alex jaffe
@alexjaf.bsky.social
(marine) microbial ecology + evolution | stanford postdoc | he/him/his
excited to see this one with @leahtaylorkearney.bsky.social @prywes.bsky.social et al. out, bringing a truly interdisciplinary (comparative genomics/phylogeny + biochemistry) lens to our favorite enzyme rubisco
Diversity-driven biochemical survey reveals dimeric structural origin of rubisco https://www.biorxiv.org/content/10.1101/2025.11.05.686826v1
November 7, 2025 at 8:05 PM
excited to see this one with @leahtaylorkearney.bsky.social @prywes.bsky.social et al. out, bringing a truly interdisciplinary (comparative genomics/phylogeny + biochemistry) lens to our favorite enzyme rubisco
while i AM looking forward to (someday) trivially assembling single contig MAGs from long-read data... picking out coherent contig clusters in #anvio will always be very satisfying!
September 24, 2025 at 5:06 AM
while i AM looking forward to (someday) trivially assembling single contig MAGs from long-read data... picking out coherent contig clusters in #anvio will always be very satisfying!
Reposted by alex jaffe
HANDS OFF OUR UC! Join us for a rally tomorrow, Sept 16, 2p at UCSF outside the Regents meeting. @uaw4811.bsky.social @calnurses.bsky.social @teamsterslocal2010.bsky.social @uptecwa.bsky.social @aaup.org @ucaftbayarea.bsky.social @afscme3299.bsky.social
September 16, 2025 at 1:30 AM
HANDS OFF OUR UC! Join us for a rally tomorrow, Sept 16, 2p at UCSF outside the Regents meeting. @uaw4811.bsky.social @calnurses.bsky.social @teamsterslocal2010.bsky.social @uptecwa.bsky.social @aaup.org @ucaftbayarea.bsky.social @afscme3299.bsky.social
Reposted by alex jaffe
My department (ecology and evolution) is hiring a core bioinformatics/comp bio person (not TT but the last person retired after 25+ years). It's a great place to work!: stonybrooku.taleo.net/careersectio...
Computational Biologist
Click the link provided to see the complete job description.
stonybrooku.taleo.net
September 10, 2025 at 9:12 PM
My department (ecology and evolution) is hiring a core bioinformatics/comp bio person (not TT but the last person retired after 25+ years). It's a great place to work!: stonybrooku.taleo.net/careersectio...
Reposted by alex jaffe
ONT has a temporary bioinformatics position (8 months) open while I'm on maternity leave. Focus will be on microbial genomics but with opportunities to work on projects across the breadth of genomics!
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
Applications Bioinformatician (8 month temporary role)
We are looking for an individual with expertise in bioinformatics and data analysis, specializing in microbial genomics and metagenomics, to join our Applications team as an Applications Bioinformatic...
ejnh.fa.em2.oraclecloud.com
August 27, 2025 at 7:04 PM
ONT has a temporary bioinformatics position (8 months) open while I'm on maternity leave. Focus will be on microbial genomics but with opportunities to work on projects across the breadth of genomics!
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
Reposted by alex jaffe
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
recruit.ap.uci.edu/JPF09601
Junior, Assistant, or Associate Specialist – Xue Lab
University of California, Irvine is hiring. Apply now!
recruit.ap.uci.edu
July 17, 2025 at 8:32 PM
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
recruit.ap.uci.edu/JPF09601
Reposted by alex jaffe
Staff scientist position (computational):
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
July 7, 2025 at 3:27 PM
Staff scientist position (computational):
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
Reposted by alex jaffe
Funded postdoc + PhD opportunities in marine microbial ecology! Please share with folks that might be interested.
Start date is flexible (fall 2025 to summer 2026)
More about the lab + applying (Postdoc rolling, PhD apps due Oct/Jan):
sites.google.com/uncc.edu/mic...
Start date is flexible (fall 2025 to summer 2026)
More about the lab + applying (Postdoc rolling, PhD apps due Oct/Jan):
sites.google.com/uncc.edu/mic...
Luo Lab - Microbial Ecology - join
The Luo Lab is accepting applications for funded Postdoc and PhD opportunities. Details below.
Lab members will have access to state-of-the art wet lab, and computing, and sequencing resources, inclu...
sites.google.com
July 8, 2025 at 2:52 PM
Funded postdoc + PhD opportunities in marine microbial ecology! Please share with folks that might be interested.
Start date is flexible (fall 2025 to summer 2026)
More about the lab + applying (Postdoc rolling, PhD apps due Oct/Jan):
sites.google.com/uncc.edu/mic...
Start date is flexible (fall 2025 to summer 2026)
More about the lab + applying (Postdoc rolling, PhD apps due Oct/Jan):
sites.google.com/uncc.edu/mic...
June 16, 2025 at 4:35 PM
an important piece of work, beyond just the marine realm - showing that long read tech not only can mean better genomes but more diverse and possibly previously unresolvable ones!
Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The planktonic microbiome of the Great Barrier Reef
Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pela...
www.biorxiv.org
May 22, 2025 at 9:05 PM
an important piece of work, beyond just the marine realm - showing that long read tech not only can mean better genomes but more diverse and possibly previously unresolvable ones!
Reposted by alex jaffe
🚨 ACTION ITEMS to stop the FDA from limiting Covid vaccine access:
1. Submit a public comment to the FDA www.regulations.gov/commenton/FD...
2. Contact your elected officials
www.usa.gov/elected-offi...
1. Submit a public comment to the FDA www.regulations.gov/commenton/FD...
2. Contact your elected officials
www.usa.gov/elected-offi...
May 20, 2025 at 6:57 PM
🚨 ACTION ITEMS to stop the FDA from limiting Covid vaccine access:
1. Submit a public comment to the FDA www.regulations.gov/commenton/FD...
2. Contact your elected officials
www.usa.gov/elected-offi...
1. Submit a public comment to the FDA www.regulations.gov/commenton/FD...
2. Contact your elected officials
www.usa.gov/elected-offi...
Reposted by alex jaffe
Marine community metabolomes in the eastern tropical North Pacific Oxygen Deficient Zone reveal glycine betaine as a metabolic link between Prochlorococcus and SAR11 www.biorxiv.org/content/10.1... #jcampubs 🌊
May 13, 2025 at 2:49 AM
Marine community metabolomes in the eastern tropical North Pacific Oxygen Deficient Zone reveal glycine betaine as a metabolic link between Prochlorococcus and SAR11 www.biorxiv.org/content/10.1... #jcampubs 🌊
Reposted by alex jaffe
As many of you know, it's been really hard for journal editors to find willing manuscript reviewers. If you are interested in reviewing for ASM's mSphere, please fill out this gform! I'm especially excited to work with early career researchers.
forms.gle/53vxpbvF3Lrk...
forms.gle/53vxpbvF3Lrk...
March 4, 2025 at 5:40 PM
As many of you know, it's been really hard for journal editors to find willing manuscript reviewers. If you are interested in reviewing for ASM's mSphere, please fill out this gform! I'm especially excited to work with early career researchers.
forms.gle/53vxpbvF3Lrk...
forms.gle/53vxpbvF3Lrk...
Reposted by alex jaffe
WHERE WILL YOU BE ON MARCH 7TH!?
Head to www.standupforscience2025.org/local-event-information/ or the link in our bio to find your closest event—or add one if you're hosting one!
#standupforscience2025
Head to www.standupforscience2025.org/local-event-information/ or the link in our bio to find your closest event—or add one if you're hosting one!
#standupforscience2025
March 2, 2025 at 2:04 AM
WHERE WILL YOU BE ON MARCH 7TH!?
Head to www.standupforscience2025.org/local-event-information/ or the link in our bio to find your closest event—or add one if you're hosting one!
#standupforscience2025
Head to www.standupforscience2025.org/local-event-information/ or the link in our bio to find your closest event—or add one if you're hosting one!
#standupforscience2025
amidst the horrors, a rejuvenating day in the field with @mlmlsci.bsky.social . thanks to the crew of the r/v jh martin!
March 2, 2025 at 4:35 AM
amidst the horrors, a rejuvenating day in the field with @mlmlsci.bsky.social . thanks to the crew of the r/v jh martin!
Reposted by alex jaffe
ACTION THIS WEDNESDAY: Researchers from New York universities are holding a rally to protest the funding cuts at Washington Square Park at 4 pm.
This will be part of a national day of action, with rallies at HHS in DC and all around the country.
RSVP HERE: docs.google.com/forms/d/e/1F...
This will be part of a national day of action, with rallies at HHS in DC and all around the country.
RSVP HERE: docs.google.com/forms/d/e/1F...
February 18, 2025 at 2:17 AM
ACTION THIS WEDNESDAY: Researchers from New York universities are holding a rally to protest the funding cuts at Washington Square Park at 4 pm.
This will be part of a national day of action, with rallies at HHS in DC and all around the country.
RSVP HERE: docs.google.com/forms/d/e/1F...
This will be part of a national day of action, with rallies at HHS in DC and all around the country.
RSVP HERE: docs.google.com/forms/d/e/1F...
Reposted by alex jaffe
Is your NSF grant on this list? Reach out if so!
Ted Cruz released a list of grants flagged for DEI or "neo-Marxist class warfare propaganda" from his Oct. report.
NSF is using keywords from that report for their review, though Cruz's list is likely larger.
www.commerce.senate.gov/2025/2/cruz-...
Ted Cruz released a list of grants flagged for DEI or "neo-Marxist class warfare propaganda" from his Oct. report.
NSF is using keywords from that report for their review, though Cruz's list is likely larger.
www.commerce.senate.gov/2025/2/cruz-...
Cruz-Led Investigation Uncovers $2 Billion in Woke DEI Grants at NSF, Releases Full Database
www.commerce.senate.gov
February 11, 2025 at 9:11 PM
Is your NSF grant on this list? Reach out if so!
Ted Cruz released a list of grants flagged for DEI or "neo-Marxist class warfare propaganda" from his Oct. report.
NSF is using keywords from that report for their review, though Cruz's list is likely larger.
www.commerce.senate.gov/2025/2/cruz-...
Ted Cruz released a list of grants flagged for DEI or "neo-Marxist class warfare propaganda" from his Oct. report.
NSF is using keywords from that report for their review, though Cruz's list is likely larger.
www.commerce.senate.gov/2025/2/cruz-...
a first try at something new - tips/tricks/superstitions, especially from those working with environmental samples, very welcome ! @nanoporetech.com
February 3, 2025 at 9:54 PM
a first try at something new - tips/tricks/superstitions, especially from those working with environmental samples, very welcome ! @nanoporetech.com
Reposted by alex jaffe
Hey, if you work for the University of California, and you are worried about public access to your research data that are currently hosted on federal sites - follow directions here to get them up on Dryad. 📈 osc.universityofcalifornia.edu/for-authors/...
@datadryad.bsky.social
@ucdavis.bsky.social
@datadryad.bsky.social
@ucdavis.bsky.social
Data Sharing Policies & Tools - Office of Scholarly Communication
Open Data is the movement to make research datasets open, thereby enabling the sharing, reuse, and transparency of research findings. Similar to the Open Access movement for articles, Open Data is cri...
osc.universityofcalifornia.edu
February 2, 2025 at 8:18 PM
Hey, if you work for the University of California, and you are worried about public access to your research data that are currently hosted on federal sites - follow directions here to get them up on Dryad. 📈 osc.universityofcalifornia.edu/for-authors/...
@datadryad.bsky.social
@ucdavis.bsky.social
@datadryad.bsky.social
@ucdavis.bsky.social
Reposted by alex jaffe
Fellow UC professors, what can we do to advocate for the NSF postdoc fellows (and potentially additional fellows next) who cannot withdraw their paychecks?
Contact the UC Federal Relations lawyers?
Contact the UC Federal Relations lawyers?
January 31, 2025 at 2:28 AM
Fellow UC professors, what can we do to advocate for the NSF postdoc fellows (and potentially additional fellows next) who cannot withdraw their paychecks?
Contact the UC Federal Relations lawyers?
Contact the UC Federal Relations lawyers?
Reposted by alex jaffe
Our most recent paper on methane seeps is out: bg.copernicus.org/articles/22/.... Two seeps in Monterey Canyon have virtually no ANME (methane oxidizers), suggesting an unabated methane flux at these and similar seeps. The microbiological methane filter in sediments is not ubiquitous.
Unexpected scarcity of ANME archaea in hydrocarbon seeps within Monterey Bay
Abstract. Marine hydrocarbon seeps typically harbor a relatively predictable microbiome, including anaerobic methanotrophic (ANME) archaea. Here, we sampled two cold seeps in Monterey Bay, CA – Clam F...
bg.copernicus.org
January 24, 2025 at 10:15 PM
Our most recent paper on methane seeps is out: bg.copernicus.org/articles/22/.... Two seeps in Monterey Canyon have virtually no ANME (methane oxidizers), suggesting an unabated methane flux at these and similar seeps. The microbiological methane filter in sediments is not ubiquitous.
i have relied heavily on coverm for years; you should too!
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
@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social
January 22, 2025 at 8:32 PM
i have relied heavily on coverm for years; you should too!
wonderful to see this tremendous piece work finally out, from @prywes.bsky.social et al.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 22, 2025 at 8:19 PM
wonderful to see this tremendous piece work finally out, from @prywes.bsky.social et al.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
calling all western geobiologists, broadly construed! come join us for the third iteration of this great little symposium, by and for early career scientists
January 17, 2025 at 8:54 PM
calling all western geobiologists, broadly construed! come join us for the third iteration of this great little symposium, by and for early career scientists
Reposted by alex jaffe
Wetting dry soil rapidly stimulates microbial activity and has important consequences for biogeochemical cycling. In our paper out today, we show that part of that response can be explained by how bacterial genomes are written (i.e. codon usage, nucleotide freq., genome size)
doi.org/10.1073/pnas...
doi.org/10.1073/pnas...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
doi.org
January 13, 2025 at 9:07 PM
Wetting dry soil rapidly stimulates microbial activity and has important consequences for biogeochemical cycling. In our paper out today, we show that part of that response can be explained by how bacterial genomes are written (i.e. codon usage, nucleotide freq., genome size)
doi.org/10.1073/pnas...
doi.org/10.1073/pnas...