Genome Research
@genomeresearch.bsky.social
Reposted by Genome Research
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
November 19, 2025 at 10:06 AM
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
Reposted by Genome Research
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
October 29, 2025 at 3:59 PM
The MARTi paper has been published in @genomeresearch.bsky.social after several years of development! genome.cshlp.org/content/earl...
Reposted by Genome Research
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
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
November 7, 2025 at 12:46 PM
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
Published in Genome Research @genomeresearch.bsky.social
Reposted by Genome Research
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...
November 7, 2025 at 9:29 PM
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...
November 7, 2025 at 3:08 PM
#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...
November 6, 2025 at 10:41 PM
#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...
November 6, 2025 at 10:35 PM
#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...
November 6, 2025 at 10:33 PM
#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...
November 3, 2025 at 10:42 PM
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...
Reposted by Genome Research
💬 “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
💻🧬 Scientists at Earlham Institute introduce MARTi, a new tool for real-time #nanopore #metagenomics.
@genomeresearch.bsky.social
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
buff.ly
October 28, 2025 at 9:02 AM
💬 “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
💻🧬 Scientists at Earlham Institute introduce MARTi, a new tool for real-time #nanopore #metagenomics.
@genomeresearch.bsky.social
Reposted by Genome Research
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...
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
October 28, 2025 at 9:36 AM
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...
genome.cshlp.org/content/earl...
Submissions Due! Call for Papers: The Genetics and Genomics of Somatic Mosaicism
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
October 24, 2025 at 8:13 PM
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
October 17, 2025 at 6:01 PM
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...
October 1, 2025 at 8:02 PM
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
September 8, 2025 at 1:07 PM
Deadline extended to November 1st!
Reposted by Genome Research
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
May 7, 2025 at 3:04 PM
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
Reposted by Genome Research
🚨 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
🧵 Check out my thread from yesterday for the details ⬇️
👨💻 Open source codes also available on my #GitHub page!
#AcademicSky
🚨 Did you know that non-invasive prenatal screening (𝗡𝗜𝗣𝗦🤰) data can be repurposed for large-scale genomics? 🧬
Our new study shows how to turn low-coverage data into valuable insights, analyzing >32,000 genomes from Belgium. #genetics #imputation #NIPS #AcademicSky
genome.cshlp.org/content/35/9...
Our new study shows how to turn low-coverage data into valuable insights, analyzing >32,000 genomes from Belgium. #genetics #imputation #NIPS #AcademicSky
genome.cshlp.org/content/35/9...
Genotype imputation from low-coverage data for medical and population genetic analyses
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
September 4, 2025 at 6:31 PM
🚨 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
🧵 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...
September 2, 2025 at 6:09 PM
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...
Reposted by Genome Research
🧬🖥️ 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
Tree-based differential testing using inferential uncertainty for RNA-seq
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
August 21, 2025 at 7:24 PM
🧬🖥️ 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
Reposted by Genome Research
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...
www.su.se/department-o...
New research shows how nerve cells can be protected against ALS - Department of Biochemistry and Biophysics
New research shows how nerve cells can be protected against ALS - Department of Biochemistry and Biophysics
www.su.se
August 20, 2025 at 8:19 AM
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...
www.su.se/department-o...
Reposted by Genome Research
🙌 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
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
August 11, 2025 at 8:40 AM
🙌 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
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...
August 1, 2025 at 5:46 PM
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...
Reposted by Genome Research
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...
About how #Wnt signalling activation induces #CTCF binding and formation of new #chromatin #loops at #CREs of target genes.
genome.cshlp.org/content/earl...
August 1, 2025 at 1:58 PM
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...
About how #Wnt signalling activation induces #CTCF binding and formation of new #chromatin #loops at #CREs of target genes.
genome.cshlp.org/content/earl...
Reposted by Genome Research
🚨 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...
📝 Now on @genomeresearch.bsky.social 👇
genome.cshlp.org/content/earl...
Genotype imputation from low-coverage data for medical and population genetic analyses
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
July 23, 2025 at 4:09 PM
🚨 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...
📝 Now on @genomeresearch.bsky.social 👇
genome.cshlp.org/content/earl...
Reposted by Genome Research
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
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
July 22, 2025 at 4:17 PM
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