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alex jaffe

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

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

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alex jaffe @alexjaf.bsky.social · 08/09/2026
that info should be at the bottom of the linked physical biosample page, e.g. www.ncbi.nlm.nih.gov/biosample/SA...
ncbi.nlm.nih.gov
MIMS Environmental/Metagenome sample from marine m... - BioSample - NCBI
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alex jaffe @alexjaf.bsky.social · 08/09/2026
out today in @asm.org journals.asm.org/doi/10.1128/...
journals.asm.org
Divergent avian strains drive an off-season influenza A peak in municipal wastewater | Microbiology Spectrum
Researchers now commonly search municipal wastewater for viral genetic material, which can indicate trends in the diversity and abundance of strains circulating in communities. Here, we show that unde...
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alex jaffe @alexjaf.bsky.social · 23/07/2026
i could see that top percentile bin being poorly represented in databases for soil, but why do you think the ecosystem in general would not also suffer from biases associated with sequencing depth?
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alex jaffe @alexjaf.bsky.social · 23/07/2026
thanks - i agree, its a neat relationship.
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alex jaffe @alexjaf.bsky.social · 23/07/2026
congratulations, steven!
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alex jaffe @alexjaf.bsky.social · 21/07/2026
thank you, steve!
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alex jaffe @alexjaf.bsky.social · 21/07/2026
my favorite, though, is that rarer microbes are (on average) more dissimilar to reference than more abundant ones, an intuitive relationship but one i'm not sure ive actually actually seen depicted.
a scientific figure showing that sequence/protein similarity to reference among ocean microbes decreases with rarity
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alex jaffe @alexjaf.bsky.social · 21/07/2026
the format really offers an opportunity to look at some sort of 'practice of science' things that one normally would not, for example, how profoundly under-sampled the deep sea is relative to the surface ocean:
a scientific plot showing that metagenomic sequencing effort decreases by orders of magnitude with physical ocean depth.
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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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alex jaffe @alexjaf.bsky.social · 12/06/2026
does this tend to skew towards euks, or would the ed board consider bacterial/archaeal genome assemblies as well?
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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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alex jaffe @alexjaf.bsky.social · 09/06/2026
out now in @natureportfolio.nature.com: www.nature.com/articles/s41...
nature.com
Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily - Nature Communications
A survey of rubisco, the enzyme behind nearly all carbon fixation on Earth, across understudied branches of its family tree finds all characterized deep-branching versions are dimers and uncovers a di...
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alex jaffe @alexjaf.bsky.social · 08/06/2026
thanks - might consider clarifying in the docs - this is an amazing set of features that i wouldn't want to go underappreciated by the community!
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alex jaffe @alexjaf.bsky.social · 08/06/2026
in the end, the default works just fine - i was wondering however, if there is a way to output an otu table corresponding to what is sequenced but not assembled, and not just what is assembled but not binned? is that --output-unaccounted-for-otu-table? if not, any suggestions for how to infer?
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alex jaffe @alexjaf.bsky.social · 30/05/2026
hi ace, we are trying to do some work with v207 (old, i know, trying to keep consistent with prev work) but are running into a corrupted tarball (gtdb_proteins_aa_reps_r207.tar.gz). any chance of getting a pair of eyes on that? i submitted a ticket a few weeks back. thanks!
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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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alex jaffe @alexjaf.bsky.social · 20/04/2026
i wonder about this - if proteins within a pathway have different turnover times, or certain enzymes serve as a bottlenecks for flux through the pathway, you could get 'meaningful' heterogeneity?
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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 · 04/03/2026
looks like they’re on bluesky thank god @redwallfeasts.bsky.social
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alex jaffe @alexjaf.bsky.social · 03/03/2026
one of the things i miss most about being off X is the RedWall Feasts bot 🥲
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alex jaffe @alexjaf.bsky.social · 06/02/2026
sample collection, filtering, extraction, sequencing of DNA or RNA using short or long-read-based approaches, the use of bioinformatic software, and more generally the computational analysis of ‘omic or amplicon data from the ocean reach out with any questions here or via email !
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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 · 28/01/2026
prepare yourself for stanford-branded everything (towels, blankets, etc.. ) 😅 and feel free to drop a line when you're on campus!
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alex jaffe @alexjaf.bsky.social · 28/01/2026
are you on university business? this is comfortable enough and was around that per diem when i stayed there last year rde.stanford.edu/stanford-gue...
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alex jaffe @alexjaf.bsky.social · 19/01/2026
if you want to do it the french way, try entrees - plats - dessert :) enjoy paris and the pasteur!
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alex jaffe @alexjaf.bsky.social · 15/01/2026
michael, i understand the draw of external postdoc funding at this time, but i do wonder if this is the kind of organization to be boosting - it could be argued that their reactionary, alarmist politics play right into us admin efforts to defund universities under the pretext of 'antisemitism'...
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alex jaffe @alexjaf.bsky.social · 14/01/2026
an essential complement to our work out last year specifically focusing on organisms with rubisco across this same transect, as well as more globally (icymi) bsky.app/profile/alex...
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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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alex jaffe @alexjaf.bsky.social · 13/01/2026
have you been able to determine what predicts pore count on start? age/temp/ randomness from manufacturing?
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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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alex jaffe @alexjaf.bsky.social · 24/12/2025
so yeah… undo all of that …
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alex jaffe @alexjaf.bsky.social · 20/12/2025
being transphobic on linkedin is so insane! odds you come across them socially with your friend/ their spouse? sounds like you might have another chance to address in person, if you want it..
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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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alex jaffe @alexjaf.bsky.social · 16/12/2025
this is what i’m concerned about in bioinformatics, working but subtly wrong is a potential nightmare come paper writing time
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alex jaffe @alexjaf.bsky.social · 10/12/2025
i get that, but is there ever a 'good time' in the admin's eyes to negotiate over much needed wage increases? i've never heard of one...
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alex jaffe @alexjaf.bsky.social · 10/12/2025
even if this is true, its not clear to me that some diversion of labor to AI is a greater harm than withholding living wages to the students...
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alex jaffe @alexjaf.bsky.social · 01/12/2025
great news! how can non-faculty support your efforts?
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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 · 25/11/2025
typical use case, just interested in seeing a few more of the abundant lineages .
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alex jaffe @alexjaf.bsky.social · 24/11/2025
yes, though i understand you run into color palette limits at a certain point …
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alex jaffe @alexjaf.bsky.social · 24/11/2025
hey ben, thanks for notifying us of the new version! any plans to allow the user to modulate the number of lineages 'colored in' in appraise plots? is that possible already?
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alex jaffe @alexjaf.bsky.social · 17/11/2025
i was wondering!
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alex jaffe @alexjaf.bsky.social · 12/11/2025
these are good but fairly pricey! eatmamahuhu.com/collections/...
eatmamahuhu.com
Potstickers
Classic Chinese-American, thoughtful ingredients. Find our gluten free frozen potstickers in grocery stores around the Bay Area.
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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 · 16/10/2025
congrats - and great to see some more rhodopsins characterized from the CPR!
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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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alex jaffe @alexjaf.bsky.social · 22/09/2025
thanks for flagging.
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