@_adameur

Associate professor @scilifelab Uppsala University. Computational biology and sequencing technologies with focus on medical applications @adameur.bsky.social

 Sweden
Joined February 2016
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The final program for the Long-Read Uppsala Meeting 2024 (#LRUA24) on Oct 21-23 is now online: lrua2024.se/ Over 300 participants have already signed up but there is still time to secure a place!
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Thrilled to share my first review in @NatureGenet with my supervisor @anaconesa: “Profiling the epigenome using long-read sequencing” under @MSCActions! We highlight how #LongReadSeq reveals new insights into DNA methylation & chromatin states. Read here: doi.org/10.1038/s41588-024-0…
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Release of DeepVariant 1.8. Large speed improvement (~67% faster) via small model for easy sites. New Pangenome-aware option. Reduces error by ~30% for vg-mapped WGS ~10% for BWA WGS ~5% BWA exome. New config for custom model users, see release notes 1/3 github.com/google/deepvarian…
Runtime figure for new version of DeepVariant with and without small model. Showing reduction in runtime of 155 minutes to 101 minutes with Illumina, 174 minutes to 71 minutes with PacBio, and 295 minutes to 114 minutes with Oxford Nanopore.

ALT Runtime figure for new version of DeepVariant with and without small model. Showing reduction in runtime of 155 minutes to 101 minutes with Illumina, 174 minutes to 71 minutes with PacBio, and 295 minutes to 114 minutes with Oxford Nanopore.

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The Long-read sequencing Special Issue is now LIVE! Guest-edited by @ahoischen, @sedlazeck, and @anaconesa!
Genome Research@genomeresearch20 Nov 2024
SPECIAL ISSUE! This month @genomeresearch publishes a diverse collection of research and review articles in a special issue highlighting advances in long-read sequencing applications in biology and medicine. tinyurl.com/Genome-Res-34-11.
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New from the lab with @sedlazeck. Brilliant analysis by ⁦@MichalIzydorcz1⁩ of long read ⁦@nanopore⁩ WGS from single human brain cells, after droplet MDA amplification in the Samplix X-drop. Funded by ⁦@ASAP_Research⁩ ⁦@UCLIoN⁩ medrxiv.org/content/10.1101/…

Single cell long read whole genome sequencing reveals somatic transposon activity in human brain

The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound...

medrxiv.org
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Surprised to see that misconceptions about long reads are still around. Maybe I'm living in a bubble.. This from a new paper: nature.com/articles/s41551-0…. Not saying anything about their work but this info is way outdated
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Revio Refresh - my latest conversation with @PacBio CEO Christian Henry omicsomics.blogspot.com/2024…
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🤝@MariekeVromman ⭕️🧬 Very happy to share that our review on extracellular circRNAs is now out in WIREs RNA! We summarize the little that is known, navigate their daunting literature, and dive into hypotheses on their extracellular existence! onlinelibrary.wiley.com/shar…
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In Sweden, we've been running a nationwide pilot project using @PacBio WGS for rare disease. Check out our results in this new paper! genome.cshlp.org/cgi/content…
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#LRUA24 has come to an end!🧬 Three days of incredible science and lots of fun. Huge thanks to all speakers, participants, and sponsors. Hope to see you back in Uppsala 2026!
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Fran from the @EarlhamInst kicked off the long read transcriptomics workshop at #LRUA24 discussing @PacBio library prep method, as well as important tips and tricks for high quality data🧬 @LongtrecEU
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#LRUA24 @CarolaGreve @LOEWE_TBG Whippet #genome with @PacBio in record time of 7 days @erga_biodiv @EBPgenome 🐕🧬
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Long reads transcriptomics workshop starting at #LRUA24 @LongtrecEU
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Adam Ameur retweeted
Ida Höijer@idaista23 Oct 2024
Last day of #LRUA24 and it's a beautiful crisp morning in Uppsala. Let's dive into the workshops hosted by our gold sponsors @PacBio @nanopore
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New preprint! With a large group of Swedish colleagues, we present a vision for Precision Omics Initiative Sweden, PROMISE, to build powerful national research data resources, and a research, healthcare and innovation ecosystem around them. 1/ papers.ssrn.com/sol3/papers.…
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What the **** ! Such an amazing opportunity to present our research to a crowd of amazingly smart people in a mind-blowing venue at LRUA in Uppsala 🇸🇪 What a HIT this ‘assembly’ was! 🧬 #LRUA24
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Fantastic talks by @anaconesa , @hagentilgner and others in this afternoon's RNA and #singlecell session chaired by @WHaerty - leaving today equipped with more information on long read data biases and spatial detection of isoforms in single cells #LRUA24
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Adam Ameur retweeted
Ida Höijer@idaista22 Oct 2024
Good morning Uppsala! @timp0 starts the morning session at #LRUA24 talking about how methylation data produced by sequencing native DNA can be used.
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Does DNA (or RNA) hold all the secrets about life and its fundamentals? What better place to learn more than at #LRUA24 in Upasala, a conference on long read sequencing at such a fancy location!
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What a stage! ✨ @Somar1987 presenting our #PacBio intro talk this morning at #LRUA24. If you have any follow-up questions, make sure to stop by our booth. #HiFiSequencing
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