OOIR: Observatory of International Research

Papers

(The TQCC of GigaScience is 9. 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 2022-06-01 to 2026-06-01.)

Article	Citations
Reducing skin microbiome exposure impacts through swine farm biosecurity	490
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	45
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	39
Characterizing a species-rich and understudied tropical insect fauna using DNA barcoding	38
Hecatomb: an integrated software platform for viral metagenomics	37
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	32
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	29
Expression-driven genetic dependency reveals targets for precision oncology	29
The probability of edge existence due to node degree: a baseline for network-based predictions	29
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome	28
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	28
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	28
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	27
TinkerHap—a novel read-based phasing algorithm with integrated multimethod support for enhanced accuracy	27
A Case for estradiol: younger brains in women with earlier menarche and later menopause	26
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	25
FAIR data station for lightweight metadata management and validation of omics studies	25
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	24
ricu: R’s interface to intensive care data	23
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis	23
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	23
Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing	23
SeuratExtend: streamlining single-cell RNA-seq analysis through an integrated and intuitive framework	23
The genomes of 5 mantises provide insights into sex chromosome evolution and Mantodea phylogeny clarification	23
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes	22

Datagraphy: toward a systematic approach to dataset discovery	22
Unveiling vertebrate development dynamics in frog Xenopus laevis using micro-CT imaging	21
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants	21
WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning	21
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	20
Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	20
Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations	20
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations	19
Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering	19
Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot	19
Chromosome-level genome assembly and transcriptomes of the leaf insect Cryptophyllium westwoodii provide insights into the evolution of leaf-like masquer	19
Computational reproducibility of Jupyter notebooks from biomedical publications	19
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	19
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	18
Unlocking the potential of Asian genomic data: a collaborative framework for precision medicine innovation	18
External validation of machine learning models—registered models and adaptive sample splitting	18
Hiding in plain sight: a research parasite’s perspective on new lessons in old data	17
Harnessing population diversity: in search of tools of the trade	17
MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections	17
Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle	16
scDenorm: a denormalization tool for integrating single-cell transcriptomics data	16
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	16
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project	15
Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	15
pyRootHair: Machine learning accelerated software for high-throughput phenotyping of plant root hair traits	15
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research	15
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata	15
NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing data	15
GADMA2: more efficient and flexible demographic inference from genetic data	15
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection	14
Retracted and Replaced: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	14
Exploring the role of normalization and feature selection in microbiome disease classification pipelines	14
An interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis	14
First chromosome-level genome assembly of the colonial chordate model Botryllus schlosseri (Tunicata)	14
Publishing data to support the fight against human vector-borne diseases	14
Interactive analysis of single-cell trajectories in 3D space with Cell Journey	14
Segmentation-based quality control of structural MRI using the CAT12 toolbox	14
ChronoRoot 2.0: an open AI-powered platform for 2D temporal plant phenotyping	14
A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps	14
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics	14
Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes	14
Challenges in structural variant calling in low-complexity regions	13
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas	13
On the benefits of self-taught learning for brain decoding	13
A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species	13
ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages	13
The effects of bioinformatics preprocessing on cell-free DNA fragment analysis	13
ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine	13
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors	13
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation	12

HeteroMRI: Robust white matter abnormality classification across multi-scanner MRI data	12
Celebrating 30 years of access to NASA Space Life Sciences data	12
New causal discovery algorithm over censored variables identifies subtype-specific drivers of breast cancer progression	12
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	12
Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma	12
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids	12
A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona	12
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species	11
Toward total recall: Enhancing data FAIRness through AI-driven metadata standardization	11
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	11
Lifting the curse from high-dimensional data: automated projection pursuit clustering for a variety of biological data modalities	11
Stereo-cell deciphers the spatial and functional heterogeneity of polyploid hepatocytes	11
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	11
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	11
nf-core/proteinfamilies: a scalable pipeline for the generation of protein families	11
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	11
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	11
AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level	11
Enhanced semantic classification of microbiome sample origins using large language models (LLMs)	10
CoCoPyE: feature engineering for learning and prediction of genome quality indices	10
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	10
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	10
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods	10
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	10
The Open Pediatric Cancer Project	10
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	10
A telomere-to-telomere genome assembly of koi carp (Cyprinus carpio) using long reads and Hi-C technology	10
Learning inherent genetic patterns and trait associations with deep generative models for discrete genotype simulation	10
PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking	10
Translating short-form Python exercises to other programming languages using diverse prompting strategies	9
A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research	9
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology	9
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing	9
Deepdefense: annotation of immune systems in prokaryotes using deep learning	9
Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)	9
Accurate proteome-wide prediction of enzymes and catalytic sites using graph deep learning and protein language model	9
Federated knowledge retrieval elevates large language model performance on biomedical benchmarks	9
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	9
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	9
M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications	9
Retraction and replacement of: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	9
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	9
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	9
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	9
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes	9
PanGIA: A universal framework for identifying association between ncRNAs and diseases	9