GigaScience

Article	Citations
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	229
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	93
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	85
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	76
MBGC: Multiple Bacteria Genome Compressor	70
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework	66
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources	62
The probability of edge existence due to node degree: a baseline for network-based predictions	61
Reducing skin microbiome exposure impacts through swine farm biosecurity	59
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	49
Hecatomb: an integrated software platform for viral metagenomics	47
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome	46
Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks	46
Preventing dataset shift from breaking machine-learning biomarkers	38
A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)	37
FAIR data station for lightweight metadata management and validation of omics studies	35
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	35
A decade of GigaScience: A perspective on conservation genetics	35
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	35
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	34
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	32
The Nencki-Symfonia electroencephalography/event-related potential dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults	31
scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues	31
X-ray microtomography imaging of craniofacial hard tissues in selected reptile species with different types of dentition	31
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis	30

A Case for estradiol: younger brains in women with earlier menarche and later menopause	29
Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing	27
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes	27
WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning	26
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	26
ricu: R’s interface to intensive care data	26
Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	26
Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering	26
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	25
A Decade of GigaScience: Milestones in Open Science	25
Harnessing population diversity: in search of tools of the trade	25
Studying mutation rate evolution in primates—the effects of computational pipelines and parameter choices	25
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations	25
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	24
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	24
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants	23
Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations	23
External validation of machine learning models—registered models and adaptive sample splitting	23
Computational reproducibility of Jupyter notebooks from biomedical publications	23
Unveiling vertebrate development dynamics in frog Xenopus laevis using micro-CT imaging	23
Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot	23
Population modeling with machine learning can enhance measures of mental health	22
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research	21
Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	21
Hiding in plain sight: a research parasite’s perspective on new lessons in old data	21
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	20
Spacemake: processing and analysis of large-scale spatial transcriptomics data	20
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	19
High-quality genome assembles from key Hawaiian coral species	19
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project	19
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata	19
De novoscreening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation	18
The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv	18
A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps	18
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics	18
Publishing data to support the fight against human vector-borne diseases	18
Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data	18
The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family	18
Retracted and Replaced: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	18
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection	17
Data standardization of plant–pollinator interactions	17
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids	17
A Decade of GigaScience: Women in Science: Past, Present, and Future	17
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach	17
HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences	17
Loop detection using Hi-C data with HiCExplorer	17
Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma	16
ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine	16
High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs	16

LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	15
On the benefits of self-taught learning for brain decoding	15
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation	15
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors	15
Lifting the curse from high-dimensional data: automated projection pursuit clustering for a variety of biological data modalities	15
NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer	15
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding	15
Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes	15
Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI	15
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	15
ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages	15
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas	15
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species	15
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	14
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification	14
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	14
Celebrating 30 years of access to NASA Space Life Sciences data	14
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	14
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	14
learnMSA: learning and aligning large protein families	13
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	13
HeteroMRI: Robust white matter abnormality classification across multi-scanner MRI data	13
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	13
A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes	13
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	13
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods	13
Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)	13
The state of Medusozoa genomics: current evidence and future challenges	13
A dataset of ant colonies’ motion trajectories in indoor and outdoor scenes to study clustering behavior	12
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	12
CoCoPyE: feature engineering for learning and prediction of genome quality indices	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 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
An in vitro whole-cell electrophysiology dataset of human cortical neurons	11
A telomere-to-telomere genome assembly of koi carp (Cyprinus carpio) using long reads and Hi-C technology	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
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET	11
A Decade of GigaScience: GigaDB and the Open Data Movement	11
Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging	11
DENTIST—using long reads for closing assembly gaps at high accuracy	11
An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	11
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology	11
M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications	11
On the variability of dynamic functional connectivity assessment methods	10
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes	10
Deepdefense: annotation of immune systems in prokaryotes using deep learning	10
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	10
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	10
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	10
Retraction and replacement of: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	10
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	10
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data	10
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	10
Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning	9
Accurate gene consensus at low nanopore coverage	9
MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model	9
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles	9
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater	9
d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes	9
Chromosome-level genome assemblies of Channa argus and Channa maculata and comparative analysis of their temperature adaptability	9
Correction to: The state of Medusozoa genomics: current evidence and future challenges	9
The chromosome-level genome assembly of an endangered herbBergenia scopulosaprovides insights into local adaptation and genomic vulnerability under climate change	9
SODAR: managing multiomics study data and metadata	9
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	9
Cerebellocerebral connectivity predicts body mass index: a new open-source Python-based framework for connectome-based predictive modeling	9
Fully resolved assembly of Cryptosporidium parvum	9
A molecular phenotypic map of malignant pleural mesothelioma	9
A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape	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
A trade-off in evolution: the adaptive landscape of spiders without venom glands	8
On the relationship between research parasites and fairness in machine learning: challenges and opportunities	8
Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning–driven data analysis	8
The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses	8
Streamlining remote nanopore data access with slow5curl	8
Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA–minus RNA sequencing data	8
MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction	8
Corrigendum to: The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics	8

Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis	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
Accurate and fast clade assignment via deep learning and frequency chaos game representation	8
Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise	8
ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks	8
SynProtX: a large-scale proteomics-based deep learning model for predicting synergistic anticancer drug combinations	7
Alignstein: Optimal transport for improved LC-MS retention time alignment	7
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators	7
Building the mega single-cell transcriptome ocular meta-atlas	7
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae	7
Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation	7
Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups	7
Genome size evolution in the diverse insect order Trichoptera	7
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes	7
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data	7
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)	7
DeePVP: Identification and classification of phage virion proteins using deep learning	7
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	7
Comparative maternal protein profiling of mouse biparental and uniparental embryos	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
epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data	6
Container Profiler: Profiling resource utilization of containerized big data pipelines	6
Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)	6
The rise of genomics in snake venom research: recent advances and future perspectives	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
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation	6
Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis)	6
A ghost moth olfactory prototype of the lepidopteran sex communication	6
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience	6
Analysis-ready VCF at Biobank scale using Zarr	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 telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance	6
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases	6
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects	6
PeptideMiner—neuropeptide discovery across the animal kingdom	6
Desiderata for the development of next-generation electronic health record phenotype libraries	6
Imputation method for single-cell RNA-seq data using neural topic model	6
Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers	6
Telomere-to-telomere genome and resequencing of 231 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	6
Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps	6
Statistical quantification of confounding bias in machine learning models	6
Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2	6
Genome resequencing reveals independent domestication and breeding improvement of naked oat	6
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl	6
Image segmentation of treated and untreated tumor spheroids by fully convolutional networks	6
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets	6
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells	6
Unlocking the power of AI for phenotyping fruit morphology in Arabidopsis	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
An interconnected data infrastructure to support large-scale rare disease research	6
A workflow reproducibility scale for automatic validation of biological interpretation results	6
Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset	6
Myth-busting the provider-user relationship for digital sequence information	5
Contrast subgraphs allow comparing homogeneous and heterogeneous networks derived from omics data	5
The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation	5
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features	5
Identifying candidate genetic variants for egg number by analyzing over 1,000 fully sequenced layers	5
DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era	5
HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences	5
CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites	5
Efficient real-time selective genome sequencing on resource-constrained devices	5
Euler characteristic curves and profiles: a stable shape invariant for big data problems	5
Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data	5
A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection	5
Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp	5
The complexity landscape of viral genomes	5
Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies	5
A telomere-to-telomere gapless genome reveals SlPRR1 control of circadian rhythm and photoperiodic flowering in tomato	5
Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing	5
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods	5
Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants	5
Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom research	5
A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation	5
Antibiotic resistance genes are differentially mobilized according to resistance mechanism	5
Association mapping across a multitude of traits collected in diverse environments in maize	5
Delineating regions of interest for mass spectrometry imaging by multimodally corroborated spatial segmentation	5
Mutation impact on mRNA versus protein expression across human cancers	5
Correction to: molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	5
SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples	5
Evolution of complex genome architecture in gymnosperms	5
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections	5
Overture: an open-source genomics data platform	5
Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences	4
Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts	4
Best genome sequencing strategies for annotation of complex immune gene families in wildlife	4
Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)	4
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data	4
A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei)	4
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology	4
Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa	4
Comparing linear and nonlinear finite element models of vertebral strength across the thoracolumbar spine: a benchmark from density-calibrated computed tomography	4
Comparative analysis of common alignment tools for single-cell RNA sequencing	4
The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology	4