Juan

Rapid terabase-scale simulation of realistic metagenomes for experimental design and pathogen detection with RandomReadsMG https://www.biorxiv.org/content/10.1101/2025.07.18.665570v1

From 🟡 to 💎: Osteoblast-inspired "osteoyeast" turns human waste into high-value biomaterial for bone and dental applications

Collaboration by @jgi.doe.gov, @molecularfoundry.lbl.gov & CABBI

doi.org/10.1038/s414...

Two-panel cartoon set in a desert with mountains and cacti. Top panel: A green box labeled “ENHANCER” stands on the left, shouting weakly “Turn on, please?!?” toward a distant blue spiky blob labeled “GENE” on the right, who is asleep with a “Zzz.” Bottom panel: The enhancer now uses a microphone connected to a large purple speaker labeled “REX,” which amplifies the message “Turn on!!” in a bold speech bubble across the desert. The gene is now awake and alert with wide eyes and a happy expression. Image credit: Emma Visel

Getting the message across from a distance:

🧬REX🧬 is a “Range EXtender” element that can turn short-range into looooooooooooong-range enhancers

Great collaboration led by @gracebower.bsky.social and @evgenykvon.bsky.social

www.nature.com/articles/s41...

@biosci.lbl.gov @berkeleylab.lbl.gov

Microbial Communities Drive Methane Fluxes From Floodplain Lakes—A Hydrological Gradient Perspective This study examined the impact of methanotrophic bacteria (MOB) and methanogenic archaea (mGen) on CH4 emissions from oxbow lakes at various successional stages, analysing their interactions with phy....

Microbial Communities Drive Methane Fluxes From Floodplain Lakes—A Hydrological Gradient Perspective enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

A genomic catalog of Earth’s bacterial and archaeal symbionts Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict...

Amongst a lot of thought-free applications of machine learning to biological problems, it's nice to see exceptions, such as this well-conceived and -executed study to identify symbionts from genomic data: www.biorxiv.org/content/10.1...

A genomic catalog of Earth’s bacterial and archaeal symbionts Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict...

Interesting AI read. 15-23% of uncultivated microbes may engage in symbiotic relationships.

www.biorxiv.org/content/10.1...

Inkscape plugin to rescale figures without distorting the text, and other useful features!
github.com/burghoff/Sci...

Image showing experimental design with map of Washington state showing increased precipitation from west to east. Soil was collected from field sites along this gradient and transplanted to the greenhouse where Camelina was grown in the soil under controlled conditions and their microbiome identified.

Another project from my time @jgi.doe.gov published @phytobiomesjournal.bsky.social ! Using a greenhouse soil transplant experiment we uncover the core microbiome of Camelina & show how past cropping regimes/precipitation can exert a legacy effect on microbiome assembly 🌾🦠🧬🧪
doi.org/10.1094/PBIO...

We are looking for additional Group Leaders to join the growing computational biology community at VIB.

If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!

https://vib.ai/en/opportunities#/job-description/110906

Updates on HPAI H5N1

Join Drs. Nina Gao and Stacey Schultz-Cherry tomorrow at 2 p.m. ET as they discuss Highly Pathogenic Avian Influenza A(HPAI H5N1), including ongoing research regarding avian flu and vaccine development. Free for all. Register now: asm.org/Webinars/Upd... #LabWeek

Data wrangling before tidyverse was a nightmare. Everything was painful. The majority of your code was marshalling data from one awkward format into another.

We are hosting a workshop titled “Genomes Online Database (GOLD) – A curated metadata resource for powering discoveries” at the Biocuration 2025 conference on April 6th, 10:30 AM to 12:30PM US CST.
Register to Join over the Zoom at t.co/WojICcd73s

Global Metagenomics Reveals Plastid Diversity and Unexplored Algal Lineages Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We captured 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originated from an early-branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes. ### Competing Interest Statement The authors have declared no competing interest.

www.biorxiv.org/content/10.1...

Global Metagenomics Reveals Hidden Protist Diversity www.biorxiv.org/content/10.1... #jcampubs

Two Berkeley Lab Scientists Named AAAS Fellows Nigel Mouncey and Phillip Messersmith were among those awarded this lifetime honor.

🎉 Congratulations to @jgi.doe.gov Director @nigelmouncey.bsky.social and Phillip Messersmith, a faculty senior scientist in our Materials Sciences Division on making the 2024 @aaas.org Fellows List for distinguished achievements in advancing or applying science. 🧪

Microbes are key to tackling climate change! A new report from the @asm.org and IUMS Scientific Advisory Group highlights microbial solutions to reduce carbon reliance, enhance food security and mitigate methane. Read the report: asm.org/climatesolutionsn.

12 days ago, Texas had 99 measles cases.
3 days ago, Texas had 159 measles cases.
Today, Texas & New Mexico have 230 measles cases. See how it works?

Measles is airborne & highly contagious, wear N95 mask😷 Measles wipes out immunity you had to everything you built up over your lifetime, get vaxxed💉

Excited to share our new study with the Müller and @SchullerJm labs, online @nature: https://www.nature.com/articles/s41586-022-04971-z

This is T. kivui, an anaerobic bacterium. It uses hydrogen energy to store #CO2. How does it do it? #CryoET revealed membrane-anchored bundles of...

Gaining insights into the complexity of specialized metabolites and their possible ecological roles These metabolites not only function as antimicrobials, but also as cue molecules among other peculiar functions

-see our paper in microLIFE of @femsjournals.bsky.social on surfactin and subtilosin A

New 🧬resource💻 for craniofacial researchers from
@justincotney.bsky.social's lab:

A single-cell RNA-seq atlas of human craniofacial development

www.biorxiv.org/content/10.1...

Three Berkeley Lab Scientists Receive PECASE Award Three scientists with Berkeley Lab were among the nearly 400 scientists and engineers awarded by President Biden to receive the Presidential Early Career Award for Scientists and Engineers (PECASE).

Congratulations to Lab scientists Raúl Briceño, Stefan Wild, and Ahmet Kusoglu for receiving the Presidential Early Career Award for Scientists and Engineers (PECASE), the highest honor the US government bestows on early-career scientists and engineers. 🧪

More ⬇️
newscenter.lbl.gov/2025/01/16/t...

The image features a banner for the "Data-Driven Science (DDS) Hub," described as a centralized resource that helps investigators access scientific data, biospecimens, experimental materials, and tools for data science-driven research and training. The banner includes the logo of the NIH National Institute of Dental and Craniofacial Research (NIDCR), accompanied by an abstract background of interconnected lines and data nodes in vibrant colors.

For researchers in 🦷dental, 👅oral, and 🙄craniofacial research, there is a now a new data science resource from NIDCR

The "DDS Data-Driven Science Hub" (built by @vv2024.bsky.social) features:
- Human phenotypes
- Multiomes
- Animals and microbiomes
- Imaging

Check it out at: www.ddshub.nih.gov

Exciting new work from @evgenykvon.bsky.social's lab:

dual-enSERT for directly comparing the in vivo activities of the 🔴reference sequence and a 🟢variant of a developmental enhancer - within the same transgenic mouse embryo!

Berkeley Lab’s Jennifer Doudna Awarded National Medal of Technology and Innovation Jennifer Doudna has been awarded the National Medal of Technology and Innovation.

“On behalf of the Berkeley Lab community, I extend my warmest congratulations to Jennifer for receiving the National Medal of Technology and Innovation. Her groundbreaking research will push the boundaries of science and benefit humanity.” - @mwitherell.bsky.social
newscenter.lbl.gov/2025/01/07/b...

Ten species comprise half of the bacteriology literature, leaving most species unstudied www.biorxiv.org/content/10.1... #jcampubs

Just a reminder that your local library has more than books! Many also have dvds, cds, video games, game systems, internet hot spots, streaming services, ebooks, audio books, park passes, museum passes, and so much more! Maybe it's time for a visit! ❤️📚

A plot showing that HMMER's recall before first false positive is 71%, nail's double-seed variant is ~62%, nail's default is ~59%, MMSeqs2's sensitive variant is ~43%, and MMSeqs2's default variant is ~33%.

Version 0.3.0 of nail is out. nail (github.com/TravisWheele...) is a tool for protein sequence annotation. It bridges most of the sensitivity gap between the two excellent tools MMSeqs2 (fast) and HMMER3 (very sensitive), and is >20x faster than HMMER3. Search with profile HMMs or single sequences.

As the year comes to a close, our social media team will be taking a well-deserved break to rest, recharge, and celebrate the season. We’ll be stepping away starting 12/24 and will return with new content in the new year. See you in 2025! 🎉☃️

Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all Comprehensive metagenomic sequence classification of diverse environmental samples faces significant computing memory challenges due to exponentially expanding genome databases. Here, we present Kun-p...

Kun-peng: claims; as fast/faster than Kraken2 with the accuracy comparable to sylph! Very cool.
The design here reinforces a strong feeling I've had for a few years - moving forward in bioinfo. system-friendly & ext. memory algorithms will come to prevail. (& rust!)
www.biorxiv.org/content/10.1...

Diverse phage communities are maintained stably on a clonal bacterial host Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...