Medhat Mahmoud

1/ 🧬 A Hitchhiker’s Guide to Long-Read Genomic Analysis is out now @genomeresearch! 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/35/4/5… 🧵👇

Stayed offline too long.. Several key papers came out (thanks to my group & great collaborators), thankful for great consortia meetings, might have a position in my lab opening, new lab homepage: fritzsedlazeck.github.io oh and got tenured (I know perfect timing ;)). Thanks all

We summarized state-of-the-art computational methods for DNA methylation analysis using long-read sequencing, covering everything from base calling to sample-level, cell-type-level, and even population-scale analysis. Huge Thanks to @sedlazeck and @timp0 for this great work!

In collaboration with @sedlazeck et al. at @BCM_HGSC we developed a long-read Dark Genes panel that allows researchers to interrogate whatever was not accessible with short-read WGS by “Closing the gap: Solving complex medically relevant genes at scale” medrxiv.org/content/10.110…

In honor of #RareDisease Week, learn more about how @GREGoR_research goes beyond exome sequencing to find causes for unsolved rare genetic diseases: Beyond the exome: What’s next in diagnostic testing for Mendelian conditions @AJHG cell.com/ajhg/fulltext/…

We are now accepting applications for scholarships to the @CSHL Biology of Genomes meeting from the @jxtxFoundation. Open to students worldwide in support of open science. Please help spread the word! jxtxfoundation.org/news/2025-2-4-…

In an unprecedented move, research-grant reviews have been suspended indefinitely at the world’s largest public funder of biomedical research go.nature.com/4gclXG0

Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data 1. Clair3-RNA pioneers as the first deep learning-based variant caller tailored for long-read RNA sequencing (lrRNA-seq), tackling challenges like uneven coverage, RNA editing events, and…

1/ 🧵 So excited to finally share our preprint! Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation (SV) on gene expression and DNA methylation- A new genomic resource for brain research! 🧠✨biorxiv.org/content/10.110…

Thanks for highlighting the Twist Alliance Dark Genes Panel (@MedhatMahmoud_ & @sedlazeck et al. medrxiv.org/content/10.110…) and the Twist Alliance Long-Read PGx Panel from @TwistBioscience twistbioscience.com/products/ngs/L… Customization is also possible! twistbioscience.com/products/ngs/c…

Our special issue is lout on long-read sequencing @PacBio / @nanopore ! Part 1 ;) genome.cshlp.org/content/34/11.… Super excited about all the new work and special thanks to all the authors! Also want to thank Hillary @genomeresearch @ahoischen @anaconesa

New from the lab with @sedlazeck. Brilliant analysis by ⁦@MichalIzydorcz1⁩ of long read ⁦@nanopore⁩ WGS from single human brain cells, after droplet MDA amplification in the Samplix X-drop. Funded by ⁦@ASAP_Research⁩ ⁦@UCLIoN⁩ medrxiv.org/content/10.110…

On Thursday I will be presenting our latest results on #mosaicSV detection with Sniffles at #ASHG2024 Come and join the Human Genetic Mosaicism Feat. Symposium

Free scientific illustrations for biologists! 😍 @NIH has released a library of 500+ free scientific illustrations to create figures, presentations, and illustrations! all freely available in the public domain. Retweet and spread the message! bioart.niaid.nih.gov

Excited to see this finally published! Our latest work demonstrates how @Illumina short-read WGS data can resolve LPA KIV-2 repeat units, which is very significant for studying cardiovascular disease risks bmcmedgenomics.biomedcentral.com/articles/10.11… @sedlazeck @MedhatMahmoud_ @lfpaulin @BCM_HGSC

STIX: Long-reads based Accurate Structural Variation Annotation at Population Scale biorxiv.org/cgi/content/sh… #biorxiv_bioinfo