Explain Podcast

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The Podcast Explain is for everyone interested in DNA/RNA sequencing or technology in general. As Iuliia doesn't have a solid background in sequencing, she keeps asking "simple" - even silly at times - questions and Daniel gives his best to make us understand.

  1. 9 oct

    The Epigenetics Epic - Part 1

    A long time coming, but here it is! Introduction: https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/Mechanisms: https://en.wikipedia.org/wiki/EpigeneticsDNA packaging: https://www.nature.com/scitable/topicpage/dna-packaging-nucleosomes-and-chromatin-310/Chromatin and gene regulation: https://learn.genetics.utah.edu/content/epigenetics/control/Histone writers, erasers and readers: https://www.nature.com/articles/emm201711DNA methylation, DNMTs and SAM: https://www.nature.com/articles/npp2012112Modified bases (5mC, N6-mA): https://en.wikipedia.org/wiki/DNA_methylationActive DNA demethylation (TET/TDG/BER): https://www.tandfonline.com/doi/full/10.1080/17501911.2025.2586452Bisulfite sequencing (WGBS): https://www.illumina.com/techniques/sequencing/methylation-sequencing/bisulfite-sequencing.htmlWGBS alignment benchmarking: https://www.sciencedirect.com/science/article/pii/S2001037022003853Illumina 5-base methylome sequencing: https://www.illumina.com/techniques/sequencing/methylation-sequencing/methylome-genome.htmlMethylationEPIC v2.0 array: https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.htmlInfinium 450K datasheet: https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_humanmethylation450.pdfPacBio HiFi methylation detection: https://www.pacb.com/revio/SMRT direct methylation detection: https://www.pacb.com/publications/direct-detection-of-dna-methylation-during-single-molecule-real-time-sequencing/Fiber-seq and cancer research: https://www.pacb.com/blog/what-a-clearer-view-of-epigenetics-can-mean-for-cancer-research/PacBio epigenetics overview: https://www.pacb.com/products-and-services/applications/epigenetics/Sequencing 101: Epigenetics: https://www.pacb.com/blog/sequencing-101-epigenetics/Oxford Nanopore modified-base calling: https://nanoporetech.com/applications/investigations/epigenetics-and-methylation-analysisNanopore sequencing accuracy: https://nanoporetech.com/platform/accuracyNanopore chromatin accessibility (EPI2ME): https://epi2me.nanoporetech.com/chromatin-acc-hg002/Nanopore 5mC/5hmC detection: https://www.nature.com/articles/s42003-025-07681-0Ultima Genomics (bisulfite, EM-seq, TAPS+): https://www.ultimagenomics.com/focus-areas/methylation-profiling/Watchmaker TAPS+: https://www.watchmakergenomics.com/taps.htmlElement AVITI methylation sequencing: https://www.elementbiosciences.com/applications/dna-sequencing/methylation-sequencingMGI DNBSEQ bisulfite sequencing: https://link.springer.com/article/10.1186/s13148-023-01543-4NEBNext EM-seq v2: https://www.neb.com/en-us/products/e8015-nebnext-enzymatic-methyl-seq-v2-kitNEBNext enzymatic 5hmC-seq: https://www.neb.com/en-us/products/e3350nebnext-enzymatic-methyl-seq-5hmc-kit5hmC detection overview: https://www.neb.com/en-us/products/epigenetics/methylation-analysis/5hmc-hydroxymethylationmeCUT&RUN: https://www.epicypher.com/product/cutana-mecutrun-kit-for-dna-methylation-sequencing/Fiber-seq chromatin profiling: https://www.epicypher.com/fiber-seq-long-read-sequencing/Fiber-seq + PacBio HiFi: https://www.pacb.com/blog/how-pairing-epicyphers-fiber-seq-with-hifi-sequencing-delivers-an-all-in-one-multiomic-view/MeDIP: https://www.activemotif.com/catalog/736/medipLINE-1 global methylation assay: https://www.activemotif.com/catalog/1043/global-dna-methylation-assay-line-1RRBS: https://www.nature.com/articles/nprot.2010.190DNA methylation biomarkers in liquid biopsies: https://www.nature.com/articles/s41388-025-03624-5 Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

    The Epigenetics Epic - Part 1

  2. 7 abr

    454.bio

    The open-source DIY Sequencer was here. Update: 454.bio is now dead, but the archives still have it: https://web.archive.org/web/20250723191639/https://454.bio/ Their GitHub: https://github.com/454bio Elements new VITARI: https://www.elementbiosciences.com/products/preorder-vitari

    454.bio

  3. 20 mar

    Special: other Nanopore Sequencing

    We have the same thing at home! - yes, but in worse, cheaper or both Qitan: https://pmc.ncbi.nlm.nih.gov/articles/PMC8985760/ https://www.qitantech.com/ The QPinnacle2: https://www.vcbeathealth.com/article/1821 CycloneSEQ, the MGI-internal clone: https://en.cyclone-seq.com/nanopTech https://www.prnewswire.com/news-releases/mgi-launches-new-nanopore-sequencing-products-with-advanced-cycloneseq-technology-302241816.html https://www.biorxiv.org/content/10.1101/2024.08.19.608720v1 https://rrwick.github.io/2024/12/17/cycloneseq.html https://gigabytejournal.com/articles/154 https://gigasciencejournal.com/blog/open-cycloneseq-benchmarking-for-complete-bacterial-genomes/ Polyseq: https://polyseq.com/ Axbio: https://www.axbio.cn/products/45.html Geneus-tech: http://www.geneus-tech.com/proddetail.aspx?id=1 Nice not up-to-date table of specs: https://github.com/zhangtianyuan666/NanoporeReview2024 ONT to double promethion throughput: https://www.genomeweb.com/sequencing/jpm-oxford-nanopore-shares-plans-double-flow-cell-output-expand-menu-biopharma-market

    Special: other Nanopore Sequencing

  4. 10 mar

    News: AlphaGenome, Vibecoding

    Artificial Intelligence everywhere, and sometimes its useful. Correction: apparently the Biostar Handbook is not free anymore :( AlphaGenome: https://omicsomics.blogspot.com/2026/02/non-coding-dnas-alpha-moment.html https://www.alphagenomedocs.com/installation.html https://www.genomeweb.com/informatics/google-alphagenome-users-scrutinize-ai-models-ability-predict-variant-effects https://deepmind.google.com/science/alphagenome/ Bioinformatics Forums: Bioinformatics mistakes on Biostars: https://www.biostars.org/p/7126/ Bioinformatics stackexchange: https://bioinformatics.stackexchange.com/ Seqanswers: https://www.seqanswers.com/forum/sequencing-technologies-companies Vibecoding (current setup, top to bottom): https://claude.ai/new https://gemini.google.com/app https://duck.ai/ If danger is something you enjoy, use this: https://openclaw.ai/ YOU HAVE BEEN WARNED Paper about old LLMs that can solve simple, old and solved bioinformatics problems: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011511 Youtube has useful bioinformatics courses: 1: https://www.youtube.com/watch?v=3XFpxQF0J74&list=PLWVKUEZ25V95IKyBrxHtRTK_6Ig8Xi9-f 2: https://www.youtube.com/watch?v=LvtPXZHNoCc&list=PLeB-Dlq-v6taAXK6ZCGfqImrNWJzFt3p3

    News: AlphaGenome, Vibecoding

  5. 20 feb

    News: PacBio, Illumina, Nanopore...

    When do you get your Illumina sticker for your ONSO? This is the first part of a two-parts news roundup. PacBio News: https://aseq.substack.com/p/pacbio-sells-short-read-tech-to-illumina https://www.pacb.com/press_releases/pacbio-completes-sale-of-short-read-sequencing-assets/ https://albertvilella.substack.com/p/pacbio-sells-short-read-ip-to-illumina The 6-base sequencing run: https://www.pacb.com/wp-content/uploads/PAG-5hmC-Portik.pdf https://www.nature.com/articles/s42003-025-07681-0 ONT's P2 solo drama: https://omicsomics.blogspot.com/2026/01/p2-solo-ont-extends-support-but-not.html

    News: PacBio, Illumina, Nanopore...

  6. 23/12/2025

    Array Sequencing

    For when matching and sticking is enough to get Links: Nice Youtube explainer: https://www.youtube.com/watch?v=NgRfc6atXQ8 Another nice one: https://www.youtube.com/watch?v=4bOY2Oh5tEQ Explaining this and more: https://berkeleygenomics.org/articles/How_many_human_genomes_have_been_sequenced_.html Since 2018, the West German Genome Center (⁠https://wggc.de/⁠) supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: ⁠https://ngs-kn.de/⁠) – network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

    Array Sequencing

  7. 18/11/2025

    Sequencing by Expansion (SBX)

    After 454 now the second try by Roche: Axelios. Preprint: https://www.biorxiv.org/content/10.1101/2025.02.19.639056v1 Read here about the PoC: https://www.pnas.org/doi/full/10.1073/pnas.1601782113 Current state (2025): https://www.nejm.org/doi/full/10.1056/NEJMc2512825 Correction: the 5B flow cell will arrive for the NovaseqX(+), not for the Nextseq2000 Also: PacBio makes sequencing cheaper: https://www.pacb.com/press_releases/pacbio-announces-major-advances-for-revio-and-vega-to-lower-genome-cost-and-expand-multiomic-capabilities/⁠ Roche about SBX: https://sequencing.roche.com/global/en/article-listing/sequencing-platform-technologies.html Roche from a conference: https://www.youtube.com/watch?v=YN2meswiCiQ Since 2018, West German Genome Center (⁠https://wggc.de/⁠) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: ⁠https://ngs-kn.de/⁠) – network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

    Sequencing by Expansion (SBX)

  8. 02/10/2025

    News: 23andMe

    This time something different. Sources: https://www.23andme.com/privacy/ https://verbraucherschutzforum.berlin/2025-03-25/23andme-meldet-insolvenz-an-was-nutzer-jetzt-wissen-sollten-357738/ https://en.wikipedia.org/wiki/23andMe_data_leak https://www.cshub.com/attacks/news/23andme-hacker-leaks-data https://www.cbsnews.com/news/dna-privacy-at-home-tests-23andme-ancestrydna-sell-data-to-third-parties/ https://techcrunch.com/2025/03/24/23andme-faces-an-uncertain-future-so-does-your-genetic-data/ https://www.theverge.com/2024/9/13/24243986/23andme-settlement-dna-data-breach-lawsuit https://newsroom.regeneron.com/news-releases/news-release-details/regeneron-enters-asset-purchase-agreement-acquire-23andmer-256/

    News: 23andMe
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The Podcast Explain is for everyone interested in DNA/RNA sequencing or technology in general. As Iuliia doesn't have a solid background in sequencing, she keeps asking "simple" - even silly at times - questions and Daniel gives his best to make us understand.

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  • Creador
    explain.pod
  • Años de actividad
    2023 - 2026
  • Episodios
    29
  • Clasificación
    Apto
  • Copyright
    © explain.pod
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    Explain Podcast

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