Lisa Karstens
lisakarstens.bsky.social
Lisa Karstens
@lisakarstens.bsky.social
Microbiome bioinformatics researcher. Open data enthusiast. R and python user; Associate Professor in Medical Informatics at OHSU.
Pinned
Applications are due 1/30/26 for the Human Microbiome Data Discovery 2-week course at OHSU!

If you're a #postdoc, junior #faculty or and advanced graduate student looking to increase your #data_science skills in #microbiome science, check it out!
Reposted by Lisa Karstens
#MVIF 46 is live!

⭐️ Highlights:
🇺🇸 Rebecca L. Knoll
🇯🇵 Akito Sakanaka

⭐️ Keynote:
🇺🇸 Simon Roux @simrouxvirus.bsky.social

⭐️ Talks:
🇦🇺 Jeremy Barr @jeremyjbarr.bsky.social
🇨🇦 Erik Bakkeren @erikbakkeren.bsky.social
🇨🇳 Guanxiang Liang

📜Full abstracts: cassyni.com/s/mvif-46
February 10, 2026 at 12:50 AM
Applications close this Friday (1/30) at 5 PM PST!
Applications are due 1/30/26 for the Human Microbiome Data Discovery 2-week course at OHSU!

If you're a #postdoc, junior #faculty or and advanced graduate student looking to increase your #data_science skills in #microbiome science, check it out!
January 27, 2026 at 2:11 AM
Reposted by Lisa Karstens
It's Friday!
...and a new #MVIF program is out! 🤩

Free registration: cassyni.com/s/mvif-46

Highlights:
🇺🇸 Rebecca L. Knoll
🇯🇵 Akito Sakanaka

Keynote:
🇺🇸 @simrouxvirus.bsky.social

⭐️ Talks:
🇦🇺 @jeremyjbarr.bsky.social
🇨🇦 @erikbakkeren.bsky.social
🇨🇳 Guanxiang Liang
January 23, 2026 at 11:53 AM
Applications are due 1/30/26 for the Human Microbiome Data Discovery 2-week course at OHSU!

If you're a #postdoc, junior #faculty or and advanced graduate student looking to increase your #data_science skills in #microbiome science, check it out!
January 21, 2026 at 4:31 PM
Reposted by Lisa Karstens
📢 JOB OPPORTUNITY We are hiring a Research Technologist (Advanced Professional) to design, implement, support, analyze, and report on rigorous research in genetics, entomology, and host-microbe interactions. Please consider and share with others in need.

psu.wd1.myworkdayjobs.com/PSU_Staff/jo...
Research Technologist - Life Sciences Advance Professional - Bordenstein Lab
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
January 17, 2026 at 11:01 PM
Applications for this #microbiome #datascience short course are due next week!

If you're in biomedical research, interested in building data science skills to study the microbiome and reusing publicly available data, this course is for you!
Applications are open for the Human Microbiome Data Discovery short course!

This is a 2-week course for postdocs and junior faculty to learn #datascience skills in #microbiome science.

Offered May 4 - 15, 2026 in Portland, OR at OHSU

Learn more at bit.ly/microbiome-data-course
Human Microbiome Data Discovery Short Course | OHSU
The Knight Cancer Institute Human Microbiome Data Discovery is a two-week training program designed for early-career researchers.
bit.ly
January 15, 2026 at 1:34 AM
Applications are open for the Human Microbiome Data Discovery short course!

This is a 2-week course for postdocs and junior faculty to learn #datascience skills in #microbiome science.

Offered May 4 - 15, 2026 in Portland, OR at OHSU

Learn more at bit.ly/microbiome-data-course
Human Microbiome Data Discovery Short Course | OHSU
The Knight Cancer Institute Human Microbiome Data Discovery is a two-week training program designed for early-career researchers.
bit.ly
December 24, 2025 at 2:46 PM
Reposted by Lisa Karstens
Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social ‬and #MVIF is OUT:
cassyni.com/s/mvif-glomi...

1/3
August 22, 2025 at 11:42 AM
Reposted by Lisa Karstens
Get Ready!

#MVIF 38 on Microbiome and Citizen Science
is live n the Pacific time zones 🌏 in less than an hour!⏰

You can still register : cassyni.com/s/mvif-38
Cassyni | Science starts with a seminar
Seamlessly organise, run and publish academic research seminars. Get started in minutes.
cassyni.com
April 15, 2025 at 12:24 AM
Reposted by Lisa Karstens
Don't miss today's #MVIF 38: A special event on on #citizenscience & #microbiome!

@patrickveiga.bsky.social @gilbertjacka.bsky.social
@waldispuhl.bsky.social Mathieu Almeida, Claudia Cappello, Daniel McDonald Mikayla Borton & Sarah Ahannach.

There's still time to register👉 cassyni.com/s/mvif-38
April 14, 2025 at 3:41 PM
Reposted by Lisa Karstens
Karstens Lab @lisakarstens.bsky.social summary of resources to identify and remove contaminated microbial DNA from seq-based microbiome studies here: github.com/KarstensLab/.... Learned this today at Urobiome 2025 @scrippsocean.bsky.social @ucsdmedschool.bsky.social
GitHub - KarstensLab/microbiome_cleaning: Summary of resources for identifying and removing contaminant microbial DNA from sequence-based microbiome studies. Includes examples of studies that have tr...
Summary of resources for identifying and removing contaminant microbial DNA from sequence-based microbiome studies. Includes examples of studies that have transparently reported their approach. ...
github.com
February 24, 2025 at 11:34 PM
Reposted by Lisa Karstens
Today/tomorrow Pacific LIVE
& on Wednesday Atlantic REPLAY!

Just register here cassyni.com/s/mvif-36

We can't wait to welcome YOU & #MVIF 36 speakers:
🇯🇵 Nodoka Chiba
🇮🇩 Patsy Tasyana Fitri
🇨🇳 Ruixin Liu
🇦🇺 @aroneys.bsky.social
🇬🇧 Maria Kardakova
🇳🇿 @theoportlock.bsky.social

#openscience #microbiomesky
Cassyni | Science starts with a seminar
Seamlessly organise, run and publish academic research seminars. Get started in minutes.
cassyni.com
February 17, 2025 at 11:26 AM
The Pacific replay for #MVIF is today at 4:30 PM PT.

There's still time to register!
It's a new year!
...and a new #MVIF program is out! 🤩

Registration here: cassyni.com/s/mvif-35

⭐️MicroTalks:
Minna Chang
@hariszaf.bsky.social

⭐️ Keynote:
@chmoei.bsky.social

⭐️Selected talks:
Pratyay Sengupta
@fatimacpereira.bsky.social
@cladigar.bsky.social
January 22, 2025 at 7:57 PM
Know #undergrads in Portland interested in summer research?

Let them know about the research opportunity fair @portlandstate Fri Jan 17th 1-3 PM.

I'll be there with @billhersh.bsky.social to chat about our #biomedical #informatics #datascience summer internship!

www.pdx.edu/events/under...
Undergraduate Research Opportunity Fair | Portland State University
www.pdx.edu
January 17, 2025 at 3:51 AM
Reposted by Lisa Karstens
Please join us in celebrating NMDC Champion Lisa Karstens’ recent NIH R25 award! The grant will support a 3-year project to develop teaching materials for early career researchers to gain essential skills in microbiome data science🧪
January 16, 2025 at 6:46 PM
Reposted by Lisa Karstens
January 13, 2025 at 10:23 AM
Reposted by Lisa Karstens
Tomorrow Atlantic replay with live Q&A!
#MVIF 34 program👇

⭐Microtalks
🇹🇼 Ha T. Doan
🇦🇺 Vedanth Ramji from bigdatabiology.bsky.social

⭐Keynote
🇺🇸 Sean Gibbons @gibbological.bsky.social

⭐Selected Talks
🇯🇵 Yuya Kiguchi
🇦🇺 Kurtis Budden
🇨🇭 Amit Halkhoree

Free registration: cassyni.com/s/mvif-34
December 4, 2024 at 10:30 AM
Reposted by Lisa Karstens
There's still time to register!
cassyni.com/s/mvif-34
November 29, 2024 at 9:40 AM
Reposted by Lisa Karstens
#MVIF 26 program is out! 🤩

⭐️ Keynote:
🇺🇸 Laura S. Weyrich

⭐️ Short talks:
🇨🇳 Ziye Wang
🇺🇸Kate Bowie
🇺🇸Richard Wolff
🇺🇸Ivan Zheludev

More about talks here: www.microbiome-vif.org/en-US/-/futu...
February 8, 2024 at 9:45 AM
📣Apps for the 2024 Undergraduate Biomedical Informatics and Data Science Summer Internship are due Feb 16th!

More info: bit.ly/ohsu-informatics-interns

What: PAID internships with research in data science & informatics

Where: Oregon Health & Science University, Portland, OR USA
February 5, 2024 at 7:33 PM
Are you an undergrad or know an undergrad interested in an internship in biomedical informatics / data science?

Join our informational webinar about the OHSU summer internship program *tomorrow* Jan 9th at 1 PM PT.

Info & Registration: bit.ly/DMICE_Internships
January 8, 2024 at 4:58 PM
Reposted by Lisa Karstens
We have an early New Year present for you
🎁 the January #MVIF program with
Jennifer Wargo
Nikolay Oskolkov
Sondra Turjeman
Mireia Valles-Colomer

Full program with abstracts: www.microbiome-vif.org/en-US/-/futu...

Registration: hopin.com/events/micro...

✨Happy holidays ✨
December 21, 2023 at 12:26 PM
Exciting!

My group's paper, microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data, was highlighted as an @ASMicrobiology Top Cited paper!

Congrats @erictleung.bsky.social @katebowie.bsky.social Emory neer and Erin Dahl!

📔 journals.asm.org/doi/10.1128/...
December 20, 2023 at 3:41 PM
Reposted by Lisa Karstens
⭐That's a wrap! So many inspiring talks!

A huge thanks to all of our speakers and attendees for making the meeting so enjoyable🦠!

And for those who missed it, you can check out the recordings later here ▶️ www.youtube.com/channel/UCJ3...
December 19, 2023 at 4:23 AM