Elinne Becket, PhD
@bielleogy.bsky.social
Assoc Prof @CSUSM | 🦠⇄🦠 MGEs & coastal metagenomes | #BlueSoup 🥣🧬 🧫 | R1→Biotech→PUI | Protective mama bear of students | She/Her
Pinned
Ok I'm outing myself here but there was forgotten beef soup in our fridge we just cleaned it out and it was BLUE?!?!? Wtf contam would make it blue??? Like BRIGHT blue!! 🤢🤮 Even w/ all my years in micro I'm not handling this well.
All important #BlueSoup updates, from me or Sebastian, will be added in line with the original thread here (it's run a little long so you need to click "show replies" at the bottom):
Current mood on the professor group chat
November 26, 2025 at 10:24 PM
Current mood on the professor group chat
Been trying to read this book loaned to me by @cawatran.bsky.social for months but ironically too distracted to finish it 🤣
November 26, 2025 at 7:26 PM
Been trying to read this book loaned to me by @cawatran.bsky.social for months but ironically too distracted to finish it 🤣
UCI is always my favorite school to submit letters of rec to. Click link, drag file, type name, click submit, DONE!
November 25, 2025 at 5:46 AM
UCI is always my favorite school to submit letters of rec to. Click link, drag file, type name, click submit, DONE!
When you have 5 research students applying for PhD programs in one cycle 😵💫 Soooooo proud of them but 😵💫😵💫
November 25, 2025 at 5:15 AM
When you have 5 research students applying for PhD programs in one cycle 😵💫 Soooooo proud of them but 😵💫😵💫
Reposted by Elinne Becket, PhD
Can we *please* stop rewarding bullying behavior in academic social media?
November 23, 2025 at 9:59 PM
Can we *please* stop rewarding bullying behavior in academic social media?
Reposted by Elinne Becket, PhD
@bielleogy.bsky.social Happy Sunday! @‘ing you in case the spreadsheet below may be of use.
hey everyone! i made a list of some useful starter packs (primarily biology/earth sciences with a few bonus things thrown in) to share with friends who have joined bsky in the last week and thought it may be useful for some people here too! 🌍🧪 #SciSky #BioSky docs.google.com/document/d/1...
Starter packs
BIOLOGY Ecology Macroecology https://go.bsky.app/GBn9pNZ Global ecology https://go.bsky.app/V6tN4cv Trait based ecology and evolution https://go.bsky.app/PThMXeX Invasion biology https://go.b...
docs.google.com
November 23, 2025 at 8:45 PM
@bielleogy.bsky.social Happy Sunday! @‘ing you in case the spreadsheet below may be of use.
Reposted by Elinne Becket, PhD
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage
Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom
academic.oup.com
November 23, 2025 at 4:39 PM
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Reposted by Elinne Becket, PhD
There are few things that frustrate me more than moving goalposts. Laziness or bad planning (or both) means more work falls on other people.
November 22, 2025 at 12:04 AM
There are few things that frustrate me more than moving goalposts. Laziness or bad planning (or both) means more work falls on other people.
Reposted by Elinne Becket, PhD
Calculating fast differential genome coverages among metagenomic sources using micov www.nature.com/articles/s42... #jcampubs
Calculating fast differential genome coverages among metagenomic sources using micov - Communications Biology
micov computes coverage breadth across genomes and samples. Its application in metagenomics highlights strain heterogeneity, uncovers associations linking genetic elements to phenotypic traits, and ai...
www.nature.com
November 21, 2025 at 4:22 PM
Calculating fast differential genome coverages among metagenomic sources using micov www.nature.com/articles/s42... #jcampubs
Reposted by Elinne Becket, PhD
Looking forward to today’s @calstate.bsky.social Bioinformatics Webinar, featuring the awesome @catalicu.bsky.social! Do join us at noon Pacific via Zoom. Deets in the flyer.
November 21, 2025 at 7:06 PM
Looking forward to today’s @calstate.bsky.social Bioinformatics Webinar, featuring the awesome @catalicu.bsky.social! Do join us at noon Pacific via Zoom. Deets in the flyer.
Reposted by Elinne Becket, PhD
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
academic.oup.com
November 20, 2025 at 2:02 PM
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
PSA: When you're at a conference, especially one like ABRCMS, and you feel the need to tell a student at their poster that their work is shit, maybe, I dunno, kick rocks???
What is wrong with people.
What is wrong with people.
November 21, 2025 at 5:36 AM
PSA: When you're at a conference, especially one like ABRCMS, and you feel the need to tell a student at their poster that their work is shit, maybe, I dunno, kick rocks???
What is wrong with people.
What is wrong with people.
Reposted by Elinne Becket, PhD
What’s the most significant advice you received from a teacher?
I had a Geology prof who always said “have strong opinions, loosely held”
Be passionate, assess alternatives with conviction, take sides. But don’t fall so in love with your opinions that you can’t change them with better data.
I had a Geology prof who always said “have strong opinions, loosely held”
Be passionate, assess alternatives with conviction, take sides. But don’t fall so in love with your opinions that you can’t change them with better data.
November 21, 2025 at 12:54 AM
What’s the most significant advice you received from a teacher?
I had a Geology prof who always said “have strong opinions, loosely held”
Be passionate, assess alternatives with conviction, take sides. But don’t fall so in love with your opinions that you can’t change them with better data.
I had a Geology prof who always said “have strong opinions, loosely held”
Be passionate, assess alternatives with conviction, take sides. But don’t fall so in love with your opinions that you can’t change them with better data.
Reposted by Elinne Becket, PhD
Deep-sea viral diversity and their role in host metabolism of complex organic matter www.nature.com/articles/s41... #jcampubs 🌊
Deep-sea viral diversity and their role in host metabolism of complex organic matter - Nature Communications
Roles of viruses in deep-sea ecosystems are poorly understood. Here, the authors use metagenomics and metatranscriptomics to profile DNA and RNA viruses in deep-sea sediments showing that these viruse...
www.nature.com
November 20, 2025 at 2:28 PM
Deep-sea viral diversity and their role in host metabolism of complex organic matter www.nature.com/articles/s41... #jcampubs 🌊
Reposted by Elinne Becket, PhD
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Elinne Becket, PhD
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:17 PM
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
Reposted by Elinne Becket, PhD
It’s hard to correctly estimate the level of fumigation that will be required to restore public trust and proper function in the CDC (and several other executive branches) after what has occurred over the past ten months (has it really only been ten months?!)
November 20, 2025 at 6:54 AM
It’s hard to correctly estimate the level of fumigation that will be required to restore public trust and proper function in the CDC (and several other executive branches) after what has occurred over the past ten months (has it really only been ten months?!)
Blue Soup pub target journal
November 19, 2025 at 6:41 AM
Blue Soup pub target journal
The lab class I teach is a course-based ugrad research experience, and I was stoked that the data we analyzed today showed that my initial hunch/hypothesis was completely wrong (in fact, the opposite). Great learning opportunity to show them it's about the data, never the ego.
November 19, 2025 at 1:51 AM
The lab class I teach is a course-based ugrad research experience, and I was stoked that the data we analyzed today showed that my initial hunch/hypothesis was completely wrong (in fact, the opposite). Great learning opportunity to show them it's about the data, never the ego.
Our lab's new CS student is working on our supercomputers in lab and wants us to move off Ubuntu bc package manager reasons, and suggests Manjaro, Pop! (even tho same pkgmngr), or Debian. For the comp (bio) people in my feed, thoughts?
November 18, 2025 at 9:50 PM
Our lab's new CS student is working on our supercomputers in lab and wants us to move off Ubuntu bc package manager reasons, and suggests Manjaro, Pop! (even tho same pkgmngr), or Debian. For the comp (bio) people in my feed, thoughts?
👇🏻👇🏻👇🏻
I am so tired of “full responsibility” that involves no action and “shame” that kicks in only upon public disclosure.
SUMMERS: “.. I am deeply ashamed of my actions and recognize the pain they have caused. I take full responsibility for my misguided decision to continue communicating with Mr. Epstein.”
@politico.com
www.politico.com/news/2025/11...
@politico.com
www.politico.com/news/2025/11...
November 18, 2025 at 2:22 AM
👇🏻👇🏻👇🏻
JFC...
POV: you are a young woman celebrating a recent academic success
November 18, 2025 at 1:53 AM
JFC...
Reposted by Elinne Becket, PhD
MedPage Today story about NIH Institute Director searches with comments from me and former NIMH Director Josh Gordon.
www.medpagetoday.com/washington-w...
www.medpagetoday.com/washington-w...
NIH Job Postings Raise Red Flags for Scientists
A dozen high-level spots are open for a short period of time
www.medpagetoday.com
November 18, 2025 at 12:05 AM
MedPage Today story about NIH Institute Director searches with comments from me and former NIMH Director Josh Gordon.
www.medpagetoday.com/washington-w...
www.medpagetoday.com/washington-w...