iiinova — where your digital self keeps evolving

Reposted by Henry Secaira

Qiyun Zhu @zhuqiyun.bsky.social · 30/07/2026

(My) last human-written bioinformatics algorithm (maybe). A parallel balanced minimum evolution tree-building algorithm up to 82x faster than FastME. Crunches all GTDB bacteria (190k taxa) within 40 min. Better than NJ as data size gro ws. Preprint online: www.biorxiv.org/content/10.6...

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Reposted by Henry Secaira

Qiyun Zhu @zhuqiyun.bsky.social · 28/07/2026

Proud to celebrate Henry Secaira-Morocho @hsecaira.bsky.social, my first PhD graduate at ASU! He has done outstanding research in evolutionary biology, computational biology and microbiome research. I'm excited to see him advance in his academic career at NLM. Congratulations, Henry!

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Quanta Magazine @quantamagazine.org · 13/07/2026

Qualia goes where curiosity leads. This week, columnist Natalie Wolchover tracks the secret of left-handedness through developmental biology, genetics, evolution, and culture. www.quantamagazine.org/why-am-i-lef...

quantamagazine.org

Why Am I Left-Handed? | Quanta Magazine

An invisible difference in 10% of humans poses deep mysteries in several fields at once.

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Reposted by Henry Secaira

Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

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Eduardo Amorim @cegamorim.bsky.social · 08/05/2026

Yesterday our article was featured on the cover of Nature. I'm incredibly proud of this team, led primarily by Latin Americans, & the result of the decade-long work by @hunemeier.bsky.social & lab. Kudos to the 1st authors too (incl @macscastro.bsky.social here on 🟦☁️) www.nature.com/nature/volum...

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Eduardo Amorim @cegamorim.bsky.social · 22/04/2026

The largest and most diverse collection of Indigenous American genomes 👉🏻 “The evolutionary history and unique genetic diversity of Indigenous Americans” @macscastro.bsky.social @hunemeier.bsky.social @chiarabarbieri.bsky.social @jrockdrigo.bsky.social 🔗 www.nature.com/articles/s41...

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Podcast de la Vaca Esférica @lavacaesferica.bsky.social · 19/04/2026

S03E10 La probabilidad son los padres. iVoox go.ivoox.com/rf/172082429 Spotify open.spotify.com/episode/3x1O... YouTube youtu.be/Zm_tK8P3H9w Y Apple Podcasts, Pocket Cast, por RSS feed, o en tu app favorita. La probabilidad de que no tengas acceso a la Vaca es despreciable.

go.ivoox.com

S03E10 La probabilidad son los padres - La vaca esférica - Podcast en iVoox

Escucha este episodio de La vaca esférica gratis en iVoox. Notas del episodio:...

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Reposted by Henry Secaira

Quanta Magazine @quantamagazine.org · 15/04/2026

Viruses evolve at an "insanely high” pace, said microbiologist Philip Kranzusch. And yet, weirdly, our immune defenses share many ancient antiviral tools with bacteria. “Why would the rules be so fixed?” www.quantamagazine.org/the-ancient-...

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Centro Nacional de Biotecnología (CNB) @cnb-csic.bsky.social · 06/04/2026

Un nuevo trabajo del @csic.es y el #INTA muestra como los virus exploran su espacio genético de forma jerárquica para adaptarse a distintos ambientes. Lee la noticia completa: f.mtr.cool/sgockakqcc DOI ( @pnas.org ): f.mtr.cool/sgdqliijsq

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CSIC @csic.es · 06/04/2026

🦠¿Cómo exploran los virus sus opciones de evolución genética? 🔬 Un estudio del #CSIC aborda esta pregunta mediante el análisis de millones de mutaciones 🔎El trabajo revela que la exploración adopta una estructura fractal y jerárquica ➡️ tiny.cc/wxe1101

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Qiyun Zhu @zhuqiyun.bsky.social · 04/03/2026

scikit-bio is participating in #GSoC 2026 via NumFOCUS! We aim to modernize core bioinformatics algorithms to support GPU acceleration and interoperability across AI-ready libraries like JAX and CuPy. Details: github.com/scikit-bio/s... Contributors are welcome! #opensource #bioinformatics #python

github.com

scikit-bio at Google Summer of Code 2026 · scikit-bio scikit-bio · Discussion #2401

We are excited to announce that scikit-bio is participating in Google Summer of Code (GSoC) 2026 as part of the NumFOCUS umbrella organization. This year, we aim to modernize fundamental bioinforma...

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Reposted by Henry Secaira

Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 25/02/2026

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨 Let me hit you with some highlights on why spatial structure matters. (and why you should care!) Sharing is appreciated 🙏 🧵👇 doi.org/10.1093/fems...

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Reposted by Henry Secaira

Qiyun Zhu @zhuqiyun.bsky.social · 12/02/2026

Introducing TM-Vec 2 and 2s -- protein language models for fast, accurate remote homology detection. Predict structural similarity from sequence alone. Major speedup, high accuracy, runs on regular hardware. Suited for proteome-scale clinical & environmental datasets. #deeplearning #bioinformatics

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Reposted by Henry Secaira

Arkadiy Garber @ironark.bsky.social · 08/02/2026

Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction. www.biorxiv.org/content/10.6...

Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”

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Reposted by Henry Secaira

Qiyun Zhu @zhuqiyun.bsky.social · 31/01/2026

We introduce a Python implementation of ANCOM-BC that is 100x faster than the original R code, while preserving statistical validity. Scales to much larger omics datasets and enables ML workflows with repeated inference (feature selection, sensitivity, stability, etc.) #Bioinformatics #Microbiome

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Ricard Solé @ricardsole.bsky.social · 15/01/2026

What if animals emerged by installing a new biological operating system that repurposed what already existed, much like the rise of the smartphone? Here's our new paper in @embojournal.org @ibe-barcelona.bsky.social @melisupf.bsky.social @sfiscience.bsky.social link.springer.com/article/10.1...

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Reposted by Henry Secaira

Science X / Phys.org @sciencex.bsky.social · 12/12/2025

New computational tools are enhancing the accuracy and scalability of microbial family tree construction and biological data analysis, supporting advances in microbiome research and environmental monitoring. doi.org/hbfhxb

phys.org

Smarter tools for peering into the microscopic world developed

The microscopic organisms that fill our bodies, soils, oceans and atmosphere play essential roles in human health and the planet's ecosystems.

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Reposted by Henry Secaira

Qiyun Zhu @zhuqiyun.bsky.social · 11/12/2025

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

nature.com

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

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Quanta Magazine @quantamagazine.org · 27/11/2025

Thanksgiving is a day of physiological extremes. 🦃 🧵

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ASM @asm.org · 30/10/2025

How did life begin, and why does it matter? Scientists are tracing early microbial life–from LUCA to multicellularity–to unlock insights for biotech, climate science and even space exploration. Read the article: asm.org/articles/202...

asm.org

Early Microbial Evolution | ASM.org

How did life begin, and why does it matter? Scientists are tracing early microbial life—from LUCA to multicellularity—to unlock insights for biotech, climate science and even space exploration.

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Reposted by Henry Secaira

Quanta Magazine @quantamagazine.org · 11/09/2025

Ancient cells called Asgard archaea were first discovered at the hydrothermal vent site called Loki's Castle in 2010. Their discovery has shaken up our view of the Tree of Life. www.quantamagazine.org/tiny-tubes-r...

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Quanta Magazine @quantamagazine.org · 28/08/2025

Punctuated equilibrium, a concept introduced by paleontologists in 1972, reimagines evolution’s tempo as a stochastic burst rather than a steady beat. A new model finds support for their theory in both molecular and fossil data. @jakebuehler.bsky.social reports www.quantamagazine.org/the-sudden-s...

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Reposted by Henry Secaira

Daan Speth @daanspeth.bsky.social · 10/06/2025

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

globdb.org

home | GlobDB

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