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alex jaffe

@alexjaf.bsky.social
822 followers 418 following 144 posts

marine microbial ecology + wastewater | stanford postdoc | he/him/his

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alex jaffe @alexjaf.bsky.social · 21/07/2026
my first 'data descriptor'! hoping this one will be useful for folks interested in tracing the distribution of genomes/genes/proteins over physicochemical gradients in the (deep) marine water column.
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bioRxivpreprint @biorxivpreprint.bsky.social · 30/06/2026
Form I and II Rubiscos Exhibit Temperature Dependent Carbon Kinetic Isotope Effects www.biorxiv.org/content/10.64898/20…
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Joshua Weitz @joshuasweitz.bsky.social · 10/06/2026
A reminder... deadline June 30, 2026 Simons Graduate Fellowships in Ecology and Evolution 👇
simonsfoundation.org
Simons Graduate Fellowships in Ecology and Evolution
The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...
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Amelia Nelson Kuhn @ameliarnelson.bsky.social · 23/05/2026
Excited to share a preprint from my postdoc research at @ucberkeleyofficial.bsky.social in the @banfieldlab.bsky.social! We surveyed soil microbiomes for autotrophy - and found it nearly everywhere, but most abundant in deep, saturated soils. Check it out below! www.biorxiv.org/content/10.6...
biorxiv.org
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Marie C. Schölmerich @mschoelmerich.bsky.social · 11/04/2026
New preprint alert 🚨: Who actually drives methane production in anoxic sediments 🧬🔥? We point to a transcriptionally dominant 🦠 clade: VadinHA17. shorturl.at/Rijc0 @bledinadede.bsky.social @taylorpriest.bsky.social
biorxiv.org
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Roland Hatzenpichler @environmicrobio.bsky.social · 08/04/2026
Again looking for (self)nominations of/by grad students and postdocs to give virtual talks (via zoom) in the fall seminar series of MSU's Thermal Biology Institute. Does >not< need to be on thermophiles. Email me!
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alex jaffe @alexjaf.bsky.social · 06/04/2026
🚨 preprint alert! check out our new pub on an unusual summer flu outbreak among shorebirds traced with targeted metagenomic sequencing of wastewater. more like this coming soon from our team at @wastewaterscan.bsky.social !
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alex jaffe @alexjaf.bsky.social · 06/02/2026
marine micro folks: @elliearrington.bsky.social and i are guest editing an issue of JOVE (journal of visualized experiments) focusing on molecular techniques: app.jove.com/methods-coll... we're looking for abstract submissions (by april) exploring best practices in..
app.jove.com
JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Jove
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alex jaffe @alexjaf.bsky.social · 14/01/2026
🚨 preprint day for a thorough investigation of the genetic potential for chemoautotrophy in the deep northeastern pacific, led by @cometkid001.bsky.social in the @annedekas.bsky.social lab
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Cameron Thrash @jcamthrash.bsky.social · 02/01/2026
Troubleshooting common errors in assemblies of long-read metagenomes www.nature.com/articles/s41... #jcampubs
nature.com
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
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Nandita Garud @nanditagarud.bsky.social · 17/12/2025
If you are interested in this work and are looking for a postdoc position, please get in touch -- we are actively looking for someone to join our group at UCLA!
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Roland Hatzenpichler @environmicrobio.bsky.social · 01/12/2025
Are you a postdoc or 4-5th year grad student working on any problem in environmental microbiology and are interested in giving a virtual seminar (via zoom) on your hard work to a crowd of interested researchers at Montana State's Thermal Biology Institute in spring? Email/DM me!
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alex jaffe @alexjaf.bsky.social · 07/11/2025
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
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alex jaffe @alexjaf.bsky.social · 24/09/2025
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!
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UC-AFT Local 1474 @ucaft.bsky.social · 16/09/2025
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
Rally flyer with colorful gradient background announcing 'Hands Off Our UC!' protest. Lists UC staff, nurses, doctors, faculty, researchers, and students as participants. Event details: Tuesday, September 16, 2 PM at William J. Rutter Center at UCSF, 1675 Owens St, San Francisco, CA. Includes logos of various unions and organizations. Lists causes they stand up for: UC workers, immigrant communities, trans youth, academic freedom, public education, healthcare for all.
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JL Weissman @jlw-ecoevo.bsky.social · 10/09/2025
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...
stonybrooku.taleo.net
Computational Biologist
Click the link provided to see the complete job description.
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Christine He @christinehe.bsky.social · 27/08/2025
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
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...
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Katherine Xue @ksxue.bsky.social · 17/07/2025
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
Junior, Assistant, or Associate Specialist – Xue Lab
University of California, Irvine is hiring. Apply now!
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Jonathan Pritchard @jkpritch.bsky.social · 07/07/2025
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
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Elaine Luo @oceanmicrobes.bsky.social · 08/07/2025
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...
sites.google.com
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...
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alex jaffe @alexjaf.bsky.social · 16/06/2025
over a year later, this one out today! link.springer.com/article/10.1...
link.springer.com
Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean - Genome Biology
Background Rubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of ...
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alex jaffe @alexjaf.bsky.social · 22/05/2025
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!
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Dr. Lucky Tran @luckytran.com · 20/05/2025
🚨 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...
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Cameron Thrash @jcamthrash.bsky.social · 13/05/2025
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 🌊
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Trina McMahon @quendi.bsky.social · 04/03/2025
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...
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Stand Up for Science! @standupforscience.net · 02/03/2025
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
Map of Stand Up for Science events, with official SUFS events in Red and solidarity events in Blue
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alex jaffe @alexjaf.bsky.social · 02/03/2025
amidst the horrors, a rejuvenating day in the field with @mlmlsci.bsky.social . thanks to the crew of the r/v jh martin!
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Dr. Lucky Tran @luckytran.com · 18/02/2025
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...
ACADEMIC WORKERS UNITE!
DEFEND PUBLIC
RESEARCH FUNDING
JOIN THE NATIONAL DAY OF ACTION
FEBRUARY 19, 4:00PM
WASHINGTON SQUARE PARK
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Jonathan Lambert @jonlambert.bsky.social · 11/02/2025
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-...
commerce.senate.gov
Cruz-Led Investigation Uncovers $2 Billion in Woke DEI Grants at NSF, Releases Full Database
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alex jaffe @alexjaf.bsky.social · 03/02/2025
a first try at something new - tips/tricks/superstitions, especially from those working with environmental samples, very welcome ! @nanoporetech.com
screenshot of a digital overview of nanopore sequencing.
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Tessa Hill @tessahill.bsky.social · 02/02/2025
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
osc.universityofcalifornia.edu
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...
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Tiffany Lowe-Power stands with Minnesota @tlowepower.bsky.social · 31/01/2025
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?
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Anne Dekas @annedekas.bsky.social · 24/01/2025
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.
bg.copernicus.org
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...
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alex jaffe @alexjaf.bsky.social · 22/01/2025
i have relied heavily on coverm for years; you should too!
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alex jaffe @alexjaf.bsky.social · 22/01/2025
wonderful to see this tremendous piece work finally out, from @prywes.bsky.social et al. www.nature.com/articles/s41...
nature.com
A map of the rubisco biochemical landscape - Nature
A massively parallel assay developed to map the essential photosynthetic enzyme rubisco showed that non-trivial biochemical changes and improvements in CO2 affinity are possible, signposting further e...
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alex jaffe @alexjaf.bsky.social · 17/01/2025
calling all western geobiologists, broadly construed! come join us for the third iteration of this great little symposium, by and for early career scientists
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Pete Chuckran @pchuckran.bsky.social · 13/01/2025
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
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...
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alex jaffe @alexjaf.bsky.social · 03/01/2025
this one out today! cc @annedekas.bsky.social academic.oup.com/ismej/articl...
academic.oup.com
Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean
Abstract. Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for ur
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Cameron Thrash @jcamthrash.bsky.social · 19/12/2024
Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus academic.oup.com/ismej/advanc... #jcampubs
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Anne Dekas @annedekas.bsky.social · 25/11/2024
Hello bluesky world! Happy to be here and looking forward to connecting/re-connecting with you all. I'm excited to share a paper just out today, led by postdoc @alexjaf.bsky.social. Prochlorococcus with two forms of rubisco! www.pnas.org/doi/10.1073/....
pnas.org
Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos | PNAS
Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all st...
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alex jaffe @alexjaf.bsky.social · 25/11/2024
published today: www.pnas.org/doi/full/10....
pnas.org
Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos | PNAS
Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all st...
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Barbara Bayer @barbarabayer.bsky.social · 18/11/2024
I am super excited to share our new preprint "Contribution of ammonia oxidizers to inorganic carbon fixation in the dark ocean". This has been my absolute favorite project from my Postdoc at the Santoro Lab (UCSB) and @dome-vienna.bsky.social 🌊🦠 biorxiv.org/cgi/content/...
biorxiv.org
Contribution of ammonia oxidizers to inorganic carbon fixation in the dark ocean
Ammonia-oxidizing archaea are the most abundant chemolithoautotrophs in the ocean, comprising up to 40% of microbial cells in deep waters, and are assumed to dominate dissolved inorganic carbon (DIC) ...
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Karthik Anantharaman @karthik-a.bsky.social · 17/10/2024
Super excited to share our new review article on the diversity and ecology of microbial sulfur metabolism. Please share widely. www.nature.com/articles/s41...
nature.com
Diversity and ecology of microbial sulfur metabolism - Nature Reviews Microbiology
In this Review, Zhou, Tran et al. provide a comprehensive overview of the metabolic reactions by which microorganisms transform inorganic sulfur compounds across varied microbiomes and ecosystems, and...
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Alex Crits-Christoph @acritschristoph.bsky.social · 19/09/2024
Modern microbiology: Embracing complexity through integration across scales A review from @merenbey.bsky.social and Jill Banfield www.cell.com/cell/abstrac...
cell.com
Modern microbiology: Embracing complexity through integration across scales
This review explores the history of microbiology and contemplates the future of this evolving discipline as microbiologists embrace rapidly emerging technologies to explore systems of great complexity...
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alex jaffe @alexjaf.bsky.social · 09/09/2024
cyanobacteria can have multiple distinct forms of rubisco! check out our new preprint to learn about the unusual carbon fixation machinery of an low O2 prochlorococcus and what we think it might mean for physiology and ecosystem biogeochem
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alex jaffe @alexjaf.bsky.social · 05/08/2024
a nice survey of chemoautotrophy in extreme environments (here, cold) + an elegant biochemical modeling approach for rubisco led by Kaitlin Harrison
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alex jaffe @alexjaf.bsky.social · 29/07/2024
this out today exploring the role of urea in the interconnected deep sea nitrogen and carbon cycles! a fun opportunity to consider how best to merge single-cell (nanosims) and bulk community (metagenomics) analyses. #MicroSky
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alex jaffe @alexjaf.bsky.social · 13/05/2024
it's preprint day! happy to share my first piece of postdoc work as well as my first in the marine space, this time, exploring the biology of bacteria and archaea fixing carbon with rubisco in the deep water column more to come soon..
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Cameron Thrash @jcamthrash.bsky.social · 23/04/2024
Selective lipid recruitment by an archaeal DPANN symbiont from its host www.nature.com/articles/s41... #jcampubs
nature.com
Selective lipid recruitment by an archaeal DPANN symbiont from its host - Nature Communications
The symbiont Ca. Nanohaloarchaeum antarcticus is dependent on its host Halorubrum lacusprofundi for lipids due to a lack of certain biosynthetic genes. Here, the authors characterize the lipidome dyna...
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Alex Crits-Christoph @acritschristoph.bsky.social · 31/03/2024
Nice genome-resolved metagenomics of 90 fermented foods - including a lot of fungal genomes www.biorxiv.org/content/10.1...
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