Kalin Nonchev
@nonchev.bsky.social
π€ 51
π₯ 81
π 44
PhD at ETH Zurich, machine learning and biomedical data
https://kalinnonchev.github.io
pinned post!
How can we predict spatial transcriptomics from histology images to enable simple, affordable, and reliable analysis of spatially resolved gene expression in routine clinical use? π€ Introducing DeepSpot β a deep learning model designed to tackle this! π§΅π
www.medrxiv.org/content/10.1...
loading . . .
10 months ago
1
6
1
reposted by
Kalin Nonchev
Andre Kahles
3 months ago
After years of research and continuous refinement, weβre thrilled to share that our paper on the MetaGraph framework β enabling Petabase-scale search across sequencing data β has been published today in Nature (
www.nature.com/articles/s41...
)
loading . . .
Efficient and accurate search in petabase-scale sequence repositories - Nature
MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.
https://www.nature.com/articles/s41586-025-09603-w
3
30
19
Older spot-level spatial transcriptomics datasets shouldn't be forgotten now that new single-cell methods exist. 𧬠Instead of discarding this rich resource, we can bridge the gap. DeepSpot2Cell helps bridge the gap π
loading . . .
3 months ago
1
0
0
reposted by
Kalin Nonchev
AI x Bio Discovery
3 months ago
DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervision
[new] Pred. sc gene expr. via DeepSet & spot sup. for spatial transcriptomics.
0
1
1
Internship Opportunity: Multimodal AI Research Scientist at the Biomedical Informatics Group at ETH Zurich π Interested in working at the intersection of computational pathology, spatial transcriptomics, LLM representation learning, and tissue generation?
5 months ago
1
0
0
reposted by
Kalin Nonchev
Moritz Schaefer
6 months ago
Just presented our new multimodal histopathology method "SpotWhisperer" at ICML, one of the largest AI conference. SpotWhisperer enables spatially resolved annotation of histopathology images using natural language. We achieved this by "transferring" annotations from transcriptomic data. More soon!
add a skeleton here at some point
0
5
2
reposted by
Kalin Nonchev
Christoph Bock Lab @ CeMM & MedUni Vienna
6 months ago
π€ Great collaboration between
@bocklab.bsky.social
(
@moritzbaio.bsky.social
, Animesh, Jake),
@nonchev.bsky.social
,
@gxxxr.bsky.social
, and pathologist Viktor KΓΆlzer. SpotWhisperer is at
#ICML25
FM4LS workshop. Visit our poster on Saturday (19 July 2025) if you're interested & attending ICML. (6/6)
0
1
1
reposted by
Kalin Nonchev
Christoph Bock Lab @ CeMM & MedUni Vienna
6 months ago
π¬ Toward histopathology 2.0: spatial transcriptomes inferred from routine diagnostic H&E images + a chat interface for cell-resolution histopathology through English language. (1/6)
loading . . .
1
8
5
reposted by
Kalin Nonchev
Peter Koo
8 months ago
Excited to share an update to D3 (DNA Discrete Diffusion) β an application of score-entropy discrete diffusion model for regulatory genomics! 𧬠Paper:
biorxiv.org/content/10.110β¦
(See thread below π) (1/n)
2
18
4
π Excited to share that we've generated the largest digital spatial transcriptomics dataset using DeepSpot - over 56 million spatial transcriptomics spots from 3 780 TCGA samples across skin melanoma, renal cell carcinoma, lung adenocarcinoma, and lung squamous cell carcinoma cohorts.
#pathology
8 months ago
1
5
1
First place award at the Autoimmune Disease Machine Learning Challenge organized by the
@broadinstitute.org
and CrunchDAO. Our approach outperformed competitors worldwide in predicting single-cell spatial transcriptomics from H&E images. π
10 months ago
1
6
0
How can we predict spatial transcriptomics from histology images to enable simple, affordable, and reliable analysis of spatially resolved gene expression in routine clinical use? π€ Introducing DeepSpot β a deep learning model designed to tackle this! π§΅π
www.medrxiv.org/content/10.1...
loading . . .
10 months ago
1
6
1
reposted by
Kalin Nonchev
Gunnar RΓ€tsch
about 1 year ago
Where RNA Science Meets AI, May 4β8, 2025, Ascona. Invited speakers:
@evamarianovoa.bsky.social
@fabiantheis.bsky.social
@rivaselenarivas.bsky.social
, Sterling Churchman, Barbara Treutlein, Rahul Satijia, Registration open
www.rna-ai.org
@hagentilgner.bsky.social
@quaidmorris.bsky.social
loading . . .
RNA-AI 2025
https://www.rna-ai.org
1
15
10
you reached the end!!
feeds!
log in