OOIR: Observatory of International Research

Papers

(The TQCC of Applications in Plant Sciences is 6. 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 2020-05-01 to 2024-05-01.)

Article	Citations
The Plant Pathology Challenge 2020 data set to classify foliar disease of apples	100
Machine learning: A powerful tool for gene function prediction in plants	68
Instance segmentation for the fine detection of crop and weed plants by precision agricultural robots	65
WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data	51
A target enrichment probe set for resolving the flagellate land plant tree of life	44
High‐throughput methods for efficiently building massive phylogenies from natural history collections	38
New targets acquired: Improving locus recovery from the Angiosperms353 probe set	37
LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens	37
Field‐based mechanical phenotyping of cereal crops to assess lodging resistance	33
Plants meet machines: Prospects in machine learning for plant biology	33
A comparison of seed germination coefficients using functional regression	28
A new fine‐grained method for automated visual analysis of herbarium specimens: A case study for phenological data extraction	28
On the potential of Angiosperms353 for population genomic studies	26
HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets	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	26
The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions	23
Digitally deconstructing leaves in 3D using X‐ray microcomputed tomography and machine learning	23
Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci	21
An algorithm competition for automatic species identification from herbarium specimens	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
Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family	19
GinJinn: An object‐detection pipeline for automated feature extraction from herbarium specimens	19
Automated trichome counting in soybean using advanced image‐processing techniques	18

Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome	18
Composite modeling of leaf shape along shoots discriminates Vitis species better than individual leaves	18
What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol	17
Algae to angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa	15
Using computer vision on herbarium specimen images to discriminate among closely related horsetails (Equisetum)	15
Early detection of black Sigatoka in banana leaves using hyperspectral images	15
Leaf Angle eXtractor: A high‐throughput image processing framework for leaf angle measurements in maize and sorghum	14
PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data	14
A new, simple, highly scalable, and efficient protocol for genomic DNA extraction from diverse plant taxa	13
Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics	13
Application of remote sensing technology to estimate productivity and assess phylogenetic heritability	13
The ecology and physiology of fern gametophytes: A methodological synthesis	12
Comparing methods for controlled capture and quantification of pollen in Cannabis sativa	11
Maximizing human effort for analyzing scientific images: A case study using digitized herbarium sheets	10
Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts	10
Species complex delimitations in the genus Hedychium: A machine learning approach for cluster discovery	10
Microsatellite marker development in the crop wild relative Linum bienne using genome skimming	9
Not that kind of tree: Assessing the potential for decision tree–based plant identification using trait databases	9
Methodologies for soil extraction and conservation analysis of ferns and lycophytes with belowground gametophytes	9
Robust mosaicking of maize fields from aerial imagery	9
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
Phenotypic characterization of Arabidopsis thaliana lines overexpressing AVP1 and MIOX4 in response to abiotic stresses	9
Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?	9
Minimizing the deleterious effects of endophytes in plant shoot tip cryopreservation	9
A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae	9
Polishing entire stems and roots using sandpaper under water: An alternative method for macroscopic analyses	9
Supporting long‐term sustainability of ex situ collections using a pedigree‐based population management approach	9
Identifying cryptic fern gametophytes using DNA barcoding: A review	8
Evaluation and application of tools for the identification of known microRNAs in plants	8
hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution	8
Harnessing the power of botanical gardens: Evaluating the costs and resources needed for exceptional plant conservation	8
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
SSRgenotyper: A simple sequence repeat genotyping application for whole‐genome resequencing and reduced representational sequencing projects	7
Selection on the gametophyte: Modeling alternation of generations in plants	7
Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq	7
Super resolution for root imaging	7
Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species	6
Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques	6
Harnessing aquatic plant growth forms to apply European nutrient‐enrichment bioindicators to Canadian waters	6
From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2	6
Development and characterization of EST‐SSR markers for Camellia reticulata	6
Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales	6