GigaScience

04/08/2025

04/08/2025

A new large-scale imaging dataset containing images of 4 staining types (DAPI, H&E, ssDNA and mIF) derived from >30 human and mouse tissues.

CellBinDB: a large-scale multimodal annotated dataset for cell segmentation with benchmarking of universal models

Abstract. In recent years, cell segmentation techniques have played a critical role in the analysis of biological images, especially for quantitative studi

01/08/2025

A new virus-focused assembler that does both assembly and polishing in a unified workflow.

PVGA: a precise viral genome assembler using an iterative alignment graph

AbstractBackground. Viral genome analysis is crucial for understanding virus evolution and mutation. Investigations into viral evolutionary dynamics and mu

28/07/2025

Investigating the potential of LLMs in improving the findability and reusability of experimental data

Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database https://doi.org/10.1093/gigascience/giaf070

25/07/2025

A new tool designed to select sparse compositional predictors and predict continuous environmental factors

CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome

AbstractBackground. Despite the surge in microbiome data acquisition, there is a limited availability of tools capable of effectively analyzing it and iden

17/07/2025

Sorry to keep carping on about our T2T genomes series...

The telomere-to-telomere gapless genome of grass carp provides insights for genetic improvement

AbstractBackground. The grass carp (Ctenopharyngodon idella) is a large herbivorous freshwater fish belonging to the Cyprinidae family. It is widely cultiv

15/07/2025

Transcriptome-wide association studies (TWAS) to identify candidate genetic variants for egg production traits

Identifying candidate genetic variants for egg number by analyzing over 1,000 fully sequenced layers

AbstractBackground. Egg production over a long laying cycle until 700 days of age is preferred for modern layer chicken breeding. It is influenced by the o

14/07/2025

A new tool for validating sample identities in whole-genome sequencing data without requiring reference information.

PISAD (Phased Intraspecies Sample Anomalies Detection): reference-free intraspecies sample anomalies detection tool based on k-mer counting

AbstractBackground. Genomic sequencing research often requires the simultaneous analysis of heterogeneous data types across single or multiple individuals,

11/07/2025

New in our Spatial Omics methods series, visualising spatial distribution of mutations by calling SNVs from spatial transcriptomics.

SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments https://doi.org/10.1093/gigascience/giaf065

09/07/2025

New Review exploring how the rapid increase in high-throughput omics data acquisition has driven the need for AI-based analysis in life sciences

Artificial intelligence: the human response to approach the complexity of big data in biology https://doi.org/10.1093/gigascience/giaf057

08/07/2025

Latest in our plant phenomics series is the Field Phenotyping Platform 1.0 data set, a comprehensive resource for winter wheat research

The FIP 1.0 Data Set: Highly resolved annotated image time series of 4,000 wheat plots grown in 6 years

AbstractBackground. Understanding genotype–environment interactions of plants is crucial for crop improvement, yet limited by the scarcity of quality pheno

03/07/2025

Combining genomics, transcriptomics, and proteomics, to characterize the main toxins of this medically important snake species.

Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii) https://doi.org/10.1093/gigascience/giaf030