Lisa Karstens
@lisakarstens.bsky.social
Microbiome bioinformatics researcher. Open data enthusiast. R and python user; Associate Professor in Medical Informatics at OHSU.
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
cassyni.com/s/mvif-glomi...
1/3
August 22, 2025 at 11:42 AM
Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social and #MVIF is OUT:
cassyni.com/s/mvif-glomi...
1/3
cassyni.com/s/mvif-glomi...
1/3
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
#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
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
#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
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
@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
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
@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
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
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
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
& 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
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
& 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
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
...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...
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
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...
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...
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
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🧪
Reposted by Lisa Karstens
January 13, 2025 at 10:23 AM
Reposted by Lisa Karstens
Today's #Microbiome digest
microbiomedigest.com/2024/12/09/d...
@elisabethbik.bsky.social
#MicrobiomeSky 🦠
microbiomedigest.com/2024/12/09/d...
@elisabethbik.bsky.social
#MicrobiomeSky 🦠
December 10, 2024
General microbiome [COMMENT]The role of pharmacomicrobiomics in HIV prevention, treatment, and women’s health – Swanson, Basting & Klatt Early life Characterization of the Gut and Skin Mi…
microbiomedigest.com
December 10, 2024 at 6:59 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
⭐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
Tomorrow Atlantic replay with live Q&A!
Reposted by Lisa Karstens
There's still time to register!
cassyni.com/s/mvif-34
cassyni.com/s/mvif-34
November 29, 2024 at 9:40 AM
There's still time to register!
cassyni.com/s/mvif-34
cassyni.com/s/mvif-34
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...
⭐️ 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
#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...
⭐️ 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...
📣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
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
📣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
More info: bit.ly/ohsu-informatics-interns
What: PAID internships with research in data science & informatics
Where: Oregon Health & Science University, Portland, OR USA
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
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
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
Join our informational webinar about the OHSU summer internship program *tomorrow* Jan 9th at 1 PM PT.
Info & Registration: bit.ly/DMICE_Internships
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 ✨
🎁 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
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 ✨
🎁 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 ✨
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/...
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
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/...
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/...
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...
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
⭐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...
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...
Reposted by Lisa Karstens
📢 Remember that you can submit your work for:
🌎Atlantic-first event in January w/ Jennifer Wargo
🌏Pacific-first event in February w/ Laura S. Weyrich
www.microbiome-vif.org/en-US/-/info...
🌎Atlantic-first event in January w/ Jennifer Wargo
🌏Pacific-first event in February w/ Laura S. Weyrich
www.microbiome-vif.org/en-US/-/info...
December 19, 2023 at 4:25 AM
📢 Remember that you can submit your work for:
🌎Atlantic-first event in January w/ Jennifer Wargo
🌏Pacific-first event in February w/ Laura S. Weyrich
www.microbiome-vif.org/en-US/-/info...
🌎Atlantic-first event in January w/ Jennifer Wargo
🌏Pacific-first event in February w/ Laura S. Weyrich
www.microbiome-vif.org/en-US/-/info...
Reposted by Lisa Karstens
Third talk for today at #MVIF.24
⭐️Analyzing microbial evolution through gene and genome phylogenies by 🇺🇸 Sarah Teichman
www.biorxiv.org/content/10.1...
⭐️Analyzing microbial evolution through gene and genome phylogenies by 🇺🇸 Sarah Teichman
www.biorxiv.org/content/10.1...
December 19, 2023 at 2:39 AM
Third talk for today at #MVIF.24
⭐️Analyzing microbial evolution through gene and genome phylogenies by 🇺🇸 Sarah Teichman
www.biorxiv.org/content/10.1...
⭐️Analyzing microbial evolution through gene and genome phylogenies by 🇺🇸 Sarah Teichman
www.biorxiv.org/content/10.1...
Reposted by Lisa Karstens
Second selected talk at #MVIF.24
⭐️ Wastewater sequencing reveals community and variant dynamics of the collective human virome by
🇺🇸 Mike Tisza
www.nature.com/articles/s41...
⭐️ Wastewater sequencing reveals community and variant dynamics of the collective human virome by
🇺🇸 Mike Tisza
www.nature.com/articles/s41...
December 19, 2023 at 2:28 AM
Second selected talk at #MVIF.24
⭐️ Wastewater sequencing reveals community and variant dynamics of the collective human virome by
🇺🇸 Mike Tisza
www.nature.com/articles/s41...
⭐️ Wastewater sequencing reveals community and variant dynamics of the collective human virome by
🇺🇸 Mike Tisza
www.nature.com/articles/s41...
Reposted by Lisa Karstens
NEXT, #MVIF short talks:
⭐️ Gut microbiota manipulation in neurodevelopmental disorders: implication from animal models of infantile epilepsy
by 🇨🇦 Chunlong Mu
Read his research at:
www.thelancet.com/journals/ebi...
⭐️ Gut microbiota manipulation in neurodevelopmental disorders: implication from animal models of infantile epilepsy
by 🇨🇦 Chunlong Mu
Read his research at:
www.thelancet.com/journals/ebi...
December 19, 2023 at 2:17 AM
NEXT, #MVIF short talks:
⭐️ Gut microbiota manipulation in neurodevelopmental disorders: implication from animal models of infantile epilepsy
by 🇨🇦 Chunlong Mu
Read his research at:
www.thelancet.com/journals/ebi...
⭐️ Gut microbiota manipulation in neurodevelopmental disorders: implication from animal models of infantile epilepsy
by 🇨🇦 Chunlong Mu
Read his research at:
www.thelancet.com/journals/ebi...
Reposted by Lisa Karstens
Our lineup of #MVIF speakers for today's dive into #microbiome science 🤩
⭐️ Keynote:
🇺🇸 @gilbertjacka
⭐️ Short talks:
🇨🇦@ChunlongMu1
🇺🇸@MikeTisza
🇺🇸@sarah_teichman
🇺🇸@GerrickElias
And thanks to our partners 🧬@Roche and 🔬@QIAGEN for supporting #MVIF!
⭐️ Keynote:
🇺🇸 @gilbertjacka
⭐️ Short talks:
🇨🇦@ChunlongMu1
🇺🇸@MikeTisza
🇺🇸@sarah_teichman
🇺🇸@GerrickElias
And thanks to our partners 🧬@Roche and 🔬@QIAGEN for supporting #MVIF!
December 19, 2023 at 1:03 AM
Our lineup of #MVIF speakers for today's dive into #microbiome science 🤩
⭐️ Keynote:
🇺🇸 @gilbertjacka
⭐️ Short talks:
🇨🇦@ChunlongMu1
🇺🇸@MikeTisza
🇺🇸@sarah_teichman
🇺🇸@GerrickElias
And thanks to our partners 🧬@Roche and 🔬@QIAGEN for supporting #MVIF!
⭐️ Keynote:
🇺🇸 @gilbertjacka
⭐️ Short talks:
🇨🇦@ChunlongMu1
🇺🇸@MikeTisza
🇺🇸@sarah_teichman
🇺🇸@GerrickElias
And thanks to our partners 🧬@Roche and 🔬@QIAGEN for supporting #MVIF!
Excited to share @katebowie.bsky.social's first first-author preprint.
This work investigated the urinary microbiome in a large observation cohort of older men and identified several interesting associations with BPH, age, BMI, and lower urinary tract symptoms.
www.biorxiv.org/content/10.1...
This work investigated the urinary microbiome in a large observation cohort of older men and identified several interesting associations with BPH, age, BMI, and lower urinary tract symptoms.
www.biorxiv.org/content/10.1...
December 16, 2023 at 1:51 AM
Excited to share @katebowie.bsky.social's first first-author preprint.
This work investigated the urinary microbiome in a large observation cohort of older men and identified several interesting associations with BPH, age, BMI, and lower urinary tract symptoms.
www.biorxiv.org/content/10.1...
This work investigated the urinary microbiome in a large observation cohort of older men and identified several interesting associations with BPH, age, BMI, and lower urinary tract symptoms.
www.biorxiv.org/content/10.1...
Had a great time presenting my group's microbiome / urobiome work today at the CAIRIBU Uromicrobiota Research Interest Group (U-RIG).
U-RIG is a monthly series for knowledge exchange and collaborations in urobiome and adjacent fields. More info/to sign up: cairibu.urology.wisc.edu
U-RIG is a monthly series for knowledge exchange and collaborations in urobiome and adjacent fields. More info/to sign up: cairibu.urology.wisc.edu
December 16, 2023 at 1:46 AM
Had a great time presenting my group's microbiome / urobiome work today at the CAIRIBU Uromicrobiota Research Interest Group (U-RIG).
U-RIG is a monthly series for knowledge exchange and collaborations in urobiome and adjacent fields. More info/to sign up: cairibu.urology.wisc.edu
U-RIG is a monthly series for knowledge exchange and collaborations in urobiome and adjacent fields. More info/to sign up: cairibu.urology.wisc.edu