GigaScience

Article	Citations
Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	111
Selection signatures in goats reveal a novel deletion mutant underlying cashmere yield and diameter	77
Protein–protein and protein–nucleic acid binding site prediction via interpretable hierarchical geometric deep learning	69
Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots	59
Interpretable network-guided epistasis detection	58
Driftage: a multi-agent system framework for concept drift detection	58
A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen	55
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	50
Erratum to: An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	50
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome	49
Triku: a feature selection method based on nearest neighbors for single-cell data	47
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework	41
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)	41
Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)	39
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification	38
The assembled and annotated genome of the masked palm civet (Paguma larvata)	38
A chromosome-level genome of the booklouse, Liposcelis brunnea, provides insight into louse evolution and environmental stress adaptation	38
The state of Medusozoa genomics: current evidence and future challenges	35
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae	35
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	34
Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations	33
DrugSim2DR: systematic prediction of drug functional similarities in the context of specific disease for drug repurposing	31
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome	30
A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes)	30
Open Data Governance at the Canadian Open Neuroscience Platform (CONP): From the Walled Garden to the Arboretum	30

Hecatomb: an integrated software platform for viral metagenomics	29
DriverMP enables improved identification of cancer driver genes	29
GSC: efficient lossless compression of VCF files with fast query	29
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants	28
Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus	28
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes	26
Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources	26
Web of venom: exploration of big data resources in animal toxin research	26
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data	25
Celebrating 30 years of access to NASA Space Life Sciences data	25
The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood	25
Genomic exploration of the endangered oriental stork, Ciconia boyciana, sheds light on migration adaptation and future conservation	24
DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology	23
Alignstein: Optimal transport for improved LC-MS retention time alignment	23
Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population	22
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	22
Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae)	22
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing	22
High-throughput imaging of powdery mildew resistance of the winter wheat collection hosted at the German Federal ex situ Genebank for Agricultural and Horticultural Crops	21
M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data	21
The curse and blessing of abundance—the evolution of drug interaction databases and their impact on drug network analysis	21
GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context	21
Correction to: A graph clustering algorithm for detection and genotyping of structural variants from long reads	21
Health record hiccups—5,526 real-world time series with change points labelled by crowdsourced visual inspection	21
High-quality phenotypic and genotypic dataset of barley genebank core collection to unlock untapped genetic diversity	21
An ecosystem for producing and sharing metadata within the web of FAIR Data	21
Computational prediction of human deep intronic variation	20
The Global Atlas of Bamboo and Rattan (GABR) Phase II: new resources for sustainable development	20
Confound-leakage: confound removal in machine learning leads to leakage	19
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection	19
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	19
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data	19
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus	18
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources	18
Genomic and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spiders	18
Maternal plasma lipids are involved in the pathogenesis of preterm birth	18
MBGC: Multiple Bacteria Genome Compressor	17
The probability of edge existence due to node degree: a baseline for network-based predictions	17
BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data	17
An analysis of performance bottlenecks in MRI preprocessing	17
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics	17
scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data	17
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks	16
Best genome sequencing strategies for annotation of complex immune gene families in wildlife	16
Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq	16
xRead: a coverage-guided approach for scalable construction of read overlapping graph	16
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology	16
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	16
Preventing dataset shift from breaking machine-learning biomarkers	16
Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)	16

Benchmarking short-read metagenomics tools for removing host contamination	15
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment	15
A ghost moth olfactory prototype of the lepidopteran sex communication	15
A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers	15
Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics	15
The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis	15
Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing	15
Correction to: Antibiotic resistance genes are differentially mobilized according to resistance mechanism	15
Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks	15
The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis	15
Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa	14
Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce	14
An interconnected data infrastructure to support large-scale rare disease research	14
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface	14
CoCoPyE: feature engineering for learning and prediction of genome quality indices	14
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators	13
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution	13
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package	13
The Nencki-Symfonia electroencephalography/event-related potential dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults	13
An analysis of security vulnerabilities in container images for scientific data analysis	13
Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a noninvasive tool for skin barrier assessment	13
Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2	13
Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes	13
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure	13
Genome size evolution in the diverse insect order Trichoptera	13
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET	12
A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)	12
A Decade of GigaScience: GigaDB and the Open Data Movement	12
X-ray microtomography imaging of craniofacial hard tissues in selected reptile species with different types of dentition	12
scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues	12
Statistical quantification of confounding bias in machine learning models	12
KOREF_S1: phased, parental trio-binned Korean reference genome using long reads and Hi-C sequencing methods	12
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data	12
A decade of GigaScience: A perspective on conservation genetics	12
Comparative maternal protein profiling of mouse biparental and uniparental embryos	11
Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective	11
CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis	11
An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	11
The germline mutational process in rhesus macaque and its implications for phylogenetic dating	11
Building the mega single-cell transcriptome ocular meta-atlas	11
DeePVP: Identification and classification of phage virion proteins using deep learning	11
Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples	11
DENTIST—using long reads for closing assembly gaps at high accuracy	11
A dataset of ant colonies’ motion trajectories in indoor and outdoor scenes to study clustering behavior	11
Hetnet connectivity search provides rapid insights into how biomedical entities are related	10
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis	10
Making Common Fund data more findable: catalyzing a data ecosystem	10
A workflow reproducibility scale for automatic validation of biological interpretation results	10
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience	10
Machine learning–based feature selection to search stable microbial biomarkers: application to inflammatory bowel disease	10
FAIR data station for lightweight metadata management and validation of omics studies	10
clevRvis: visualization techniques for clonal evolution	10
Chromosome-level genome and recombination map of the male buffalo	10
The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology	10
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	10
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	10
Allele-specific regulatory effects on the pig transcriptome	9
KGML-xDTD: a knowledge graph–based machine learning framework for drug treatment prediction and mechanism description	9
Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps	9
Leveraging citizen science for monitoring urban forageable plants	9
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes	9
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods	9
Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases	9
ricu: R’s interface to intensive care data	8
Halvade somatic: Somatic variant calling with Apache Spark	8
Comparative analysis of common alignment tools for single-cell RNA sequencing	8
Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows	8
The telomere-to-telomere genome of flowering cherry (Prunus campanulata) reveals genomic evolution of the subgenus Cerasus	8
Genome resequencing reveals independent domestication and breeding improvement of naked oat	8
learnMSA: learning and aligning large protein families	8
Learning a generalized graph transformer for protein function prediction in dissimilar sequences	8
Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution	8
Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma	8
Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts	8
CAT: a computational anatomy toolbox for the analysis of structural MRI data	7
Correction to: mechanisms of hepatic steatosis in chickens: integrated analysis of the host genome, molecular phenomics and gut microbiome	7
demuxSNP: supervised demultiplexing single-cell RNA sequencing using cell hashing and SNPs	7
Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes	7
An in vitro whole-cell electrophysiology dataset of human cortical neurons	7
Correction to: DivBrowse—interactive visualization and exploratory data analysis of variant call matrices	7

Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit	7
Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)	7
Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing	7
The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis	7
Correction to: Scientists without borders: lessons from Ukraine	7
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy	7
Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups	7
Healthy microbiome—moving towards functional interpretation	7
Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis)	6
Fluorescence microscopy datasets for training deep neural networks	6
Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus	6
ExTaxsI: an exploration tool of biodiversity molecular data	6
CAT Bridge: an efficient toolkit for gene–metabolite association mining from multiomics data	6
A dataset profiling the multiomic landscape of the prefrontal cortex in amyotrophic lateral sclerosis	6
Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature	6
Retraction: Dissection of soybean populations according to selection signatures based on whole-genome sequences	6
StoatyDive: Evaluation and classification of peak profiles for sequencing data	6
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality	6
U-Limb: A multi-modal, multi-center database on arm motion control in healthy and post-stroke conditions	6
High-throughput microscopy reveals the impact of multifactorial environmental perturbations on colorectal cancer cell growth	6
Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines	6
Studying mutation rate evolution in primates—the effects of computational pipelines and parameter choices	6
Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus	5
Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies	5
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data	5
Data management strategy for a collaborative research center	5
The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics	5
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	5
LED color gradient as a new screening tool for rapid phenotyping of plant responses to light quality	5
A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of the number one Chinese cotton variety CRI-12	5
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	5
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation	5
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection	5
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants	5
Genome assemblies of Vigna reflexo-pilosa (créole bean) and its progenitors, Vigna hirtella and Vigna trinervia, revealed homoeolog expression bias and expression-level dominance	5
Imputation method for single-cell RNA-seq data using neural topic model	5
Clonality, inbreeding, and hybridization in two extremotolerant black yeasts	5
Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging	5
Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle	5
A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability	5
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	5
Variability analysis of LC-MS experimental factors and their impact on machine learning	5
The founding charter of the Omic Biodiversity Observation Network (Omic BON)	5
Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes	5
Generation and application of pseudo–long reads for metagenome assembly	5
A Decade of GigaScience: Milestones in Open Science	5
NETMAGE: A human disease phenotype map generator for the network-based visualization of phenome-wide association study results	5
Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season	5
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data	4
Evolutionary genomics of three agricultural pest moths reveals rapid evolution of host adaptation and immune-related genes	4
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes	4
Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfishOplegnathus fasciatus	4
The rise of genomics in snake venom research: recent advances and future perspectives	4
A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei)	4
Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors	4
Toward genome assemblies for all marine vertebrates: current landscape and challenges	4
MetGENE: gene-centric metabolomics information retrieval tool	4
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells	4
Multi-omic dataset of patient-derived tumor organoids of neuroendocrine neoplasms	4
Unveiling vertebrate development dynamics in frog Xenopus laevis using micro-CT imaging	4
Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake	4
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl	4
Design and implementation of a scalable high-performance computing (HPC) cluster for omics data analysis: achievements, challenges and recommendations in LMICs	4
MMV_Im2Im: an open-source microscopy machine vision toolbox for image-to-image transformation	4
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations	4
A multi-omics data analysis workflow packaged as a FAIR Digital Object	4
Chromosome-level genome of the poultry shaft louse Menopon gallinae provides insight into the host-switching and adaptive evolution of parasitic lice	4
Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts	4
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	4
The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity	4
Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences	4
On the variability of dynamic functional connectivity assessment methods	4
d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes	3
FAIR Island: real-world examples of place-based open science	3
Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios	3
Myth-busting the provider-user relationship for digital sequence information	3
A scalable software solution for anonymizing high-dimensional biomedical data	3
Studying mutation rate evolution in primates—a need for systematic comparison of computational pipelines	3
NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data	3
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects	3
Genome assembly of 3 Amazonian Morpho butterfly species reveals Z-chromosome rearrangements between closely related species living in sympatry	3
Identification of candidate sex-specific genomic regions in male and female Asian arowana genomes	3
Accurate gene consensus at low nanopore coverage	3
Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim	3
Bias-invariant RNA-sequencing metadata annotation	3
Chromosome-level genome assemblies of Channa argus and Channa maculata and comparative analysis of their temperature adaptability	3
0s and 1s in marine molecular research: a regional HPC perspective	3
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy	3
Cell type–specific interpretation of noncoding variants using deep learning–based methods	3
Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning	3
The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe	3
SCIGA: Software for large-scale, single-cell immunoglobulin repertoire analysis	3
ISA API: An open platform for interoperable life science experimental metadata	3
A high-throughput multiplexing and selection strategy to complete bacterial genomes	3
Improved integration of single-cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humans	3