OOIR: Observatory of International Research

Papers

(The TQCC of Applications in Plant Sciences is 4. 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 2020-11-01 to 2024-11-01.)

Article	Citations
A target enrichment probe set for resolving the flagellate land plant tree of life	52
New targets acquired: Improving locus recovery from the Angiosperms353 probe set	49
High‐throughput methods for efficiently building massive phylogenies from natural history collections	45
HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets	34
On the potential of Angiosperms353 for population genomic studies	28
Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci	24
The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions	24
What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol	23
Composite modeling of leaf shape along shoots discriminates Vitis species better than individual leaves	21
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae	21
Toward genomic selection inPinus taeda: Integrating resources to support array design in a complex conifer genome	20
Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family	19
Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics	17
Algae to angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa	17
A new, simple, highly scalable, and efficient protocol for genomic DNA extraction from diverse plant taxa	17
The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques	16
The ecology and physiology of fern gametophytes: A methodological synthesis	15
PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data	15
Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes	14
Application of remote sensing technology to estimate productivity and assess phylogenetic heritability	14
Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?	12
hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution	12
Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts	11
Methodologies for soil extraction and conservation analysis of ferns and lycophytes with belowground gametophytes	11
Supporting long‐term sustainability of ex situ collections using a pedigree‐based population management approach	11

Evaluation and application of tools for the identification of known microRNAs in plants	10
Identifying cryptic fern gametophytes using DNA barcoding: A review	10
Minimizing the deleterious effects of endophytes in plant shoot tip cryopreservation	10
Comparative chloroplast genomes and phylogenetic analysis of Aquilegia	10
High‐molecular‐weight DNA extraction for long‐read sequencing of plant genomes: An optimization of standard methods	10
Polishing entire stems and roots using sandpaper under water: An alternative method for macroscopic analyses	10
Accelerating gametophytic growth in the model hornwort Anthoceros agrestis	9
From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2	9
A sick plot–based protocol for dry root rot disease assessment in field‐grown chickpea plants	9
Harnessing the power of botanical gardens: Evaluating the costs and resources needed for exceptional plant conservation	8
Selection on the gametophyte: Modeling alternation of generations in plants	8
Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales	8
Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species	8
SSRgenotyper: A simple sequence repeat genotyping application for whole‐genome resequencing and reduced representational sequencing projects	7
Optimizing the lysis step in CTAB DNA extractions of silica‐dried and herbarium leaf tissues	7
Modified CTAB protocols for high‐molecular‐weight DNA extractions from ferns	7
Seed dormancy and germination of the endangered exceptional Hawaiian lobelioid Brighamia rockii	7
Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq	7
Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques	6
Genotypic confirmation of a biased phenotypic sex ratio in a dryland moss using restriction fragment length polymorphisms	6
Asymbiotic in vitro seed germination, in vitro seedling development, and ex vitro acclimatization of Spiranthes	6
Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana)	6
Target capture and genome skimming for plant diversity studies	6
Harnessing aquatic plant growth forms to apply European nutrient‐enrichment bioindicators to Canadian waters	6
Providing the missing links in fern life history: Insights from a phenological survey of the gametophyte stage	5
Long‐read genotyping with SLANG (Simple Long‐read loci Assembly of Nanopore data for Genotyping)	5
Integrating tissue‐direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field	5
A metabarcoding protocol targeting two DNA regions to analyze root‐associated fungal communities in ferns and lycophytes	5
Using marsh organs to test seed recruitment in tidal freshwater marshes	5
Digital morphometrics: Application of MorphoLeaf in shape visualization and species delimitation, using Cucurbitaceae leaves as a model	5
A low‐cost high‐throughput phenotyping system for automatically quantifying foliar area and greenness	5
Photographic analysis of field‐monitored fern gametophyte development and response to environmental stress	5
A field‐capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring	5
An image‐based technique for automated root disease severity assessment using PlantCV	5
A dormant resource for genome size estimation in ferns: C‐value inference of the Ophioglossaceae using herbarium specimen spores	5
Calculation of the ovule number in the genus Salix: A method for taxa differentiation	5
Virus‐induced gene silencing as a tool for functional studies in Cleome violacea	4
Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos	4
An automated pipeline for supervised classification of petal color from citizen science photographs	4
Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens	4
Informed cover measurement: Guidelines and error for point‐intercept approaches	4
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids	4
Measuring volatile emissions from moss gametophytes: A review of methodologies and new applications	4
Using acetone for rapid PCR‐amplifiable DNA extraction from recalcitrant woody plant taxa	4
Can alpine plant species “bank” on conservation?: Using artificial aging to understand seed longevity	4
Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits	4
A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming	4
TagSeq for gene expression in non‐model plants: A pilot study at the Santa Rita Experimental Range NEON core site	4