GigaScience

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
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
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	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
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
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	20
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
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
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
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	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
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
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection	14
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
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 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
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
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
AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level	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
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
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
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
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
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
Cerebellocerebral connectivity predicts body mass index: a new open-source Python-based framework for connectome-based predictive modeling	8
On the variability of dynamic functional connectivity assessment methods	8
SurGen: 1020 H&E-stained whole-slide images with survival and genetic markers	8
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles	8
SODAR: managing multiomics study data and metadata	8
A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks	8
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	8
A framework to mine laser microdissection-based omics data and uncover regulators of pancreatic cancer heterogeneity	8
The chromosome-level genome assembly of an endangered herbBergenia scopulosaprovides insights into local adaptation and genomic vulnerability under climate change	8
Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes	8
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data	8
Metaphor—A workflow for streamlined assembly and binning of metagenomes	8
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	8
MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model	8
Open RGB imaging workflow for morphological and morphometric analysis of fruits using deep learning: a case study on almonds	8
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	8
Streamlining remote nanopore data access with slow5curl	7
Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination	7
MRanalysis: a comprehensive online platform for integrated, multimethod Mendelian randomization and associated post-GWAS analyses	7
SynProtX: a large-scale proteomics-based deep learning model for predicting synergistic anticancer drug combinations	7
Accurate and fast clade assignment via deep learning and frequency chaos game representation	7
Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning–driven data analysis	7
Cell type transcriptomic modules reveal shared molecular mechanisms in Alzheimer’s and Parkinson’s disease	7
Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis	7
A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human	7
Comparative analysis of 163 ant genomes reveals recurrent horizontal gene transfer from bacteria to ants	7
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data	7
A trade-off in evolution: the adaptive landscape of spiders without venom glands	7
Genos: a human-centric genomic foundation model	7
Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family	7
Improving the reliability, quality, and maintainability of bioinformatics pipelines with nf-test	7
A molecular phenotypic map of malignant pleural mesothelioma	7
Patterns of aDNA damage through time and environments—lessons from herbarium specimens	7
The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses	7

Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation	7
An evaluation of computational methods for reconstruction of human viral DNA genomes	7
4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians	7
Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise	7
MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction	7
Interspecific hybridization in Brassica species leads to changes in agronomic traits through the regulation of gene expression by chromatin accessibility and DNA methylation	7
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience	6
Cord blood DNA methylation and cell-type composition are not significantly associated with severe preeclampsia after cell-type and clinical covariate adjustment	6
Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence	6
Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset	6
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells	6
Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups	6
CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology	6
Analysis-ready VCF at Biobank scale using Zarr	6
An interconnected data infrastructure to support large-scale rare disease research	6
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes	6
Telomere-to-telomere genome and resequencing of 231 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	6
Charting human organogenesis across the Carnegie stages from a whole-embryo perspective	6
Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers	6
Chromosome-level reference genome for the medically important Arabian horned viper ( Cerastes gasperettii )	6
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	6
A workflow reproducibility scale for automatic validation of biological interpretation results	6
A ghost moth olfactory prototype of the lepidopteran sex communication	6
Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps	6
Genome resequencing reveals independent domestication and breeding improvement of naked oat	6
HVRLocator: a computationally efficient tool for identifying hypervariable regions in large 16S rRNA datasets	6
Correction to: Scientists without borders: lessons from Ukraine	6
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants	6
Giant chromosomes of a tiny plant—the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermannio	6
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	6
Image segmentation of treated and untreated tumor spheroids by fully convolutional networks	5
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation	5
Imputation method for single-cell RNA-seq data using neural topic model	5
ZNF331 modulates early embryonic transcription during zygotic genome activation in goat	5
epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data	5
Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data	5
A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation	5
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections	5
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data	5
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases	5
PeptideMiner—neuropeptide discovery across the animal kingdom	5
A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance	5
Container Profiler: Profiling resource utilization of containerized big data pipelines	5
Comparative genomics and multiomics analyses reveal the evolution and physiological basis of rubber biosynthesis in Hevea species	5
Efficient real-time selective genome sequencing on resource-constrained devices	5
Reproducible processing of TCGA regulatory networks	5
Improved reference assembly and core collection resequencing to facilitate exploration of important agronomical traits for the improvement of oilseed crop, Carthamus tinctorius<	5
Contrast subgraphs allow comparing homogeneous and heterogeneous networks derived from omics data	5
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets	5
Unsupervised multiscale clustering of single-cell transcriptomes to identify hierarchical structures of cell subtypes	5
Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis)	5
The complete genome assembly of Astragalus membranaceus: enabling more accurate genetic research	5
Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution	5
Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies	5
Nanopore- and AI-empowered microbial viability inference	5
Overture: an open-source genomics data platform	5
Euler characteristic curves and profiles: a stable shape invariant for big data problems	5
Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing	5
Unlocking the power of AI for phenotyping fruit morphology in Arabidopsis	5
A telomere-to-telomere gapless genome reveals SlPRR1 control of circadian rhythm and photoperiodic flowering in tomato	4
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes	4
Draft assemblies for 177 bird species enhance genus-level coverage	4
Identifying candidate genetic variants for egg number by analyzing over 1,000 fully sequenced layers	4
The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology	4
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure	4
Network-based anomaly detection algorithm reveals proteins with major roles in human tissues	4
Charting immune variation through genetics and single-cell genomics	4
eNRSA: a faster and more powerful approach for nascent transcriptome analysis	4
An integrative multiomics random forest framework for robust biomarker discovery	4
RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations	4
Delineating regions of interest for mass spectrometry imaging by multimodally corroborated spatial segmentation	4
Population-level allelic dispersion modeling by maelstRom yields genome-wide maps of allele-specific dysregulation during early carcinogenesis	4
A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection	4
HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences	4
Confound-leakage: confound removal in machine learning leads to leakage	4
Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)	4
Comparing linear and nonlinear finite element models of vertebral strength across the thoracolumbar spine: a benchmark from density-calibrated computed tomography	4
PVGA: a precise viral genome assembler using an iterative alignment graph	4
Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat	4
GSC: efficient lossless compression of VCF files with fast query	4
DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era	4
Mutation impact on mRNA versus protein expression across human cancers	4
Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp	4
Correction to: molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	4
CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites	4
The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation	4
Selection signatures in goats reveal a novel deletion mutant underlying cashmere yield and diameter	4
MIReVTD, a minimum information standard for reporting vector trait data	4
SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis	4
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation	4
Open Data Governance at the Canadian Open Neuroscience Platform (CONP): From the Walled Garden to the Arboretum	4
Emerging AI approaches for cancer spatial omics	4
The telomere-to-telomere gap-free reference genome and taxonomic reassessment of Siniperca roulei	4
Finding easy regions for short-read variant calling from pangenome data	4