungal symbionts	4
A new spin on chemotaxonomy: Using non‐proteogenic amino acids as a test case	4
	4
A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming	4
Optogenetic control of transgene expression in Marchantia polymorpha	4
expowo: An R package for mining global plant diversity and distribution data	4
DNA assays for genetic discrimination of threePhragmites australissubspecies in the United States	4
Issue Information	4
	4
InDelGT: An integrated pipeline for extracting indel genotypes for genetic mapping in a hybrid population using next‐generation sequencing data	4
Using disposable food packaging materials as printing, embedding, and sectioning media in the plant anatomy lab	4
Correction to GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data	4
Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana)	3
Whole‐genomic DNA amplifications from individually isolated sweet sorghum microspores	3

What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol	3
Digital morphometrics: Application of MorphoLeaf in shape visualization and species delimitation, using Cucurbitaceae leaves as a model	3
Embryo excision in Compositae, with implications for combating biodiversity loss	3
Issue Information	3
Evaluation of floral volatile patterns in the genus Narcissus using gas chromatography–coupled ion mobility spectrometry	3
FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes	3
PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data	3
Stable isotope mixing models demonstrate the role of an invasive plant in wetland songbird food webs	3
Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts	3
Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?	3
florabr: An R package to explore and spatialize species distribution using Flora e Funga do Brasil	3
BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more	3
A field‐capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring	3
Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales	3
Issue Information	2
The impact of extraction method and pollen concentration on community composition for pollen metabarcoding	2
Using photogrammetry to create virtual permanent plots in rare and threatened plant communities	2
A simple and cost‐effective method for studying anoxia tolerance in plants	2
	2
Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems	2
Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos	2
	2
Acclimation and hardening of a slow‐growing woody species emblematic to western North America from in vitro plantlets	2
Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits	2
Ensemble automated approaches for producing high‐quality herbarium digital records	2
Efficient homology‐based annotation of transposable elements using minimizers	2
Optimizing the lysis step in CTAB DNA extractions of silica‐dried and herbarium leaf tissues	2
Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans	2
The sensitivity of reconstructed carbon dioxide concentrations to stomatal preparation methods using a leaf gas exchange model	2
Issue Information	2
Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference	2
Rapid character scoring and tabulation of large leaf‐image libraries using Adobe Bridge	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
Novel method for the quantification of rosette area from images of Arabidopsis seedlings grown on agar plates	2
A comparison of methods for excluding light from stems to evaluate stem photosynthesis	2
Calculation of the ovule number in the genus Salix: A method for taxa differentiation	2
From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?	2
Variant calling in polyploids for population and quantitative genetics	2
	2
	2
Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data	2
Issue Information	2
Improving culture initiation of mature oak shoots through use of silver thiosulfate	1
Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes	1
A comprehensive illustrated protocol for clearing, mounting, and imaging leaf venation networks	1
Issue Information	1
RootBot: High‐throughput root stress phenotyping robot	1
Issue Information	1
A machine learning approach to study plant functional trait divergence	1
	1
An image‐based technique for automated root disease severity assessment using PlantCV	1
CuticleTrace: A toolkit for capturing cell outlines from leaf cuticle with implications for paleoecology and paleoclimatology	1
Easy as piadcs: A low‐cost, ultra‐high‐resolution data acquisition system using a Raspberry Pi	1
Spatially resolved detection of small molecules from press‐dried plant tissue using MALDI imaging	1
nQuack: An R package for predicting ploidal level from sequence data using site‐based heterozygosity	1
Calceolariaceae809: A bait set for targeted sequencing of nuclear loci	1
A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae	1
Carbon balance: A technique to assess comparative photosynthetic physiology in poikilohydric plants	1
Can alpine plant species “bank” on conservation?: Using artificial aging to understand seed longevity	1
Issue Information	1
FlowerMate: Multidimensional reciprocity and inaccuracy indices for style‐polymorphic plant populations	1
Unfurling an improved method for visualizing mitotic chromosomes in ferns	1
Measuring volatile emissions from moss gametophytes: A review of methodologies and new applications	1
Tailoring convolutional neural networks for custom botanical data	1
Looking to the past to inform the future: What eDNA from herbarium specimens can tell us about plant–animal interactions	1
Issue Information	1
hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution	1
Acknowledgment of Reviewers	1
Seed classification with random forest models	1