GigaScience

15/01/2025

A new deep learning framework integrating single-cell datasets and gene–gene interaction networks.

scGraph2Vec: a deep generative model for gene embedding augmented by graph neural network and single-cell omics data

AbstractBackground. Exploring the cellular processes of genes from the aspects of biological networks is of great interest to understanding the properties

14/01/2025

New highly complete reference of a unique breed indigenous to China, alongside a variant database comprising 332 individuals.

Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality

AbstractBackground. Mongolian cattle, a unique breed indigenous to China, represent valuable genetic resources and serve as important sources of meat and m

13/01/2025

GigaBlog covers the s*x chromosome madness in the iconic echidna http://gigasciencejournal.com/blog/5982-2-s*x-chromosomes/

Read the research in GigaScience: Chromosome-level echidna genome illuminates evolution of multiple s*x chromosome system in monotremes https://doi.org/10.1093/gigascience/giae112

10/01/2025

Great resource from the ELIXIR Machine Learning Focus Group promoting transparency and reproducibility of ML in the life sciences.

DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology

Abstract. Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recom

08/01/2025

Another paper in our T2T series, this time presenting the genome of a prized hemiparasitic plant highly sought in the commercial market because of its wonderful aroma.

The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood

AbstractBackground. Sandalwood, a prized hemiparasitic plant, is highly sought in the commercial market because of its aromatic core materia. The structure

07/01/2025

GADES is a new tool for processing large multidimensional datasets that allows for massively paralleled Kendall-distance matrices computation (a statistical tool used to measure the association between two sets of ranked data).

GPU-accelerated Kendall distance computation for large or sparse data

AbstractBackground. Current experimental practices typically produce large multidimensional datasets. Distance matrix calculation between elements (e.g., s

03/01/2025

A new, generalized approach to function prediction for proteins from previously unseen sequence space.

Learning a generalized graph transformer for protein function prediction in dissimilar sequences https://doi.org/10.1093/gigascience/giae093

28/12/2024

With the Pacific Symposium on Biocomputing (PSB) starting next week, read winner of a award at Michael Skinnider, on the lessons learned from his work.

Hiding in plain sight: a research parasite’s perspective on new lessons in old data https://doi.org/10.1093/gigascience/giae097

26/12/2024

Presenting a comprehensive catalog and epigenome of rainbow trout. 🌈🐟

Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution

Abstract. Rainbow trout (RBT) has gained widespread attention as a biological model across various fields and has been rapidly adopted for aquaculture and

24/12/2024

A new supervised algorithm for demultiplexing scRNA-seq which leverages both cell hashing and genetic variation between individuals.

demuxSNP: supervised demultiplexing single-cell RNA sequencing using cell hashing and SNPs https://doi.org/10.1093/gigascience/giae090

23/12/2024

Round three for GigaByte Journal’s vectors of human disease series http://gigasciencejournal.com/blog/round-three-for-vectors/

23/12/2024

Reference for a rare plant from the mountains Southern Shaanxi with resequenced individuals spanning its geographic range.

The chromosome-level genome assembly of an endangered herb Bergenia scopulosa provides insights into local adaptation and genomic vulnerability under climate change

AbstractBackground. Global climate change poses severe threats to biodiversity and ecosystem stability. Rapid climate oscillations potentially lead to spec

19/12/2024

Presenting the largest diatom image dataset thus far, aimed at facilitating the application and benchmarking of new machine learning methods.

“UDE DIATOMS in the Wild 2024”: a new image dataset of freshwater diatoms for training deep learning models

AbstractBackground. Diatoms are microalgae with finely ornamented microscopic silica shells. Their taxonomic identification by light microscopy is routinel

18/12/2024

It's that time of year again. Read the 2024 GigaScience Press year-in-review from Hans Zauner.

Urban fruits, 3D printed frog legs and gapless genomes: 2024 was wild http://gigasciencejournal.com/blog/gigascience-2024-was-wild/

17/12/2024

New multimodal geometric deep learning method in our Spatial Omics series.

stMMR: accurate and robust spatial domain identification from spatially resolved transcriptomics with multimodal feature representation

AbstractBackground. Deciphering spatial domains using spatially resolved transcriptomics (SRT) is of great value for characterizing and understanding tissu

17/12/2024

More complete genomes for our T2T Series.

Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis)

AbstractBackground. Sweet orange (Citrus sinensis Osbeck) is a fruit crop of high nutritional value that is widely consumed around the world. However, its

16/12/2024

New genome of the Piauçu, offering insights into the evolutionary dynamics of Z and W s*x chromosomes in fish.

De novo assembly and characterization of a highly degenerated ZW s*x chromosome in the fish Megaleporinus macrocephalus

AbstractBackground. Megaleporinus macrocephalus (piauçu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW s*x

12/12/2024

New toolkit for analyzing multiple sequences in multi-FASTA format using alignment-free methodologies. And scalable to millions of sequences, making it ideal for scenarios involving endemic or epidemic outbreaks with vast amounts of available sequence data.

AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data

AbstractBackground. Most viral genome sequences generated during the latest pandemic have presented new challenges for computational analysis. Analyzing mi