GigaScience

Article	Citations
Reducing skin microbiome exposure impacts through swine farm biosecurity	209
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	90
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	82
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	71
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	65
MBGC: Multiple Bacteria Genome Compressor	62
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework	61
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources	60
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	59
Hecatomb: an integrated software platform for viral metagenomics	48
The probability of edge existence due to node degree: a baseline for network-based predictions	47
A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)	46
A decade of GigaScience: A perspective on conservation genetics	45
Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks	38
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis	35
The Nencki-Symfonia electroencephalography/event-related potential dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults	35
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	34
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes	34
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	34
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	32
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
Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing	30
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	30
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome	29

A Case for estradiol: younger brains in women with earlier menarche and later menopause	28
FAIR data station for lightweight metadata management and validation of omics studies	26
Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering	26
ricu: R’s interface to intensive care data	26
Preventing dataset shift from breaking machine-learning biomarkers	26
Harnessing population diversity: in search of tools of the trade	25
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations	25
Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations	25
A 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	25
External validation of machine learning models—registered models and adaptive sample splitting	25
Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	25
Studying mutation rate evolution in primates—the effects of computational pipelines and parameter choices	24
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	24
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	23
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants	23
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	23
A Decade of GigaScience: Milestones in Open Science	23
Unveiling vertebrate development dynamics in frog Xenopus laevis using micro-CT imaging	23
Computational reproducibility of Jupyter notebooks from biomedical publications	22
Spacemake: processing and analysis of large-scale spatial transcriptomics data	21
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research	21
Population modeling with machine learning can enhance measures of mental health	21
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project	21
Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	21
Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle	21
Hiding in plain sight: a research parasite’s perspective on new lessons in old data	21
High-quality genome assembles from key Hawaiian coral species	20
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	20
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata	19
GADMA2: more efficient and flexible demographic inference from genetic data	19
Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection	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 whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv	18
Retracted and Replaced: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis	18
The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family	18
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach	18
ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine	17
A Decade of GigaScience: Women in Science: Past, Present, and Future	17
Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes	17
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids	17
Loop detection using Hi-C data with HiCExplorer	17
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics	17
Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma	17
Data standardization of plant–pollinator interactions	17
HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences	17
De novoscreening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation	17
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors	16
On the benefits of self-taught learning for brain decoding	16
High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs	16

Lifting the curse from high-dimensional data: automated projection pursuit clustering for a variety of biological data modalities	15
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification	15
Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI	15
ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages	15
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	15
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	15
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation	15
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding	15
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	15
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	15
NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer	15
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas	15
The state of Medusozoa genomics: current evidence and future challenges	14
Celebrating 30 years of access to NASA Space Life Sciences data	14
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species	14
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	14
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	14
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	14
CoCoPyE: feature engineering for learning and prediction of genome quality indices	13
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	13
DENTIST—using long reads for closing assembly gaps at high accuracy	13
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET	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
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	13
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	13
learnMSA: learning and aligning large protein families	13
An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	13
A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research	12
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	12
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	12
A Decade of GigaScience: GigaDB and the Open Data Movement	12
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	12
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	12
A dataset of ant colonies’ motion trajectories in indoor and outdoor scenes to study clustering behavior	12
An in vitro whole-cell electrophysiology dataset of human cortical neurons	12
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	12
Metaphor—A workflow for streamlined assembly and binning of metagenomes	11
Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging	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
A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks	11
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	11
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	11
On the variability of dynamic functional connectivity assessment methods	11
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	11
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	10
Deepdefense: annotation of immune systems in prokaryotes using deep learning	10
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data	10
d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes	10
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes	10
Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning	10
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater	9
ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks	9
Cerebellocerebral connectivity predicts body mass index: a new open-source Python-based framework for connectome-based predictive modeling	9
Chromosome-level genome assemblies of Channa argus and Channa maculata and comparative analysis of their temperature adaptability	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
The chromosome-level genome assembly of an endangered herbBergenia scopulosaprovides insights into local adaptation and genomic vulnerability under climate change	9
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor	9
The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses	9
Accurate gene consensus at low nanopore coverage	9
Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis	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
SODAR: managing multiomics study data and metadata	9
Accurate and fast clade assignment via deep learning and frequency chaos game representation	9
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles	9
Fully resolved assembly of Cryptosporidium parvum	9
Correction to: The state of Medusozoa genomics: current evidence and future challenges	9
MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model	9
On the relationship between research parasites and fairness in machine learning: challenges and opportunities	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
Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning–driven data analysis	8
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)	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
Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise	8
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes	8
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae	8
Corrigendum to: The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics	8

A trade-off in evolution: the adaptive landscape of spiders without venom glands	8
Streamlining remote nanopore data access with slow5curl	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 workflow reproducibility scale for automatic validation of biological interpretation results	7
Analysis-ready VCF at Biobank scale using Zarr	7
Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2	7
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data	7
DeePVP: Identification and classification of phage virion proteins using deep learning	7
Building the mega single-cell transcriptome ocular meta-atlas	7
Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset	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
Genome size evolution in the diverse insect order Trichoptera	7
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators	7
Myth-busting the provider-user relationship for digital sequence information	6
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl	6
Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution	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
Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)	6
Container Profiler: Profiling resource utilization of containerized big data pipelines	6
A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance	6
Imputation method for single-cell RNA-seq data using neural topic model	6
Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom research	6
epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data	6
The rise of genomics in snake venom research: recent advances and future perspectives	6
LED color gradient as a new screening tool for rapid phenotyping of plant responses to light quality	6
Statistical quantification of confounding bias in machine learning models	6
A ghost moth olfactory prototype of the lepidopteran sex communication	6
Genome resequencing reveals independent domestication and breeding improvement of naked oat	6
An interconnected data infrastructure to support large-scale rare disease research	6
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets	6
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation	6
Correction to: Scientists without borders: lessons from Ukraine	6
Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants	6
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases	6
Unlocking the power of AI for phenotyping fruit morphology in Arabidopsis	6
Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers	6
Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis)	6
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants	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
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience	6
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells	6
Desiderata for the development of next-generation electronic health record phenotype libraries	6
Efficient real-time selective genome sequencing on resource-constrained devices	6
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects	6
Image segmentation of treated and untreated tumor spheroids by fully convolutional networks	6
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features	5
Association mapping across a multitude of traits collected in diverse environments in maize	5
Mutation impact on mRNA versus protein expression across human cancers	5
HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences	5
Evolution of complex genome architecture in gymnosperms	5
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods	5
Antibiotic resistance genes are differentially mobilized according to resistance mechanism	5
Overture: an open-source genomics data platform	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
Identifying candidate genetic variants for egg number by analyzing over 1,000 fully sequenced layers	5
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing	5
Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing	5
CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites	5
SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples	5
A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation	5
DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era	5
Delineating regions of interest for mass spectrometry imaging by multimodally corroborated spatial segmentation	5
Correction to: molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	5
Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies	5
Contrast subgraphs allow comparing homogeneous and heterogeneous networks derived from omics data	5
Euler characteristic curves and profiles: a stable shape invariant for big data problems	5
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections	5
Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data	5
A telomere-to-telomere gapless genome reveals SlPRR1 control of circadian rhythm and photoperiodic flowering in tomato	5
The telomere-to-telomere gap-free reference genome and taxonomic reassessment of Siniperca roulei	5
Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database	4
A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei)	4
Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus	4
Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences	4
Generation and application of pseudo–long reads for metagenome assembly	4
A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability	4
The founding charter of the Omic Biodiversity Observation Network (Omic BON)	4
demuxSNP: supervised demultiplexing single-cell RNA sequencing using cell hashing and SNPs	4
Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies	4
Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle	4
The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology	4
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data	4
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology	4
Data management strategy for a collaborative research center	4
Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature	4
Design and implementation of a scalable high-performance computing (HPC) cluster for omics data analysis: achievements, challenges and recommendations in LMICs	4
Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts	4
Correction to: DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	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
What the Phage: a scalable workflow for the identification and analysis of phage sequences	4