Medhat Mahmoud

YouTube video by Stowers Institute for Medical Research How Stowers Scientists Found the DNA Site Where Robertsonian Chromosomes Fuse

🚂 The T2T train keeps rolling: "The formation and propagation of human Robertsonian chromosomes" with Gerton and Garrison labs is out! What's a Robertsonian chromosome? Let Jen tell you herself in this great video, or read our paper: [1/3]
📺 youtu.be/JmlY5omxQVc
📄 www.nature.com/articles/s41...

5/ Big thanks to @sedlazeck.bsky.social and Daniel Agustinho for their support and insight on this work!

Would love to hear your thoughts, feedback, or what tools you are using in your long-read work. 👇

#Genomics #Bioinformatics #PacBio #Nanopore #VariantCalling #GenomeAssembly #T2T #Epigenetics

4/ We also dig into:

⚠️ Key challenges still facing the field
🔬 Areas where accuracy or scalability can improve
🚀 Where we think long-read tech is heading next

3/ In this review, we cover:

🧩 Reference-based + de novo assembly workflows
🧬 Structural + small variant calling
🧠 Epigenetic insights (methylation, etc.)
🛠️ Bioinformatics tools and pipelines that power it all

2/ Over the past decade, long-read sequencing (e.g., ONT, PacBio) has reshaped how we explore the genome, enabling breakthroughs like:

✅ Telomere-to-telomere assembly
✅ Structural variant discovery
✅ Epigenetic profiling
✅ Complex repeat resolution

1/ 🧬 A Hitchhiker’s Guide to Long-Read Genomic Analysis is out now!

This mini-review walks through the latest advances in long-read DNA sequencing — from assemblies to variant calling to epigenetics.

Link 🔗 genome.cshlp.org/content/35/4...
🧵👇

Transcriptomics in the era of long-read sequencing - Nature Reviews Genetics Advances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read RNA sequencing, including expe...

Transcriptomics in the era of long-read sequencing. #RNAseq #LongReads #Bioinformatics @naturerevgenet.bsky.social 🧬🖥️
www.nature.com/articles/s41...

@sedlazeck.bsky.social AMPath24 talk about long reads highlighting TRGT tool by @egor-dolzhenko.bsky.social and @guilhermesena1.bsky.social and others for HiFi sequencing by @pacbio.bsky.social

Good read about how the NIH functions. After 2 years as a new investigator I only now feel like I am starting to understand the process. This is one of the challenges for new investigators: why is the learning curve so steep?

Thank you!!

I created a long-read sequencing starter pack. I'm still finding people on here, so apologies if I missed you. Please suggest people who should be added and I'll add them! go.bsky.app/JGkefsJ

New method out for structural variants studies called Kanpig. Huge improvements on tandem repeat regions where 70% of sv are. Great new method from Adam English!

www.biorxiv.org/content/10.1...

I'm going to be advertising a PhD studentship (open to international students) working on long read pangenome / assembly algorithms in bacteria. Would suit someone with maths/compsci background. Aptitude and interest more important than experience. Do please spread the word. Advert to follow

GitHub - RILAB/statements: Successful Job Applications and Grants Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

Also, for folks submitting NSF postdoc fellowships, we have a few successful examples of those here too. And please if you got one last year, consider submitting!

github.com/RILAB/statem...

Sharing on behalf of Andy Clark @ Cornell. Their Dept of Mol Bio and Genetics has an Asst Prof opening with a focus on human genetics and genomics this year: academicjobsonline.org/ajo/jobs/28554

Thank you for this initiative, please include me.

Join the T2T consortium next Thursday, Apr 4, 12-4pm EDT for a webinar focused on the wet side of ultra-long read sequencing. We will have a half-day of seminars from top experts in the field sharing their advice plus a Q&A. Free and open to all. Register here: ucsc-seqtech-events.online

Import your Twitter follows to Bluesky

I imported 15 friends from Twitter to Bluesky

With an increasing number of suspected genetic disorders, there is a need for new tools to improve diagnostics rate. At @nanopore, I will discuss the potential of nanopore sequencing to uncover variants of complex mendelian bit.ly/40Go3rB

NCI Spring School on Algorithmic Cancer Biology is happening again Apr 1-5 2024! The registration is now open, we invite trainees broadly interested in computational cancer biology to participate. Please apply and spread the word! ncifrederick.cancer.gov/events/confe...

Bioconductor is leaving Twitter/X

blog.bioconductor.org/posts/2023-1...

Exciting news: We’re taking another step to making Bluesky an open network for public conversations.

Around the end of this month, we’ll release a public web interface. With this, you’ll be able to view posts on Bluesky without being logged in on an account.

Distinguished Lecture: Dr. Adam Phillippy A Ken Kennedy Institute Distinguished Lecture by Dr. Adam Phillippy, Senior Investigator at National Human Genome Research Institute, National Inst...

I was waiting for a great topic for my first Bluesky post, and I cannot thing of a better one: I’m thrilled to be hosting @aphillippy.bsky.social at Rice University today and looking forward to his talk at 4pm! events.rice.edu/event/345896...

A reminder of this faculty opening in the Dept of Human Genetics at UU. Applications are due Dec. 8. Please share!

Attending #ASHG2023? Come check out my poster on Nov 2nd 3 to 5PM. I'll be presenting my research on @PacBio #longread application on complex medically relevant genes. Poster number PB3340. Can't wait to see you there! 🧬

Excited to be attending the ASHG 2023 Meeting next week in Washington, DC! I will be introducing the use of long-read sequencing technology to solve complex genomic regions. Looking forward to learning about the latest advances in human genetics and genomics research. #ASHG2023 #genetics #genomics