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Medhat Mahmoud

@medhat.bsky.social

490 followers 56 following 12 posts

Postdoc, HGSC, Baylor college of medicine. Interests: Bioinformatics | SVs | SNVs | comparative genomics | data science

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Medhat Mahmoud @medhat.bsky.social · May 5

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...
🧵👇

Reposted by Medhat Mahmoud

Adam Phillippy @aphillippy.bsky.social · 14d

🚂 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...

How Stowers Scientists Found the DNA Site Where Robertsonian Chromosomes Fuse

YouTube video by Stowers Institute for Medical Research

Medhat Mahmoud @medhat.bsky.social · May 5

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

Medhat Mahmoud @medhat.bsky.social · May 5

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

Medhat Mahmoud @medhat.bsky.social · May 5

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

Medhat Mahmoud @medhat.bsky.social · May 5

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

Medhat Mahmoud @medhat.bsky.social · May 5

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...
🧵👇

Reposted by Medhat Mahmoud

Javier Santoyo @jsantoyo.bsky.social · Mar 29

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

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...

Reposted by Medhat Mahmoud

Sarah Doom @sarahdoom.bsky.social · Nov 23

@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

Reposted by Medhat Mahmoud

Danny Miller, MD, PhD @danrdanny.bsky.social · Nov 24

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?

Sasha Gusev @sashagusevposts.bsky.social · Nov 24

I wrote about the National Institutes of Health and the various serious and unserious proposals for NIH reform that have been floating around. It is important to understand how this agency actually functions and point criticism at the right problems. A short 🧵:

Distinguishing real from invented problems with the NIH

How does the NIH work and where does it work well?

open.substack.com

Medhat Mahmoud @medhat.bsky.social · Nov 13

Thank you!!

Reposted by Medhat Mahmoud

Danny Miller, MD, PhD @danrdanny.bsky.social · Nov 11

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

Reposted by Medhat Mahmoud

Fritz Sedlazeck @sedlazeck.bsky.social · Oct 26

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...

Reposted by Medhat Mahmoud

Zamin Iqbal @zaminiqbal.bsky.social · Oct 22

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

Reposted by Medhat Mahmoud

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · Oct 23

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...

GitHub - RILAB/statements: Successful Job Applications and Grants

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

Reposted by Medhat Mahmoud

Adam Phillippy @aphillippy.bsky.social · Oct 22

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

Cornell University, CALS Molecular Biology and Genetics

Full service online faculty recruitment and application management system for academic institutions worldwide. We offer unique solutions tailored for academic communities.

academicjobsonline.org

Medhat Mahmoud @medhat.bsky.social · Oct 23

Thank you for this initiative, please include me.

Reposted by Medhat Mahmoud

Adam Phillippy @aphillippy.bsky.social · Mar 27

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

T2T Nanopore Ultra-Long Workshop |

ucsc-seqtech-events.online

Medhat Mahmoud @medhat.bsky.social · Dec 29

I imported 15 friends from Twitter to Bluesky

Import your Twitter follows to Bluesky

Medhat Mahmoud @medhat.bsky.social · Dec 4

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

Reposted by Medhat Mahmoud

Mikhail Kolmogorov @mishakolmogorov.bsky.social · Nov 20

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...

Medhat Mahmoud @medhat.bsky.social · Nov 18

Bioconductor is leaving Twitter/X

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

Reposted by Medhat Mahmoud

Bluesky @bsky.app · Nov 16

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.

Reposted by Medhat Mahmoud

Todd J. Treangen @treangen.bsky.social · Nov 14

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...

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...

events.rice.edu

Reposted by Medhat Mahmoud

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · Nov 12

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

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · Oct 16

The Dept of Human Genetics is hiring computational genomics faculty again this year! Last year we recruited Xiaoxu Yang - please apply to join him and our human, computational, developmental, and evolutionary genetics faculty. Please spread the word!
utah.peopleadmin.com/postings/153...

Medhat Mahmoud @medhat.bsky.social · Nov 2

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! 🧬