Explain Podcast

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/s41388-025-03624-5Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).Podcast Title: Explain PodcastCreators: Iuliia Novoselova, Daniel RickertWebsite: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

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/454bioElements new VITARI: https://www.elementbiosciences.com/products/preorder-vitari

We have the same thing at home!- yes, but in worse, cheaper or bothQitan:https://pmc.ncbi.nlm.nih.gov/articles/PMC8985760/https://www.qitantech.com/The QPinnacle2: https://www.vcbeathealth.com/article/1821CycloneSEQ, the MGI-internal clone:https://en.cyclone-seq.com/nanopTechhttps://www.prnewswire.com/news-releases/mgi-launches-new-nanopore-sequencing-products-with-advanced-cycloneseq-technology-302241816.htmlhttps://www.biorxiv.org/content/10.1101/2024.08.19.608720v1https://rrwick.github.io/2024/12/17/cycloneseq.htmlhttps://gigabytejournal.com/articles/154https://gigasciencejournal.com/blog/open-cycloneseq-benchmarking-for-complete-bacterial-genomes/Polyseq:https://polyseq.com/Axbio:https://www.axbio.cn/products/45.htmlGeneus-tech:http://www.geneus-tech.com/proddetail.aspx?id=1Nice not up-to-date table of specs:https://github.com/zhangtianyuan666/NanoporeReview2024ONT to double promethion throughput: https://www.genomeweb.com/sequencing/jpm-oxford-nanopore-shares-plans-double-flow-cell-output-expand-menu-biopharma-market

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.htmlhttps://www.alphagenomedocs.com/installation.htmlhttps://www.genomeweb.com/informatics/google-alphagenome-users-scrutinize-ai-models-ability-predict-variant-effectshttps://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-companiesVibecoding (current setup, top to bottom):https://claude.ai/newhttps://gemini.google.com/apphttps://duck.ai/If danger is something you enjoy, use this: https://openclaw.ai/YOU HAVE BEEN WARNEDPaper about old LLMs that can solve simple, old and solved bioinformatics problems:https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011511Youtube has useful bioinformatics courses:1: https://www.youtube.com/watch?v=3XFpxQF0J74&list=PLWVKUEZ25V95IKyBrxHtRTK_6Ig8Xi9-f2: https://www.youtube.com/watch?v=LvtPXZHNoCc&list=PLeB-Dlq-v6taAXK6ZCGfqImrNWJzFt3p3

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-illuminahttps://www.pacb.com/press_releases/pacbio-completes-sale-of-short-read-sequencing-assets/https://albertvilella.substack.com/p/pacbio-sells-short-read-ip-to-illuminaThe 6-base sequencing run:https://www.pacb.com/wp-content/uploads/PAG-5hmC-Portik.pdfhttps://www.nature.com/articles/s42003-025-07681-0ONT's P2 solo drama:https://omicsomics.blogspot.com/2026/01/p2-solo-ont-extends-support-but-not.html