Lightnews — Scholar-powered news

GigaScience Journal @gigascience.bsky.social · 21d

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...

2 6 6

GigaScience Journal @gigascience.bsky.social · 22d

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

2

GigaScience Journal @gigascience.bsky.social · 24d

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...

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

doi.org

GigaScience Journal @gigascience.bsky.social · 26d

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

1

GigaScience Journal @gigascience.bsky.social · 26d

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...

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

doi.org

1

GigaScience Journal @gigascience.bsky.social · 27d

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...

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

doi.org

Reposted by GigaScience Journal

Center for Evolutionary Hologenomics @hologenomics.bsky.social · 27d

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

@ehologenome.bsky.social 🦠💡

Find it in
@gigascience.bsky.social
👇

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

academic.oup.com

4 2

GigaScience Journal @gigascience.bsky.social · 28d

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...

GigaScience Journal @gigascience.bsky.social · Sep 8

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...

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

doi.org

GigaScience Journal @gigascience.bsky.social · Sep 6

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...

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

doi.org

GigaScience Journal @gigascience.bsky.social · Sep 5

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...

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

doi.org

1

GigaScience Journal @gigascience.bsky.social · Sep 3

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...

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

doi.org

1

GigaScience Journal @gigascience.bsky.social · Sep 2

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...

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

doi.org

2 1

GigaScience Journal @gigascience.bsky.social · Sep 2

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...

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

doi.org

GigaScience Journal @gigascience.bsky.social · Aug 29

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

1

GigaScience Journal @gigascience.bsky.social · Aug 29

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?...

Charley Yen on Conservation Genomics and Epigenomics of Loggerhead Turtles

YouTube video by GigaScience Press

youtu.be

1 1

GigaScience Journal @gigascience.bsky.social · Aug 27

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...

GigaScience Journal @gigascience.bsky.social · Aug 26

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

GigaScience Journal @gigascience.bsky.social · Aug 22

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...

GigaScience Journal @gigascience.bsky.social · Aug 24

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...

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

doi.org

1 1

GigaScience Journal @gigascience.bsky.social · Aug 24

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?...

1

GigaScience Journal @gigascience.bsky.social · Aug 22

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...

1 2

GigaScience Journal @gigascience.bsky.social · Aug 21

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...

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

doi.org

Reposted by GigaScience Journal

Aurora Ruiz-Herrera @aruizherrera.bsky.social · Aug 19

🎉 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 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

academic.oup.com

21 63

GigaScience Journal @gigascience.bsky.social · Aug 19

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...

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

doi.org

GigaScience Journal @gigascience.bsky.social · Aug 19

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-...

1 2