GigaScience

Article	Citations
Hecatomb: an integrated software platform for viral metagenomics	459
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	39
Characterizing a species-rich and understudied tropical insect fauna using DNA barcoding	38
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	38
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	36
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	29
Expression-driven genetic dependency reveals targets for precision oncology	28
The probability of edge existence due to node degree: a baseline for network-based predictions	28
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	28
Reducing skin microbiome exposure impacts through swine farm biosecurity	28
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	27
The genomes of 5 mantises provide insights into sex chromosome evolution and Mantodea phylogeny clarification	26
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
TinkerHap—a novel read-based phasing algorithm with integrated multimethod support for enhanced accuracy	25
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes	24
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	24
Datagraphy: toward a systematic approach to dataset discovery	24
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	23
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	23
SeuratExtend: streamlining single-cell RNA-seq analysis through an integrated and intuitive framework	22
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome	22
ricu: R’s interface to intensive care data	22
FAIR data station for lightweight metadata management and validation of omics studies	22
WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning	22
Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing	21

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

TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors	12
Celebrating 30 years of access to NASA Space Life Sciences data	11
AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level	11
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	11
A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona	11
HeteroMRI: Robust white matter abnormality classification across multi-scanner MRI data	11
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	11
nf-core/proteinfamilies: a scalable pipeline for the generation of protein families	11
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	11
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	11
Lifting the curse from high-dimensional data: automated projection pursuit clustering for a variety of biological data modalities	10
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	10
A telomere-to-telomere genome assembly of koi carp (Cyprinus carpio) using long reads and Hi-C technology	10
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods	10
Stereo-cell deciphers the spatial and functional heterogeneity of polyploid hepatocytes	10
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species	10
CoCoPyE: feature engineering for learning and prediction of genome quality indices	10
PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking	10
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	10
Toward total recall: Enhancing data FAIRness through AI-driven metadata standardization	10
A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research	10
Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)	10
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	9
Enhanced semantic classification of microbiome sample origins using large language models (LLMs)	9
Retraction and replacement of: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	9
Deepdefense: annotation of immune systems in prokaryotes using deep learning	9
Translating short-form Python exercises to other programming languages using diverse prompting strategies	9
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	9
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	9
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	9
M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications	9
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	9
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	9
The Open Pediatric Cancer Project	9
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	9
Federated knowledge retrieval elevates large language model performance on biomedical benchmarks	9
PanGIA: A universal framework for identifying association between ncRNAs and diseases	9
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing	9
Learning inherent genetic patterns and trait associations with deep generative models for discrete genotype simulation	9
On the variability of dynamic functional connectivity assessment methods	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
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
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	8
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	8
Cerebellocerebral connectivity predicts body mass index: a new open-source Python-based framework for connectome-based predictive modeling	8
Interspecific hybridization in Brassica species leads to changes in agronomic traits through the regulation of gene expression by chromatin accessibility and DNA methylation	8
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	8
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology	8
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes	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
Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes	8
A framework to mine laser microdissection-based omics data and uncover regulators of pancreatic cancer heterogeneity	7
Comparative analysis of 163 ant genomes reveals recurrent horizontal gene transfer from bacteria to ants	7
MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction	7
Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise	7
Improving the reliability, quality, and maintainability of bioinformatics pipelines with nf-test	7
Streamlining remote nanopore data access with slow5curl	7
SODAR: managing multiomics study data and metadata	7
Accurate and fast clade assignment via deep learning and frequency chaos game representation	7
MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model	7
Patterns of aDNA damage through time and environments—lessons from herbarium specimens	7
A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human	7
Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning–driven data analysis	7
Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis	7
The chromosome-level genome assembly of an endangered herbBergenia scopulosaprovides insights into local adaptation and genomic vulnerability under climate change	7
A molecular phenotypic map of malignant pleural mesothelioma	7
The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses	7
A trade-off in evolution: the adaptive landscape of spiders without venom glands	7
Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination	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
Open RGB imaging workflow for morphological and morphometric analysis of fruits using deep learning: a case study on almonds	7
CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology	6
Genos: a human-centric genomic foundation model	6
MRanalysis: a comprehensive online platform for integrated, multimethod Mendelian randomization and associated post-GWAS analyses	6
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience	6
An interconnected data infrastructure to support large-scale rare disease research	6
Cord blood DNA methylation and cell-type composition are not significantly associated with severe preeclampsia after cell-type and clinical covariate adjustment	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
Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers	6
HVRLocator: A Computationally Efficient Tool for Identifying Hypervariable Regions in Large 16S rRNA Datasets	6
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes	6
An evaluation of computational methods for reconstruction of human viral DNA genomes	6
Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset	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
Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps	6
Analysis-ready VCF at Biobank scale using Zarr	6
Telomere-to-telomere genome and resequencing of 231 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	6
A ghost moth olfactory prototype of the lepidopteran sex communication	6
Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence	6
Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation	6
SynProtX: a large-scale proteomics-based deep learning model for predicting synergistic anticancer drug combinations	6
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data	6
Giant chromosomes of a tiny plant—the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermannio	6
A workflow reproducibility scale for automatic validation of biological interpretation results	6
Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups	6
Genome resequencing reveals independent domestication and breeding improvement of naked oat	6
The complete genome assembly of Astragalus membranaceus: enabling more accurate genetic research	5
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets	5
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants	5
PeptideMiner—neuropeptide discovery across the animal kingdom	5
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases	5
Image segmentation of treated and untreated tumor spheroids by fully convolutional networks	5
Unsupervised multiscale clustering of single-cell transcriptomes to identify hierarchical structures of cell subtypes	5
CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites	5
A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance	5
Imputation method for single-cell RNA-seq data using neural topic model	5
Correction to: Scientists without borders: lessons from Ukraine	5
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation	5
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data	5
ZNF331 modulates early embryonic transcription during zygotic genome activation in goat	5
A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection	5
Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution	5
Euler characteristic curves and profiles: a stable shape invariant for big data problems	5
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells	5
Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis)	5
Unlocking the power of AI for phenotyping fruit morphology in Arabidopsis	5
Container Profiler: Profiling resource utilization of containerized big data pipelines	5
epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data	5
HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences	5
Chromosome-level reference genome for the medically important Arabian horned viper ( Cerastes gasperettii )	5
Contrast subgraphs allow comparing homogeneous and heterogeneous networks derived from omics data	4
A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation	4
Efficient real-time selective genome sequencing on resource-constrained devices	4
Comparative genomics and multiomics analyses reveal the evolution and physiological basis of rubber biosynthesis in Hevea species	4
RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations	4
Network-based anomaly detection algorithm reveals proteins with major roles in human tissues	4
Open Data Governance at the Canadian Open Neuroscience Platform (CONP): From the Walled Garden to the Arboretum	4
SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis	4
DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era	4
Nanopore- and AI-empowered microbial viability inference	4
Mutation impact on mRNA versus protein expression across human cancers	4
Delineating regions of interest for mass spectrometry imaging by multimodally corroborated spatial segmentation	4
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections	4
Reproducible processing of TCGA regulatory networks	4
Overture: an open-source genomics data platform	4
Improved reference assembly and core collection resequencing to facilitate exploration of important agronomical traits for the improvement of oilseed crop, Carthamus tinctorius<	4
The telomere-to-telomere gap-free reference genome and taxonomic reassessment of Siniperca roulei	4
Charting immune variation through genetics and single-cell genomics	4
Confound-leakage: confound removal in machine learning leads to leakage	4
eNRSA: a faster and more powerful approach for nascent transcriptome analysis	4
A telomere-to-telomere gapless genome reveals SlPRR1 control of circadian rhythm and photoperiodic flowering in tomato	4
The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation	4
Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies	4
Selection signatures in goats reveal a novel deletion mutant underlying cashmere yield and diameter	4
Population-level allelic dispersion modeling by maelstRom yields genome-wide maps of allele-specific dysregulation during early carcinogenesis	4
Correction to: molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	4
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes	4
Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing	4
An integrative multiomics random forest framework for robust biomarker discovery	4
Emerging AI approaches for cancer spatial omics	4
Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat	4
Finding easy regions for short-read variant calling from pangenome data	4
GSC: efficient lossless compression of VCF files with fast query	4
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation	4
Identifying candidate genetic variants for egg number by analyzing over 1,000 fully sequenced layers	4
Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data	4
Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp	4