GigaScience

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
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

CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome	31
ricu: R’s interface to intensive care data	30
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	29
Datagraphy: toward a systematic approach to dataset discovery	29
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	29
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
The genomes of five mantises provide insights into sex chromosome evolution and Mantodea phylogeny clarification	28
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants	27
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
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
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
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	20
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
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
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
Publishing data to support the fight against human vector-borne diseases	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
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
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
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
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
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
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
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
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
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
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
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	10
Metaphor—A workflow for streamlined assembly and binning of metagenomes	10
SurGen: 1020 H&E-stained whole-slide images with survival and genetic markers	10
Accurate gene consensus at low nanopore coverage	10
On the variability of dynamic functional connectivity assessment methods	10
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	10
Translating short-form Python exercises to other programming languages using diverse prompting strategies	10
d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes	10
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes	10
Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging	10
Cerebellocerebral connectivity predicts body mass index: a new open-source Python-based framework for connectome-based predictive modeling	10
Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning	10
Fully resolved assembly of Cryptosporidium parvum	9
Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes	9
A molecular phenotypic map of malignant pleural mesothelioma	9
MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model	9
The chromosome-level genome assembly of an endangered herbBergenia scopulosaprovides insights into local adaptation and genomic vulnerability under climate change	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

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles	9
Correction to: The state of Medusozoa genomics: current evidence and future challenges	9
ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks	9
Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits using Deep Learning: A Case Study on Almonds	9
Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis	9
SODAR: managing multiomics study data and metadata	9
A framework to mine laser microdissection-based omics data and uncover regulators of pancreatic cancer heterogeneity	9
A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape	9
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater	9
Streamlining remote nanopore data access with slow5curl	9
A trade-off in evolution: the adaptive landscape of spiders without venom glands	8
Accurate and fast clade assignment via deep learning and frequency chaos game representation	8
The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses	8
Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation	8
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae	8
Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning–driven data analysis	8
Improving the reliability, quality, and maintainability of bioinformatics pipelines with nf-test	8
MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction	8
MRanalysis: a comprehensive online platform for integrated, multimethod Mendelian randomization and associated post-GWAS analyses	8
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	8
SynProtX: a large-scale proteomics-based deep learning model for predicting synergistic anticancer drug combinations	8
Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family	8
Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise	8
Genos: a human-centric genomic foundation model	8
Alignstein: Optimal transport for improved LC-MS retention time alignment	8
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data	8
Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps	7
Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset	7
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	7
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience	7
CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology	7
Telomere-to-telomere genome and resequencing of 231 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	7
Analysis-ready VCF at Biobank scale using Zarr	7
Correction to: Scientists without borders: lessons from Ukraine	7
Imputation method for single-cell RNA-seq data using neural topic model	7
Genome size evolution in the diverse insect order Trichoptera	7
DeePVP: Identification and classification of phage virion proteins using deep learning	7
Comparative maternal protein profiling of mouse biparental and uniparental embryos	7
Giant chromosomes of a tiny plant - the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermann	7
Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence	7
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators	7
Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups	7
Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers	7
Statistical quantification of confounding bias in machine learning models	7
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera	7
Genome resequencing reveals independent domestication and breeding improvement of naked oat	7
A ghost moth olfactory prototype of the lepidopteran sex communication	7
An evaluation of computational methods for reconstruction of human viral DNA genomes	7
An interconnected data infrastructure to support large-scale rare disease research	7
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes	7
The complete genome assembly of Astragalus membranaceus: enabling more accurate genetic research	7
A workflow reproducibility scale for automatic validation of biological interpretation results	7
Nanopore- and AI-empowered microbial viability inference	6
Antibiotic resistance genes are differentially mobilized according to resistance mechanism	6
HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences	6
Unlocking the power of AI for phenotyping fruit morphology in Arabidopsis	6
Container Profiler: Profiling resource utilization of containerized big data pipelines	6
Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution	6
LED color gradient as a new screening tool for rapid phenotyping of plant responses to light quality	6
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants	6
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl	6
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases	6
Improved reference assembly and core collection re-sequencing to facilitate exploration of important agronomical traits for the improvement of oilseed crop, Carthamus tinctorius L.	6
Comparative genomics and multiomics analyses reveal the evolution and physiological basis of rubber biosynthesis in Hevea species	6
Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing	6
Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants	6
PeptideMiner—neuropeptide discovery across the animal kingdom	6
epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data	6
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells	6
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation	6
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data	6
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets	6
Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies	6
CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites	6
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections	6
A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection	6
Image segmentation of treated and untreated tumor spheroids by fully convolutional networks	6
Unsupervised multiscale clustering of single-cell transcriptomes to identify hierarchical structures of cell subtypes	6
The rise of genomics in snake venom research: recent advances and future perspectives	6
Chromosome-level reference genome for the medically important Arabian horned viper ( Cerastes gasperettii )	6
Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis)	6
A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance	6
Overture: an open-source genomics data platform	6
Delineating regions of interest for mass spectrometry imaging by multimodally corroborated spatial segmentation	5
DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era	5
RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations	5
The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation	5
Finding easy regions for short-read variant calling from pangenome data	5
Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies	5
The complexity landscape of viral genomes	5
The telomere-to-telomere gap-free reference genome and taxonomic reassessment of Siniperca roulei	5
Association mapping across a multitude of traits collected in diverse environments in maize	5
Mutation impact on mRNA versus protein expression across human cancers	5
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features	5
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation	5