Workshops and Meetings

Next Workshop: April 18-25, 2026

Course principles: BioInformatics Workshop for Xenopus Researchers:

I am pleased to announce that the NXR Bioinformatics workshop will be held next year, from April 18, 2026 (Sat) to April 25, 2026 (Sat). The tentative schedule for the workshop can be downloaded below.

This time, we have changed the workshop format to a wet-dry-hybrid exercise, specifically emphasizing single-cell analysis. Many Xenopus researchers are working on single-cell data these days, but it seems that we are a bit behind other model organisms (based on the number of data and papers published recently). By working together for two days on tissue dissociation and cell quality checks, participants may get an idea of how to apply this approach in their own experiments (if you already have experience, it is also a good opportunity to share it with colleagues). Basic topics in bioinformatics, such as environment setup and RNA-seq/ChIP-seq/Proteomics analysis, will also be covered briefly.

This year, in addition to crews in the 2023 workshop, John Young at Simmons University and Wil Ratzan at Harvard Medical School will join for this special event, together with several crews from the NXR and Xenbase.

If you are curious about single-cell analysis (and other bioinformatics skills), come to Woods Hole next Spring. The registration will be available shortly.

Instructors:

Taejoon Kwon (UNIST, Korea), John Young (Simmons), ChangHee Lee (HMS), Wil Ratzan (HMS), Malcolm Fisher (Xenbase/CCHMC), Konrad Thorner (Xenbase/CCHMC) & staffs from the NXR and Xenbase.

Workshop Costs:

TBA

Schedule:

Please click here to view 2026 BioInformatics Workshop Schedule.

Registration:

Coming soon. 

For additional information, please contact:

Marko Horb, Ph.D.
Director, National Xenopus Resource (NXR)
Associate Scientist, Bell Center for Regenerative Biology and Tissue Engineering
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA 02543
Email: mhorb@mbl.edu
Office: (508) 289-7627
Lab: (508) 289-7370

Feedback from the Community

“One of our post-docs attended the 2013 Bioinformatics workshop, and the training in RNA-seq analysis and general bioinformatics approaches he learned have been crucial for our research on Xenopus tropicalis embryo development. We are now pursuing several high-throughput sequencing projects–including RNA-seq and ChIP-seq–in early Xenopus embryos, and the design of these experiments and analysis of sequencing reads would not have been possible without the specialized knowledge he gained from the Bioinformatics workshop.”

“Great! I have sent one student to the bioinformatics course and he loved the course and came back and was immediately able to help many folks in the lab with bioinformatic issues.”

“I have sent three lab members to the Bioinformatics workshop. These lab members have learned the basic skills of genomic work and now routinely perform RNA-seq and ChIP-seq analyses.”

Next Workshop: TBD

Topics covered:

• Theoretical and practical aspects of CRISPR/Cas9 and TALENs
• Methods for genotyping (DSP, HRMA, T7E1, and others)
• Maximizing target site choice and sgRNA design
• Applications for the maternal host transfer technique combined with genome editing
• Gene targeting and homology-directed repair
• Circumventing lethal phenotypes
• Xenopus genetics and husbandry issues arising in the creation of mutant lines
• Both laevis and tropicalis will be used

The goal is for you to practice the techniques using known sgRNAs and TALENs and then use your own. Ideally, you will become competent in the techniques and implement them in your own lab. In addition for those who have limited experience in tropicalis, this is a perfect time to get comfortable with them.

Next Workshop:  TBA

Check out this article about Gary McDowell’s experience in last year’s course:
More than Just Meetings- Xenopus, Advanced Imaging Workshop

The following instructors will be returning to teach this exciting workshop once again:

• John Wallingford, University of Texas, Austin
• Lance Davidson, University of Pittsburgh
• Laura Anne Lowery, Boston College
• Jakub Sedzinski, Danish Stem Cell Institute, Copenhagen
• Scott Fraser, University of Southern California      

Topics to be covered in this imaging workshop include:

• A primer on microscopes and optics with a focus on practical considerations.
• Imaging immunostained Xenopus embryos in whole-mount.
• Live imaging of cells and tissues in intact Xenopus using fluorescent fusion proteins.
• Live imaging of cells and tissues in explants.
• Computational post-processing of images for presentation/display.
• Development of custom imaging assays for students.

Participation will be limited to 15 students. The course will be team taught by experts in Xenopus and imaging. If you have any questions, please email Xenopus@mbl.edu.