Emanuel
@ebioman.bsky.social
Multi-omics advocate, working on cancer and CLD questions in industry, Rust programming, trail running, mountains and hip-hop
Pinned
Emanuel
@ebioman.bsky.social
· Nov 21
GitHub - ngs-ai-org/splitty: Tool suite around gene fusion detection and analysis
Tool suite around gene fusion detection and analysis - ngs-ai-org/splitty
github.com
Just released our tool "splitty" github.com/ngs-ai-org/s... for fusion detection from transcripts. It's a BAM-based fusion caller in #rust for short- and long-reads, as well as tools around BND VCF entries (clustering, filtering,...).
Soon hopefully a publication with it's application will follow 🤞
Soon hopefully a publication with it's application will follow 🤞
Chilled snowboard day with the family
December 29, 2024 at 4:26 PM
Chilled snowboard day with the family
Fire and snow outside make for a perfect Sunday morning mood
December 8, 2024 at 9:31 AM
Fire and snow outside make for a perfect Sunday morning mood
Enjoying Frankfort and the IABS meeting for NGS in adventitious virus detection. Great conference so far
December 4, 2024 at 5:07 AM
Enjoying Frankfort and the IABS meeting for NGS in adventitious virus detection. Great conference so far
Enjoyed a quick morning run at the lake. Holds work problems again at bay
November 30, 2024 at 2:04 PM
Enjoyed a quick morning run at the lake. Holds work problems again at bay
Just released our tool "splitty" github.com/ngs-ai-org/s... for fusion detection from transcripts. It's a BAM-based fusion caller in #rust for short- and long-reads, as well as tools around BND VCF entries (clustering, filtering,...).
Soon hopefully a publication with it's application will follow 🤞
Soon hopefully a publication with it's application will follow 🤞
GitHub - ngs-ai-org/splitty: Tool suite around gene fusion detection and analysis
Tool suite around gene fusion detection and analysis - ngs-ai-org/splitty
github.com
November 21, 2024 at 4:24 PM
Just released our tool "splitty" github.com/ngs-ai-org/s... for fusion detection from transcripts. It's a BAM-based fusion caller in #rust for short- and long-reads, as well as tools around BND VCF entries (clustering, filtering,...).
Soon hopefully a publication with it's application will follow 🤞
Soon hopefully a publication with it's application will follow 🤞
Reposted by Emanuel
Another very insightful paper on #methylation and long-read sequencing by @gangfang.bsky.social, describing some important but frequently overlooked caveats.
Gang provides a fantastic summary in his post, but here's my take too😅:
Gang provides a fantastic summary in his post, but here's my take too😅:
November 20, 2024 at 7:25 PM
Another very insightful paper on #methylation and long-read sequencing by @gangfang.bsky.social, describing some important but frequently overlooked caveats.
Gang provides a fantastic summary in his post, but here's my take too😅:
Gang provides a fantastic summary in his post, but here's my take too😅:
Reposted by Emanuel
(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n
November 20, 2024 at 11:41 AM
(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n
Reposted by Emanuel
New interval lookup library just hit for Rust, C++ and Python — claims best in class performance! Pretty cool : github.com/kcleal/super...
GitHub - kcleal/superintervals: Fast interval intersection library
Fast interval intersection library. Contribute to kcleal/superintervals development by creating an account on GitHub.
github.com
November 20, 2024 at 3:18 PM
New interval lookup library just hit for Rust, C++ and Python — claims best in class performance! Pretty cool : github.com/kcleal/super...
Great work and intriguing story. I am glad that I could contribute a bit, too. #🧪
Very proud of the work of Ganesh Nawkar & Martina Legris
with invaluable help from many others: Air channels create a directional light signal to regulate hypocotyl phototropism. www.science.org/doi/10.1126/...
with invaluable help from many others: Air channels create a directional light signal to regulate hypocotyl phototropism. www.science.org/doi/10.1126/...
November 29, 2023 at 7:36 AM
Great work and intriguing story. I am glad that I could contribute a bit, too. #🧪
Reposted by Emanuel
So @ctitusbrown.bsky.social gave a talk for our Genome Center faculty meeting & I got reacquainted with sourmash -- github.com/sourmash-bio... really easy to install - got it to work in a few minutes on my laptop and desktop -- lots of interesting findings already ...
Thanks Titus et al.
Thanks Titus et al.
GitHub - sourmash-bio/sourmash: Quickly search, compare, and analyze genomic and metagenomic data se...
Quickly search, compare, and analyze genomic and metagenomic data sets. - GitHub - sourmash-bio/sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets.
github.com
November 17, 2023 at 4:54 PM
So @ctitusbrown.bsky.social gave a talk for our Genome Center faculty meeting & I got reacquainted with sourmash -- github.com/sourmash-bio... really easy to install - got it to work in a few minutes on my laptop and desktop -- lots of interesting findings already ...
Thanks Titus et al.
Thanks Titus et al.
Reposted by Emanuel
Relaxing a bit after a demanding week
October 8, 2023 at 2:30 PM
Relaxing a bit after a demanding week
Reposted by Emanuel
This is the dirty secret of the ctDNA field. The false positives will absolutely bankrupt the medical system if they're rolled out as is (not to mention the mental trauma!)
Blood tests for cancer may be useful someday, but the hype needs to be kept in check until the results are there.
Blood tests for cancer may be useful someday, but the hype needs to be kept in check until the results are there.
Blood-based tests for multicancer early detection (PATHFINDER): a prospective cohort study
#grail
www.thelancet.com/journals/lan...
A cancer signal was detected in 92 (1·4%) of 6621 participants.[...] 57 (62%) had no cancer diagnosis (false positives). 😱
#grail
www.thelancet.com/journals/lan...
A cancer signal was detected in 92 (1·4%) of 6621 participants.[...] 57 (62%) had no cancer diagnosis (false positives). 😱
October 7, 2023 at 11:14 PM
This is the dirty secret of the ctDNA field. The false positives will absolutely bankrupt the medical system if they're rolled out as is (not to mention the mental trauma!)
Blood tests for cancer may be useful someday, but the hype needs to be kept in check until the results are there.
Blood tests for cancer may be useful someday, but the hype needs to be kept in check until the results are there.
Reposted by Emanuel
Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing https://www.biorxiv.org/content/10.1101/2023.10.05.561129v1
Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing https://www.biorxiv.org/content/10.1101/2023.10.05.561129v1
Chromatin accessibility demonstrates accessible DNA regions that usually have regulatory function. S
www.biorxiv.org
October 6, 2023 at 9:33 PM
Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing https://www.biorxiv.org/content/10.1101/2023.10.05.561129v1
Looking forward to read that one 👍🧪
Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition https://www.biorxiv.org/content/10.1101/2023.09.26.559521v1
Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition https://www.biorxiv.org/content/10.1101/2023.09.26.559521v1
Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse
www.biorxiv.org
September 27, 2023 at 3:48 PM
Looking forward to read that one 👍🧪
Unfortunately Bioinformatics rejected our Pacbio methylation Algo manuscript www.biorxiv.org/content/10.1... . Reviews were constructive and easy to address, none questioned method itself, results or that it should be published. Strange.. off to the next publisher then 🧪
September 21, 2023 at 6:33 AM
Unfortunately Bioinformatics rejected our Pacbio methylation Algo manuscript www.biorxiv.org/content/10.1... . Reviews were constructive and easy to address, none questioned method itself, results or that it should be published. Strange.. off to the next publisher then 🧪
Getting slowly a hang on these intervals
September 19, 2023 at 8:29 PM
Getting slowly a hang on these intervals
Enjoyed a family weekend hike in the nearby mountains, Les Moss
September 18, 2023 at 9:26 AM
Enjoyed a family weekend hike in the nearby mountains, Les Moss
Thrilled to see that the approach to which I contributed is going forward and might eventually help in the early detection of pancreatic cancer
blog.crownbio.com/a-novel-panc...
blog.crownbio.com/a-novel-panc...
September 16, 2023 at 9:50 AM
Thrilled to see that the approach to which I contributed is going forward and might eventually help in the early detection of pancreatic cancer
blog.crownbio.com/a-novel-panc...
blog.crownbio.com/a-novel-panc...
Announcing myself here with a genome announcement coming out of our group recently 🤗 academic.oup.com/g3journal/ad...
Reference genomes for BALB/c Nude and NOD/SCID mouse models
Reference genomes for BALB/c Nude and NOD/SCID mouse models
September 13, 2023 at 6:35 PM
Announcing myself here with a genome announcement coming out of our group recently 🤗 academic.oup.com/g3journal/ad...
Reference genomes for BALB/c Nude and NOD/SCID mouse models
Reference genomes for BALB/c Nude and NOD/SCID mouse models