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 2022-08-01 to 2026-08-01.)

Article	Citations
Reducing skin microbiome exposure impacts through swine farm biosecurity	581
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	56
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	45
Expression-driven genetic dependency reveals targets for precision oncology	41
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	40
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	40
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	39
Characterizing a species-rich and understudied tropical insect fauna using DNA barcoding	35
The probability of edge existence due to node degree: a baseline for network-based predictions	35
Hecatomb: an integrated software platform for viral metagenomics	34
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	32
TinkerHap—a novel read-based phasing algorithm with integrated multimethod support for enhanced accuracy	30
Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing	29
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	29
The genomes of 5 mantises provide insights into sex chromosome evolution and Mantodea phylogeny clarification	29
ricu: R’s interface to intensive care data	28
WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning	28
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	28
Datagraphy: toward a systematic approach to dataset discovery	27
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	27
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes	27
FAIR data station for lightweight metadata management and validation of omics studies	26
A Case for estradiol: younger brains in women with earlier menarche and later menopause	26
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome	25
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis	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	25
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants	23
SeuratExtend: streamlining single-cell RNA-seq analysis through an integrated and intuitive framework	23
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	23
Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	22
Harnessing population diversity: in search of tools of the trade	22
Unlocking the potential of Asian genomic data: a collaborative framework for precision medicine innovation	21
Chromosome-level genome assembly and transcriptomes of the leaf insect Cryptophyllium westwoodii provide insights into the evolution of leaf-like masquer	21
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations	21
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	20
Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot	20
Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations	20
Unveiling vertebrate development dynamics in frog Xenopus laevis using micro-CT imaging	20
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	20
External validation of machine learning models—registered models and adaptive sample splitting	19
MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections	19
Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering	19
Hiding in plain sight: a research parasite’s perspective on new lessons in old data	19
Computational reproducibility of Jupyter notebooks from biomedical publications	19
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	18
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project	18
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research	18
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata	18
GADMA2: more efficient and flexible demographic inference from genetic data	17
Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle	17
scDenorm: a denormalization tool for integrating single-cell transcriptomics data	17
Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	17
First chromosome-level genome assembly of the colonial chordate model Botryllus schlosseri (Tunicata)	16
ChronoRoot 2.0: an open AI-powered platform for 2D temporal plant phenotyping	16
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection	16
NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing data	16
Interactive analysis of single-cell trajectories in 3D space with Cell Journey	16
A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps	15
An interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis	15
A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species	15
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors	15
pyRootHair: Machine learning accelerated software for high-throughput phenotyping of plant root hair traits	15
Retracted and Replaced: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	15
Exploring the role of normalization and feature selection in microbiome disease classification pipelines	15
ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine	15
Publishing data to support the fight against human vector-borne diseases	15
Segmentation-based quality control of structural MRI using the CAT12 toolbox	15
Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes	15
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics	15
New causal discovery algorithm over censored variables identifies subtype-specific drivers of breast cancer progression	14
ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages	14
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids	14
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas	14
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	13
Challenges in structural variant calling in low-complexity regions	13

HeteroMRI: Robust white matter abnormality classification across multi-scanner MRI data	13
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	13
Stereo-cell deciphers the spatial and functional heterogeneity of polyploid hepatocytes	13
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	13
Toward total recall: Enhancing data FAIRness through AI-driven metadata standardization	13
On the benefits of self-taught learning for brain decoding	13
The effects of bioinformatics preprocessing on cell-free DNA fragment analysis	13
AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level	13
A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona	13
Lifting the curse from high-dimensional data: automated projection pursuit clustering for a variety of biological data modalities	13
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	13
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation	13
Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma	13
nf-core/proteinfamilies: a scalable pipeline for the generation of protein families	13
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	13
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	13
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species	13
A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research	12
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	12
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	12
CoCoPyE: feature engineering for learning and prediction of genome quality indices	12
Accurate proteome-wide prediction of enzymes and catalytic sites using graph deep learning and protein language model	12
PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking	12
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	12
Celebrating 30 years of access to NASA Space Life Sciences data	12
A telomere-to-telomere genome assembly of koi carp (Cyprinus carpio) using long reads and Hi-C technology	12
Learning inherent genetic patterns and trait associations with deep generative models for discrete genotype simulation	12
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods	12
The Open Pediatric Cancer Project	11
Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)	11
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	11
M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications	11
Enhanced semantic classification of microbiome sample origins using large language models (LLMs)	11
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	11
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	11
Deepdefense: annotation of immune systems in prokaryotes using deep learning	11
MPLID (Membrane Protein–Lipid Interaction Database): A Large-Scale Experimental Resource of Residue-Level Protein–Lipid Contacts	11
Federated knowledge retrieval elevates large language model performance on biomedical benchmarks	11
Retraction and replacement of: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	11
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	11
A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks	10
Comparison of deep learning approaches for extreme low-SNR image restoration	10
Translating short-form Python exercises to other programming languages using diverse prompting strategies	10
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	10
On the variability of dynamic functional connectivity assessment methods	10
Metaphor—A workflow for streamlined assembly and binning of metagenomes	10
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	10
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology	10
A molecular phenotypic map of malignant pleural mesothelioma	9
Cell type transcriptomic modules reveal shared molecular mechanisms in Alzheimer’s and Parkinson’s disease	9
The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses	9
The chromosome-level genome assembly of an endangered herbBergenia scopulosaprovides insights into local adaptation and genomic vulnerability under climate change	9
SurGen: 1020 H&E-stained whole-slide images with survival and genetic markers	9
Cerebellocerebral connectivity predicts body mass index: a new open-source Python-based framework for connectome-based predictive modeling	9
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	9
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data	9
A framework to mine laser microdissection-based omics data and uncover regulators of pancreatic cancer heterogeneity	9
Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes	9
Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis	9
Improving the reliability, quality, and maintainability of bioinformatics pipelines with nf-test	9
ChatMDV: Reducing Technical Barriers in Bioinformatics Analysis using Large Language Models	9
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing	9
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	9
Open RGB imaging workflow for morphological and morphometric analysis of fruits using deep learning: a case study on almonds	9
Interspecific hybridization in Brassica species leads to changes in agronomic traits through the regulation of gene expression by chromatin accessibility and DNA methylation	9
SODAR: managing multiomics study data and metadata	9
Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family	9
4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians	9
MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model	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
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles	9
PathoFact 2.0: an integrative pipeline for the prediction of antimicrobial resistance genes, virulence factors, toxins and toxin-associated proteins, and biosynthetic gene clusters in metagenomes	9