Chrystine, PhD
@joyeuphField Application Scientist @MGI_BGI, aspiring bioinformatician and poet but most of all a daydreamer. I make love in microlitres.
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Tried something new and although I didn't win any prizes, it was a fun experience besides doing science! PS - the 2nd half of the video is (unedited) done purely using command-line with a lot of programming tweaks. bridges.monash.edu/articles/prese… #visualizeyourthesis #vyt2020 #shrimp
Build a mini MiSeq i100 Series with us! Do you want to see the MiSeq i100 Series and maybe get a mini model of your own? Stop by our booth at #ASHG24!
STAMP Single-Cell Transcriptomics Analysis & Multimodal Profiling through Sequencing-free, Imaging-based #SpatialOmics system CosMx Xenium Single-cell suspension cytospinned to slides 100 ~ >1M cells ⏫cell capture ⏬doublets Able to identify ultra-rare cell population…
Just when you think you’ve seen most things in the lab… saw this outside the lab
Systematic comparison of sequencing-based spatial transcriptomic methods | Nature Methods nature.com/articles/s4159…
Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs frontiersin.org/articles/10.33…
Someone sent me an example of a Manhattan plot used in a GWAS study... 👀 seems legit...
A difference of 100-fold reduction in reagent consumption per cycle, which makes the system more cost effective than "traditional methods". The multivalency is key: the fluorophore is attached to many avidites.
A short video showing the cycle by cycle 100bp targetted sequencing of @ElemBio AVITI24 multi-omics instrument. It's called in vitro 3D ABC sequencing. #AGBT
1/ Do you want to gain practical computational biology skills in industry? I made this challenge for you buff.ly/48TcalB In this task, you are going to use public TCGA data to answer some questions on immune infiltration.
same library sequenced on @illumina #Novaseq6000 (PE250) and @ElemBio #aviti (PE300). what you are looking at are Phix error rates per cycle. #Aviti wins this round, I think
454.bio went the Open Source way for their DIY sequencer. 454.bio/blog/2024/01/2…
More on #LiquidBiopsy methods to increase the amount of cfDNA per blood sample science.org/doi/10.1126/sc…
With improvement in @nanopore basecalling we now get reads of Q20+ (soon Q30?). Are anyone actively working on establishing a standardized workflow for 16S rRNA gene #amplicon processing to generate OTUs/ASVs in the style of QIIME/Mothur/USEARCH? #bioinformatics
Spatial transcriptomics trade offs that sometimes are not realized. Here are some examples, simplified for twitter
Jokes aside I'm genuinely excited about ORA to replace fastq.gz soon. It would be a proper game changer since 2000 fastq first ever release: emea.illumina.com/science/genomi…
mosdepth calculates depth quickly from bam/cram. @LudvigOlsen added the ability to filter on fragment length (e.g. to count only cfDNA reads) for latest release: github.com/brentp/mosdept…
I'm excited to introduce Genomic Sequence Encryption (GSE): a DNA-based cryptography scheme in living cells! Using simultaneous multi-site base editing, we implement GSE in cell populations and individual stem cells. doi.org/10.1101/2023.1… 1/8
Based on the table of @AlbertVilella I created this graph of (minimum) sequencing cost vs (maximum) yield. Pretty strong correlation. Long read sequencing methods from @PacBio and @nanopore doing remarkably well #NGS #Bioinformatics.
Updated the #NextGenerationSequencing specs table now with the numbers of the NovaSeq X vs NovaSeq X Plus. The former can do 1 fcell at a time, including the 25B type. NovaSeq X Plus can do 2 fcells at a time.
Visualization of package dependencies in R, here e.g. DESeq2. My takeaways: -they can be enormous -the spectacular collaborativity of the R& BioC communities. Developers can reliably reuse inputs from 10s/100s of other projects, distributed around the world& across disciplines.
New blog post: Package dependencies in your R session jokergoo.github.io/2023/11/16/pac… The diagram below shows strong dependency relations when only loading Seurat in a new R session.
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