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alex jaffe @alexjaf.bsky.social · 15d

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 · 16d

thanks for flagging.

Reposted by alex jaffe

UC-AFT Local 1474 @ucaft.bsky.social · 23d

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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Reposted by alex jaffe

JL Weissman @jlw-ecoevo.bsky.social · 28d

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

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Reposted by alex jaffe

Christine He @christinehe.bsky.social · Aug 27

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...

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

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alex jaffe @alexjaf.bsky.social · Aug 27

@tendersombrero.bsky.social may have some thoughts?

alex jaffe @alexjaf.bsky.social · Aug 26

fingers crossed for good data!

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alex jaffe @alexjaf.bsky.social · Aug 23

cool, im interested - will send you an email!

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alex jaffe @alexjaf.bsky.social · Aug 23

is research on mesophilic environments eligible ?!

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alex jaffe @alexjaf.bsky.social · Aug 18

amen. feel like i need a print-out version for my desk, or something!

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alex jaffe @alexjaf.bsky.social · Aug 8

tested for what, exactly? in any case, there are nice examples from marine micro - HOTS/BATS/ san pedro for long term time series, geotraces malaspina and tara for geographic breadth …

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alex jaffe @alexjaf.bsky.social · Jul 31

yep

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alex jaffe @alexjaf.bsky.social · Jul 23

you are correct - thanks for flagging that!

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alex jaffe @alexjaf.bsky.social · Jul 23

one other quick question for you - seeing lots of otu coverage vals with 0.31 decimal increments - expected behavior? if so, related to default kmer len?

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alex jaffe @alexjaf.bsky.social · Jul 18

ah, that's great! working mostly with illumina right now but this may be useful in the future. kudos on your documentation, by the way - very clear

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alex jaffe @alexjaf.bsky.social · Jul 18

great - thanks!

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alex jaffe @alexjaf.bsky.social · Jul 17

congrats to the team and thanks for the great tool! curious if you have any tips/tricks for 'supplement' - im concerned for ex. that adding more erroneous MAGs from current nanopore chemistry might mess with smafa

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Reposted by alex jaffe

Katherine Xue @ksxue.bsky.social · Jul 17

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

Junior, Assistant, or Associate Specialist – Xue Lab

University of California, Irvine is hiring. Apply now!

recruit.ap.uci.edu

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alex jaffe @alexjaf.bsky.social · Jul 17

this was me using rclone yesterday - why u so slow!?

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alex jaffe @alexjaf.bsky.social · Jul 13

we love to see it.. also neat they derived their expected breadth calculation from an '88 paper

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Reposted by alex jaffe

Jonathan Pritchard @jkpritch.bsky.social · Jul 7

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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alex jaffe @alexjaf.bsky.social · Jul 10

and then there’s infant gut…

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alex jaffe @alexjaf.bsky.social · Jul 9

but even without that you could get a sense for % of reads composed by your genome(s) of interest - an imperfect (of course) proxy.

i also love branchwater.jgi.doe.gov but im not sure that will give you rel abund, simply presence across all SRA - a very useful starting point for more detailed work

Branchwater Metagenome Query

branchwater.jgi.doe.gov

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alex jaffe @alexjaf.bsky.social · Jul 9

interesting scenario! relative abundance is tricky, because to me that would imply mapping reads against a relatively representative set of [genomes, gene regions, etc] present in that sample, rather than a select subset.

Branchwater Metagenome Query

branchwater.jgi.doe.gov

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Reposted by alex jaffe

Elaine Luo @oceanmicrobes.bsky.social · Jul 8

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...

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

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