GigaScience Journal

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

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...

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...

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...

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...

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...

📣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...

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 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...

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...

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...

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...

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...

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 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...

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...

🎉 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/...

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...

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 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...

New #opensource pipeline that can uncover hidden gene transfer patterns in microbiomes. Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp doi.org/10.1093/giga...

Help! I need curation. Our write up of Birthdays, BOSC, Beatles and Bioinformatics at ISMB2025 in Liverpool gigasciencejournal.com/blog/help-i-...

Write up from Chris Hunter in GigaBlog on the recent Genomic Standards Consortium meeting in Cambridge #GSC2025 gigasciencejournal.com/blog/gsc25-c...

GigaScience Press FTW! youtu.be/yp_pYwb78G4?...

A new large-scale imaging dataset containing images of 4 staining types (DAPI, H&E, ssDNA, and mIF) derived from over 30 human and mouse tissues. CellBinDB: a large-scale multimodal annotated dataset for cell segmentation with benchmarking of universal models doi.org/10.1093/giga...

MetaboSERV—a platform for selecting, exchanging, and visualizing metabolomics data with controlled data access #Gigascience academic.oup.com/gigascience/...

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 doi.org/10.1093/giga...

Great visit to @institutpasteur.bsky.social today, thanks Herve Menager for showing us around and talking bioinformatics and workflows

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 doi.org/10.1093/giga...

During the #BOSC2025 closing remarks, chair @nomiharris.bsky.social thanked the BOSC sponsors (@cziscience.bsky.social @seqera.io @gigascience.bsky.social) for covering registration for 12 BOSC presenters.

A new tool designed to select sparse compositional #microbiome predictors and predict continuous environmental factors CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome doi.org/10.1093/giga...

Fantastic #BOSC2025 panel on data sustainability to cap off the conference. #ISMBECCB2025

Asked about the “human in the loop”, David Baker says despite the incredible rise of AI, there will be a role for human scientists by 2045. Phew. #ISMBECCB2025

Live from Palestine, Daniel Voskergian from Al-Quds University is presenting a virtual talk in #CAMDA2025 on diabetes complication prediction from synthetic EHR data #ISMBECCB2025

Quick shout out for the Make Data Count challenge to improve data citation from @gigascience.bsky.social's Scott Edmunds. Looks cool and 💲prizes! #BOSC2025 #ISMBECCB2025 www.kaggle.com/competitions...