GigaScience Journal

Dear Authors, Readers, Editorial Board Members and Colleagues in the Academic Community, we are delighted to announce that Dr. Xun Xu has officially been appointed as Editor-in-Chief of GigaScience. See the announcement here: gigasciencejournal.com/blog/dr-xun-...

And it’s goodbye from me. Final GigaBlog from outgoing EiC @scedmunds.bsky.social on the major changes at GigaScience Press gigasciencejournal.com/blog/and-its...

Happy #PeerReviewWeek: To celebrate we have a proposal in GigaBlog: Why we need a FAIR Principles for Peer Review? gigasciencejournal.com/blog/peerrev... #PRW2025

WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning AbstractBackground. Influenza A virus (IAV) poses a significant threat to animal health globally, with its ability to overcome species barriers and cause p

A novel deep learning model for accurate and rapid prediction of IAV subtypes and host source

WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning doi.org/10.1093/giga...

The Return of Asia Nature Challenge #ANC2025
gigasciencejournal.com/blog/the-ret... #AsiaNatureChallenge #ANC2025 #CitizenScience

DeepAnnotation: A novel interpretable deep learning–based genomic selection model that integrates comprehensive functional annotations AbstractBackground. Genomic selection, which leverages genomic information to predict the breeding value of individuals, has dramatically accelerated the i

A new #opensource interpretable genomic selection model designed for phenotype prediction.

DeepAnnotation: A novel interpretable deep learning–based genomic selection model that integrates comprehensive functional annotations doi.org/10.1093/giga...

HeteroMRI: Robust white matter abnormality classification across multi-scanner MRI data AbstractBackground. Magnetic resonance imaging (MRI) is commonly used for analyzing white matter abnormalities in the human brain. Integrating machine lear

Presenting new avenues for white matter abnormality-related classification of heterogeneous MRI data

HeteroMRI: Robust white matter abnormality classification across multi-scanner MRI data doi.org/10.1093/giga...

The Earth Hologenome Initiative: Data Release 1 AbstractBackground. The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from

📣Another publication from our amazing researchers and colleagues: The Earth Hologenome Initiative: Data Release 1

@ehologenome.bsky.social 🦠💡

Find it in
@gigascience.bsky.social
👇

New in our T2T series, and the first published plant (and T2T) genome using CycloneSeq nanopore reads.

Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation doi.org/10.1093/giga...

A holistic genome dataset of bacteria and archaea of mangrove sediments AbstractBackground. Mangroves are one of the most productive marine ecosystems with high ecosystem service value. The sediment microbial communities contri

Presenting metagenomic data from the analysis of microbial communities in mangrove sediments across Southeast China

A holistic genome dataset of bacteria and archaea of mangrove sediments doi.org/10.1093/giga...

PeptideMiner—neuropeptide discovery across the animal kingdom Abstract. Neuropeptides represent the largest and most diverse class of cell-to-cell signaling molecules, holding important roles in animal physiology and

A new platform for discovering new bioactive peptides and family-specific analogues, accelerating both natural product discovery and evolutionary research.

PeptideMiner—neuropeptide discovery across the animal kingdom doi.org/10.1093/giga...

SynProtX: a large-scale proteomics-based deep learning model for predicting synergistic anticancer drug combinations AbstractMotivation. Drug combination therapy plays a pivotal role in addressing the molecular heterogeneity of cancer, improving treatment efficacy, minimi

A new GNN+DNN model, which combines molecular graphs and fingerprints through a graph attention network architecture.

SynProtX: a large-scale proteomics-based deep learning model for predicting synergistic anticancer drug combinations doi.org/10.1093/giga...

Reducing skin microbiome exposure impacts through swine farm biosecurity AbstractBackground. Livestock work is unique due to worker exposure to animal-associated microbiomes within the workplace. Swine workers are a unique cohor

Old MacDonald had animal-associated microbiome contamination, E-I-E-I-O

Reducing skin microbiome exposure impacts through swine farm biosecurity doi.org/10.1093/giga...

MetaboSERV—a platform for selecting, exchanging, and visualizing metabolomics data with controlled data access AbstractBackground. The growing number of metabolomics studies, based on high-dimensional data measured by hyphenated mass spectrometry (MS) and/or nuclear

A new #opensource #metabolomics platform dedicated to the selection, integration, and secure (controlled access) sharing of quantitative metabolomics data

MetaboSERV—a platform for selecting, exchanging, and visualizing metabolomics data with controlled data access doi.org/10.1093/giga...

Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes AbstractBackground. Koi carp, a variant of the common carp, is one of the most popular ornamental fish. Its genomic resources can help us better understand

New in our T2T series: Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes doi.org/10.1093/giga...

And read the research in GigaScience here doi.org/10.1093/giga...

YouTube video by GigaScience Press Charley Yen on Conservation Genomics and Epigenomics of Loggerhead Turtles

Watch this new explainer video from @eugeniecyen.bsky.social on her labs work on on conservation #genomics and #epigenomics of endangered Loggerhead Turtles youtu.be/3C4D43mEBBk?...

Cassyni screenshot

If you missed our cracking Cassyni webinar yesterday with Arthur Georges and Qiye Li talking about reptile sex-determination and CycloneSeq, the Q&A was a treat as we had many of the worlds top sex chromosome researchers join the discussion. You can watch it here cassyni.com/events/SWHRe...

Tune it to our amazing sex changing reptile genomics webinar starting in about an hour...

The telomere-to-telomere gap-free reference genome and taxonomic reassessment of Siniperca roulei Abstract. Siniperca roulei is primarily distributed in the eastern waters of China, with its population being both scarce and vulnerable. Research on this

The long-bodied mandarin fish joins the T2T genome club (and our T2T genomes thematic series)

The telomere-to-telomere gap-free reference genome and taxonomic reassessment of Siniperca roulei doi.org/10.1093/giga...

See also this video where you can see the loss of eyes during development of the olm from 3D imaging data we published youtu.be/OJYafv5lzSk?...

Sign up for our webinar on Tuesday 26th August on how new long read technologies (including the first CycloneSeq vertebrate genomes) are helping elucidate the sex determination of sex-changing reptiles cassyni.com/events/SWHRe...

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot AbstractBackground. Uncovering the epigenomic regulation of immune response is essential for a comprehensive understanding of host defense mechanisms, thou

New work providing an improved understanding of the epigenomic basis of turbot immune response to mimics of viral and bacterial stimuli

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot doi.org/10.1093/giga...

A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps AbstractBackground. The central bearded dragon (Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among

🎉 Another exciting contribution from our lab this summer!

🧬 Nearly complete, gapless genome of the sex-changing central bearded dragon (Pogona vitticeps) shed new light on the mystery of reptile sex determination.

Proud to be part of this collaborative effort!

academic.oup.com/gigascience/...

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes AbstractBackground. Vertebrate sex is typically determined either by genetic factors, such as sex chromosomes, or by environmental cues like temperature. T

Read more:
A near-complete genome assembly of the bearded dragon P. vitticeps provides insights into the origin of Pogona sex chromosomes doi.org/10.1093/giga...

A near telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon doi.org/10.1093/giga...

Double Dragon Genomes Helping Explain Sex Determination of Reptiles. Two almost complete and gapless genomes of the sex-changing central bearded dragon (Pogona vitticeps) have just been published back-to-back in GigaScience gigasciencejournal.com/blog/double-...

SeuratExtend: streamlining single-cell RNA-seq analysis through an integrated and intuitive framework Abstract. Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity, but the rapid expansion of analytical tools has pr

New tool extending upon the popular Seurat framework to harness the full potential of scRNA-seq data, making complex analyses accessible to a wider audience.

SeuratExtend: streamlining single-cell RNA-seq analysis through an integrated and intuitive framework doi.org/10.1093/giga...

eNRSA: a faster and more powerful approach for nascent transcriptome analysis Abstract. Nascent RNA sequencing tracks primary transcriptional events, making it crucial for studying the immediate regulatory changes of genes and enhanc

New enhanced NRSA tool to extract newly transcribed RNAs from the total pool of cellular RNA.

eNRSA: a faster and more powerful approach for nascent transcriptome analysis doi.org/10.1093/giga...

A new complete tomato reference joins our T2T series.

A telomere-to-telomere gapless genome reveals SlPRR1 control of circadian rhythm and photoperiodic flowering in tomato doi.org/10.1093/giga...

The genome of Hippophae salicifolia provides new insights into the sexual differentiation of sea buckthorn AbstractBackground. Dioecy, a common reproductive strategy in angiosperms, has evolved independently in various plant lineages, and this has resulted in th

The sex lives of sea buckthorns. Comparative genomics of male and female Hippophae angiosperms to understand its XY sex determination system.

The genome of Hippophae salicifolia provides new insights into the sexual differentiation of sea buckthorn doi.org/10.1093/giga...