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Simon Roux @simrouxvirus.bsky.social · 12/06/2026

🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0

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Simon Roux @simrouxvirus.bsky.social · 07/06/2026

Last day of #ASMicrobe, with a lot of exciting talks and sessions still to come ! Including one near and dear to my heart: long-term dynamics of environmental microbiomes, where we'll hear all about time-series 'omics datasets across many ecosystems, from rivers to soils to insects (and more) 🎉

Screenshot of the ASM Microbe program showing the session AEM-402 "long-term dynamics of environmental microbiomes" Sunday June 7, at 10:45 in room 147AB

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Simon Roux @simrouxvirus.bsky.social · 04/06/2026

Almost time to kick-off this year's ASM Microbe, including some very cool sessions in the next few days in the AEM meeting ! If you're around and want to chat anything metagenomes, phages, viruses, and all that, let me know !

Two doors with signs saying "ASM Applied & Environmental Microbiology Meeting" "session rooms"

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Simon Roux @simrouxvirus.bsky.social · 17/03/2026

🧬🦠🔬📣 First announcement for the 2026 edition of our Viral EcoGenomics and Applications symposium - VEGA26 will take place November 18 and 19 at UC Berkeley. We'll add more information at jgi.doe.gov/work-with-us... , but save the date already for 2 exciting days of viral ecogenomics !

A poster announcing the next edition of the VEGA (Viral EcoGenomics and Applications) symposium, to be hosted on November 18-19, 2026 in the Pauley Ballroom at UC Berkeley. The text is surrounded by various drawings of phages and viruses, and an capsid-shaped Earth map.

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Simon Roux @simrouxvirus.bsky.social · 28/02/2026

Post a pic you took, no context, to bring some zen to the feed.

A cat (tortie) sleeping on a round cushion. The cat is sleeping with its tail between its paws, and nicely matching the round shape of the cushion

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Simon Roux @simrouxvirus.bsky.social · 09/12/2025

What really seems to happen is not just too much coverage, but too much population diversity in the dataset without a clear dominant genotype, leading to a very complex assembly graph that can't be resolved from short read alone (just look at this tangled mess 😮)

A metagenome assembly graph, showing a lot of small fragments connected to each other, without any obvious path through it. Or said otherwise: a bunch of black and red lines all mixed up together that form no specific shape or form, really.

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Simon Roux @simrouxvirus.bsky.social · 18/08/2025

I wish it wasn't so, but some days it feels like we could generalize this meme further 🥲

The Scooby-Doo unmasking meme. The "masked" ghost is labeled "Some cool bioinformatic result", the "unmasked" ghost is labeled "a method artifact/error"

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Simon Roux @simrouxvirus.bsky.social · 22/06/2025

And wrapping up an amazing session with a very nice (and modular) phage-host network 🤩 Really great to see some fascinating phage research from anoxic lakes to soils to zebrafish (and human) gut, all informing each other ! And a reminder that these session topics are coming from you: the community

A picture of a scientist presenting at a conference. The scientist is at a podium on the left, pointing to a slide projected in the middle, and some of the audience is visible on the right

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Simon Roux @simrouxvirus.bsky.social · 22/06/2025

Kicking off Sunday morning #ASMicrobe with an entire phage ecology session \o/ thanks to @cathyhernandez.bsky.social and @phagebeelicious.bsky.social . And first, @cynthiasilveira.bsky.social on phages and geochemistry 🤩

The picture shows a conference room with a speaker on a podium on the left, a large screen with a scientific diagram in the middle and the audience on the right.

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Simon Roux @simrouxvirus.bsky.social · 21/06/2025

Jonelle Basso @jgi.doe.gov reminding everyone that phages are in every microbiome, and will influence host-microbiome interactions (here with a plant, but applies to all hosts ! ) #ASMicrobe

A scientist (Jonelle Basso) presenting her work, pointing at a slide on the left, with the audience sitting and standing on the right

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Simon Roux @simrouxvirus.bsky.social · 18/04/2025

- hey, he's never replying to our great credit card offers ! What should we do ? - I dunno, maybe send 5 the same day ? - yeah that should do it, I'm sure that'll make him super happy and will make our offer irresistible to just see it 5 times #MarketingStrategy(probably)

A photo of five (5) envelopes from the same credit card company offering the same credit card deal to the same person, all received the same day

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Simon Roux @simrouxvirus.bsky.social · 05/12/2024

New custom stamp just dropped 👀👀👀 (thanks @maureenbug.bsky.social and Jonelle !) #VEGA24

The picture shows on the left a post-it note stamped with the acronym VEGA followed by a diagram of a phage particle. On the right is the custom stamp used to stamp the note, and the writing and phage diagram are visible.

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Simon Roux @simrouxvirus.bsky.social · 27/11/2024

Another great-looking EEB session at the upcoming ASM Microbe 25: "Standardizing Success: Best Practices for Microbial Data Collection and Reuse in Diverse and Extreme Environments" www.abstractsonline.com/pp8/#!/20974... co-organized by Julia Kelliher (LANL/NMDC) and Jessica Lee (NASA Ames)

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Simon Roux @simrouxvirus.bsky.social · 21/11/2024

It was really great to host the #VEGA24 conference last week, thanks again to everyone for joining us, and thanks to NIST for the co-organization ! And since we are on the topic of conferences, abstracts for ASM Microbe 25 are open (asm.org/events/asm-m...) with some fantastic EEB sessions !

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Simon Roux @simrouxvirus.bsky.social · 13/11/2024

Last talk of the conference (already !) at #VEGA24 : @bkoskella.bsky.social showing that phages clearly influence microbiome composition (always nice to see it confirmed in actual experiment ☺️), including helping plants fight against microbial pathogens !

The picture is of a speaker (Britt Koskella) at the VEGA 2024 conference, presenting from behind a lectern. In the background is a projected screen with a slide showing scientific graphs, on a dark curtain background

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Simon Roux @simrouxvirus.bsky.social · 13/11/2024

More information on (one of) the most common phages in human gut - pCrassphage, thanks to Danica Schmidtke who managed to grow them in culture ! #VEGA24

The picture shows a projected screen with a slide from a scientific talk. The speaker (Danica Schmidtke) can be seen in the foreground)

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Simon Roux @simrouxvirus.bsky.social · 13/11/2024

Starting the afternoon with the challenging world of soil RNA viruses (but made a bit less challenging by a little DMSO !) with Luke Hillary from the Emerson Lab #VEGA24

The picture shows a projected slide on a wide screen in front of dark curtains, and the speaker (Luke Hillary) in front presenting his research

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Simon Roux @simrouxvirus.bsky.social · 13/11/2024

Why would you need a black background for your slides ? To show really neat pictures of jumbo phages infecting a host cell 🤩 by Deepto Mozumdar at #VEGA24

A speaker (Deepto Mozumdar) at a lectern presenting results at the VEGA 24 conference. A projected slide is visible behind and has an unusual black background, which helps the audience to better see fluorescent microscopy observation

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Simon Roux @simrouxvirus.bsky.social · 13/11/2024

Next up at #VEGA24, Nacho de la Higuera from the Stedman Lab on the emergence and evolution of cruciviruses (the story was so neat and simple when we only knew a few of these, but now of course with more data everything becomes super complex 😳)

A speaker (Nacho de la Higuera) is behind a lectern and presenting at the VEGA24 conference. Behind is a projected slide that shows a complex network of genomes connected to each other

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Simon Roux @simrouxvirus.bsky.social · 13/11/2024

Getting ready for #VEGA24 day 2, which will feature the poster prizes 👀👀

The picture shows two custom 3D printed trophies shaped like phages, with "VEGA 2024" written on the phage head. In the background is the stage and banner of the VEGA 24 conference

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Simon Roux @simrouxvirus.bsky.social · 12/11/2024

Working groups starting to self-organize for the next session at #VEGA24, with discussions around all the unknown sequences in viruses and how to deal with them, what are the best ways to leverage AI for viromics, and how do we better communicate around our favorite (viral) topics !

The picture shows a conference room with linear tables, and scientists gathering in small groups between tables to discuss. In the back a stage and a screen are visible as well.

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Simon Roux @simrouxvirus.bsky.social · 12/11/2024

Starting the afternoon with Angela Hickey from the group of Ami Bhatt in Stanford, telling us about how long reads really help to better "see" prophages in human gut #VEGA24 (also trying another orientation for picture that hopefully will work better, apologies for the previous distorted ones :-) )

A speaker (Angela Hickey) at the VEGA 24 conference presenting a slide about the human gut phageome. The speaker is behind a lectern and the slide is visible behind

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Simon Roux @simrouxvirus.bsky.social · 12/11/2024

Next: an overview of the Human Virome Program at NIH, by Liliana Brown. If you didn't hear about it yet, you can learn more at commonfund.nih.gov/humanvirome - essentially an ambitious goal to characterize all viruses found in and on humans ! #VEGA24

A speaker (Liliana Brown) is presenting a slide about the NIH Human Virome Program at the VEGA24 conference. The speaker is on a stage behind a podium, and the slide is visible behind

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Simon Roux @simrouxvirus.bsky.social · 12/11/2024

Katrine Whiteson starting us off with "22 years in the virome wolrd", and a recommendation to "consider something viral in your research" (which I wholeheartedly agree with) #VEGA24

The speaker (Katrine Whiteson) is at the podium and presenting a slide about her research at the VEGA 2024 conference

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Simon Roux @simrouxvirus.bsky.social · 12/11/2024

The VEGA 2024 symposium is almost here ! Starting tomorrow, what should be two fun days of talks and discussions on everything viromics and viral ecology and virus evolution and virus-inspired biotech and therapeutic applications. Plus custom trophies for best posters 👀👀 #VEGA24

A picture of 2 3d printed trophies, shaped like a T4 phage with a blue head and white tail on a black base. They are labeled VEGA 2024 (the name of the conférence) and Best Student Poster / Best Visualization. They are displayed in front of a fireplace

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Simon Roux @simrouxvirus.bsky.social · 19/10/2024

show me your pet and what they're named after.

A picture of Mimi (Zola) the cat. she's a tortoiseshell, pictured here laying on her side, sleeping, on a big cushion.

A picture of the famous French writer Emile Zola

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Simon Roux @simrouxvirus.bsky.social · 30/09/2024

"In-N-out" is such a perfect name for a soil carbon framework (and title for a paper, of course onlinelibrary.wiley.com/doi/full/10....) Francesca Cotrufo with a fascinating keynote to open #JGI2024

Picture of a presentation slide that shows the title "The In-N-out framework"

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Simon Roux @simrouxvirus.bsky.social · 17/06/2024

Thank you ASM community, 2024 was really fun, and interesting, and mind-blowing, and inspiring. Looking forward to #ASMicrobe 2025 in Los Angeles ! And remember, you'll want to get these session proposals in soon !! So any topic you feel should be (better) covered, etc, don't be shy !!!

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Simon Roux @simrouxvirus.bsky.social · 16/06/2024

Full house (again) for the EEB track hub presentation, this time @luiszaman.bsky.social making us all think about the limits of evolution in microbes #ASMicrobe

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Simon Roux @simrouxvirus.bsky.social · 15/06/2024

Next year's president forum at #ASMicrobe : AI and ML for Microbiology!! Get ready for ASM 2025 in LA (although don't forget the last two days of ASM Microbe 2024 first !)

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Simon Roux @simrouxvirus.bsky.social · 15/06/2024

Massive combined assembly of soil metagenomes \o/ thanks to collaboration between NEON / NMDC / @jgi.doe.gov #ASMicrobe

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Simon Roux @simrouxvirus.bsky.social · 15/06/2024

Everything about single-cell transcriptomics *for bacteria* 🤩 exciting EEB track hub talk by Anna Kuchina from ISB at #ASMicrobe

Picture of the speaker, Anna Kuchina, and the first rows of the audience at the EEB track hub

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Simon Roux @simrouxvirus.bsky.social · 14/06/2024

Standing room only for the "AI in Environmental Biology" session, a great way to kick off this Friday! #ASMicrobe

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Simon Roux @simrouxvirus.bsky.social · 13/06/2024

Scott Jackson from NIST presenting the new NIST-managed collection of bacterial strains. Open for donation so get your favorite bug ready ! #ASMicrobe

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Simon Roux @simrouxvirus.bsky.social · 13/06/2024

In Atlanta for #ASMicrobe. DM open if anyone want to chat ! Also if you have (or are) PhD student(s) looking for postdocs, we have positions now for RNA phage discovery and wastewater phage bioinformatics !

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Simon Roux @simrouxvirus.bsky.social · 16/01/2024

Virus tattoo: the (overdue) 10-year upgrade ☺️ (left: before, 3 right: after upgrade), thanks to www.instagram.com/quiana.tattoo

Old(ish) tattoo of (relatively) simple viral capsid shapes on the upper arm

The same upper arm with new more complex virus tattoo, here showing two archaeal viruses in the inner arm

Large virus capsid tattoo including a T4 phage on the back of the upper arm

Combination of viral capsid tattoos on upper arm (inovirus, podovirus) and around the shoulder (giant virus)

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Simon Roux @simrouxvirus.bsky.social · 29/11/2023

Ten years (and two weeks) later, it's so great to be back in Tucson even for a short visit. Thanks again @surtlab.bsky.social ☺️

Picture of a sunset over Downtown/University in Tucson

Picture of a palm tree on university of Arizona campus

Picture of a building, some trees, and a sunset sky on the University of Arizona campus

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