Wet lab scientist, into all kinds of microbiology and sequencing. Tweets are my own.

København, Danmark
Joined June 2016
Last day on X for me, the posts in here are getting more and more crazy. The amount of bots is insane at this time. Hope the alternatives will provide more of the old twitter spirit.
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We are happy to test it out and see what the future brings! So far we are relieved to see it handle all the different species we throw at it. I’m super thankful for the ONT Nordic and implementation team, a smooth ride so far. @nanopore @Rigshospitalet #turbot
TurBOT's ready to go! The team at @RegionH are leveraging the fully automated, cutting-edge device to enhance their microbial and clinical research capabilities. Learn more about TurBOT: bit.ly/3wDdL12 More updates coming next week at #nanoporeconf. @Born2bewildtype
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I don’t know if it ever will feel normal to place your samples on the machine and just go home 😀 It truly is walk away and come back next day and look at the sequencing report.
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Martin S. Pedersen retweeted
TurBOT's ready to go! The team at @RegionH are leveraging the fully automated, cutting-edge device to enhance their microbial and clinical research capabilities. Learn more about TurBOT: bit.ly/3wDdL12 More updates coming next week at #nanoporeconf. @Born2bewildtype
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Kindly: please retweet if you see this important notice. Today at @officialatcc, we announced a change to the access model for the ATCC Genome Portal (genomes.atcc.org). In order to maintain its long term sustainability, we are transitioning to a Supporting Membership access model on May 1st, 2024. Members, groups, or institutions who opt in to support the AGP will continue to have access to ALL our microbial genomics data, our REST-API, recieve quarterly updates as we release new authenticated genome references to the portal (~1,000 new genomes per year), and get access to new tools for assessing the quality and accuracy of existing genomics data and reference genomes. We have many such tools on the roadmap, the first of which will be Descrepency Report tool that will compare raw sequencing data provided by end-users against our reference genomes, and provide both an easy to interpret (human-readible) report (PDF) and a machine-readable JSON, BAM, BED, and VCF files. More tools, additional data types, phenotypic data, and extensive re-curation efforts are planned, but I would love to hear feedback about what sorts of things might be of most use to you. Finally, access to the entire database and tools we develop doesn't require purchasing physical materials from ATCC, only that you opt-in to be a supporting member. For ATCC customers who decide not to opt-in for supporting the ATCC Genome Portal, we will still provide them with access to authenticated reference genome assemblies for the microbes they purchase from ATCC. So, if you purchased (for example) a bacterial strain from ATCC in the past, you will be able to still access the reference genome, annotations, and metadata for that strain directly from the ATCC Genome Portal. It's extremely important that we continue to provide customers with access to verified/authenticated reference genomes for the materials they obtain from us. These data is produced by our ISO-certified genomics lab (the ATCC Sequencing & Bioinformatics Center, my group ☺️), and is not found anywhere else. The last three years has been a wild ride as we started sequencing the entire collection. About 30% of the microbes we've sequences have never been sequenced before by anyone anywhere in history. It's very cool when you think about it! ☺️ And - wow... my team has grown from 5 to 20 in that time, and both our sequencing and bioinformatics capabilities have increased by orders of magnitude. This has been, and continues to be, a major investment by ATCC into the authenticity of both our biological materials and the data associated with those organisms. I'm really looking forward to the next three years too - and beyond - as we continue to sequence all these interesting bugs. But do to this, we'll need the help of the community to continue supporting this extensive program. I'm very happy to answer questions and take suggestions from the community as well - so please feel free to send me DM via Twitter or LinkedIn (see profile for link). And thanks again to everyone for their continued support 🥰🧬 -- Jonathan #genomics #microbiology #bioinformatics #dataprovenance #science #reproducibility #bacteriology #virology #mycology genomes.atcc.org
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Martin S. Pedersen retweeted
We have a strong interdisciplinary team of wet-lab, bioinformaticians, and data scientists - but will be hiring several positions to help us realize this bold mission! Reach out if you want to develop the next long-read based @nanopore @PacBio genome-centric metagenomics methods!
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Martin S. Pedersen retweeted
An international cohort of scientists, many of whom helped propose the new #monkeypox clade names in June, have formed a group to designate new monkeypox lineages. Initially, 5 new lineages stemming from the B.1 ('outbreak') clade have been designated. 1/12
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Martin S. Pedersen retweeted
Coverage at 30x coverage depth: - Ct value <20:>99% - Ct value 20-25: 98% coverage (drop-out primer 22) -Ct value 25-30: >94,5% coverage (drop-out primer 22, 29 and 50) Coverage (depth) plots: 3
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Martin S. Pedersen retweeted
The PCR tiling method contains out of: - 2 pools - 44 primer sets per pool (88 in total) designed by Martin S Pedersen ( @Born2bewildtype ) from @Rigshospitalet Copenhagen, Denmark - Generating 2.5 kB amplicon fragments covering the whole genome of Monkeypox 2
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Martin S. Pedersen retweeted
Together with @amsterdamumc @Flahless1 @viroloog we developed a PCR tiling method for #Monkeypox using @nanopore. Method is tested on 40 monkeypox samples in a 42 minute #NextGenPCR program. This method is inspired by Midnight, @freed_nikki and @NetworkArtic 🧵 First data⬇️
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Martin S. Pedersen retweeted
Danish Covid-19 Genome Consortium modtager årets Fritz Kauffmann pris for deres omfattende arbejde med covid-19-data. Et arbejde som fik international betydning. ssi.dk/aktuelt/nyheder/2022/…
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Martin S. Pedersen retweeted
Wanna do your Postdoc on RNA viruses? In a pleasant, ambitious and international environment? In wonderful Copenhagen? With a lab view all the way to Sweden? Apply here: 👇 jobportal.ku.dk/phd/?show=15… Deadline 20 Feb! #virus #RNA #postdoc 🧪🧬🔬💊
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Martin S. Pedersen retweeted
Wanna do your PhD on RNA viruses? In a pleasant, ambitious and international environment? In wonderful Copenhagen? With a lab view all the way to Sweden? With this great crowd? Apply here: 👇 jobportal.ku.dk/phd/?show=15… #virus #RNA #PhD #jobs @uni_copenhagen @UCPH_health
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Martin S. Pedersen retweeted
2022: A Wild Year for Short Reads?omicsomics.blogspot.com/2022…
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Enjoy the game, Munich💪Tonight, we’ll turn on the lights to celebrate diversity. With love from Copenhagen 🌈 #euro2020 #gerhun
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Before SARS-CoV-2 took over, we developed a Cell culture system for hepatitis C virus genotype 4 that is finally out in @Gut_BMJ . If SARS-CoV-2 is your first RNA virus encounter then you will love the diversity in Hepatitis C virus. #openaccess gut.bmj.com/content/early/20…
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Martin S. Pedersen retweeted
Replying to @firefoxx66
We are working hard to get the DK human-related sequences on GISAID as we speak (Got approval to resume upload last week). We have sequenced 25% of all positive cases in DK. Note: we are not involved in the specific case, so we know as little as you. covid19genomics.dk/
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Martin S. Pedersen retweeted
For anyone doing SARS-CoV-2 genome sequencing (Nanopore or Illumina) - the primer pool we (@freed_nikki & @m_vlkova) designed for superfast and supereasy genome sequencing is now available from @idtdna as: SARS-Cov2-Midnight-1200, 500rxn, Product no. 10007184.
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Martin S. Pedersen retweeted
Hi there! I am officially looking for a postdoc abroad (great timing!). My expertise is in animal #microbiome (mainly skin and GI 🐕) and I have been playing with #nanopore sequencing 🧬 for a while. I would love to expand my #metagenomics knowledge. Please RT & many thanks!
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