The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on ancient DNA yields in stapes and incus, genetic and epigenetic divergence in barn swallows, and more! tinyurl.com/Genome-Res-3...
Genome Research
@genomeresearch.bsky.social
A leading peer-reviewed genomics journal. https://genome.cshlp.org Submit: http://submit.genome.org
In @genomeresearch.bsky.social: @atothezphd.bsky.social "Cross-species variant-to-function analyses implicate MEIS1 in conferring sleep abnormalities and impaired cerebellar development". Co-led with Allan Pack @chopresearch.bsky.social @penngenetics.bsky.social genome.cshlp.org/content/earl...
Just got our @genomeresearch.bsky.social article by Margarita Geleta. 📬 I love hard copies...still here's a link genome.cshlp.org/content/36/2... Rita's article was a tour de force of genomic uses for the autoencoder architecture: compression, dim reduction, ancestry, synthetic genomes.
Dr. @grahamerwin.bsky.social @bcmhouston.bsky.social, M. Snyder @stanford.edu et al's study made @genomeresearch.bsky.social cover! They found that long-read HiFi #sequencingtechnology could provide answers when a small amount of DNA is available. genome.cshlp.org/content/36/7...
Our paper on genetic load in an invasive guppy population is now published in @genomeresearch.bsky.social It was a fantastic journey — from field sampling to analysis and finally publication. I hope readers will enjoy the story as much as we enjoyed working on it. genome.cshlp.org/content/36/7...
genome.cshlp.org
K. Wang, A. Cera, @grahamerwin.bsky.social, & colleagues report in @genomeresearch.bsky.social that a new low-input HiFi long-read sequencing method provides a more complete view of genetic variation from less DNA samples, helping advance disease & cancer research. genome.cshlp.org/content/36/7...
Call for Papers! @genomeresearch.bsky.social is now encouraging submissions for a Special Issue: "Spatial Omics: Technologies, Computation, and Biological Discovery", Guest Edited by Drs. Christina Leslie, Jian Ma, and Jeffrey Moffitt. Submission deadline: Nov. 1, 2026. tinyurl.com/Call-for-pap...
The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on variant detection from ultralow input tumor samples, genetic load in an invasive guppy population, and more! tinyurl.com/Genome-Res-3...
Our previously preprinted study "Influence of cis-regulatory elements on expression divergence in human segmental duplications" is now published in @genomeresearch.bsky.social! Please check it out: genome.cshlp.org/content/earl...
genome.cshlp.org
Megan Dennis@mydennis.bsky.social · 10mo agoHappy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.
The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on allele-specific splicing in Alzheimer's disease, tissue-specific gene regulation by vitamin B, and more! tinyurl.com/Genome-Res-3...
So proud to annouce our new paper in Genome Research ! genome.cshlp.org/content/36/5... Here we present scDynaBar, a CRISPR-based molecular recording system that enables the study of dynamic biological processes at single-cell resolution by accumulating and tracking genomic edits over time ⏰ 🧬 📈
Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution
Biological processes are inherently dynamic, yet current methods for capturing temporal changes remain limited. Here, we present scDynaBar, a novel approach that combines CRISPR-Cas9 dynamic barcoding with single-cell sequencing. In this system, genetic barcodes gradually accumulate mutations over time; these barcodes are sequenced alongside the transcriptome of individual cells. We propose that the divergence of these barcodes from the original sequence can serve as a record of the timing of cellular events. To demonstrate the potential of this method, we track the transition from a pluripotent state to a two-cell (2C)-like state in mouse embryonic stem cells (mESCs), providing evidence for the transient nature of the 2C-like state. Additionally, our system shows consistent mutation rates across diverse cell types in a mouse gastruloid model, highlighting its applicability to other biological systems. This approach not only improves our ability to study single-cell dynamics but also opens up new possibilities for recording other temporal signals—in other words, using dynamic barcoding as a molecular clock in individual cells.
genome.cshlp.org
Genome Research @genomeresearch.bsky.social · 3mo agoThe new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on single-cell CRISPR barcoding, Drosophila immune response enhancers, 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 CRISPR barcoding, Drosophila immune response enhancers, and more! tinyurl.com/Genome-Res-3...
📢 A new @genomeresearch.bsky.social paper shows processed pseudogenes break the rules: they’re transcribed without classic epigenetic marks, linked to enhancers and enriched for YY1 motifs. Study co-led by @beaborsari.bsky.social @geneticsub.bsky.social and Yunzhe Jiang 1/2
The new issue of @genomeresearch.bsky.social arch is now live. Follow the link to new research on somatic mutant alleles in bulk tumor samples, honey bee gut microbiota, and more! tinyurl.com/Genome-Res-3...
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...
Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
Genome Research @genomeresearch.bsky.social · 5mo agoThe 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 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! 🧬
AGBT@agbt.bsky.social · 5mo agoWe are ready for the 2026 AGBT General Meeting! For the next four days, leaders in genomics and technology will come together to share discoveries, spark collaborations, and shape the future of genomics. Let’s make this an unforgettable meeting. #AGBTGM26
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...
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 👇
Genome Research @genomeresearch.bsky.social · 7mo agoThe 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...
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!
Genome Research @genomeresearch.bsky.social · 7mo agoThe 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...
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...
🧪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
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
doi.org
The MARTi paper has been published in @genomeresearch.bsky.social after several years of development! genome.cshlp.org/content/earl...
Real-time analysis and visualization of nanopore metagenomic samples with MARTi
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
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
Loss of multilevel 3D genome organization during breast cancer progression
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
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.
Genome Research @genomeresearch.bsky.social · 9mo ago#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 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...