OOIR: Observatory of International Research

Papers

(The TQCC of GigaScience is 11. 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 2021-04-01 to 2025-04-01.)

Article	Citations
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	111
Selection signatures in goats reveal a novel deletion mutant underlying cashmere yield and diameter	77
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	69
Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots	59
Driftage: a multi-agent system framework for concept drift detection	58
Interpretable network-guided epistasis detection	58
A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen	55
Erratum to: An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	50
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	50
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome	49
Triku: a feature selection method based on nearest neighbors for single-cell data	47
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework	41
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)	41
Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)	39
The assembled and annotated genome of the masked palm civet (Paguma larvata)	38
A chromosome-level genome of the booklouse, Liposcelis brunnea, provides insight into louse evolution and environmental stress adaptation	38
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification	38
The state of Medusozoa genomics: current evidence and future challenges	35
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae	35
A novel ground truth multispectral image dataset with weight, anthocyanins, and Brix index measures of grape berries tested for its utility in machine learning pipelines	34
Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations	33
DrugSim2DR: systematic prediction of drug functional similarities in the context of specific disease for drug repurposing	31
A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes)	30
Open Data Governance at the Canadian Open Neuroscience Platform (CONP): From the Walled Garden to the Arboretum	30
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	30

DriverMP enables improved identification of cancer driver genes	29
GSC: efficient lossless compression of VCF files with fast query	29
Hecatomb: an integrated software platform for viral metagenomics	29
Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus	28
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	28
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	26
Web of venom: exploration of big data resources in animal toxin research	26
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes	26
Celebrating 30 years of access to NASA Space Life Sciences data	25
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	25
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data	25
Genomic exploration of the endangered oriental stork, Ciconia boyciana, sheds light on migration adaptation and future conservation	24
Alignstein: Optimal transport for improved LC-MS retention time alignment	23
DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology	23
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	22
Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae)	22
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing	22
Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population	22
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	21
GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context	21
Correction to: A graph clustering algorithm for detection and genotyping of structural variants from long reads	21
Health record hiccups—5,526 real-world time series with change points labelled by crowdsourced visual inspection	21
High-quality phenotypic and genotypic dataset of barley genebank core collection to unlock untapped genetic diversity	21
An ecosystem for producing and sharing metadata within the web of FAIR Data	21
High-throughput imaging of powdery mildew resistance of the winter wheat collection hosted at the German Federal ex situ Genebank for Agricultural and Horticultural Crops	21
M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data	21
The Global Atlas of Bamboo and Rattan (GABR) Phase II: new resources for sustainable development	20
Computational prediction of human deep intronic variation	20
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	19
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	19
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data	19
Confound-leakage: confound removal in machine learning leads to leakage	19
Genomic and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spiders	18
Maternal plasma lipids are involved in the pathogenesis of preterm birth	18
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	18
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources	18
BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data	17
An analysis of performance bottlenecks in MRI preprocessing	17
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	17
scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data	17
MBGC: Multiple Bacteria Genome Compressor	17
The probability of edge existence due to node degree: a baseline for network-based predictions	17
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	16
xRead: a coverage-guided approach for scalable construction of read overlapping graph	16
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology	16
Similar, but not the same: multiomics comparison of human valve interstitial cells and osteoblast osteogenic differentiation expanded with an estimation of data-dependent and data-independent PASEF pr	16
Preventing dataset shift from breaking machine-learning biomarkers	16
Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)	16
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	16
Best genome sequencing strategies for annotation of complex immune gene families in wildlife	16

A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers	15
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	15
The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis	15
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	15
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	15
Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks	15
The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis	15
Benchmarking short-read metagenomics tools for removing host contamination	15
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment	15
A ghost moth olfactory prototype of the lepidopteran sex communication	15
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	14
An interconnected data infrastructure to support large-scale rare disease research	14
CoCoPyE: feature engineering for learning and prediction of genome quality indices	14
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	14
Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa	14
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	13
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package	13
The Nencki-Symfonia electroencephalography/event-related potential dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults	13
An analysis of security vulnerabilities in container images for scientific data analysis	13
Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a noninvasive tool for skin barrier assessment	13
Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2	13
Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes	13
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure	13
Genome size evolution in the diverse insect order Trichoptera	13
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators	13
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET	12
A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)	12
A Decade of GigaScience: GigaDB and the Open Data Movement	12
X-ray microtomography imaging of craniofacial hard tissues in selected reptile species with different types of dentition	12
scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues	12
Statistical quantification of confounding bias in machine learning models	12
KOREF_S1: phased, parental trio-binned Korean reference genome using long reads and Hi-C sequencing methods	12
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data	12
A decade of GigaScience: A perspective on conservation genetics	12
Comparative maternal protein profiling of mouse biparental and uniparental embryos	11
Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective	11
CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis	11
An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	11
The germline mutational process in rhesus macaque and its implications for phylogenetic dating	11
Building the mega single-cell transcriptome ocular meta-atlas	11
DeePVP: Identification and classification of phage virion proteins using deep learning	11
Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples	11
DENTIST—using long reads for closing assembly gaps at high accuracy	11
A dataset of ant colonies’ motion trajectories in indoor and outdoor scenes to study clustering behavior	11