SCSEQ is a new zero-code web platform for single-cell RNA-seq analysis, published in #GigaScience. doi.org/10.1093/giga...

SCSEQ: A web tool for analyzing single-cell RNA-seq data

AbstractBackground. Single-cell RNA sequencing has emerged as a powerful approach to reveal cellular heterogeneity within biological systems. With the cont

doi.org

New tool alert! MicroFinder, just published in GigaScience, helps assemble notoriously tricky bird genomes—faster & more accurately than ever before. doi.org/10.1093/giga...; www.sanger.ac.uk/news_item/ne...

MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes

AbstractBackground. Obtaining chromosomally complete genome assemblies across the tree of life is an important goal of biodiversity genomics. However, some

doi.org

Giant chromosomes of a tiny plant - the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta): doi.org/10.1093/giga...

Giant chromosomes of a tiny plant - the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta)

AbstractBackground. The liverwort A. endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability, genomic

doi.org

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

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

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

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

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

📣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

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...

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

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

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

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

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

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

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

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...

GigaScience Journal@gigascience.bsky.social · 12mo ago

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...

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

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?...

Visualizing a sightless world: 3D Imaging of the Proteus reveals adaptation for life in the dark

YouTube video by GigaScience Press

youtu.be

Harriet Carroll: Long Covid Scientific Consultancy@angryhacademic.bsky.social · 12mo ago

Fun fact: olms "lose" their eyes & eyesight as they develop into adulthood, retaining light sensing only. However other senses compensate, including mechano-, electro-, magneto-, & chemo-receptors academic.oup.com/gigascience/... journals.uchicago.edu/doi/10.2307/... www.amnh.org/explore/news...

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...

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

🎉 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

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-...

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...

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

doi.org

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...

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

doi.org

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...