Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

Joanna Masel@joannamasel.bsky.social · 8mo ago

Sequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10

New @isbscience.org research shows how microbial teamwork behind denitrification can collapse in polluted environments, threatening ecosystem balance and resilience. isbscience.org/news/environ...

Microbes That Keep Ecosystems in Balance Can Fall Apart Easily, New Study Finds

Microbial teamwork behind denitrification can collapse in polluted environments, threatening ecosystem balance and resilience.

isbscience.org

🚨 BREAKING: Nearly 4 months the NIH cut its first grants, a judge has ruled that the directives and process that led to cuts are arbitrary and capricious. "The explanations are bereft of reasoning — virtually in their entirety... unsupported by [facts]." Each of them are VOID and ILLEGAL, he says.

the reissued NOFO for the Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral Fellowship (Parent F31) is finally published! grants.nih.gov/grants/guide...

🦠🧬Exciting news! BFVD predicted viral protein structures are now available in @InterProDB! For the first time, explore InterPro functional annotations directly on 3D structures of viral proteins not covered by AlphaFold DB. This bridges a critical gap in structural virology research.

The Koonin Law of Computatoinal Biology: Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.

The spread of Mpox in Sierra Leone is unlike anything we have ever seen - and we have been keeping an eye on this bug in the region for >15 years. Given geographical spread, 50/50 men vs women, this is no "sexual network". This could be the next one. clt.npha.gov.sl/outbreak.aspx

Who's calling the shots at NIH? Sworn testimonies and internal e-mails reveal for the first time the breadth of DOGE's control over the world's largest public biomedical funder. DOGE has provided lists of hundreds of grants to cut, and DOGE is now reviewing ALL NIH awards before they're released

NIH killed grants on orders from Elon Musk’s DOGE

Court documents and internal correspondence show the cost-cutting force has broad control over the world’s largest public biomedical funder.

nature.com

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

bioRxiv Molecular Biology@biorxiv-molbio.bsky.social · last yr.

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes https://www.biorxiv.org/content/10.1101/2025.05.14.653371v1

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

an old redraw of one of my fav microbe memes, by @prokaryota.bsky.social "eAT The DiRT bRöTHer" 🦠 #SciArt #microbes

Having a hard time processing this. HHMI is pausing all competitions. Very demoralizing for early career scientists like me @hhmi.org

New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

Optometrist: you should really probably spend less time on screens Me, a computational biologist: I’ll… just take that under advisement, shall I?

Nine cases of Middle East Respiratory Syndrome (MERS) have been reported in Saudi Arabia including two fatalities and a cluster of seven cases linked to healthcare associated transmission. http://spr.ly/63329Nk0yX

New Notice on No Cost Extensions (or lack thereof) grants.nih.gov/grants/guide...

The Spencer Foundation is offering rapid response bridge funding for those who lost NSF research grants. www.spencer.org/grant_types/...

Rapid Response Bridge Funding Program

In the face of recent abrupt shifts in federal funding for education research, including large-scale terminations of National Science Foundation (NSF) research grant awards, we have developed a rap...

spencer.org

BREAKING: Reports that Trump would try to cut NIH's budget by 40% have come true. The request released moments ago would: - Cut $18 BILLION to NIH's $47b budget - Eliminate NIMHD, NCCIH, FIC - Collapse ICs into five 'focus areas' There's also a long screed about NIH's deficiencies.

NEW: Starting May 5, NSF will implement an across-the-board 15% indirect cost rate (mirroring policies at DOE, NIH) Also, NSF staff expect 341 additional terminations today, bringing the total number of terminations to ~1,380.

BREAKING: NSF has frozen all grant funding, as of yesterday. It's unclear when they will resume funding awards, or why the pause has been put in place. www.nature.com/articles/d41...

Exclusive: NSF stops awarding new grants and funding existing ones

US science funder also plans to screen grant applications for compliance with ‘agency priorities’.

nature.com

🦟🦠 NEW! We looked at every experiment going back to the 1960s, and found that mosquitoes are almost certainly not primary or secondary vectors of Oropouche virus - a common claim in both the scientific literature and public health communication. #EpiSky #IDSky 😷🧪 journals.plos.org/plosntds/art...

Vector competence for Oropouche virus: A systematic review of pre-2024 experiments

Oropouche virus has recently become an urgent threat to public health in Central and South America. OROV is mainly transmitted by biting midges; however, some public health agencies and scientific sou...

journals.plos.org

Calling all US and Canadian students thinking about graduate studies! Come study science at #SFU in beautiful British Columbia, Canada. Graduate admissions have been reopened. Apply by April 25th. ⚛️ 🧪👩‍🔬🎢 🇨🇦

SFU Faculty of Science@sfuscience.bsky.social · last yr.

Applications are open for select graduate studies programs at #SFU, including biomedical physiology, chemistry, molecular biology and @sfuphysics.bsky.social. Canadian and US students encouraged to apply by April 25. www.sfu.ca/gradstudies/...

GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.

We're all going to learn about suppy chains the hard way...again.

Karen Attiah@karenattiah.bsky.social · last yr.

Right now, I’m paying attention to news from the shipping and trucking industries of leading indicators of how bad things are going to get. And the trends are alarming. Beginning to stock up on essentials *now*.

Per source, NIH has been instructed to hold off from issuing ALL awards to Harvard, Cornell, Columbia, Brown, and Northwestern (including med schools) Agency staff have also been instructed to not speak about this funding freeze to grantees and applicants

This is ridiculous. NSF is pausing *all* outgoing grants awarded this cycle and subjecting them to a “secondary review” by DOGE. Gumming up the funding pipeline like this threatens the job security of nearly a million graduate students and post docs, to say nothing of the science…

David Malakoff@davidmalakoff.bsky.social · last yr.

BREAKING:The National Science Foundation (NSF) has put a cork in its grantmaking pipeline after billionaire Elon Musk’s Department of Government Efficiency (DOGE) set up shop at the agency this week. | Science | AAAS www.science.org/content/arti...

SCOOP: Internal budget doc reveals extent of Trump’s proposed health cuts. About 1/3 of HHS discretionary budget. Our story w @carolynyjohnson.bsky.social @rachelroubein.bsky.social @joelachenbach.bsky.social @laurenweberhp.bsky.social www.washingtonpost.com/health/2025/...

Internal budget document reveals extent of Trump’s proposed health cuts

HHS would be asked to absorb a $40 billion cut, about one third of its discretionary budget.

washingtonpost.com

Hurray, it is finally out! Meet bacteriophage Bxb1 - the subject of my first full-phage cryo-EM study. My structures are beautifully complemented by the Park Lab’s cryo-ET analysis, shedding light on mycobacteriophage structural changes during infection. www.sciencedirect.com/science/arti...

Structure and infection dynamics of mycobacteriophage Bxb1

Mycobacteriophage Bxb1 is a well-characterized virus of Mycobacterium smegmatis with double-stranded DNA and a long, flexible tail. Mycobacteriophages…

sciencedirect.com