Foivos Gypas
@fgypas.bsky.social
Bioinformatics Software Engineer @ Novartis
🖥️ 🧬 🐧
#Bioinformatics #SoftwareDevelopment #RNABiology #oncology #fair
Reposted by Foivos Gypas
Excited to share the #Snakemake monitoring tool I've been working on:
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3
June 3, 2025 at 2:52 PM
Excited to share the #Snakemake monitoring tool I've been working on:
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3
Reposted by Foivos Gypas
An exciting first day of the #SnakemakeHackathon2025 at @cern.bsky.social is ending now. I have already merged several pull requests and many very productive teams have formed!
March 10, 2025 at 4:52 PM
An exciting first day of the #SnakemakeHackathon2025 at @cern.bsky.social is ending now. I have already merged several pull requests and many very productive teams have formed!
Reposted by Foivos Gypas
Job opening in my research group!! Please share.
I'm looking for a lab technician to join my small team investigating how chromatin structure regulates gene expression in C. elegans.
www.fmi.ch/education-ca...
I'm looking for a lab technician to join my small team investigating how chromatin structure regulates gene expression in C. elegans.
www.fmi.ch/education-ca...
Friedrich Miescher Institute, open position
Friedrich Miescher Institute, open position
www.fmi.ch
March 14, 2025 at 8:24 AM
Job opening in my research group!! Please share.
I'm looking for a lab technician to join my small team investigating how chromatin structure regulates gene expression in C. elegans.
www.fmi.ch/education-ca...
I'm looking for a lab technician to join my small team investigating how chromatin structure regulates gene expression in C. elegans.
www.fmi.ch/education-ca...
Reposted by Foivos Gypas
#snakemakehackathon2025 ! We started!
At the CERN for better #reproduciblecomputing and #ReproducibleResearch .
At the CERN for better #reproduciblecomputing and #ReproducibleResearch .
March 10, 2025 at 3:53 PM
#snakemakehackathon2025 ! We started!
At the CERN for better #reproduciblecomputing and #ReproducibleResearch .
At the CERN for better #reproduciblecomputing and #ReproducibleResearch .
Reposted by Foivos Gypas
New paper from my PhD provides genomic evidence that white shark livers are on the menu for Aussie killer whales!
See more here: onlinelibrary.wiley.com/doi/epdf/10....
See more here: onlinelibrary.wiley.com/doi/epdf/10....
January 28, 2025 at 4:38 AM
New paper from my PhD provides genomic evidence that white shark livers are on the menu for Aussie killer whales!
See more here: onlinelibrary.wiley.com/doi/epdf/10....
See more here: onlinelibrary.wiley.com/doi/epdf/10....
Reposted by Foivos Gypas
I agree. UMAP/t-SNE esse delendam. Two quibbles. You present UMAP as a function of the high-dimensional input vectors to the 2D output space, and that the problem is people do not understand what that function is. But it isn't even a function! There's no way to ask: where would this additional 1/n
December 24, 2024 at 1:44 PM
I agree. UMAP/t-SNE esse delendam. Two quibbles. You present UMAP as a function of the high-dimensional input vectors to the 2D output space, and that the problem is people do not understand what that function is. But it isn't even a function! There's no way to ask: where would this additional 1/n
Reposted by Foivos Gypas
Reposted by Foivos Gypas
Our group CBG at ETHZ:
We are excited to share that our new tool VILOCA has been published! VILOCA is a novel method for mutation calling and local haplotype reconstruction from diverse viral short-read and long-read sequencing data. It has already proven to be useful in various settings […]
We are excited to share that our new tool VILOCA has been published! VILOCA is a novel method for mutation calling and local haplotype reconstruction from diverse viral short-read and long-read sequencing data. It has already proven to be useful in various settings […]
Original post on mstdn.science
mstdn.science
December 20, 2024 at 1:04 PM
Our group CBG at ETHZ:
We are excited to share that our new tool VILOCA has been published! VILOCA is a novel method for mutation calling and local haplotype reconstruction from diverse viral short-read and long-read sequencing data. It has already proven to be useful in various settings […]
We are excited to share that our new tool VILOCA has been published! VILOCA is a novel method for mutation calling and local haplotype reconstruction from diverse viral short-read and long-read sequencing data. It has already proven to be useful in various settings […]
Reposted by Foivos Gypas
A great post on "How to generate SAM/BAM records and files for testing with SamBuilder" written by Alison Meynert. It's part of how we rigorously and programmatically test our #bioinformatics #genomics tools @fulcrumgenomics.bsky.social!
fulcrumgenomics.com/2024-11-test...
fulcrumgenomics.com/2024-11-test...
November 25, 2024 at 6:25 PM
A great post on "How to generate SAM/BAM records and files for testing with SamBuilder" written by Alison Meynert. It's part of how we rigorously and programmatically test our #bioinformatics #genomics tools @fulcrumgenomics.bsky.social!
fulcrumgenomics.com/2024-11-test...
fulcrumgenomics.com/2024-11-test...
Reposted by Foivos Gypas
The hallmarks of cancer immune evasion
The hallmarks of cancer immune evasion
Cancer cells often evade the host immune system, challenging the effectiveness of
immunotherapy. In this comprehensive review, Galassi et al. summarize key mechanisms
of immune evasion within the “thr...
www.cell.com
November 25, 2024 at 3:45 AM
The hallmarks of cancer immune evasion
Reposted by Foivos Gypas
GENCODE 2025: reference gene annotation for human and mouse. #Gencode #GeneAnnotations #Genomics #NAR 🧬
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GENCODE 2025: reference gene annotation for human and mouse
Abstract. GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as n
academic.oup.com
November 24, 2024 at 11:39 PM
GENCODE 2025: reference gene annotation for human and mouse. #Gencode #GeneAnnotations #Genomics #NAR 🧬
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Welcome to #bsky @giorgiocorfu.bsky.social
November 23, 2024 at 6:19 PM
Welcome to #bsky @giorgiocorfu.bsky.social
Reposted by Foivos Gypas
You can now run tximport in Python with pytximport thanks to @compmed.bsky.social et al. academic.oup.com/bioinformati...
Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python
AbstractSummary. Transcript quantification tools efficiently map bulk RNA sequencing reads to reference transcriptomes. However, their output consists of t
academic.oup.com
November 21, 2024 at 12:19 AM
You can now run tximport in Python with pytximport thanks to @compmed.bsky.social et al. academic.oup.com/bioinformati...
Reposted by Foivos Gypas
Welcome to Biozentrum @Bluesky account: @biozentrum.bsky.social. Follow us to get the latest news on research, education and events.
November 19, 2024 at 11:05 AM
Welcome to Biozentrum @Bluesky account: @biozentrum.bsky.social. Follow us to get the latest news on research, education and events.