Shubhankar Londhe
@slondhe.bsky.social
PhD student @gagneurlab.bsky.social (TU Munich and Helmholtz Munich).
Interested in rare variant genetics.
https://shubhankarlondhe.github.io/
Interested in rare variant genetics.
https://shubhankarlondhe.github.io/
Why be satisfied with coding variant gene impairments? Check out Eva’s poster to learn how we scale DeepRVAT to the WGS UKBiobank. It’s been great fun being a part of this project!
#ASHG25
#ASHG25
DeepRVATv2 is in the making! We learn from >60M WGS variants, >90 features, and 500k UKB participants to predict gene impairment beyond coding regions and showcase how DeepRVAT can advance rare disease diagnostics and gene constraint measurement.
Learn more at my Poster 5058W, Wed 2:30pm #ASHG25
Learn more at my Poster 5058W, Wed 2:30pm #ASHG25
October 14, 2025 at 9:56 PM
Why be satisfied with coding variant gene impairments? Check out Eva’s poster to learn how we scale DeepRVAT to the WGS UKBiobank. It’s been great fun being a part of this project!
#ASHG25
#ASHG25
Excited to share UKBBGym at #ASHG25, a new benchmark for variant effect predictors using WGS, proteomics and phenotypes from 500K UKBiobank participants. Stop by for insights on the impact of non-coding variants and how computational scores stack up against exp assays.
Poster 5022W, Wed 2:30-4:30.
Poster 5022W, Wed 2:30-4:30.
October 14, 2025 at 3:40 PM
Excited to share UKBBGym at #ASHG25, a new benchmark for variant effect predictors using WGS, proteomics and phenotypes from 500K UKBiobank participants. Stop by for insights on the impact of non-coding variants and how computational scores stack up against exp assays.
Poster 5022W, Wed 2:30-4:30.
Poster 5022W, Wed 2:30-4:30.
Reposted by Shubhankar Londhe
The Solvathons have been one of our most exciting research community experiences: Hands-on, effective – solving real cases during the events, and multidisciplinary – from clinicians to bioinformaticians. Thumbs up to the SolveRD community. Looking for more now with @erdera.bsky.social
rdcu.be/eFaqO
rdcu.be/eFaqO
The Solve-RD Solvathons as a pan-European interdisciplinary collaboration to diagnose patients with rare disease
Nature Genetics - This Perspective presents the Solve-RD Solvathon model, an innovative, pan-European framework uniting clinical and bioinformatics experts to diagnose rare diseases through...
rdcu.be
September 9, 2025 at 11:42 AM
The Solvathons have been one of our most exciting research community experiences: Hands-on, effective – solving real cases during the events, and multidisciplinary – from clinicians to bioinformaticians. Thumbs up to the SolveRD community. Looking for more now with @erdera.bsky.social
rdcu.be/eFaqO
rdcu.be/eFaqO
Reposted by Shubhankar Londhe
[1/8] *New Open-Access Long Read Resource*. We sequenced 1,019 genomes from the 1000 Genomes Project sample cohort using @nanoporetech.com long-read sequencing (LRS) to median 17x coverage. Publication at go.nature.com/4ffPb8f.
@hhu.de @crg.eu @embl.org @impvienna.bsky.social
@hhu.de @crg.eu @embl.org @impvienna.bsky.social
July 24, 2025 at 9:26 AM
[1/8] *New Open-Access Long Read Resource*. We sequenced 1,019 genomes from the 1000 Genomes Project sample cohort using @nanoporetech.com long-read sequencing (LRS) to median 17x coverage. Publication at go.nature.com/4ffPb8f.
@hhu.de @crg.eu @embl.org @impvienna.bsky.social
@hhu.de @crg.eu @embl.org @impvienna.bsky.social
Reposted by Shubhankar Londhe
Today at 12:20 in the HIT-Seq COSI, @lauradmartens.bsky.social Laura Martens will present her results on spatial chromatin accessibility data deconvolution #ISMBECCB2025. Great collab with Sarah Ouologuem and @fabiantheis.bsky.social
Proceedings paper:
doi.org/10.1093/bioi...
Proceedings paper:
doi.org/10.1093/bioi...
Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
AbstractMotivation. Spatially resolved chromatin accessibility profiling offers the potential to investigate gene regulatory processes within the spatial c
doi.org
July 23, 2025 at 8:35 AM
Today at 12:20 in the HIT-Seq COSI, @lauradmartens.bsky.social Laura Martens will present her results on spatial chromatin accessibility data deconvolution #ISMBECCB2025. Great collab with Sarah Ouologuem and @fabiantheis.bsky.social
Proceedings paper:
doi.org/10.1093/bioi...
Proceedings paper:
doi.org/10.1093/bioi...
Reposted by Shubhankar Londhe
@thbec.bsky.social is going to share preliminary results on Meta-DeepRVAT, a new approach for deep learning based meta-analysis improving the power of rare variant association studies using population scale external control cohorts. #MLCSB
📅 July 21 |📍 Poster A-312
📅 July 21 |📍 Poster A-312
July 19, 2025 at 5:33 PM
@thbec.bsky.social is going to share preliminary results on Meta-DeepRVAT, a new approach for deep learning based meta-analysis improving the power of rare variant association studies using population scale external control cohorts. #MLCSB
📅 July 21 |📍 Poster A-312
📅 July 21 |📍 Poster A-312
Reposted by Shubhankar Londhe
Join us for our next Kipoi Seminar with Katherine Pollard, Gladstone Institute of Data Science & Biotechnology,UCSF, Biohub
@gladstoneinst.bsky.social @czbiohub.bsky.social
👉Human variant interpretation with sequence-to-activity models
📅Wed June 4,5:30pm CET🧬 kipoi.org/seminar/🦋@kipoizoo.bsky.social
@gladstoneinst.bsky.social @czbiohub.bsky.social
👉Human variant interpretation with sequence-to-activity models
📅Wed June 4,5:30pm CET🧬 kipoi.org/seminar/🦋@kipoizoo.bsky.social
https://kipoi.org/seminar/🦋kipoizoo.bsky
May 28, 2025 at 1:06 PM
Join us for our next Kipoi Seminar with Katherine Pollard, Gladstone Institute of Data Science & Biotechnology,UCSF, Biohub
@gladstoneinst.bsky.social @czbiohub.bsky.social
👉Human variant interpretation with sequence-to-activity models
📅Wed June 4,5:30pm CET🧬 kipoi.org/seminar/🦋@kipoizoo.bsky.social
@gladstoneinst.bsky.social @czbiohub.bsky.social
👉Human variant interpretation with sequence-to-activity models
📅Wed June 4,5:30pm CET🧬 kipoi.org/seminar/🦋@kipoizoo.bsky.social
Excited to present at #eshg2025. Catch my talk on improving rare variant association studies using functional gene embeddings, on Monday at 11:45am (C26.06).
Shubhankar Londhe @slondhe.bsky.social presents his work on RVAT in the talk “Functional gene embeddings improve rare variant polygenic risk scores” at session C26 – Computational models in human genetics. Catch it on Monday at 11:45am. 2/n
May 25, 2025 at 10:33 AM
Excited to present at #eshg2025. Catch my talk on improving rare variant association studies using functional gene embeddings, on Monday at 11:45am (C26.06).
Reposted by Shubhankar Londhe
Excited to be back at #eshg2025! Come by my poster today to check out fresh results on how rare high impact variants influence gene expression across immune cells—analyzed in 5,000 UK Biobank participants
Eva Holtkamp @evaholtkamp.bsky.social shares insights on rare variant effects on cell type-specific gene expression in immune cells across 4,978 UK Biobank participants - catch poster P18.066.A (Sunday, 1pm)
May 25, 2025 at 7:40 AM
Excited to be back at #eshg2025! Come by my poster today to check out fresh results on how rare high impact variants influence gene expression across immune cells—analyzed in 5,000 UK Biobank participants
Reposted by Shubhankar Londhe
Tomorrow Johannes Hingerl @johahi.bsky.social gives a talk on scooby at #probgen25. Enjoy learning in the legendary CSHL auditorium how to model RNA-seq and ATAC-seq profiles in individual cells from half a megabase of genomic sequence. Preprint:
doi.org/10.1101/2024...
doi.org/10.1101/2024...
March 6, 2025 at 9:04 PM
Tomorrow Johannes Hingerl @johahi.bsky.social gives a talk on scooby at #probgen25. Enjoy learning in the legendary CSHL auditorium how to model RNA-seq and ATAC-seq profiles in individual cells from half a megabase of genomic sequence. Preprint:
doi.org/10.1101/2024...
doi.org/10.1101/2024...
Reposted by Shubhankar Londhe
Excited to share that PROTRIDER, our method to call outliers on mass spectrometry-based proteomics data, is out now!! #proteomics #massspectrometry #raredisease doi.org/10.1101/2025...
PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder
Motivation Detection of gene regulatory aberrations enhances our ability to interpret the impact of inherited and acquired genetic variation for rare disease diagnostics and tumor characterization. Wh...
doi.org
February 19, 2025 at 8:15 AM
Excited to share that PROTRIDER, our method to call outliers on mass spectrometry-based proteomics data, is out now!! #proteomics #massspectrometry #raredisease doi.org/10.1101/2025...
Reposted by Shubhankar Londhe
Join us for our next Kipoi Seminar with with Pedro Tomaz da Silva @pedrotomazdasilva.bsky.social @gagneurlab.bsky.social @TU_Muenchen!
👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements
📅Wed Feb 5, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky
👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements
📅Wed Feb 5, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky
February 3, 2025 at 4:11 PM
Join us for our next Kipoi Seminar with with Pedro Tomaz da Silva @pedrotomazdasilva.bsky.social @gagneurlab.bsky.social @TU_Muenchen!
👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements
📅Wed Feb 5, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky
👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements
📅Wed Feb 5, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky
Reposted by Shubhankar Londhe
Hey reg genomics folks, here is our little x-mas present: Flashzoi. Borzoi. Just as good. 3x faster. Thumbs up to @johahi.bsky.social for the great initiative, conception & implementation. Big thanks to Johannes Linder, David Kelley and colleagues to have created Borzoi and shared it freely.
Flashzoi: An enhanced Borzoi model for accelerated genomic analysis https://www.biorxiv.org/content/10.1101/2024.12.18.629121v1
December 23, 2024 at 9:15 AM
Hey reg genomics folks, here is our little x-mas present: Flashzoi. Borzoi. Just as good. 3x faster. Thumbs up to @johahi.bsky.social for the great initiative, conception & implementation. Big thanks to Johannes Linder, David Kelley and colleagues to have created Borzoi and shared it freely.