Mike Schatz
@mikeschatz.bsky.social
Bloomberg Distinguished Professor at Johns Hopkins University. http://schatz-lab.org
Pinned
Mike Schatz
@mikeschatz.bsky.social
· Jun 2
Today (June 1) marks the 20th anniversary of Galaxy! Thanks to all the developers, admins, researchers, trainers, educators, students and more that have made up this amazing community. Here is to the next 20 years! @galaxyproject.bsky.social @jxtxfoundation.bsky.social galaxyproject.org
November 6, 2025 at 12:39 AM
Reposted by Mike Schatz
Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory.
List of talks and posters: meetings.cshl.edu/abstracts.as...
List of talks and posters: meetings.cshl.edu/abstracts.as...
November 6, 2025 at 12:38 AM
Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory.
List of talks and posters: meetings.cshl.edu/abstracts.as...
List of talks and posters: meetings.cshl.edu/abstracts.as...
Reposted by Mike Schatz
On the last day of #ASHG25, attending a telomere session entitled "end results" seems fitting. It's been a great meeting talking with vibrant young geneticists, and on this note, I'm hiring a postdoc! thejacksonlaboratory.wd503.myworkdayjobs.com/External_JAX...
Postdoctoral Associate
The Beck Lab is seeking an enthusiastic, independent, and highly motivated postdoctoral fellow to join our innovative research group at the Jackson Laboratory for Genomic Medicine and University of Co...
thejacksonlaboratory.wd503.myworkdayjobs.com
October 18, 2025 at 2:45 PM
On the last day of #ASHG25, attending a telomere session entitled "end results" seems fitting. It's been a great meeting talking with vibrant young geneticists, and on this note, I'm hiring a postdoc! thejacksonlaboratory.wd503.myworkdayjobs.com/External_JAX...
Reposted by Mike Schatz
🚨Don't miss the GREGoR Consortium's Ancillary Session at #ASHG25 on Thursday at 11:45 am.
Featuring: Dr. Ben Heavner, Dr. Alex Wagner (@alexphd.bsky.social) & Dr. Mike Schatz (@mikeschatz.bsky.social)
#RareDisease #Research
Featuring: Dr. Ben Heavner, Dr. Alex Wagner (@alexphd.bsky.social) & Dr. Mike Schatz (@mikeschatz.bsky.social)
#RareDisease #Research
October 16, 2025 at 1:45 PM
🚨Don't miss the GREGoR Consortium's Ancillary Session at #ASHG25 on Thursday at 11:45 am.
Featuring: Dr. Ben Heavner, Dr. Alex Wagner (@alexphd.bsky.social) & Dr. Mike Schatz (@mikeschatz.bsky.social)
#RareDisease #Research
Featuring: Dr. Ben Heavner, Dr. Alex Wagner (@alexphd.bsky.social) & Dr. Mike Schatz (@mikeschatz.bsky.social)
#RareDisease #Research
Getting excited for #ASHG25. The must see talk is tomorrow at 1:30 by Qiuhui (Iris) Li presenting the first large-scale integration of long-read genome sequencing with electronic health record data across >1000 All of Us participants meetings.ashg.org/event/ASHG25...
PheedLoop
PheedLoop: Hybrid, In-Person & Virtual Event Software
meetings.ashg.org
October 14, 2025 at 5:40 PM
Getting excited for #ASHG25. The must see talk is tomorrow at 1:30 by Qiuhui (Iris) Li presenting the first large-scale integration of long-read genome sequencing with electronic health record data across >1000 All of Us participants meetings.ashg.org/event/ASHG25...
Reposted by Mike Schatz
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
docs.google.com
October 8, 2025 at 4:03 PM
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
After vibe coding a little swift this summer, I feel totally validated by this post! holdtherobot.com/blog/xcode-i...
Xcode is the Worst Piece of Professional Software I Have Ever Used | Hold The Robot
The compiler is unable to type-check this expression in reasonable time; try breaking up the expression into distinct sub-expressions
holdtherobot.com
September 23, 2025 at 12:56 AM
After vibe coding a little swift this summer, I feel totally validated by this post! holdtherobot.com/blog/xcode-i...
This is amazing
Zstandard's --long range mode works wonders for assemblies, but needs uninterrupted single line sequences.
*AllTheBacteria 661k, multiline fasta*
gzip (pigz): 751GB
zstandard --long: 641GB (30% original size)
*Single line fasta*
gzip (pigz): 700GB
zstandard --long: 232GB (10% original size)
*AllTheBacteria 661k, multiline fasta*
gzip (pigz): 751GB
zstandard --long: 641GB (30% original size)
*Single line fasta*
gzip (pigz): 700GB
zstandard --long: 232GB (10% original size)
September 15, 2025 at 3:54 PM
This is amazing
Reposted by Mike Schatz
after a long effort, gathering a lot of input from many people, we finaly put it all together:
Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)
https://www.preprints.org/manuscript/202509.0823
Thank you very much to all people involved !
Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)
https://www.preprints.org/manuscript/202509.0823
Thank you very much to all people involved !
September 10, 2025 at 10:22 AM
after a long effort, gathering a lot of input from many people, we finaly put it all together:
Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)
https://www.preprints.org/manuscript/202509.0823
Thank you very much to all people involved !
Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)
https://www.preprints.org/manuscript/202509.0823
Thank you very much to all people involved !
Reposted by Mike Schatz
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Phishing site : minimap2.com · Issue #1316 · lh3/minimap2
Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...
github.com
September 9, 2025 at 3:40 PM
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Reposted by Mike Schatz
🎉 Big news! Galaxy Training Network workflows are now automatically registered on WorkflowHub.
Easier discovery, citation, & direct Galaxy execution → boosting FAIR & accessible training!
training.galaxyproject.org/training-mat...
Easier discovery, citation, & direct Galaxy execution → boosting FAIR & accessible training!
training.galaxyproject.org/training-mat...
GTN is now integrated with WorkflowHub
Thanks to a collaborative effort between the teams at Galaxy Training Network (GTN), WorkflowHub, and Australian BioCommons, GTN workflows are now registered automatically with WorkflowHub. The existi...
training.galaxyproject.org
September 8, 2025 at 4:32 PM
🎉 Big news! Galaxy Training Network workflows are now automatically registered on WorkflowHub.
Easier discovery, citation, & direct Galaxy execution → boosting FAIR & accessible training!
training.galaxyproject.org/training-mat...
Easier discovery, citation, & direct Galaxy execution → boosting FAIR & accessible training!
training.galaxyproject.org/training-mat...
Reposted by Mike Schatz
Please repost!
We have an open rank, tenure-line faculty position in biomechanics in the School of Kinesiology at the University of Michigan Ann Arbor. At U-M we have great colleagues, exceptional resources, and biomechanics can be found all across the campus. #BiomechSky
We have an open rank, tenure-line faculty position in biomechanics in the School of Kinesiology at the University of Michigan Ann Arbor. At U-M we have great colleagues, exceptional resources, and biomechanics can be found all across the campus. #BiomechSky
Tenure-track Faculty Position in Biomechanics (Open Rank), University of Michigan, Ann Arbor, MI, USA -
Biomch-L
The School of Kinesiology (http://kines.umich.edu) at the University of Michigan invites applications and nominations for a tenure-track faculty position at the level of Assistant Professor, Associate...
biomch-l.isbweb.org
August 28, 2025 at 9:44 PM
Please repost!
We have an open rank, tenure-line faculty position in biomechanics in the School of Kinesiology at the University of Michigan Ann Arbor. At U-M we have great colleagues, exceptional resources, and biomechanics can be found all across the campus. #BiomechSky
We have an open rank, tenure-line faculty position in biomechanics in the School of Kinesiology at the University of Michigan Ann Arbor. At U-M we have great colleagues, exceptional resources, and biomechanics can be found all across the campus. #BiomechSky
Scholarships available for Genome Informatics - just include a brief summary on your open science work plus your conference abstract. If you have already paid to register, we will work with CSHL to refund you the $$$. Apply today! jxtxfoundation.org/news/2025-6-... @jxtxfoundation.bsky.social
JXTX + CSHL 2025 Genome Informatics Scholarship
JXTX + CSHL 2025 Genome Informatics Scholarships
jxtxfoundation.org
August 26, 2025 at 11:21 PM
Scholarships available for Genome Informatics - just include a brief summary on your open science work plus your conference abstract. If you have already paid to register, we will work with CSHL to refund you the $$$. Apply today! jxtxfoundation.org/news/2025-6-... @jxtxfoundation.bsky.social
Reposted by Mike Schatz
📢🚨📢🚨 Genome Informatics deadline extended to September 8! meetings.cshl.edu/meetings.asp....
Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!
Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!
Genome Informatics
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
August 26, 2025 at 8:38 PM
📢🚨📢🚨 Genome Informatics deadline extended to September 8! meetings.cshl.edu/meetings.asp....
Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!
Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!
Genome Informatics abstract deadline now Sept 8! h/t @benlangmead.bsky.social meetings.cshl.edu/meetings.asp...
Genome Informatics
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
August 26, 2025 at 5:44 PM
Genome Informatics abstract deadline now Sept 8! h/t @benlangmead.bsky.social meetings.cshl.edu/meetings.asp...
Reposted by Mike Schatz
Johns Hopkins researchers including @mikeschatz.bsky.social & @vikramshivakumar.bsky.social have developed Uncalled4, a new software toolkit that can detect epigenetic changes—chemical modifications to normal DNA and RNA that control which genes are turned off and on—with unprecedented accuracy.
Researchers build a smarter tool for reading genetic code
The Hopkins team’s new, open-source software dramatically improves scientists’ ability to detect genetic modifications that control gene activity.
www.cs.jhu.edu
August 22, 2025 at 1:44 PM
Johns Hopkins researchers including @mikeschatz.bsky.social & @vikramshivakumar.bsky.social have developed Uncalled4, a new software toolkit that can detect epigenetic changes—chemical modifications to normal DNA and RNA that control which genes are turned off and on—with unprecedented accuracy.
Reposted by Mike Schatz
🎉 Galaxy has passed 21,000 citations on Google Scholar!
A huge thank you to the global community of researchers who use and advance Galaxy for open, reproducible science.
A huge thank you to the global community of researchers who use and advance Galaxy for open, reproducible science.
August 18, 2025 at 5:23 PM
🎉 Galaxy has passed 21,000 citations on Google Scholar!
A huge thank you to the global community of researchers who use and advance Galaxy for open, reproducible science.
A huge thank you to the global community of researchers who use and advance Galaxy for open, reproducible science.
Reposted by Mike Schatz
Missed GBCC2025? Want to rewatch your favorite talks?
All session recordings (including Galaxy Live!) are now available on our YouTube channel. Revisit the presentations, explore new tools and workflows, and catch up on sessions you may have missed.
Watch here: youtube.com/playlist?lis...
All session recordings (including Galaxy Live!) are now available on our YouTube channel. Revisit the presentations, explore new tools and workflows, and catch up on sessions you may have missed.
Watch here: youtube.com/playlist?lis...
Galaxy and Bioconductor Community Conference 2025 - YouTube
Cold Spring Harbor Laboratory, New York June 23–26, 2025
youtube.com
August 6, 2025 at 3:49 PM
Missed GBCC2025? Want to rewatch your favorite talks?
All session recordings (including Galaxy Live!) are now available on our YouTube channel. Revisit the presentations, explore new tools and workflows, and catch up on sessions you may have missed.
Watch here: youtube.com/playlist?lis...
All session recordings (including Galaxy Live!) are now available on our YouTube channel. Revisit the presentations, explore new tools and workflows, and catch up on sessions you may have missed.
Watch here: youtube.com/playlist?lis...
Just failed a CAPTCHA challenge to join a MS Teams call, but I cant decide if this is a feature or a bug
August 6, 2025 at 8:58 PM
Just failed a CAPTCHA challenge to join a MS Teams call, but I cant decide if this is a feature or a bug
Congratulations @benlangmead.bsky.social!
Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬
July 22, 2025 at 7:17 PM
Congratulations @benlangmead.bsky.social!
Reposted by Mike Schatz
Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬
July 22, 2025 at 6:52 PM
Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬
Reposted by Mike Schatz
Reposted by Mike Schatz
ggplot2 4.0.0 is coming soon, and is moving some of the internals from S3 to the new S7 OOP system. This is worth a read if you're developing packages with ggplot2 (bioconductor or otherwise) blog.bioconductor.org/posts/2025-0... #Rstats
Bioconductor and ggplot2 4.0.0: What’s Changing and How to Prepare – Bioconductor community blog
Preparing for the upcoming update - key changes, potential breakages, and what developers and users can do
blog.bioconductor.org
July 7, 2025 at 3:31 PM
ggplot2 4.0.0 is coming soon, and is moving some of the internals from S3 to the new S7 OOP system. This is worth a read if you're developing packages with ggplot2 (bioconductor or otherwise) blog.bioconductor.org/posts/2025-0... #Rstats