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Anders Kiledal

@akiledal.bsky.social
128 followers 270 following 7 posts

Microbial ecology of Great Lakes toxic cyano. blooms @MichiganEarth and graft vs. host disease @umichmedicine PhD @UDelaware, 🦠 in/on concrete

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Reposted by Anders Kiledal
ace-gtdb.bsky.social @ace-gtdb.bsky.social · 15/04/2026
GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.
gtdb.ecogenomic.org
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
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Reposted by Anders Kiledal
Sebastian Schmidt @tsbschm.bsky.social · 03/04/2026
Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!
nature.com
Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
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Aldert Zomer @aldertzomer.bsky.social · 08/12/2025
MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...
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Greg Dick @greatlakesgreg.bsky.social · 26/11/2025
I am searching for a lab manager/researcher to come and work with a friendly, collaborative, and interdisciplinary group of students, postdocs, and staff on the microbial ecology of cyanobacterial blooms. careers.umich.edu/job_detail/2...
careers.umich.edu
Research Lab Specialist | U-M Careers
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Samuel Aroney @aroneys.bsky.social · 13/11/2025
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6
Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA
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Michael Baym @baym.lol · 28/10/2025
The only thing more scientifically dispiriting than reading a potentially exciting paper that turns out to be a ton of hype and little else is seeing your colleagues uncritically holding it up as a breakthrough
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Reposted by Anders Kiledal
plasmidsaurus @plasmidsaurus.bsky.social · 15/10/2025
🦖 Something HUGE just hatched. Plasmidsaurus now offers RNA sequencing for gene expression analysis: • As fast as 3 day turnaround • $50/sample for academia, $80 for industry • Up to ~10M unique transcript 3’ end reads per sample • Interactive results Explore Plasmidsaurus RNA-Seq today.
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Reposted by Anders Kiledal
Andre Kahles @akkah21.bsky.social · 08/10/2025
After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)
nature.com
Efficient and accurate search in petabase-scale sequence repositories - Nature
MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.
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Reposted by Anders Kiledal
Rob Patro @robp.bsky.social · 08/10/2025
Another amazing opportunity at UMD in Mihai Pop's lab! Mihai is looking for a bioinformatics software engineer. Consider applying here if you're interested: umd.wd1.myworkdayjobs.com/en-US/UMCP/j...
umd.wd1.myworkdayjobs.com
Bioinformatics engineer
Job Description Summary Organization's Summary Statement: We are seeking to hire a bioinformatics engineer in the Pop lab within the University of Maryland Institute for Advanced Computer Studies (UMI...
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Reposted by Anders Kiledal
The Probst Lab @probstlab.bsky.social · 30/09/2025
Our own @alexjprobst.bsky.social @geomicrosoares.bsky.social and Cristina Moraru have recently authored a @natmicrobiol.nature.com Consensus Statement where they discuss new mechanisms for sequencing data reuse! 🧬💻 Check out their manuscript here: www.nature.com/articles/s41...
nature.com
A roadmap for equitable reuse of public microbiome data - Nature Microbiology
In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.
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Joy Buongiorno, PhD @joybuongiorno.bsky.social · 22/09/2025
My team is hiring again! 📣 springernature.wd3.myworkdayjobs.com/SpringerNatu...
springernature.wd3.myworkdayjobs.com
Associate or Senior Editor, Nature Communications (Geosciences)
Job Title: Associate or Senior Editor, Nature Communications (Geosciences) Location(s): Shanghai, Beijing, Nanjing, New York, Washington, Jersey City, Madrid, Milan (hybrid) Closing date: 8th October,...
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Nature Methods @natmethods.nature.com · 16/09/2025
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...
nature.com
De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods
This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.
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Jim Shaw @jimshaw.bsky.social · 13/08/2025
skani v0.3.0 is released. github.com/bluenote-157... - 30-40% potential reduction in memory with approximately the same runtime. - Breaking changes to indexing and searching databases Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.
github.com
GitHub - bluenote-1577/skani: Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. - bluenote-1577/skani
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Reposted by Anders Kiledal
Will Ratcliff @wcratcliff.bsky.social · 12/08/2025
Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.
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Matt Hutchings @matthutchings.bsky.social · 01/07/2025
Useful paper: "The Transcriptional Architecture of Bacterial Biosynthetic Gene Clusters" #microsky #streptomyces pubs.acs.org/doi/abs/10.1...
pubs.acs.org
The Transcriptional Architecture of Bacterial Biosynthetic Gene Clusters
Bacterial biosynthetic gene clusters (BGCs) drive the production of diverse bioactive specialized metabolites regulated by transcription factors (TFs) in response to environmental signals. In this met...
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Reposted by Anders Kiledal
Jim Shaw @jimshaw.bsky.social · 28/05/2025
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
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ProPublica @propublica.org · 06/05/2025
NEW: The Trump administration’s slashing of budgets and staff have Great Lakes scientists concerned that they have lost the ability to protect the public from toxic algal blooms, which can kill animals and sicken people. By @annaleighclark.bsky.social
propublica.org
Millions of People Depend on the Great Lakes’ Water Supply. Trump Decimated the Lab Protecting It.
The Trump administration’s slashing of budgets and staff have Great Lakes scientists concerned that they have lost the ability to protect the public from toxic algal blooms, which can kill animals…
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Anders Kiledal @akiledal.bsky.social · 30/04/2025
Agree, and looks like a nice new tool! I'll also make a plug for the fantastic Kingfisher from @benjwoodcroft.bsky.social that can flexibly pull from either ENA or SRA, and also cloud providers: github.com/wwood/kingfi...
github.com
GitHub - wwood/kingfisher-download: Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP. - wwood/kingfisher-download
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Reposted by Anders Kiledal
Florian Trigodet @floriantrigodet.bsky.social · 28/04/2025
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵
biorxiv.org
Assemblies of long-read metagenomes suffer from diverse errors
Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 25/04/2025
High-quality metagenome assembly from nanopore reads with nanoMDBG www.biorxiv.org/content/10.1101/202…
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Anders Kiledal @akiledal.bsky.social · 23/04/2025
From #CIGLR on the other place: 🚨 Cuts would cripple NOAA’s wide-ranging science partnerships, because of the ongoing funding delays, “we’re looking at having to lay off a substantial number of our workers in the next few months,” said #CIGLR Dir. Greg Dick: #GreatLakes
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Reposted by Anders Kiledal
Tominaga K. (tomiken) @pacyc184.bsky.social · 16/04/2025
Release 10-RS226 (16th April 2025) GTDB - Genome Taxonomy Database gtdb.ecogenomic.org
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Reposted by Anders Kiledal
Janelle Shane @janelleshane.com · 13/04/2025
1. LLM-generated code tries to run code from online software packages. Which is normal but 2. The packages don’t exist. Which would normally cause an error but 3. Nefarious people have made malware under the package names that LLMs make up most often. So 4. Now the LLM code points to malware.
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Reposted by Anders Kiledal
Paul Voosen @voosen.me · 11/04/2025
BREAKING from @science.org: The Trump admin is seeking to kill nearly all climate research at NOAA, its climate science agency. Its near-final budget proposal would end all NOAA research labs, academic institutes, and regional climate centers. And it wants to fully end the NOAA Research division.
science.org
Trump seeks to end climate research at premier U.S. climate agency
White House aims to end NOAA’s research office; NASA also targeted
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Anders Kiledal @akiledal.bsky.social · 11/04/2025
Great to see this paper from Paul Den Uyl's MS work out in ES&T "Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms" doi.org/10.1021/acs.... @GreatLakesGreg @pubs.acs.org #greatlakes #ciglr #noaaglerl
doi.org
Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms
Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.
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Reposted by Anders Kiledal
Zack Labe @zacklabe.com · 10/04/2025
NOAA just fired us, again 🤡 Retroactive to February 🤡
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Reposted by Anders Kiledal
ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 11/04/2025
Wow ⓁⓄⒸⒶⓉⒾⓄⓃ ⓁⓄⒸⒶⓉⒾⓄⓃ ⓁⓄⒸⒶⓉⒾⓄⓃ Thought bacterial gene regulation is all about promoters and repressors? 𝙏𝙃𝙄𝙉𝙆 𝘼𝙂𝘼𝙄𝙉 WHERE a gene sits on the chromosome can dictate its expression—especially in fast growing bacteria Evolution won’t leave genome layout to chance Hu et al SCIENCE
science.org
Most bacterial gene families are biased toward specific chromosomal positions
The arrangement of genes along bacterial chromosomes influences their expression through growth rate–dependent gene copy number changes during DNA replication. Although translation- and transcription-...
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Cameron Thrash @jcamthrash.bsky.social · 09/04/2025
CoverM is published! CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
academic.oup.com
CoverM: Read alignment statistics for metagenomics
AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r
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Randall Munroe @xkcd.com · 17/03/2025
Lungfish xkcd.com/3064
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National Microbiome Data Collaborative (NMDC) @microbiomedata.org · 04/02/2025
📣 Our 2025 Ambassador cohort applications are officially OPEN! Are you an early career researcher passionate about open science and FAIR microbiome data? Head to microbiomedata.org/ambassadors to learn more & apply!
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Reposted by Anders Kiledal
Stephen Turner @stephenturner.us · 04/02/2025
clustur: an R package for clustering features using sparse distance matrices journals.asm.org/doi/10.1128/mra.01… #Rstats 🧬🖥️🧪 github.com/schlosslab/clustur
journals.asm.org
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Wilhelm Lab at the University of Tennessee @tn-marine-micro.bsky.social · 24/01/2025
Nice to see this important work make the news cycle when there is a lot of news in the world. Kudos to @laurenhart.bsky.social, @zepernickbn.bsky.social and others. journals.asm.org/doi/10.1128/... And very nice of Newsweek to pick it up! www.newsweek.com/lake-erie-la...
newsweek.com
Worrying signs for Lake Erie uncovered 7,500 miles away in Africa
New research from Africa's Lake Victoria has revealed critical clues about toxic algal blooms and their potential impact on Lake Erie and beyond.
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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 23/01/2025
This is me :) Go read about the incredible microbes and currents of Lake Ontario!
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Cameron Thrash @jcamthrash.bsky.social · 09/01/2025
Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya journals.asm.org/doi/full/10.... #jcampubs
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Samuel Aroney @aroneys.bsky.social · 22/01/2025
Excited to introduce the preprint for CoverM: the Swiss Army knife of coverage calculators for metagenomics! 🧬🖥️ DOI: doi.org/10.48550/arX... @benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social
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Teun van den Brand @teunbrand.bsky.social · 14/12/2024
Hi folks! I know it is the weekend, but I'd like to quickly announance an update to {legendry} version 0.2.0: teunbrand.github.io/teunbrand_bl... #rstats #ggplot2
A scatterplot of the gapminder dataset, showing GDP per capita on the x-axis and life expectancy on the y-axis. The points are sized by population, which has a legend with overlapping circles.A correlation heatmap of the mtcars dataset. Car names on the left are decorated with a dendrogram. The bottom cells also have a dendrogram, whereas the labels are on the top.
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Kelly Sovacool @kelly.sova.cool · 20/11/2024
I'm deliberately not importing my old tweets, but I do want to re-share a tutorial I made a couple of years ago -- check it out if you're an R user interested in leveling up your Python & Snakemake skills! sovacool.dev/posts/just-e... #rstats #python #snakemake #bioinformatics
sovacool.dev
Just enough Python for Snakemake – sovacool.dev
A tutorial for R users who want to write advanced Snakemake workflows
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Anders Kiledal @akiledal.bsky.social · 29/01/2024
Want to determine Microcystis diversity in your samples? We evaluated all Microcystis core genes to identify the best markers and developed optimal primers for sequencing. Markers also predictive of gene content, including for bioactive compound synthesis. doi.org/10.1016/j.ha...
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