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...

💬 “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...

🧬🖥️ Thrilled that our paper "Tree-based differential testing using inferential uncertainty for RNA-seq" genome.cshlp.org/content/earl..., led by @noorpratap.bsky.social, & in collab with @mikelove.bsky.social, @fennecpaaaw.bsky.social and Jason Fan is now accepted at @genomeresearch.bsky.social. 1/4

By analyzing millions of messenger RNA molecules during the course of ALS, researchers have identified why certain nerve cells are resistant to the disease and what happens in the sensitive nerve cells when they are affected. New study in @genomeresearch.bsky.social #ALS www.su.se/department-o...

🙌 New advances on rare diseases! Within the Solve_RD, @pacbio.bsky.social HiFi long-read whole-genome sequencing has proven instrumental in uncovering previously undetectable genetic variants, leading to new diagnoses genome.cshlp.org/content/35/4... @genomeresearch.bsky.social @erdera.bsky.social

The new issue of @genomeresearch.bsky.social search is now live. Follow the link to new research on oxygen stress and gene regulation in the brain, a new C. elegans reference genome, and more! tinyurl.com/Genome-Res-3...

Now out @genomeresearch.bsky.social this fantastic work in collaboration with Claudio Cantù's lab. About how #Wnt signalling activation induces #CTCF binding and formation of new #chromatin #loops at #CREs of target genes. genome.cshlp.org/content/earl...

🚨 Excited to share my new paper! We imputed 32,769 ultra-low coverage genomes from #NIPS 🫃and show how our custom filtering (GDI) impacts ancestry and PGS analyses. Big thanks to the team behind this long and rewarding work! 🧬 📝 Now on @genomeresearch.bsky.social 👇 genome.cshlp.org/content/earl...

Very happy that this (last?) piece of my PhD time in the Dekker lab is now out in Genome Research! genome.cshlp.org/content/earl... @jobdekker.bsky.social @pablonavarrolab.bsky.social @genomeresearch.bsky.social

A 6-year long study from the Lab is finally out @genomeresearch.bsky.social Mastered by @annanordin.bsky.social in collaboration with Chaitali Chakraborty from @remeseiro-lab.bsky.social Why is our work Important? Discover it in the quick Bluetorial 👇 genome.cshlp.org/content/earl...

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on single-cell multiomics of muscle response to endurance exercise, a method for Nanopore data compression, and more! tinyurl.com/Genome-Res-3...

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on single-cell multiomics of muscle response to endurance exercise, a method for Nanopore data compression, and more! tinyurl.com/Genome-Res-3...

Making the rounds here on behalf of @lsajournal.org ! Great visit with my colleagues at @genesdev.bsky.social and @genomeresearch.bsky.social today to discuss our manuscript transfer procedures, towards better serving authors. And admiring all the @cshlpress.bsky.social books 😍

Happy to share that our latest research study is out now @genomeresearch.bsky.social Androgen receptor-mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells genome.cshlp.org/content/earl... pubmed.ncbi.nlm.nih.gov/40456604/

The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on TP53 regulation of transposable elements in cancer, gut microbiome–associated protists, and more! tinyurl.com/Genome-Res-3...

Glad we found the perfect home in a community journal including a read and publish open access agreement. "Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus" genome.cshlp.org/content/earl...

New paper out in @genomeresearch.bsky.social on using contrastive self-supervised learning for spatial domain detection with multi-omics data! Huge congratulations to Jianing Yao and coauthors Jinglun Yu, Brian Caffo Stephanie Page & @martinowk.bsky.social! 🧬 🖥️ 🧪 doi.org/10.1101/gr.2...

Last night of another great #BOG25! Thanks to everyone who came to chat with us at our Meet the Editors sessions. Had a great year putting together this special double issue! Now, on to the next! #somaticmosaicism @genomeresearch.bsky.social @cshlmeetings.bsky.social

This Wednesday and Friday, meet the editors of @genomeresearch.bsky.social . We will be available to discuss your latest research and to answer any questions about the journal. In addition, hear about our upcoming issue on Somatic Mosaicism. #BOG25

Prof Dan Mishmar's latest paper is on the cover of CSHL’s “Genome Research” Journal — “Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth.” (My artwork on the cover). @genomeresearch.bsky.social @cshlmeetings.bsky.social

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

The 38th annual Biology of Genomes meeting starts TONIGHT! Make sure to use #BOG25 for all of your posts and have a great week 🧬

@fxquah.bsky.social 's paper is finally out @genomeresearch.bsky.social and we made the cover!! This was only possible due to the brilliant illustration by @sonhita.bsky.social Paper here: genome.cshlp.org/content/35/5... See below for more details 🧵

🐡 My new cover art highlights research from the Miska lab @miskalab.bsky.social at U of Cambridge @cambiochem.bsky.social 🧪 The authors present the first pangenome for Lake Malawi cichlids built from the genomes of seven representative species. Full paper 🔗 genome.cshlp.org/content/35/5... (1/3)

The new issue of genomeresearch.bsky.social is now live! Follow the link to a new ultra-long nanopore sequencing toolkit, a unified analysis of atlas single-cell data, and more! tinyurl.com/Genome-Res-3...

Great to see our research on heterogenous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids published as part of Long-read sequencing special issue in Genome Research, along fantastic collection of articles on long reads!

Siyu Xie’s paper is out now @genomeresearch.bsky.social. A remarkable story about this remarkable creature -Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad genome.cshlp.org/content/earl...

One of the gems from the last @genomeresearch.bsky.social #long-reads special issue, Part II. Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resol… pubmed.ncbi.nlm.nih.gov/40086881/

Our newest collab paper showing an interplay between common regulatory SNVs and rare coding variants in SHROOM3 in Craniofacial Microsomia is now online ahead of print @genomeresearch.bsky.social: pubmed.ncbi.nlm.nih.gov/40234029/. Huge shoutout to Yong-Biao Zhang’s team again.

Great to see our work on GNASTy made it into the long-read special issue at Genome Research alongside some super innovative applications and methods!

We hope your as excited as us to dig into all the wonderful science in this special issue of @genomeresearch.bsky.social related to all things #LongReads (transcriptomics and beyond). Curated in part by our #LongTRECs very own @anaconesa.bsky.social

I had a great time working with @genomeresearch.bsky.social on these two covers that combine to form a single image for part 1 and 2 of their long-read sequencing special issues

Part 2 of the #longreads @genomeresearch.bsky.social special issue is out! Thanks to @ahoischen.bsky.social and @sedlazeck.bsky.social for the great collaboration. The issue features many novel tools and applications showing the strong advance of this field @longtrec.bsky.social @hitseq.bsky.social

Part 1 and 2 of the Long-read sequencing Special Issues are now live! tinyurl.com/Genome-Res-LRS