GigaScience

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

Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples	30
FAIR data station for lightweight metadata management and validation of omics studies	30
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants	30
Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks	30
Harnessing population diversity: in search of tools of the trade	29
A Decade of GigaScience: Milestones in Open Science	28
Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering	28
Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	28
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	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	26
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations	25
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	25
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	25
Hiding in plain sight: a research parasite’s perspective on new lessons in old data	24
Computational reproducibility of Jupyter notebooks from biomedical publications	24
Studying mutation rate evolution in primates—the effects of computational pipelines and parameter choices	24
Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations	24
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	23
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project	23
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata	23
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research	23
GADMA2: more efficient and flexible demographic inference from genetic data	22
Spacemake: processing and analysis of large-scale spatial transcriptomics data	22
Population modeling with machine learning can enhance measures of mental health	22
High-quality genome assembles from key Hawaiian coral species	22
Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	21
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics	21
Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data	21
The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv	20
BiSulfite Bolt: A bisulfite sequencing analysis platform	20
Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	20
The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family	19
BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data	19
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection	19
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach	19
De novoscreening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation	19
Publishing data to support the fight against human vector-borne diseases	19
ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine	18
Data standardization of plant–pollinator interactions	18
A Decade of GigaScience: Women in Science: Past, Present, and Future	18
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation	18
ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages	17
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors	17
High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs	17
Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma	17
On the benefits of self-taught learning for brain decoding	17
HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences	17
Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI	17
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas	16

NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer	16
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids	16
Loop detection using Hi-C data with HiCExplorer	16
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding	16
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	16
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	15
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification	15
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	15
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	15
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	15
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	15
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species	14
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	14
M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data	14
Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots	14
Celebrating 30 years of access to NASA Space Life Sciences data	14
The state of Medusozoa genomics: current evidence and future challenges	14
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	14
DENTIST—using long reads for closing assembly gaps at high accuracy	13
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	13
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	13
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET	13
A Decade of GigaScience: GigaDB and the Open Data Movement	13
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	13
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	13
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods	13
An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	13
CoCoPyE: feature engineering for learning and prediction of genome quality indices	13
A dataset of ant colonies’ motion trajectories in indoor and outdoor scenes to study clustering behavior	13
An in vitro whole-cell electrophysiology dataset of human cortical neurons	12
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	12
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	12
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes	12
learnMSA: learning and aligning large protein families	12
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data	11
U-Limb: A multi-modal, multi-center database on arm motion control in healthy and post-stroke conditions	11
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	11
Deepdefense: annotation of immune systems in prokaryotes using deep learning	11
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	11
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology	11
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	11
On the variability of dynamic functional connectivity assessment methods	11
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	11
Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging	11
A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks	11
Metaphor—A workflow for streamlined assembly and binning of metagenomes	11
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	11
Accurate gene consensus at low nanopore coverage	10
The chromosome-level genome assembly of an endangered herbBergenia scopulosaprovides insights into local adaptation and genomic vulnerability under climate change	10
Correction to: The state of Medusozoa genomics: current evidence and future challenges	10
MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model	10
Fully resolved assembly of Cryptosporidium parvum	10
NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data	10
Cerebellocerebral connectivity predicts body mass index: a new open-source Python-based framework for connectome-based predictive modeling	10
ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks	10
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles	10
A molecular phenotypic map of malignant pleural mesothelioma	10
Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning	10
Chromosome-level genome assemblies of Channa argus and Channa maculata and comparative analysis of their temperature adaptability	10
SODAR: managing multiomics study data and metadata	10
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor	10
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater	10
d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes	10
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 decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape	9
Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis	9
Accurate and fast clade assignment via deep learning and frequency chaos game representation	9
Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family	9
Corrigendum to: The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics	9
The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses	8
Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA–minus RNA sequencing data	8
Streamlining remote nanopore data access with slow5curl	8
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes	8
On the relationship between research parasites and fairness in machine learning: challenges and opportunities	8
Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise	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
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
A trade-off in evolution: the adaptive landscape of spiders without venom glands	8
Driftage: a multi-agent system framework for concept drift detection	8

MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction	8
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data	7
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience	7
Statistical quantification of confounding bias in machine learning models	7
A ghost moth olfactory prototype of the lepidopteran sex communication	7
Alignstein: Optimal transport for improved LC-MS retention time alignment	7
Comparative maternal protein profiling of mouse biparental and uniparental embryos	7
Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups	7
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)	7
A workflow reproducibility scale for automatic validation of biological interpretation results	7
Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2	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
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
Genome size evolution in the diverse insect order Trichoptera	6
Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers	6
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl	6
epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data	6
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation	6
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells	6
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants	6
The germline mutational process in rhesus macaque and its implications for phylogenetic dating	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
Imputation method for single-cell RNA-seq data using neural topic model	6
An interconnected data infrastructure to support large-scale rare disease research	6
The rise of genomics in snake venom research: recent advances and future perspectives	6
Container Profiler: Profiling resource utilization of containerized big data pipelines	6
Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)	6
Correction to: Scientists without borders: lessons from Ukraine	6
DeePVP: Identification and classification of phage virion proteins using deep learning	6
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators	6
Building the mega single-cell transcriptome ocular meta-atlas	6
LED color gradient as a new screening tool for rapid phenotyping of plant responses to light quality	6
Desiderata for the development of next-generation electronic health record phenotype libraries	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
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
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets	5
Overture: an open-source genomics data platform	5
Euler characteristic curves and profiles: a stable shape invariant for big data problems	5
Evolution of complex genome architecture in gymnosperms	5
Delineating regions of interest for mass spectrometry imaging by multimodally corroborated spatial segmentation	5
Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data	5
CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites	5
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects	5
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods	5
Contrast subgraphs allow comparing homogeneous and heterogeneous networks derived from omics data	5
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections	5
Antibiotic resistance genes are differentially mobilized according to resistance mechanism	5
Correction to: molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	5
Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants	5
SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples	5
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases	5
Myth-busting the provider-user relationship for digital sequence information	5
Efficient real-time selective genome sequencing on resource-constrained devices	5
A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation	5
Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom research	5
The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation	5
Best genome sequencing strategies for annotation of complex immune gene families in wildlife	4
xRead: a coverage-guided approach for scalable construction of read overlapping graph	4
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure	4
GSC: efficient lossless compression of VCF files with fast query	4
Confound-leakage: confound removal in machine learning leads to leakage	4
DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era	4
Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies	4
Open Data Governance at the Canadian Open Neuroscience Platform (CONP): From the Walled Garden to the Arboretum	4
Halvade somatic: Somatic variant calling with Apache Spark	4
Comparative analysis of common alignment tools for single-cell RNA sequencing	4
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology	4
The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology	4
Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa	4
BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data	4
Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae)	4
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features	4
Mutation impact on mRNA versus protein expression across human cancers	4
Association mapping across a multitude of traits collected in diverse environments in maize	4
Healthy microbiome—moving towards functional interpretation	4
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data	4
Maternal plasma lipids are involved in the pathogenesis of preterm birth	4
CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis	4
Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)	4
Selection signatures in goats reveal a novel deletion mutant underlying cashmere yield and diameter	4
Network-based anomaly detection algorithm reveals proteins with major roles in human tissues	4
The complexity landscape of viral genomes	4
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation	4
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing	4
The Global Atlas of Bamboo and Rattan (GABR) Phase II: new resources for sustainable development	4
Correction to: DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	4
Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts	4