Ryan Ziels
@ryanziels.bsky.social
Associate Professor of Environmental Engineering | UBC | Engineer | Microbiologist | Surfer of mountains & waves
https://emberrlab.civil.ubc.ca/
https://emberrlab.civil.ubc.ca/
Reposted by Ryan Ziels
Some researchers get their boost from papers or grants.
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 22, 2025 at 6:55 PM
Some researchers get their boost from papers or grants.
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
Reposted by Ryan Ziels
Very excited to finally have my thesis work out in the world! Hopefully it just got easier to understand the role of specific microbes in complex communities, even when they are really rare!
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 11:15 PM
Very excited to finally have my thesis work out in the world! Hopefully it just got easier to understand the role of specific microbes in complex communities, even when they are really rare!
Reposted by Ryan Ziels
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism www.nature.com/articles/s41... #jcampubs
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 22, 2025 at 4:38 AM
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism www.nature.com/articles/s41... #jcampubs
Reposted by Ryan Ziels
Nice work by @ryanziels.bsky.social lab that combines BONCAT, FACS, and genome-resolved metaproteomics using affinity capture of newly made proteins.
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
October 21, 2025 at 6:25 PM
Nice work by @ryanziels.bsky.social lab that combines BONCAT, FACS, and genome-resolved metaproteomics using affinity capture of newly made proteins.
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 5:08 PM
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
Reposted by Ryan Ziels
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 1:38 PM
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Excited for this opportunity to work with excellent research scientists at EMSL and the @jgi.doe.gov to study the microbes driving clean biofuel production! 🙏🦠⚡️🔥
Welcome the six researchers accepted to the FICUS program for FY26! Focus areas for projects include biofuels, biomaterials & bioproducts; hydrobiogeochemistry; & novel applications of molecular techniques.
🖥️🧬 @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
🖥️🧬 @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
Six join FICUS program in 2026 | Joint Genome Institute
Pictured from left to right are: [above] Allegra Aron, Jana Pilatova and Ryan Ziels; [below] Andrew Vander Yacht, Itamar Shabtai and Victoria Orphan The JGI is excited to welcom
jgi.doe.gov
September 18, 2025 at 1:23 AM
Excited for this opportunity to work with excellent research scientists at EMSL and the @jgi.doe.gov to study the microbes driving clean biofuel production! 🙏🦠⚡️🔥
Reposted by Ryan Ziels
Welcome the six researchers accepted to the FICUS program for FY26! Focus areas for projects include biofuels, biomaterials & bioproducts; hydrobiogeochemistry; & novel applications of molecular techniques.
🖥️🧬 @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
🖥️🧬 @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
Six join FICUS program in 2026 | Joint Genome Institute
Pictured from left to right are: [above] Allegra Aron, Jana Pilatova and Ryan Ziels; [below] Andrew Vander Yacht, Itamar Shabtai and Victoria Orphan The JGI is excited to welcom
jgi.doe.gov
September 16, 2025 at 3:26 PM
Welcome the six researchers accepted to the FICUS program for FY26! Focus areas for projects include biofuels, biomaterials & bioproducts; hydrobiogeochemistry; & novel applications of molecular techniques.
🖥️🧬 @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
🖥️🧬 @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
Reposted by Ryan Ziels
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.
Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!
www.biorxiv.org/content/10.1...
Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!
www.biorxiv.org/content/10.1...
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome
Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed...
www.biorxiv.org
July 29, 2025 at 2:18 AM
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.
Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!
www.biorxiv.org/content/10.1...
Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!
www.biorxiv.org/content/10.1...
Reposted by Ryan Ziels
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Are you interested in microbes that are rare but active? We combined BONCAT with SIP and metaproteomics to improve the recovery of labeled proteins from such microbes. In this case, it illuminated a new anaerobic syntrophic acetate-oxidizing bacterium.
tinyurl.com/a8j29dsr
#microbiomesky #microsky
tinyurl.com/a8j29dsr
#microbiomesky #microsky
Activity-targeted metaproteomics enhances the ecophysiological characterization of cryptic syntrophic metabolisms
Syntrophic microbial consortia can contribute significantly to the activity and function of anoxic ecosystems, yet are often too rare to study their in situ physiologies using traditional molecular me...
tinyurl.com
July 16, 2025 at 3:49 PM
Are you interested in microbes that are rare but active? We combined BONCAT with SIP and metaproteomics to improve the recovery of labeled proteins from such microbes. In this case, it illuminated a new anaerobic syntrophic acetate-oxidizing bacterium.
tinyurl.com/a8j29dsr
#microbiomesky #microsky
tinyurl.com/a8j29dsr
#microbiomesky #microsky
Reposted by Ryan Ziels
UC-Berkeley has an open-rank faculty position in our incredible Climate Equity and Environmental Justice (CEEJ) research cluster. It is an extraordinary interdisciplinary group working across multiple colleges and departments at the university! More information here: aprecruit.berkeley.edu/JPF04842
Assistant/Associate/Full Professor - Climate Equity and Environmental Justice - Rausser College of Natural Resources
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
July 12, 2025 at 12:02 AM
UC-Berkeley has an open-rank faculty position in our incredible Climate Equity and Environmental Justice (CEEJ) research cluster. It is an extraordinary interdisciplinary group working across multiple colleges and departments at the university! More information here: aprecruit.berkeley.edu/JPF04842
Reposted by Ryan Ziels
Interesting new study on emergence and disruption of cooperativity in a denitrifying microbial community, by postdoc in the lab Alex Carr (from his PhD work with Nitin Baliga). academic.oup.com/ismej/articl...
Emergence and disruption of cooperativity in a denitrifying microbial community
Abstract. Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the em
academic.oup.com
June 13, 2025 at 9:09 PM
Interesting new study on emergence and disruption of cooperativity in a denitrifying microbial community, by postdoc in the lab Alex Carr (from his PhD work with Nitin Baliga). academic.oup.com/ismej/articl...
Reposted by Ryan Ziels
High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the #Nanopore platform #microbiome
High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform
Abstract. Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms
academic.oup.com
November 15, 2024 at 5:00 PM
High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the #Nanopore platform #microbiome
Reposted by Ryan Ziels
Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration journals.asm.org/doi/full/10.... #jcampubs
February 29, 2024 at 2:33 PM
Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration journals.asm.org/doi/full/10.... #jcampubs
Reposted by Ryan Ziels
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium www.nature.com/articles/s41... #jcampubs
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing c...
The ISME Journal - Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
www.nature.com
October 26, 2023 at 1:31 PM
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium www.nature.com/articles/s41... #jcampubs
~70% of CH4 in anoxic ecosystems comes from acetate, but what microbes are catalyzing its oxidation, and how? We shed some new light on this question using long-term enrichments along with metabolic modeling informed by SIP-metaproteogenomics. #MicrobiomeSky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing c...
The ISME Journal - Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
www.nature.com
October 25, 2023 at 4:33 PM
~70% of CH4 in anoxic ecosystems comes from acetate, but what microbes are catalyzing its oxidation, and how? We shed some new light on this question using long-term enrichments along with metabolic modeling informed by SIP-metaproteogenomics. #MicrobiomeSky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ryan Ziels
#IndigenousPeoplesDay is Monday. My challenge to non-Natives: dig into the history of the people who were displaced from your land, learn about the history of how they were displaced, find out where they are now, and support them financially or by protesting with them. Go beyond platitudes.
October 6, 2023 at 1:10 PM
#IndigenousPeoplesDay is Monday. My challenge to non-Natives: dig into the history of the people who were displaced from your land, learn about the history of how they were displaced, find out where they are now, and support them financially or by protesting with them. Go beyond platitudes.
Reposted by Ryan Ziels
capitalism ruins everything
How Google Alters Search Queries to Get at Your Wallet
Testimony during Google’s antitrust case revealed that the company may be altering billions of queries a day to generate results that will get you to buy more stuff.
www.wired.com
October 3, 2023 at 4:28 PM
capitalism ruins everything
Reposted by Ryan Ziels
🚨 #anvio v8 (marie) is out 🚨
This version includes new toys for integrated studies of microbial metabolism, genomic inversions, & phylogeography of proteins among many fixes and improvements.
Release notes:
github.com/merenlab/anv...
Installation page:
anvio.org/install
This version includes new toys for integrated studies of microbial metabolism, genomic inversions, & phylogeography of proteins among many fixes and improvements.
Release notes:
github.com/merenlab/anv...
Installation page:
anvio.org/install
Release anvi'o v8, "marie" · merenlab/anvio
We are happy to announce anvi'o v8 with the code name, "marie"!
After about 4,200 changes that introduced over 36,000 new lines of code, this stable release of anvi'o represents significant advance...
github.com
October 1, 2023 at 2:21 PM
🚨 #anvio v8 (marie) is out 🚨
This version includes new toys for integrated studies of microbial metabolism, genomic inversions, & phylogeography of proteins among many fixes and improvements.
Release notes:
github.com/merenlab/anv...
Installation page:
anvio.org/install
This version includes new toys for integrated studies of microbial metabolism, genomic inversions, & phylogeography of proteins among many fixes and improvements.
Release notes:
github.com/merenlab/anv...
Installation page:
anvio.org/install
Reposted by Ryan Ziels
Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing
-in ISME Comms
www.nature.com/articles/s43...
-in ISME Comms
www.nature.com/articles/s43...
October 1, 2023 at 8:56 AM
Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing
-in ISME Comms
www.nature.com/articles/s43...
-in ISME Comms
www.nature.com/articles/s43...
Reposted by Ryan Ziels
Our department is hiring! We have a wide variety of expertise in molecular & cell bio & work with with many different systems. We are interested in candidates using cutting-edge and innovative techniques conduct novel research on molecular structure & function 🧪
academicjobsonline.org/ajo/jobs/25945
academicjobsonline.org/ajo/jobs/25945
University of Connecticut, Molecular and Cell Biology
Full service online faculty recruitment and application management system for academic institutions worldwide. We offer unique solutions tailored for academic communities.
academicjobsonline.org
September 27, 2023 at 3:31 PM
Our department is hiring! We have a wide variety of expertise in molecular & cell bio & work with with many different systems. We are interested in candidates using cutting-edge and innovative techniques conduct novel research on molecular structure & function 🧪
academicjobsonline.org/ajo/jobs/25945
academicjobsonline.org/ajo/jobs/25945
Reposted by Ryan Ziels
I'm excited to announce that the UNC-Chapel Hill Department of Biology has TWO openings for tenure track Assistant Professors using genomics-informed methods to study critical questions in Plant and/or Microbial Biology.
unc.peopleadmin.com/postings/265...
unc.peopleadmin.com/postings/265...
Assistant Professor
The Department of Biology at UNC Chapel Hill (https://bio.unc.edu/) is searching for two tenure track Assistant Professors using genomics-informed methods to study critical questions in Plant and Micr...
unc.peopleadmin.com
September 27, 2023 at 12:17 AM
I'm excited to announce that the UNC-Chapel Hill Department of Biology has TWO openings for tenure track Assistant Professors using genomics-informed methods to study critical questions in Plant and/or Microbial Biology.
unc.peopleadmin.com/postings/265...
unc.peopleadmin.com/postings/265...
Reposted by Ryan Ziels
three microbiology tenure track positions at Texas State San Marcos
General research areas of particular interest include Microbial Functional Genomics, Microbial Ecology, and Molecular Microbiology.
jobs.hr.txstate.edu/...
deadline nov 6th 2023 🦠🧬🖥️
General research areas of particular interest include Microbial Functional Genomics, Microbial Ecology, and Molecular Microbiology.
jobs.hr.txstate.edu/...
deadline nov 6th 2023 🦠🧬🖥️
September 24, 2023 at 12:12 PM
three microbiology tenure track positions at Texas State San Marcos
General research areas of particular interest include Microbial Functional Genomics, Microbial Ecology, and Molecular Microbiology.
jobs.hr.txstate.edu/...
deadline nov 6th 2023 🦠🧬🖥️
General research areas of particular interest include Microbial Functional Genomics, Microbial Ecology, and Molecular Microbiology.
jobs.hr.txstate.edu/...
deadline nov 6th 2023 🦠🧬🖥️