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 2020-03-01 to 2024-03-01.)

Article	Citations
The Plant Pathology Challenge 2020 data set to classify foliar disease of apples	96
Machine learning: A powerful tool for gene function prediction in plants	64
Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants	63
Instance segmentation for the fine detection of crop and weed plants by precision agricultural robots	63
WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data	47
A target enrichment probe set for resolving the flagellate land plant tree of life	41
High‐throughput methods for efficiently building massive phylogenies from natural history collections	36
LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens	36
New targets acquired: Improving locus recovery from the Angiosperms353 probe set	35
Field‐based mechanical phenotyping of cereal crops to assess lodging resistance	33
Plants meet machines: Prospects in machine learning for plant biology	30
A new fine‐grained method for automated visual analysis of herbarium specimens: A case study for phenological data extraction	27
A comparison of seed germination coefficients using functional regression	26
A two‐tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae	26
Generating segmentation masks of herbarium specimens and a data set for training segmentation models using deep learning	25
Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi	24
On the potential of Angiosperms353 for population genomic studies	24
Inferring the impacts of evolutionary history and ecological constraints on spore size and shape in the ferns	23
Digitally deconstructing leaves in 3D using X‐ray microcomputed tomography and machine learning	23
The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions	22
HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets	22
A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera	22
An algorithm competition for automatic species identification from herbarium specimens	21
Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci	21
Applying machine learning to investigate long‐term insect–plant interactions preserved on digitized herbarium specimens	20

Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae	20
GinJinn: An object‐detection pipeline for automated feature extraction from herbarium specimens	19
What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol	17
Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family	17
Automated trichome counting in soybean using advanced image‐processing techniques	16
Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome	16
Low‐cost observations and experiments return a high value in plant phenology research	15
Early detection of black Sigatoka in banana leaves using hyperspectral images	15
Composite modeling of leaf shape along shoots discriminates Vitis species better than individual leaves	15
Using computer vision on herbarium specimen images to discriminate among closely related horsetails (Equisetum)	15
PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data	14
A step‐by‐step protocol for meiotic chromosome counts in flowering plants: A powerful and economical technique revisited	14
Leaf Angle eXtractor: A high‐throughput image processing framework for leaf angle measurements in maize and sorghum	14
Algae to angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa	13
A new, simple, highly scalable, and efficient protocol for genomic DNA extraction from diverse plant taxa	12
Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics	12
Application of remote sensing technology to estimate productivity and assess phylogenetic heritability	12
Comparing methods for controlled capture and quantification of pollen in Cannabis sativa	11
Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts	10
Comparative chloroplast genomes and phylogenetic analysis of Aquilegia	9
Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes	9
Robust mosaicking of maize fields from aerial imagery	9
A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae	9
Methodologies for soil extraction and conservation analysis of ferns and lycophytes with belowground gametophytes	9
Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?	9
Species complex delimitations in the genus Hedychium: A machine learning approach for cluster discovery	9
Maximizing human effort for analyzing scientific images: A case study using digitized herbarium sheets	9
Microsatellite marker development in the crop wild relative Linum bienne using genome skimming	8
Polishing entire stems and roots using sandpaper under water: An alternative method for macroscopic analyses	8
Evaluation and application of tools for the identification of known microRNAs in plants	8
Phenotypic characterization of Arabidopsis thaliana lines overexpressing AVP1 and MIOX4 in response to abiotic stresses	8
Minimizing the deleterious effects of endophytes in plant shoot tip cryopreservation	8
Harnessing the power of botanical gardens: Evaluating the costs and resources needed for exceptional plant conservation	8
Supporting long‐term sustainability of ex situ collections using a pedigree‐based population management approach	8
SSRgenotyper: A simple sequence repeat genotyping application for whole‐genome resequencing and reduced representational sequencing projects	7
An efficient low‐cost xylem sap isolation method for bacterial wilt assays in tomato	7
The ecology and physiology of fern gametophytes: A methodological synthesis	7
Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq	7
Using clear plastic CD cases as low‐cost mini‐rhizotrons to phenotype root traits	7
Identifying cryptic fern gametophytes using DNA barcoding: A review	7
High‐molecular‐weight DNA extraction for long‐read sequencing of plant genomes: An optimization of standard methods	7
Accelerating gametophytic growth in the model hornwort Anthoceros agrestis	7
A sick plot–based protocol for dry root rot disease assessment in field‐grown chickpea plants	7
Selection on the gametophyte: Modeling alternation of generations in plants	6
Development and characterization of EST‐SSR markers for Camellia reticulata	6
Not that kind of tree: Assessing the potential for decision tree–based plant identification using trait databases	6
Super resolution for root imaging	6
Harnessing aquatic plant growth forms to apply European nutrient‐enrichment bioindicators to Canadian waters	6
Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales	6
Extraction of high‐quality, high‐molecular‐weight DNA depends heavily on cell homogenization methods in green microalgae	6

hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution	6
From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2	6
Integrating tissue‐direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field	5
A low‐cost high‐throughput phenotyping system for automatically quantifying foliar area and greenness	5
The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques	5
Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana)	5
Long‐read genotyping with SLANG (Simple Long‐read loci Assembly of Nanopore data for Genotyping)	5
A simple high‐throughput protocol for the extraction and quantification of inorganic phosphate in rice leaves	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
Modified CTAB protocols for high‐molecular‐weight DNA extractions from ferns	5
Optimizing the lysis step in CTAB DNA extractions of silica‐dried and herbarium leaf tissues	5
Seed dormancy and germination of the endangered exceptional Hawaiian lobelioid Brighamia rockii	5
Asymbiotic in vitro seed germination, in vitro seedling development, and ex vitro acclimatization of Spiranthes	4
Genotypic confirmation of a biased phenotypic sex ratio in a dryland moss using restriction fragment length polymorphisms	4
A dormant resource for genome size estimation in ferns: C‐value inference of the Ophioglossaceae using herbarium specimen spores	4
Using acetone for rapid PCR‐amplifiable DNA extraction from recalcitrant woody plant taxa	4
Digital morphometrics: Application of MorphoLeaf in shape visualization and species delimitation, using Cucurbitaceae leaves as a model	4
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids	4
Photographic analysis of field‐monitored fern gametophyte development and response to environmental stress	4
Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species	4
Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques	4
Three‐dimensional digital image construction of metaxylem vessels in root tips of Zea mays subsp. mexicana from thin transverse sections	4
Enabling automated herbarium sheet image post‐processing using neural network models for color reference chart detection	4
TagSeq for gene expression in non‐model plants: A pilot study at the Santa Rita Experimental Range NEON core site	4
An automated pipeline for supervised classification of petal color from citizen science photographs	3
Using microcontrollers and sensors to build an inexpensive CO₂ control system for growth chambers	3
Rapid imaging in the field followed by photogrammetry digitally captures the otherwise lost dimensions of plant specimens	3
A novel, rapid technique for clearing leaf tissues	3
Target capture and genome skimming for plant diversity studies	3
Efficient homology‐based annotation of transposable elements using minimizers	3
Using a portable hydrogen cyanide gas meter to uncover a dynamic phytochemical landscape	3
Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest	3
An image‐based technique for automated root disease severity assessment using PlantCV	3
Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos	3
Research inequity in the plant sciences	3
Measuring volatile emissions from moss gametophytes: A review of methodologies and new applications	3
Stable isotope mixing models demonstrate the role of an invasive plant in wetland songbird food webs	3
Using marsh organs to test seed recruitment in tidal freshwater marshes	3
A field‐capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring	3
Virus‐induced gene silencing as a tool for functional studies in Cleome violacea	3
An efficient protocol for functional studies of apple transcription factors using a glucocorticoid receptor fusion system	3
Rapid character scoring and tabulation of large leaf‐image libraries using Adobe Bridge	2
FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes	2
Informed cover measurement: Guidelines and error for point‐intercept approaches	2
An efficient, high‐throughput method for the simultaneous exposure of drought stress and bacterial infection in plants	2
Estimating herbarium specimen digitization rates: Accounting for human experience	2
Does sorting by color using visible and high‐energy violet light improve classification of taxa in honey bee pollen pellets?	2
Optimizing efficient PCR‐amplifiable DNA extraction from herbarium specimens	2
Recognition of Latin scientific names using artificial neural networks	2
Can alpine plant species “bank” on conservation?: Using artificial aging to understand seed longevity	2
Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits	2
Techniques for locating and analyzing subterranean Lycopodium and Diphasiastrum gametophytes in the field	2
A simple, non‐toxic method for separating seeds based on density, and its application in isolating Arabidopsis thaliana seed oil mutants	2
Evaluation of sampling effort required to assess pollen species richness on pollinators using rarefaction	2
A metabarcoding protocol targeting two DNA regions to analyze root‐associated fungal communities in ferns and lycophytes	2
An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex	2
Combining rare alleles and grouped pollen donors to assign paternity in pollen dispersal studies	2
A pipeline for the rapid collection of color data from photographs	2
Improving culture initiation of mature oak shoots through use of silver thiosulfate	2
A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming	2
Choices on sampling, sequencing, and analyzing DNA influence the estimation of community composition of plant fungal symbionts	2
Low‐cost FloPump for regulated air sampling of volatile organic compounds	2
Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens	2