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GigaScience Journal

@gigascience.bsky.social
766 followers 887 following 235 posts

The #OpenScience journal from BGI & OUP publishing articles using/generating large datasets. And linked to GigaDB #opendata hosting/analysis repository. Website: gigasciencejournal.com

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GigaScience Journal @gigascience.bsky.social · 27/05/2026
SCSEQ is a new zero-code web platform for single-cell RNA-seq analysis, published in #GigaScience. doi.org/10.1093/giga...
doi.org
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
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GigaScience Journal @gigascience.bsky.social · 27/05/2026
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...
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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
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GigaScience Journal @gigascience.bsky.social · 02/12/2025
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...
doi.org
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
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GigaScience Journal @gigascience.bsky.social · 13/10/2025
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-...
gigasciencejournal.com
Dr. Xun Xu has been appointed as Editor-in-Chief of GigaScience |
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GigaScience Journal @gigascience.bsky.social · 17/09/2025
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...
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GigaScience Journal @gigascience.bsky.social · 16/09/2025
Happy #PeerReviewWeek: To celebrate we have a proposal in GigaBlog: Why we need a FAIR Principles for Peer Review? gigasciencejournal.com/blog/peerrev... #PRW2025
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GigaScience Journal @gigascience.bsky.social · 14/09/2025
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...
doi.org
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
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GigaScience Journal @gigascience.bsky.social · 12/09/2025
The Return of Asia Nature Challenge #ANC2025 gigasciencejournal.com/blog/the-ret... #AsiaNatureChallenge #ANC2025 #CitizenScience
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GigaScience Journal @gigascience.bsky.social · 12/09/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 11/09/2025
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...
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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
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Reposted by GigaScience Journal
Center for Evolutionary Hologenomics @hologenomics.bsky.social · 11/09/2025
📣Another publication from our amazing researchers and colleagues: The Earth Hologenome Initiative: Data Release 1 @ehologenome.bsky.social 🦠💡 Find it in @gigascience.bsky.social 👇
academic.oup.com
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
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GigaScience Journal @gigascience.bsky.social · 10/09/2025
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...
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GigaScience Journal @gigascience.bsky.social · 08/09/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 06/09/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 05/09/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 03/09/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 02/09/2025
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...
doi.org
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
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GigaScience Journal @gigascience.bsky.social · 02/09/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 29/08/2025
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?...
youtu.be
Charley Yen on Conservation Genomics and Epigenomics of Loggerhead Turtles
YouTube video by GigaScience Press
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GigaScience Journal @gigascience.bsky.social · 27/08/2025
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...
Cassyni screenshot
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GigaScience Journal @gigascience.bsky.social · 26/08/2025
Tune it to our amazing sex changing reptile genomics webinar starting in about an hour...
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GigaScience Journal @gigascience.bsky.social · 24/08/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 24/08/2025
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?...
youtu.be
Visualizing a sightless world: 3D Imaging of the Proteus reveals adaptation for life in the dark
YouTube video by GigaScience Press
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GigaScience Journal @gigascience.bsky.social · 22/08/2025
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...
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GigaScience Journal @gigascience.bsky.social · 21/08/2025
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...
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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
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Reposted by GigaScience Journal
Aurora Ruiz-Herrera @aruizherrera.bsky.social · 20/08/2025
🎉 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/...
academic.oup.com
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
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GigaScience Journal @gigascience.bsky.social · 19/08/2025
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-...
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GigaScience Journal @gigascience.bsky.social · 15/08/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 14/08/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 13/08/2025
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...
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GigaScience Journal @gigascience.bsky.social · 12/08/2025
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...
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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
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GigaScience Journal @gigascience.bsky.social · 11/08/2025
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...
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Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp
AbstractBackground. Comparative genomics, genetic spread analysis, and context-aware ranking are crucial in understanding microbial dynamics’ impact on pub
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GigaScience Journal @gigascience.bsky.social · 08/08/2025
Help! I need curation. Our write up of Birthdays, BOSC, Beatles and Bioinformatics at ISMB2025 in Liverpool gigasciencejournal.com/blog/help-i-...
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GigaScience Journal @gigascience.bsky.social · 07/08/2025
Write up from Chris Hunter in GigaBlog on the recent Genomic Standards Consortium meeting in Cambridge #GSC2025 gigasciencejournal.com/blog/gsc25-c...
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GigaScience Journal @gigascience.bsky.social · 07/08/2025
GigaScience Press FTW! youtu.be/yp_pYwb78G4?...
youtu.be
GigaScience Press: An Award-Winning Publisher
YouTube video by GigaScience Press
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GigaScience Journal @gigascience.bsky.social · 04/08/2025
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...
doi.org
CellBinDB: a large-scale multimodal annotated dataset for cell segmentation with benchmarking of universal models
Abstract. In recent years, cell segmentation techniques have played a critical role in the analysis of biological images, especially for quantitative studi
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Reposted by GigaScience Journal
BioMassSpec @realbiomassspec.bsky.social · 02/08/2025
MetaboSERV—a platform for selecting, exchanging, and visualizing metabolomics data with controlled data access #Gigascience academic.oup.com/gigascience/...
academic.oup.com
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
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GigaScience Journal @gigascience.bsky.social · 01/08/2025
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...
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PVGA: a precise viral genome assembler using an iterative alignment graph
AbstractBackground. Viral genome analysis is crucial for understanding virus evolution and mutation. Investigations into viral evolutionary dynamics and mu
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GigaScience Journal @gigascience.bsky.social · 29/07/2025
Great visit to @institutpasteur.bsky.social today, thanks Herve Menager for showing us around and talking bioinformatics and workflows
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GigaScience Journal @gigascience.bsky.social · 28/07/2025
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...
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Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database
Abstract. BioSample is a repository of experimental sample metadata. It is a comprehensive archive that enables searches of experiments, regardless of type
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Reposted by GigaScience Journal
Bioinformatics Open Source Conference (BOSC) @bosc.bsky.social · 27/07/2025
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.
BOSC chair Nomi Harris
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GigaScience Journal @gigascience.bsky.social · 25/07/2025
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...
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CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome
AbstractBackground. Despite the surge in microbiome data acquisition, there is a limited availability of tools capable of effectively analyzing it and iden
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Jason “Obstacle to Progress” Williams @jasonwilliamsny.bsky.social · 22/07/2025
Fantastic #BOSC2025 panel on data sustainability to cap off the conference. #ISMBECCB2025
Panelists on stage
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GigaScience Journal @gigascience.bsky.social · 24/07/2025
Final closing #ISMBECCB2025 keynote from Fabian Theis. Nice to have the meeting bookended by opening and closing talks from people that have published in GigaScience (see our MetaMap paper doi.org/10.1093/giga...) #ISMB2025
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GigaScience Journal @gigascience.bsky.social · 24/07/2025
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
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GigaScience Journal @gigascience.bsky.social · 24/07/2025
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
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Jake Lever @jakelever.bsky.social · 22/07/2025
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...
kaggle.com
Make Data Count - Finding Data References
Identify scientific data use in papers and classify how they are mentioned.
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GigaScience Journal @gigascience.bsky.social · 22/07/2025
Closing session at #BOSC2025, Guy Cochrane talking about the Global Biodata Infrastructure, hopefully framing things for the sustainability panel (which our EiC @scedmunds.bsky.social is participating in #ISMB2025 #ISMBECCB2025
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GigaScience Journal @gigascience.bsky.social · 22/07/2025
Phill Read presenting RO-Crate in #BOSC2025, we’ve been increasing numbers of papers with associated RO-Crates, and have a summer internship working on it at the moment #ISMBECCB2025
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GigaScience Journal @gigascience.bsky.social · 22/07/2025
Gavin Farrell from ELIXIR presenting on the DOME Registry in the #BOSC2025 AI track #ISMBECCB2025 #ISMB2025
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