Sam Kovaka (@samkovaka) header
Sam Kovaka (@samkovaka) profile picture

Sam Kovaka

@samkovaka

Computational biology postdoc at JHU

Joined August 2011
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  • Followers240
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Photo by Sam Kovaka (@samkovaka)
Very excited to announce "Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment" by @samkovaka et al. biorxiv.org/content/10.1101/…
Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal...

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal...

Nanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic/transcriptomic and epigenetic information without additional...

biorxiv.org
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Bioinformatics advancements unleash the full potential of long-read sequencing in various areas of genomics. A Comment from Michael Schatz (@mike_schatz) and colleagues highlights this thriving domain of active methods development. @JohnsHopkins nature.com/articles/s41592-0…
Image from Nature Methods (@naturemethods)
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Thank you! So happy to finally (pretty much) be a doctor. Also excited to announce that I'll be staying at Hopkins as a postdoc with @mike_schatz!
Michael Schatz (@mike_schatz) profile pictureMichael Schatz@mike_schatz11 Mar 2022
Congratulations to @samkovaka for defending his thesis on Computational Methods for Genomic, Transcriptomic, and Epi-Omic Analysis with Long-Read Sequencing! @timp0, @elapertea and I are so proud! @nanopore @PacBio @JHUCompSci @HopkinsEngineer
Image from Michael Schatz (@mike_schatz)
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Come to my talk on December 2nd! Despite being in the adaptive sampling session, I'll be talking more about general analysis and visualization of nanopore signal. If you think that's uncalled for, well...
Oxford Nanopore Events (@NanoporeConf) profile pictureOxford Nanopore Events@NanoporeConf5 Nov 2021
At #nanoporeconf, @Samkovaka will present UNCALLED4: an adaptive sampling toolkit for nanopore signal alignment & analysis. UNCALLED4 features interactive alignment visualisations & comparisons, & epigenetic modification detection stats: bit.ly/3Gy20sX
Image from Oxford Nanopore Events (@NanoporeConf)
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Need lots and lots of reads from your @nanopore for copy number analysis of cancer genomes? Try short molecule sequencing! Impactful project with @TimourBaslan @samkovaka @sedlazeck @shgoodwin1 et al. academic.oup.com/nar/advance…
High resolution copy number inference in cancer using short-molecule nanopore sequencing

High resolution copy number inference in cancer using short-molecule nanopore sequencing

Abstract. Genome copy number is an important source of genetic variation in health and disease. In cancer, Copy Number Alterations (CNAs) can be inferred f

academic.oup.com
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Pan-genomic Matching Statistics for Targeted Nanopore Sequencing biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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DNA SEQUENCING: Complex targeted sequencing in real time go.nature.com/3rSXVbe #ResearchHighlight
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A very simple yet very effective approach: High resolution copy number inference in cancer using short-molecule @nanopore sequencing. Great work with @TimourBaslan @samkovaka @sedlazeck @shgoodwin1 et al. biorxiv.org/content/10.1101/… – at Clarksburg, MD
High resolution copy number inference in cancer using short-molecule nanopore sequencing

High resolution copy number inference in cancer using short-molecule nanopore sequencing

Genome copy number is an important source of genetic variation in health and disease. In cancer, clinically actionable Copy Number Alterations (CNAs) can be inferred from short-read sequencing data,...

biorxiv.org
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Want to find out about how a class project turned into an @NatureBiotech paper? Read this "Behind the Paper" blog post I wrote about the UNCALLED paper! bioengineeringcommunity.natu…
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A nice way to end two weeks of quarantine!
Michael Schatz (@mike_schatz) profile pictureMichael Schatz@mike_schatz30 Nov 2020
Excited to announce: Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Awesome work with @samkovaka, Yunfan Fan, @bohan_ni & @timp0 that will forever change how sequencing is done. @JHUCompSci @JHUBME @nanopore nature.com/articles/s41587-0…
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Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED biorxiv.org/cgi/content/shor… #bioRxiv
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StringTie2 from @samkovaka, @elapertea and co. An update of the popular reference-guided transcriptome assembler, now includes the ability to assemble long reads. It's more accurate than other assemblers, while being quicker with lower memory requirements genomebiology.biomedcentral.…
Image from Genome Biology (@GenomeBiology)
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