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 2022-01-01 to 2026-01-01.)

Article	Citations
Reducing skin microbiome exposure impacts through swine farm biosecurity	338
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	109
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	86
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	76
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	72
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework	67
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	58
Hecatomb: an integrated software platform for viral metagenomics	56
MBGC: Multiple Bacteria Genome Compressor	54
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources	50
The probability of edge existence due to node degree: a baseline for network-based predictions	46
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	38
A decade of GigaScience: A perspective on conservation genetics	38
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis	38
The Nencki-Symfonia electroencephalography/event-related potential dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults	38
On the path to reference genomes for all biodiversity: laboratory protocols and lessons learned from processing over 2,000 species in the Sanger Tree of Life	37
X-ray microtomography imaging of craniofacial hard tissues in selected reptile species with different types of dentition	37
A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)	36
TinkerHap—a novel read-based phasing algorithm with integrated multimethod support for enhanced accuracy	33
Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing	32
Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks	32
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	32
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome	31
WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning	31
A Case for estradiol: younger brains in women with earlier menarche and later menopause	31

FAIR data station for lightweight metadata management and validation of omics studies	31
ricu: R’s interface to intensive care data	30
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	29
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	29
Datagraphy: toward a systematic approach to dataset discovery	29
The genomes of five mantises provide insights into sex chromosome evolution and Mantodea phylogeny clarification	28
scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues	28
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes	28
A virtual library for behavioral performance in standard conditions—rodent spontaneous activity in an open field during repeated testing and after treatment with drugs or brain lesions	27
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants	27
Unveiling vertebrate development dynamics in frog Xenopus laevis using micro-CT imaging	25
Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot	25
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations	25
Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations	25
A Decade of GigaScience: Milestones in Open Science	25
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	24
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	24
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	23
Computational reproducibility of Jupyter notebooks from biomedical publications	23
Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering	23
External validation of machine learning models—registered models and adaptive sample splitting	22
Spacemake: processing and analysis of large-scale spatial transcriptomics data	22
Harnessing population diversity: in search of tools of the trade	22
Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	22
Hiding in plain sight: a research parasite’s perspective on new lessons in old data	22
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project	22
Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	22
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata	21
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	20
Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle	20
GADMA2: more efficient and flexible demographic inference from genetic data	20
High-quality genome assembles from key Hawaiian coral species	20
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research	20
Segmentation-Based Quality Control of Structural MRI using the CAT12 Toolbox	19
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection	19
First chromosome-level genome assembly of the colonial chordate model Botryllus schlosseri (Tunicata)	19
Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data	19
pyRootHair: Machine Learning Accelerated Software for High-Throughput Phenotyping of Plant Root Hair Traits	19
The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv	19
Publishing data to support the fight against human vector-borne diseases	18
Exploring the role of normalization and feature selection in microbiome disease classification pipelines	18
Retracted and Replaced: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	18
A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps	18
NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing data	17
Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes	17
HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences	17
The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family	17
A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species	17
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics	17
ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine	17

High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs	16
A Decade of GigaScience: Women in Science: Past, Present, and Future	16
NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer	16
The effects of bioinformatics preprocessing on cell-free DNA fragment analysis	16
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors	16
Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma	16
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation	16
Challenges in structural variant calling in low-complexity regions	16
On the benefits of self-taught learning for brain decoding	16
Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI	16
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids	16
Loop detection using Hi-C data with HiCExplorer	16
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding	16
Data standardization of plant–pollinator interactions	15
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	15
ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages	15
HeteroMRI: Robust white matter abnormality classification across multi-scanner MRI data	15
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	15
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas	15
AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level	15
A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona	14
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification	14
Lifting the curse from high-dimensional data: automated projection pursuit clustering for a variety of biological data modalities	14
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species	14
Celebrating 30 years of access to NASA Space Life Sciences data	13
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	13
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	13
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	13
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	13
The state of Medusozoa genomics: current evidence and future challenges	13
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	13
A telomere-to-telomere genome assembly of koi carp (Cyprinus carpio) using long reads and Hi-C technology	13
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	13
An in vitro whole-cell electrophysiology dataset of human cortical neurons	12
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	12
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	12
A Decade of GigaScience: GigaDB and the Open Data Movement	12
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET	12
learnMSA: learning and aligning large protein families	12
A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research	12
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	12
Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)	12
DENTIST—using long reads for closing assembly gaps at high accuracy	12
PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking	12
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods	12
CoCoPyE: feature engineering for learning and prediction of genome quality indices	12
A dataset of ant colonies’ motion trajectories in indoor and outdoor scenes to study clustering behavior	12
The Open Pediatric Cancer Project	12
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	11
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	11
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	11
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology	11
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing	11
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	11
PanGIA: A universal framework for identifying association between ncRNAs and diseases	11
Deepdefense: annotation of immune systems in prokaryotes using deep learning	11
Retraction and replacement of: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	11
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data	11
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	11
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	11
A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks	11
M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications	11