Genome Research

Work from my M.Sc. with @guilbourque.bsky.social is in this month's issue of Genome Research, detailing my short tandem repeat (STR) genotyping tool for long-read data!

Article: genome.cshlp.org/content/36/3...
STRkit: github.com/davidloughee...

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on chromosome engineering in 8p syndrome, convergent evolution in arid rodents, and more! tinyurl.com/Genome-Res-3...

The Editors of @genomeresearch.bsky.social are here! Looking forward to all of the great talks! 🧬

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on transposable elements in pancreatic cancer, genomic evolution in living fossils, and more! tinyurl.com/Genome-Res-3...

You can access the full issue here: genome.cshlp.org/content/36/2....

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on transposable elements in pancreatic cancer, genomic evolution in living fossils, and more! tinyurl.com/Genome-Res-3...

Associate professor of Medicine @agoren.bsky.social and graduate student Yuwei Cao's new method for an end-to-end single pot automated (spa) ChIP-seq made the cover of @genomeresearch.bsky.social! 🧬

Read their article, focused on developing spa-ChIP-seq, below 👇

Our new method for an end-to-end single pot automated (spa) ChIP-seq made the cover of @genomeresearch.bsky.social! A fun spa day for the DNA ;)
(Sorry, I had to, please don’t tell my wife).
Shoutout to my graduate student Yuwei Cao which led this effort amazingly!

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research the 3D genome organization in breast cancer, assisted reproductive technology mutation rate, and more! tinyurl.com/Genome-Res-3...

This month, @genomeresearch.bsky.social publishes a special RECOMB issue highlighting algorithmic innovations in haplotype assembly and phasing, analysis of genomic variation and its association to phenotype, metagenomic analyses, and more.

Link to full issue: genome.cshlp.org/content/35/1...

This month @genomeresearch.bsky.social publishes a special @recombconf.bsky.social issue highlighting algorithmic innovations in haplotype assembly and phasing, analysis of genomic variation and its association to phenotype, metagenomic analyses, and more. genome.cshlp.org/content/35/1...

Summary of dynamic changes in shrew metabolism associated with seasonal size change, with proposed regulation of Dehnel’s cycle. Depleted lipid metabolites in the blood and increased RNA expression of genes involved in fatty acid metabolism indicate rapid fat turnover in winter juveniles. FOXO signaling regulates gluconeogenesis, also upregulated in winter juveniles, providing another energy source. Both FOXO signaling and fatty acid metabolism promote changes in oxidative phosphorylation, as was found in both the transcriptomic and proteomic analyses, and have large effects on mitochondrial respiration in the liver.

🧪New #shrewcrew #OA @genomeresearch.bsky.social 📃shows how tiny shrews remain active in ❄️❄️! As it gets 🥶tiny mammals hibernate or migrate, but not shrews. They shrink, thus reducing their overall⚡️demand 👉🏽 genome.cshlp.org/content/earl... 1/4

Surveillance getting GNASTy! Improving our ability to detect variants that haven’t been seen before! Optimizing nanopore adaptive sampling for pneumo surveillance in @genomeresearch.bsky.social 👇 doi.org/10.1101/gr.2... @imperialcollegeldn.bsky.social @ox.ac.uk @rebecca-and.bsky.social @ebi.embl.org

The MARTi paper has been published in @genomeresearch.bsky.social after several years of development! genome.cshlp.org/content/earl...

New publication: "Loss of multilevel 3D genome organization during breast #cancer progression" with Roberto Rossini @robomics.bsky.social, Saleh Oshaghi, Jonas Paulsen @jonnings.bsky.social from @biovitenskap.bsky.social
Published in Genome Research @genomeresearch.bsky.social

Really excited to see our new work in scaling Mumemto to any size pangenome published in Genome Research this morning. And right on cue with the great opportunity to present this work at #GI2025 this week.

#GI2025 Vikram Shivakumar from Ben Langmead's lab (@benlangmead.bsky.social) presents "MumemtoM - partitioned Multi-MUM finding for scalable pangenomics ". Now published in Genome Research @genomeresearch.bsky.social. Read full text here ➡️ tinyurl.com/Genome-Res-2...

#GI2025 Ilias Georgakopoulos-Soares presents "Quadrupia - a comprehensive catalog of G-quadruplexes across genomes from the tree of life". Now published in Genome Research @genomeresearch.bsky.social Read full text here ➡️ tinyurl.com/Genome-Res-2...

#GI2025 Chirag Jain presents "Pangenome-based genome inference using integer programming". Now published in GenomeResearch @genomeresearch.bsky.social Read the full text here ➡️ tinyurl.com/Genome-Res-2...

#GI2025 Mile Sikic @msikic.bsky.social presents "Geometric deep learning framework for de novo genome assembly" Now published in GenomeResearch @genomeresearch.bsky.social Full text here ➡️ tinyurl.com/Genome-Res-2...

The new issue of @genomeresearch.bsky.social h is now live. Follow the link to new research on wheat centromere adaptation, Quadrupia - a G-quadruplex database, and more! tinyurl.com/Genome-Res-3...

New software tool MARTi fast-tracks identification and response to microbial threats. An open-source software tool that powers real-time analysis and visualisation of metagenomic data

💬 “It’s operationally very lightweight, you can use it in-field for taxonomic classification on a standard laptop, or undertake larger, complex analysis using HPC.”

💻🧬 Scientists at Earlham Institute introduce MARTi, a new tool for real-time #nanopore #metagenomics.

@genomeresearch.bsky.social

Our MARTi @nanoporetech.com paper is now out in @genomeresearch.bsky.social after several years of development (particularly Ned Peel and Sam Martin). We'd love to hear from users about how you're using it, or suggestions for new features. @earlhaminst.bsky.social

genome.cshlp.org/content/earl...

Submissions Due! Call for Papers: The Genetics and Genomics of Somatic Mosaicism

Call for papers deadline is quickly approaching! More information on the topic of interests can be found here: tinyurl.com/Call-for-pap.... #ASHG25 #BOG25 #KSMosaicism25 #MITS25 #somaticmosaicism

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on microglia in neurodegenerative diseases, intron retention in nuclear RNA complexes, and more! tinyurl.com/Genome-Res-3...

Deadline extended to November 1st!

Call for Papers! @genomeresearch.bsky.social is now encouraging submissions for a Special Issue on The Genetics and Genomics of Somatic Mosaicism, Guest Edited by Drs. Gilad Evrony, Eunjung (Alice) Lee, and Raheleh Rahbari. tinyurl.com/Call-for-pap... #BOG25 #KSMosaicism25 #MITS25 #somaticmosaicism

🚨 My new paper is out in the latest issue of @genomeresearch.bsky.social! 🧬

🧵 Check out my thread from yesterday for the details ⬇️

👨‍💻 Open source codes also available on my #GitHub page!

#AcademicSky

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on HER2 isoform diversity and drug resistance in breast cancer, off-target site detection in prime editing, and more! tinyurl.com/Genome-Res-3...