alex jaffe

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 !

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..

prepare yourself for stanford-branded everything (towels, blankets, etc.. ) 😅

and feel free to drop a line when you're on campus!

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...

if you want to do it the french way, try entrees - plats - dessert :) enjoy paris and the pasteur!

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'...

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...

🚨 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

have you been able to determine what predicts pore count on start? age/temp/ randomness from manufacturing?

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Troubleshooting common errors in assemblies of long-read metagenomes www.nature.com/articles/s41... #jcampubs

so yeah… undo all of that …

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..

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!

this is what i’m concerned about

in bioinformatics, working but subtly wrong is a potential nightmare come paper writing time

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...

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...

great news! how can non-faculty support your efforts?

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!

typical use case, just interested in seeing a few more of the abundant lineages .

yes, though i understand you run into color palette limits at a certain point …

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?

i was wondering!

Potstickers Classic Chinese-American, thoughtful ingredients. Find our gluten free frozen potstickers in grocery stores around the Bay Area.

these are good but fairly pricey! eatmamahuhu.com/collections/...

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

congrats - and great to see some more rhodopsins characterized from the CPR!

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!

thanks for flagging.

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.

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

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...

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...