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Reposted by Simone Andrea Biagini 🏳️‍🌈

SMBE IDEA taskforce @smbe-idea.bsky.social · 36m

🤝 In 2024, the 𝗜𝗗𝗘𝗔 𝗴𝗿𝗮𝗻𝘁 from @official-smbe.bsky.social went to Drs. Rori Rohlfs and Emilia Huerta-Sanchez for their podcast ScienceWise!

✨ We are happy to have contributed to their project!

🎙️ @sciencewisepod.bsky.social

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · 5d

🔥 Time's ticking! Share your vision for inclusion & equity in science!

⏰ Deadline: 𝗢𝗰𝘁 𝟭𝟬

@official-smbe.bsky.social
@smbe-idea.bsky.social
#AcademicSky

SMBE IDEA taskforce @smbe-idea.bsky.social · 5d

⏳ Don't miss out! Submit your proposals by 𝗢𝗰𝘁 𝟭𝟬 and help shape a more inclusive science community!

@official-smbe.bsky.social #AcademicSky

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Reposted by Simone Andrea Biagini 🏳️‍🌈

Society for Molecular Biology and Evolution @official-smbe.bsky.social · 7d

❗REMINDER - the call for proposals for SMBE IDEA initiatives for 2025/2026 will close soon - apply by October 10th

Categories:

💡 IDEA ($25k)
🪂 Non-Parachute Science ($10k)
🗣️ Outreach ($10k)

More info
smbe.org/idea-initiatives
@smbe-idea.bsky.social

Society for Molecular Biology and Evolution @official-smbe.bsky.social · 29d

📢 Call for proposals - SMBE IDEA 2026

@smbe-idea.bsky.social invites all SMBE members to propose initiatives for 2025/2026 to reduce inequities in our field.

Categories:

💡 IDEA ($25k)
🪂 Non-Parachute Science ($10k)
🗣️ Outreach ($10k)

Deadline: Oct. 10 2025

More info: smbe.org/idea-initiatives

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · 8d

🔥 Don't miss the opportunity! Submit your proposal 𝙉𝙊𝙒! 🌈

#AcademicSky #IDEA #SMBE2026
@official-smbe.bsky.social

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · 9d

Moving to another country for a few months. #academiclife #academicsky

Excited but also:

a woman in a suit says everything hurts and i 'm dying .

ALT: a woman in a suit says everything hurts and i 'm dying .

media.tenor.com

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · 21d

thanks 🩷✨

Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · 22d

✨ In my latest paper, I used 𝙥𝙧𝙚𝙜𝙣𝙖𝙣𝙩 𝙥𝙚𝙤𝙥𝙡𝙚 instead of “pregnant women", because pregnancy is not exclusive to those who identify as women 🤰

📢 Using inclusive language is part of our responsibility as scientists to fight erasure of transgender and nonbinary people 🏳️‍⚧️ #AcademicSky #QueerInSTEM

Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

🚨 Did you know that non-invasive prenatal screening (𝗡𝗜𝗣𝗦🤰) data can be repurposed for large-scale genomics? 🧬

Our new study shows how to turn low-coverage data into valuable insights, analyzing >32,000 genomes from Belgium. #genetics #imputation #NIPS #AcademicSky

genome.cshlp.org/content/35/9...

Genotype imputation from low-coverage data for medical and population genetic analyses

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

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Reposted by Simone Andrea Biagini 🏳️‍🌈

SMBE IDEA taskforce @smbe-idea.bsky.social · 28d

🌍✨ SMBE IDEA 2026 – Call for Proposals!

We support initiatives that tackle inequities in evolutionary biology.

Funding available:
💡 IDEA ($25k)
🪂 Non-Parachute Science ($10k)
🗣️ Outreach ($10k)

📅 Deadline: Oct 10, 2025
🔗 docs.google.com/forms/d/1we2...

IDEA Initiatives

SMBE, through the IDEA (Inclusion, Diversity, Equity, and Access) Task Force, aims to address systemic racism, sexism, colonialism, and other exclusion in our society. SMBE DIVERSITY STATEMENT Our goa...

smbe.org

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Reposted by Simone Andrea Biagini 🏳️‍🌈

Stephen Turner @stephenturner.us · Sep 3

Genotype imputation from low-coverage data for medical and population genetic analyses genome.cshlp.org/content/35/9... 🧬🖥️🧪 github.com/SABiagini/GDI

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Reposted by Simone Andrea Biagini 🏳️‍🌈

Bioinformatics Advances @bioinfoadv.bsky.social · Sep 9

🧬 Now published in Bioinformatics Advances: "DNPcall: A new pipeline for accurate double nucleotide polymorphism calling"

Read the full paper here: https://doi.org/10.1093/bioadv/vbaf209

Authors include: @eugeniadat.bsky.social

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 8

Neanderthals lived ~350,000 years without governments, capitalism, or wrecking ecosystems.

We Homo sapiens, in just 300,000 years (and especially the last 200), have trashed the planet.

Just saying.

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 4

Anything to promote my new paper (and yes that includes this photo). I put six years of my mental health into this one 😅🧬🔥

📝 Go read it! ⬇️

🔗 genome.cshlp.org/content/35/9...

#AcademicSky

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 4

🚨 My new paper is out in the latest issue of @genomeresearch.bsky.social! 🧬

🧵 Check out my thread from yesterday for the details ⬇️

👨‍💻 Open source codes also available on my #GitHub page!

#AcademicSky

Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

🚨 Did you know that non-invasive prenatal screening (𝗡𝗜𝗣𝗦🤰) data can be repurposed for large-scale genomics? 🧬

Our new study shows how to turn low-coverage data into valuable insights, analyzing >32,000 genomes from Belgium. #genetics #imputation #NIPS #AcademicSky

genome.cshlp.org/content/35/9...

Genotype imputation from low-coverage data for medical and population genetic analyses

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

Also, check out our 𝗚𝗶𝘁𝗛𝘂𝗯 for all tools from this study 👨‍💻 𝗙𝘂𝗹𝗹𝘆 𝗼𝗽𝗲𝗻 𝘀𝗼𝘂𝗿𝗰𝗲:

• 𝗚𝗗𝗜 𝗳𝗶𝗹𝘁𝗲𝗿: github.com/SABiagini/GDI

• 𝗣𝗼𝘀𝘁-𝗶𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝘀𝘁𝗮𝘁𝘀: github.com/SABiagini/Po...

A useful resource for low-coverage genomic data! #bioinformatics #AcademicSky #GitHub #OpenSource #Genetics #imputation #popgen

GitHub - SABiagini/GDI

Contribute to SABiagini/GDI development by creating an account on GitHub.

github.com

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

In short, NIPS data are a goldmine for genomics but need tailored strategies. There is no one-size-fits-all filter.

Curious to learn more? 🔬 The full paper compares QUILT and GLIMPSE2, shows the impact of fetal fraction and coverage, the GDI filter development and validation, and more! ✨

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

When applied to 𝗽𝗼𝗹𝘆𝗴𝗲𝗻𝗶𝗰 𝘀𝗰𝗼𝗿𝗲𝘀 (PGS) for height, GDI was less effective. GDI-filtered data explained 14% of the variance, while the best-performing approach (PGSHapMap) explained 23.7% using a smaller set of common variants.

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

✅ 𝗔𝗳𝘁𝗲𝗿 𝗮𝗽𝗽𝗹𝘆𝗶𝗻𝗴 𝗚𝗗𝗜, 𝘁𝗵𝗲 𝗯𝗮𝘁𝗰𝗵 𝗲𝗳𝗳𝗲𝗰𝘁 𝗱𝗶𝘀𝗮𝗽𝗽𝗲𝗮𝗿𝘀! ✨

PCA/UMAP of >27,000 Belgian samples.

🇪🇺 89.17% European ancestry

🌍🌏 10.83% African/Asian ancestries

🇧🇪 A snapshot of Belgium’s current diversity!

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

❌ Without GDI, both PCA and UMAP show a strong batch effect. NIPS samples cluster apart due to low imputation quality.

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

We introduce 🅶🅳🅸 (GenotypeProbability-Dosage-INFOscore), a 𝗯𝗮𝘁𝗰𝗵-𝗹𝗲𝘃𝗲𝗹 𝗳𝗶𝗹𝘁𝗲𝗿𝗶𝗻𝗴 𝗮𝗽𝗽𝗿𝗼𝗮𝗰𝗵.

GDI combines three QC metrics to maximize accuracy while minimizing variant loss ✨

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

In a test on a batch of 3 genomes, the standard filter (GP≥0.99) keeps only 49.2% of sites. 𝗪𝗶𝘁𝗵 𝗹𝗮𝗿𝗴𝗲𝗿 𝗰𝗼𝗵𝗼𝗿𝘁𝘀, 𝘁𝗵𝗲 𝗹𝗼𝘀𝘀 𝗯𝗲𝗰𝗼𝗺𝗲𝘀 𝗱𝗿𝗮𝗺𝗮𝘁𝗶𝗰 😭

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

On average, our NIPS data has very low coverage (~0.15x). Standard quality filters applied per sample cause 𝗰𝘂𝗺𝘂𝗹𝗮𝘁𝗶𝘃𝗲 𝗺𝗶𝘀𝘀𝗶𝗻𝗴𝗻𝗲𝘀𝘀: when combining thousands of genomes, most variants get lost.

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Sep 3

🚨 Did you know that non-invasive prenatal screening (𝗡𝗜𝗣𝗦🤰) data can be repurposed for large-scale genomics? 🧬

Our new study shows how to turn low-coverage data into valuable insights, analyzing >32,000 genomes from Belgium. #genetics #imputation #NIPS #AcademicSky

genome.cshlp.org/content/35/9...

Genotype imputation from low-coverage data for medical and population genetic analyses

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Aug 30

Great experience this year at #ISBA11 amazing talks and posters ✨👏

ISBA - Intl. Soc. for Biomolecular Archaeology @isbarchaeology.bsky.social · Aug 29

What a week! 🎉 Big thanks to @isba11.bsky.social for hosting an incredible ISBA conference — so well organized and full of great science.

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Aug 29

Let's talk about legends coming true at poster 8! 🧬☠️ #ISBA11 @isba11.bsky.social

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Simone Andrea Biagini 🏳️‍🌈 @sabiagini.bsky.social · Aug 9

I’m from Southern Europe. We are built for quiescence in August.

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