OOIR: Observatory of International Research

Papers

(The H4-Index of Molecular Ecology Resources is 37. 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
ASAP: assemble species by automatic partitioning	795
pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data	293
CPGView: A package for visualizing detailed chloroplast genome structures	256
Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest	79
SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways	73
Experimental support for genomic prediction of climate maladaptation using the machine learning approach Gradient Forests	66
Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas	56
Reference genome and demographic history of the most endangered marine mammal, the vaquita	56
Chromosomal‐level genomes of three rice planthoppers provide new insights into sex chromosome evolution	54
Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem	54
Improving the reliability of eDNA data interpretation	53
pr2‐primers: An 18S rRNA primer database for protists	53
eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity	53
Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot	53
Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses	52
A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes	51
Strategies for sample labelling and library preparation in DNA metabarcoding studies	50
LEA 3: Factor models in population genetics and ecological genomics with R	49
Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification	48
A high‐quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis	48
SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets	46
High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes	46
Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses	45
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding	45
The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes	44

DiversityScanner: Robotic handling of small invertebrates with machine learning methods	44
Automatic inference of demographic parameters using generative adversarial networks	43
RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data	43
DILS: Demographic inferences with linked selection by using ABC	43
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens	43
Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron	40
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes	39
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species	39
f‐Statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat	38
Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod	37
A large genome with chromosome‐scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans)	37
Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data	37