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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 · 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 · 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 · 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...

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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 · 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 · 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 · 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 · 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 · 24/07/2025

Great to hear about Fabian’s efforts in improving Spatial Omics standards and best practices through scverse and squidpy #ISMBECCB2025

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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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GigaScience Journal @gigascience.bsky.social · 22/07/2025

Guy ending his talk telling the #BOSC2025 audience if they value global data infrastructure sign their open letter globalbiodata.org/open-letter-... #ISMBECCB2025

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GigaScience Journal @gigascience.bsky.social · 22/07/2025

Thinking globally, Guy telling us the Global Biodata coalition, with 11 funders in the coalition and many more observing organisations #BOSC2025 #ISMBECCB2025

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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 presenting on how we’ve used the DOME guidelines, wizard and registry in our peer review of ML papers (we presented on this in BOSC last year). Calling for more journals to use this. Read the Registry paper academic.oup.com/gigascience/... #BOSC2025 #ISMB2025

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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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GigaScience Journal @gigascience.bsky.social · 22/07/2025

Chris outlining the different AI coding agents that can be used for ontology development. Working on documenting best practices for this ai4curation.GitHub.io/aidocs #BOSC2025 #ISMBECCB2025

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GigaScience Journal @gigascience.bsky.social · 22/07/2025

Nice Chris is raising the topic of AI-assisted coding. There are huge advantages of Agentic AI applications here, but there are also risks (watch this space for more on this topic) #ISMBECCB2025 #BOSC2025

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GigaScience Journal @gigascience.bsky.social · 22/07/2025

Chris Mungall asking can LLMs help with ontology production? Tl;dr: nope. Superficially look impressive but prone to hallucination and has memory issues with medium to large ontologies #BOSC2025 #ISMBECCB2025

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GigaScience Journal @gigascience.bsky.social · 22/07/2025

Today #BOSC2025 and #BOKR (formerly Bioontologies) COSI’s, Chris Mungall is doing the keynote on Open KBs in the age of generative AI #ISMBECCB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Great “rant of the day” from Susheel Varna that the I in FAIR (interoperability) is the part that currently doesn’t work. APIs don’t count #BOSC2025 #ISMBECCB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Interesting evaluations of AI-readiness of the different Bridge2AI grand challenges datasets via radar plots. Lots of variation, especially as some data types don’t have standards. Read more in their preprint www.biorxiv.org/content/10.1... #BOSC2025 #ISMBECCB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Now up in #BOSC2025 is our Ed Board Member @monimunozto.bsky.social talking about the AI/ML readiness of biomedical data through the Bridge2AI project #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Now in the #BOSC2025 Analytic tools and pipelines track, Jose Espinosa-Carrasco presenting on @nextflow.io and associated nf-core community, best practice workflows and coding guidelines. #ISMBECCB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Kristi plugging #datacitation and the related @makedatacount.bsky.social metrics and Kaggle competition. Still time to participate (and win $100K) here www.kaggle.com/competitions... #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

InvinioRDM is highly scalable, proven to work with the 5M records in Zenodo. Supports large files, has versioning, easy to deploy, customisable #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Kristi Holmes in the NIH #ISMB2025 track giving on an update on the Zenodo modular InvenioRDM infrastructure underlying it. Kristi calling it “The best #opensource community I have ever worked with”. slides here zenodo.org/records/1627... #ISMBECCB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

In the #ISMBECCB2025 NIH track Nick Weber is talking about their usage of AI, LLMs on top of their massive computational infrastructure (395+ PBs and counting) #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Now up in the #ISMBECCB2025 publishing track @mmmarksman.bsky.social is telling us about the @elife.bsky.social Publish Review Curate model. Our sister @gigabytejournal.bsky.social is grateful for their @scietyhq.bsky.social infrastructure to allow linking of their reviews to preprints

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Like us, Michael is seeing a huge rise in Machine Learning paper (see our talk on ML standards www.youtube.com/watch?v=EQM0...). Very concerned about data leakage. Mustn’t have the same protein in the training and testing (some journals have holdback sets). #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

Michael Sternberg (IC and Editor for JMB and NAR) talking about special issues and how Editors decide on accepting papers on highly similar topics. #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

In the publishing track at #ISMBECCB2025, and Feilim Mac Gabhann from Plos Comp Biol giving their experience on how they make editorial decisions. Saying they are celebrating their 20th birthday this month. #ISMB2025 is our 13th birthday too (check out our party tomorrow)

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GigaScience Journal @gigascience.bsky.social · 21/07/2025

The OG of biocuration Amos Bairoch giving us insight into what makes a good biocurator (an autistic Samurai to knowledge) in the morning keynote at #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 20/07/2025

Seemingly one of the only good things to come out of the COVID pandemic, JJ saying the need to predict SARS-CoV2 structure predictions pushed them to produce a new confidence measure called pLDDT #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 20/07/2025

JJ saying in late 2018/early 2019 started over in using evolutionary data – introduced use of LMs like BERT, created rawBERT (raw MSA BERT) to do this. This model allowed rapid improvements, getting first end-to-end networks #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 20/07/2025

JJ taking us from AlphaFold1 to 2 - the CASP13 conference forced them to go back to the drawing board, updating beliefs about structure to more iterative updating and new direct folding systems #ISMBECCB2025 #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 20/07/2025

Pretty cool to start #ISMBECCB2025 with the latest winner of the Nobel Prize in Chemistry (John Jumper, who is also a GigaScience author doi.org/10.1093/giga...) giving the secrets of DeepMind's success #ISMB2025

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GigaScience Journal @gigascience.bsky.social · 20/07/2025

And we’re off. @iscb.bsky.social President Predrag Radivojac and Christophe Dessimoz are announcing the start of #ISMBECCB2025 in Liverpool. Possibly the biggest ever with 2225 in-person and 300 online attendees

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GigaScience Journal @gigascience.bsky.social · 20/07/2025

GigaPanda is enjoying the fab Liverpool vibes, and is getting ready for #ISMBECCB2025 kicking off today

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GigaScience Journal @gigascience.bsky.social · 19/07/2025

The GigaScience team are on the road to Liverpool for ISMB, where we'll be celebrating our birthday at the always fab #ISMBECCB2025 conference

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GigaScience Journal @gigascience.bsky.social · 04/07/2025

Turtley cool usage of @nanoporetech.com sequencing to simultaneously generate genomic and epigenomic resources simultaneously. Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles doi.org/10.1093/giga...

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GigaScience Journal @gigascience.bsky.social · 13/06/2025

Was great to visit and talk at a "meet the editors" event at Siriraj Hospital, Mahidol University Thailand. Thanks to GigaScience author Sakda Khoomrung for helping set the event up

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GigaScience Journal @gigascience.bsky.social · 12/06/2025

Help @makedatacount.bsky.social, join the @kaggle.com "Finding Data References" competition, and win fame and fortune (well, a $100,000 USD prize) #DataCitation kaggle.com/competitions...

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GigaScience Journal @gigascience.bsky.social · 26/05/2025

If you are in Bangkok we are doing a "Meet the Editors" event at the Faculty of Medicine Siriraj Hospital, Mahidol University on 11th June. You can sign up via the QR code.

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GigaScience Journal @gigascience.bsky.social · 14/05/2025

Exploring the epigenomic landscape of Brassica allotriploid hybrids Interspecific hybridization in Brassica species leads to changes in agronomic traits through the regulation of gene expression by chromatin accessibility and DNA methylation doi.org/10.1093/giga...

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