Patrick Rynkiewicz
@ngsorcerer.bsky.social
NGS sorcerer, computational biologist, cat dad, homebrewer.
Obsessed with beer yeast, human microbiomes, and writing decent code for science. Happy to collaborate.
🇵🇱🇺🇸
Views my own.
Obsessed with beer yeast, human microbiomes, and writing decent code for science. Happy to collaborate.
🇵🇱🇺🇸
Views my own.
Cool service and idea. Microbiome science benefits greatly from efforts like this and BugSigDB, among others, to better curate data.
straininfo.dsmz.de/about
straininfo.dsmz.de/about
straininfo.dsmz.de
November 14, 2025 at 12:09 PM
Cool service and idea. Microbiome science benefits greatly from efforts like this and BugSigDB, among others, to better curate data.
straininfo.dsmz.de/about
straininfo.dsmz.de/about
Working on a tool for pulling Oura Ring data into a Postgres database:
github.com/patrynk/oura...
Claude helped. Not vibe-coded. Nice exercise in learning new data engineering techniques while playing with new development toys.
github.com/patrynk/oura...
Claude helped. Not vibe-coded. Nice exercise in learning new data engineering techniques while playing with new development toys.
GitHub - patrynk/oura_sync: Service for extracting Oura Ring data to PostgreSQL database with OAuth2 authentication
Service for extracting Oura Ring data to PostgreSQL database with OAuth2 authentication - patrynk/oura_sync
github.com
November 12, 2025 at 9:44 PM
Working on a tool for pulling Oura Ring data into a Postgres database:
github.com/patrynk/oura...
Claude helped. Not vibe-coded. Nice exercise in learning new data engineering techniques while playing with new development toys.
github.com/patrynk/oura...
Claude helped. Not vibe-coded. Nice exercise in learning new data engineering techniques while playing with new development toys.
Reposted by Patrick Rynkiewicz
When you buy a cutting board from bioinformaticians
October 26, 2025 at 10:56 PM
When you buy a cutting board from bioinformaticians
Excited to see Anthropic leaning into streamlining life sciences research with the Claude for Life Sciences initiative. Should be interrogated for accuracy like any other LLM output but it could help define research questions and make bioinformatics more accessible
www.anthropic.com/news/claude-...
www.anthropic.com/news/claude-...
Claude for Life Sciences
Discover how Claude accelerates life sciences research with new scientific connectors, skills, and improved performance for drug discovery and clinical work.
www.anthropic.com
October 21, 2025 at 1:35 PM
Excited to see Anthropic leaning into streamlining life sciences research with the Claude for Life Sciences initiative. Should be interrogated for accuracy like any other LLM output but it could help define research questions and make bioinformatics more accessible
www.anthropic.com/news/claude-...
www.anthropic.com/news/claude-...
Reposted by Patrick Rynkiewicz
ICYMI: New online! Clostridioides difficile pathogenesis and control
Clostridioides difficile pathogenesis and control
Nature Reviews Microbiology, Published online: 02 October 2025; doi:10.1038/s41579-025-01242-2Clostridioides difficile infection is challenging to diagnose and treat and is associated with considerable mortality, morbidity and economic costs worldwide. In this Review, Chilton et al. discuss changes in global epidemiology, breakthroughs in pathogenesis and antibiotic resistance, the role of microbiota dysbiosis and the potential for microbiota-based therapeutics for Clostridioides difficile infection.
www.nature.com
October 9, 2025 at 1:08 PM
ICYMI: New online! Clostridioides difficile pathogenesis and control
Looking forward to this special issue!
REMINDER: only two weeks left to submit papers to the special issue of "Yeast in microbiomes". There will be no further extensions.
The deadline for submissions to the special issue "Yeast in Microbiomes" has been extended to 15 October. We accept manuscripts exploring yeast diversity, interactions, and adaptations in diverse host environments. Hurry up and don't miss this opportunity!!!
onlinelibrary.wiley.com/page/journal...
onlinelibrary.wiley.com/page/journal...
October 3, 2025 at 12:40 PM
Looking forward to this special issue!
Reposted by Patrick Rynkiewicz
New research article
Single-gene transcripts for subclinical #tuberculosis: an individual participant data meta-analysis
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #TB #OpenAccess #OA
Single-gene transcripts for subclinical #tuberculosis: an individual participant data meta-analysis
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #TB #OpenAccess #OA
October 3, 2025 at 8:13 AM
New research article
Single-gene transcripts for subclinical #tuberculosis: an individual participant data meta-analysis
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #TB #OpenAccess #OA
Single-gene transcripts for subclinical #tuberculosis: an individual participant data meta-analysis
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #TB #OpenAccess #OA
Really interested to see how the phenomenon of fungal domestication across food microbiomes plays into this discussion around phylosymbiosis. We exogenously select for traits in beer yeast like flavor and fermentation performance, and then endogenously interact with these living microbes. Incredible
Human gut fungi are largely presumed to be negligible, transient, and diet-derived. While this assumption may hold water for many taxa, science has a long way to go in testing the full depths of eco-evolutionary influences in the gut mycobiome.
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Gut fungal profiles reveal phylosymbiosis and codiversification across humans and nonhuman primates
Fungi in the gut microbiome (the "mycobiome") are a neglected component of the human holobiont. This study of gut fungal profiles across natural populations of humans and non-human primates reveals si...
journals.plos.org
September 24, 2025 at 5:52 PM
Really interested to see how the phenomenon of fungal domestication across food microbiomes plays into this discussion around phylosymbiosis. We exogenously select for traits in beer yeast like flavor and fermentation performance, and then endogenously interact with these living microbes. Incredible
Reposted by Patrick Rynkiewicz
The gut MYCOBIOME is akin to the tiny group of kids in the corner of a huge homecoming dance. Their story is largely unknown. In our latest, @emilyvansyoc.bsky.social dives into the evolutionary associations of gut fungi with @erdavenport.bsky.social & Andres Gomez
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Gut fungal profiles reveal phylosymbiosis and codiversification across humans and nonhuman primates
Fungi in the gut microbiome (the "mycobiome") are a neglected component of the human holobiont. This study of gut fungal profiles across natural populations of humans and non-human primates reveals si...
journals.plos.org
September 24, 2025 at 5:36 PM
The gut MYCOBIOME is akin to the tiny group of kids in the corner of a huge homecoming dance. Their story is largely unknown. In our latest, @emilyvansyoc.bsky.social dives into the evolutionary associations of gut fungi with @erdavenport.bsky.social & Andres Gomez
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Reposted by Patrick Rynkiewicz
A salient experiment that elegantly examines how context dependent is hologenome evolution in response to selection on diet quality? The short answer. It is resilient, even when faced with abiotic and biotic disruptors such as post-selection socialization and diet. Brilliant evaluation; a must read
Pleased to share new work tinkering with and testing the concept of the holobiont
@isme-microbes.bsky.social
"Experimental evolution of a mammalian holobiont: bank voles selected for herbivorous capability evolved distinct and robust gut bacterial communities"
🌾🐭🦠
academic.oup.com/ismecommun/a...
@isme-microbes.bsky.social
"Experimental evolution of a mammalian holobiont: bank voles selected for herbivorous capability evolved distinct and robust gut bacterial communities"
🌾🐭🦠
academic.oup.com/ismecommun/a...
Experimental evolution of a mammalian holobiont: bank voles selected for herbivorous capability evolved distinct and robust gut bacterial communities
Abstract. According to the “hologenome” theory of evolution natural selection and evolution can act through a conglomerate biological unit, the “holobiont”
academic.oup.com
September 16, 2025 at 10:58 PM
A salient experiment that elegantly examines how context dependent is hologenome evolution in response to selection on diet quality? The short answer. It is resilient, even when faced with abiotic and biotic disruptors such as post-selection socialization and diet. Brilliant evaluation; a must read
Reposted by Patrick Rynkiewicz
Just FYI: while CDC is no longer tracking much of anything, wastewater data is still being reported. COVID-19 levels have just been nationally upgraded to “high”
September 15, 2025 at 3:22 PM
Just FYI: while CDC is no longer tracking much of anything, wastewater data is still being reported. COVID-19 levels have just been nationally upgraded to “high”
Looking forward to the peer-reviewed version but very exciting direction.
Therapeutic Salmonella induces long-term protective trained immunity in NK cells against cancer metastasis @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 4, 2025 at 12:25 PM
Looking forward to the peer-reviewed version but very exciting direction.
Reposted by Patrick Rynkiewicz
When other journals were too nervous to lean into this topic, this one leaned in. They specifically have a discovery report section for new insights based on initial observations. Can’t recommend this @plosbiology.org team enough!
What determines the human gut fungal community? @emilyvansyoc.bsky.social @erdavenport.bsky.social @symbionticism.bsky.social &co present the first #GWAS of human genetic loci that influence the abundance of gut #fungi, linking these to disease risk #mycobiome @plosbiology.org 🧪 plos.io/42bCKou
September 3, 2025 at 12:29 PM
When other journals were too nervous to lean into this topic, this one leaned in. They specifically have a discovery report section for new insights based on initial observations. Can’t recommend this @plosbiology.org team enough!
Reposted by Patrick Rynkiewicz
Great pop-sci digest by Alex Carr of his recent C. diff modeling work in Cell Systems youtu.be/shp-TjniW48?...
here's the paper --> doi.org/10.1016/j.ce...
@isbscience.org
here's the paper --> doi.org/10.1016/j.ce...
@isbscience.org
Forecasting Gut Health: Predicting C. diff Risk with Digital Twins
YouTube video by Institute for Systems Biology
youtu.be
August 28, 2025 at 7:50 PM
Great pop-sci digest by Alex Carr of his recent C. diff modeling work in Cell Systems youtu.be/shp-TjniW48?...
here's the paper --> doi.org/10.1016/j.ce...
@isbscience.org
here's the paper --> doi.org/10.1016/j.ce...
@isbscience.org
Reposted by Patrick Rynkiewicz
Severe, refractory lupus successfully treated with engineered T cells derived from a healthy donor
nature.com/articles/s41...
nature.com/articles/s41...
Allogeneic CD19-targeting T cells for treatment-refractory systemic lupus erythematosus: a phase 1 trial - Nature Medicine
In a small trial of patients with severe systemic lupus erythematosus and nephritis, treatment with allogeneic T cells with a CD19 chimeric antigen receptor inserted into the T cell receptor locus and...
nature.com
August 27, 2025 at 3:06 PM
Severe, refractory lupus successfully treated with engineered T cells derived from a healthy donor
nature.com/articles/s41...
nature.com/articles/s41...
Reposted by Patrick Rynkiewicz
🎙️ JOB ANNOUNCEMENT: @ciddpsu.bsky.social Ctr for Infectious Disease Dynamics at PSU is searching for a Full or Associate Professor in Infectious Disease Modeling. This is a unique, cross-university search for someone to become a leader in our community!
psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...
psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...
Full or Associate Professor in Infectious Disease Modeling
APPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a...
psu.wd1.myworkdayjobs.com
August 27, 2025 at 4:25 PM
🎙️ JOB ANNOUNCEMENT: @ciddpsu.bsky.social Ctr for Infectious Disease Dynamics at PSU is searching for a Full or Associate Professor in Infectious Disease Modeling. This is a unique, cross-university search for someone to become a leader in our community!
psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...
psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...
"using our custom designed experimental set-up, we found that mosquitoes are drawn to those who avoid sunscreen, drink beer, and share their bed. They simply have a taste for the hedonists among us."
LOL
LOL
August 27, 2025 at 11:04 PM
"using our custom designed experimental set-up, we found that mosquitoes are drawn to those who avoid sunscreen, drink beer, and share their bed. They simply have a taste for the hedonists among us."
LOL
LOL
Love when great scientists amplify each others' work!
Happy to team up with @microbe-enjoyer.bsky.social to highlight fantastic work by @gibbological.bsky.social, Alex Carr, and colleagues using community scale metabolic models to predict risk for C. difficile colonization!
See the initial study here: www.cell.com/cell-systems...
See the initial study here: www.cell.com/cell-systems...
August 20, 2025 at 4:42 PM
Love when great scientists amplify each others' work!
It had to be from Spongebob of course 😂
August 15, 2025 at 9:00 AM
It had to be from Spongebob of course 😂
Reposted by Patrick Rynkiewicz
solid foundation in statistics is even more important in the age of AI.
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
August 12, 2025 at 2:15 PM
solid foundation in statistics is even more important in the age of AI.
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
Reposted by Patrick Rynkiewicz
ICYMI: New online! The human skin microbiome: from metagenomes to therapeutics
The human skin microbiome: from metagenomes to therapeutics
Nature Reviews Microbiology, Published online: 04 August 2025; doi:10.1038/s41579-025-01211-9In this Review, Oh and Voigt explore the major characteristics and functions of the skin microbiome, and they highlight potential therapeutic targets in the skin microbiome and ongoing progress in the development of skin microbiome-based therapeutics.
www.nature.com
August 11, 2025 at 5:37 PM
ICYMI: New online! The human skin microbiome: from metagenomes to therapeutics
Reposted by Patrick Rynkiewicz
I'm beyond excited to share that our last work is now published in Nature Communications.
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations - Nature Communications
Here, Valderrama et al., introduced ‘saMBA’, the largest collection of uniformly analyzed microbiome data from South America, the worlds most biodiverse yet less characterized region. The article prop...
shorturl.at
August 11, 2025 at 1:33 PM
I'm beyond excited to share that our last work is now published in Nature Communications.
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
Reposted by Patrick Rynkiewicz
The updated version of the database of PhD fellowships produced and maintained by my team can be downloaded by anyone here:
research.jhu.edu/rdt/funding-...
For each of the 187 fellowships, you will find a short description, deadline, $ amount, link, etc.
Good luck!
research.jhu.edu/rdt/funding-...
For each of the 187 fellowships, you will find a short description, deadline, $ amount, link, etc.
Good luck!
August 8, 2025 at 10:59 AM
The updated version of the database of PhD fellowships produced and maintained by my team can be downloaded by anyone here:
research.jhu.edu/rdt/funding-...
For each of the 187 fellowships, you will find a short description, deadline, $ amount, link, etc.
Good luck!
research.jhu.edu/rdt/funding-...
For each of the 187 fellowships, you will find a short description, deadline, $ amount, link, etc.
Good luck!
Tal does great work! Check his group out.
We are hiring a postdoc - come work with us (www.koremlab.science) at the intersection of #microbiome, data science, and women's health!
Message or email me if interested. 🖥️ 🧬
Message or email me if interested. 🖥️ 🧬
Korem Lab - Microbiome Systems Biology @ Columbia | New York, USA
We apply systems biology approaches to decipher the metabolic interactions between the microbiome and its human host in diverse clinical settings, aiming towards personalized microbiome-based therapeu...
www.koremlab.science
August 8, 2025 at 2:32 PM
Tal does great work! Check his group out.
Reposted by Patrick Rynkiewicz
Have you explored the NMDC Field Notes mobile app yet? Check out our new tutorial video for a quick walkthrough! buff.ly/Dohg4gH 🧪
August 7, 2025 at 8:21 PM
Have you explored the NMDC Field Notes mobile app yet? Check out our new tutorial video for a quick walkthrough! buff.ly/Dohg4gH 🧪