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 2021-05-01 to 2025-05-01.)

Article	Citations
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework	131
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	81
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	74
Hecatomb: an integrated software platform for viral metagenomics	61
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	61
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	55
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	55
The probability of edge existence due to node degree: a baseline for network-based predictions	54
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources	50
MBGC: Multiple Bacteria Genome Compressor	50
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	49
A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers	42
Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing	42
Preventing dataset shift from breaking machine-learning biomarkers	41
ricu: R’s interface to intensive care data	41
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	40
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes	39
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	38
The Nencki-Symfonia electroencephalography/event-related potential dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults	36
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	33
X-ray microtomography imaging of craniofacial hard tissues in selected reptile species with different types of dentition	33
scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues	32
A decade of GigaScience: A perspective on conservation genetics	31
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants	30
Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks	30

Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis	30
A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)	30
Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples	30
FAIR data station for lightweight metadata management and validation of omics studies	30
Harnessing population diversity: in search of tools of the trade	29
Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	28
A Decade of GigaScience: Milestones in Open Science	28
Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering	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
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	27
Unveiling vertebrate development dynamics in frog Xenopus laevis using micro-CT imaging	26
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	25
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations	25
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	25
Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations	24
Hiding in plain sight: a research parasite’s perspective on new lessons in old data	24
Computational reproducibility of Jupyter notebooks from biomedical publications	24
Studying mutation rate evolution in primates—the effects of computational pipelines and parameter choices	24
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata	23
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research	23
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	23
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project	23
High-quality genome assembles from key Hawaiian coral species	22
GADMA2: more efficient and flexible demographic inference from genetic data	22
Spacemake: processing and analysis of large-scale spatial transcriptomics data	22
Population modeling with machine learning can enhance measures of mental health	22
Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data	21
Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	21
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics	21
The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv	20
BiSulfite Bolt: A bisulfite sequencing analysis platform	20
Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	20
De novoscreening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation	19
Publishing data to support the fight against human vector-borne diseases	19
The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family	19
BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data	19
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection	19
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach	19
A Decade of GigaScience: Women in Science: Past, Present, and Future	18
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation	18
ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine	18
Data standardization of plant–pollinator interactions	18
HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences	17
Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI	17
ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages	17
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors	17
High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs	17
Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma	17
On the benefits of self-taught learning for brain decoding	17
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding	16

Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	16
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas	16
NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer	16
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids	16
Loop detection using Hi-C data with HiCExplorer	16
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	15
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	15
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	15
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification	15
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	15
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	15
Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots	14
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species	14
The state of Medusozoa genomics: current evidence and future challenges	14
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	14
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	14
M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data	14
Celebrating 30 years of access to NASA Space Life Sciences data	14
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET	13
A Decade of GigaScience: GigaDB and the Open Data Movement	13
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	13
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	13
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods	13
An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	13
CoCoPyE: feature engineering for learning and prediction of genome quality indices	13
A dataset of ant colonies’ motion trajectories in indoor and outdoor scenes to study clustering behavior	13
DENTIST—using long reads for closing assembly gaps at high accuracy	13
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	13
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	13
An in vitro whole-cell electrophysiology dataset of human cortical neurons	12
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	12
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	12
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes	12
learnMSA: learning and aligning large protein families	12
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	11
Deepdefense: annotation of immune systems in prokaryotes using deep learning	11
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	11
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology	11
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	11
On the variability of dynamic functional connectivity assessment methods	11
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	11
Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging	11
A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks	11
Metaphor—A workflow for streamlined assembly and binning of metagenomes	11
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	11
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data	11
U-Limb: A multi-modal, multi-center database on arm motion control in healthy and post-stroke conditions	11