I haven't posted in a while, and i was in grind against OptKnock so i couldn't do it but i am back! and i have the progress updated!✨ it was mostly about learning, and intro to Metabolic Engineering, and using COBRApy. (and alot of code debugging XD). 🖥️ Check it out! 🚀

Project Menhed Update #1: The Math Won (For Now)

The Silence (And The Grind)

djosergenomics.github.io

Introducing Project Menhed 🎨 Ancient Egyptian scribes used a palette (Menhed) to mix ink. I'm using Python to mix genes. Phase 1: Design a bacteria that produces a Red Dye with high efficiency & 100% In Silico. I'll share Updates Publicly Read More 👇 djosergenomics.github.io/Introducing-...

Tried out Google's Antigravity today! For a while wanted to introduce a dark mode for the @djosergenomics.github.io Website so decided to let Antigravity's AI Agent take on the task and it performed very well done. Saved me a lot of time indeed! djosergenomics.github.io

Week 4 of HTGAA (Protein Design) is done & I'm amazed! I was always intimidated by 3D protein models in papers & never thought I'd understand them one day! Today, I loaded a PDB file into PyMOL, saw the alpha helices & beta sheets of my Tyrosinase enzyme. This is so cool. 🚀 #HTGAA #proteindesign

I'm really enjoying the HTGAA course so far 🥳

Djoser Genomics@djosergenomics.github.io · 11mo ago

Week 3 of HTGAA is all about lab automation! 🤖 I wrote a script to program a virtual Opentrons robot to draw my Djoser Genomics pyramid. It simulates robots pipetting 100+ dots of fluorescent E.coli because manually it is slow & error-prone. #HTGAA #synbio #Opentrons #automation #bioinformatics

🥳 Happy 1st Birthday to Djoser Genomics! 🥳 From starting Djoser Genomics, Learning and Exploring Various Projects, to publishing my first preprint and creating the Bulk RNAseq Tutorial Codex! Thank you for being part of this journey so far. Here’s to Year Two. 🚀 #Bioinformatics #DjoserGenomics

Djoser Genomics: Year One

Today marks Djoser Genomics’ 1st Birthday.

djosergenomics.github.io

🎊 Scroll 1 of Djoser’s Bulk RNAseq Tutorial Codex: Imhotep's Insights 🎊 We start by collecting real RNA-seq data from ENA using Google Colab. Inspired by Imhotep - ancient Egypt’s architect of the Pyramid of Djoser. 📜 Check it out: djosergenomics.github.io/Scroll-1-Imh... #bioinformatics #RNAseq

I'm planning on making a series of mini blog tutorials on bulk RNAseq, they'll be beginner friendly to help someone who's just starting. I'm also planning to theme it around ancient Egypt just like Djoser ;D So stay tuned! #Bioinfomatics #RNAseq

🚀New Blog Post! Just finished a training project on variant calling using zebrafish data from @uofglasgow.bsky.social study on fisheries selection (PRJNA630223) Walked through the full pipeline: QC → alignment → variant calling → VEP annotation #Genomics #Zebrafish #Bioinformatics #VariantCalling

Discovering Mutations in fisheries-induced Selection of Zebrafish

Zebrafish Variant Calling Training Project

djosergenomics.github.io

📚Looking for some textbooks or reviews for learning genomics, gene editing, and molecular biology. Trying to build a solid foundation, Any recommendations?

⚙️ Back to Training! This time, I’m diving into Genomics & Variant Calling. I’ll share some insights throughout my learning process and present some of my findings 🔍 This time I'll be going with a Marine Theme 🐟 Stay tuned. #Bioinformatics #Genomics #Variants #Mutation #Marine #Fish

Broke down the key findings, plots, and major themes from the SCG reanalysis into a blog post for anyone not up for the full RNAseq reanalysis preprint 🖥️🧬 Read it here: djosergenomics.github.io/Human-SCG-RN... #bioinformatics #rnaSeq #transcriptomics

When Heart Disease Meets the Nervous System: Uncovering Immune Signatures in the Superior Cervical Ganglion

Djoser Genomics: Advancing Transcriptomics & Bioinformatics, One Step at a Time

djosergenomics.github.io

A major milestone: my first RNAseq preprint is now live on bioRxiv 🎉🎊 I reanalyzed public data from the human SCG to uncover neuroimmune signatures during cardiac disease.🧬🖥️ This was an awesome learning experience and I am excited use everything I learned for new project ideas :D. #Bioinformatics

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

Transcriptomic Signatures of Neuroinflammation and Adaptive Immunity in the Human SCG During Cardiac Disease: A Bulk RNA-seq Reanalysis https://www.biorxiv.org/content/10.1101/2025.05.18.654713v1

Trying to level up my ability to extract biological insights from GSEA results, FEA GO terms, & my list of DEGs. Any tips or recommended approaches for making sense of the data and connecting it to real biological mechanisms? Would love to hear how others tackle this! 🧬🖥️🔬 #Bioinformatics #RNAseq

🚨 Differential Expression Analysis (DEA) results! 🚨 My analysis compares healthy samples (HS) vs. cardiac disease (CD) samples. 🔬🧬 Time to dive into the key findings and visualizations—let's see what the data reveals! 📊 🖥️ #Bioinformatics #RNAseq

Please share 🧪 We seek 2 postdocs to work on Vancouver Island marmots in the following areas : 1 - demographic models. 2 - conservation genomics. Positions based at UNBC, working with MRF. Full details here marmots.org/recovery-eff... #conservation #jobs

New RNA-seq Project! 🧬 Reanalyzing PRJNA967653 from the Technical University of Munich to explore how cardiac disease disrupts sleep cycles & melatonin levels via the superior cervical ganglia (SCG). 🖥️ Uncovering key genes & pathways behind this disruption. Stay tuned! 🔬✨ #Bioinformatics #RNAseq

🚀 Just wrapped up the DIY Transcriptomics course! It’s been an incredible dive into RNAseq, learned alot about kallisto, QC, differential expression, heatmaps, volcano plots, FEA, GSEA & more. Now, it's time to put this to work in my next RNAseq project. Stay tuned! 🧬🖥️ #Bioinformatics #RNAseq

The First Milestone of my Djoser Genomics Journey 🎉🎉

Djoser Genomics@djosergenomics.github.io · 2y ago

🚀 Exciting news! The Djoser Genomics website is now live at djosergenomics.github.io 🖥️🧬 This will be the central hub for all my bioinformatics articles, guides, & projects. Whether you’re a Student, Researcher, Lecturer, or just want to follow my journey, this is the place to be! #Bioinformatics

It is important that we take this poll www.nature.com/articles/d41...

Has Bluesky replaced X for scientists? Take Nature’s poll

The research community has flocked to the social-media platform Bluesky. Tell us about your experience.

nature.com

Kelp farming has completely captured my interest lately! Especially after I took the introduction to seaweed course on coursera. Its environmental benefits & beauty are so inspiring. Hoping to visit a kelp farm someday and see this amazing process up close! #KelpFarming #Aquaculture

Stuart Ryan@skeeberr.bsky.social · 2y ago

Hey Bluesky! I’m an oyster and kelp farmer in Maine. I haven’t seen much aquaculture content here yet, so here’s a quick video of seeding my kelp farm recently. Seed line is densely covered in tiny kelp sporophytes. By May they will grow 6-8 feet long! #kelp #kelpfarming #Aquaculture #Maine

🚀 From Zero to Bioinformatics Beginner🧬 From knowing nothing to completing beginner projects The transformation feels incredible!🎉 Each step no matter how simple, has been a giant leap forward for me This journey is just starting, & I’m excited to push further in 2025 🖥️✨ #Bioinformatics #Genomics

📣 Project Update 🧬🖥️: I started by aligning using HISAT2 & then sorted & Marked Duplicates in my BAM files. Then FeatureCounts to quantify gene expression. Then, I ran DESeq2 for differential expression analysis. #Bioinformatics #RNAseq

Super Excited to use what I learned in the previous project and see if I can pull this one off :D #Bioinformatics #RNAseq

Djoser Genomics@djosergenomics.github.io · 2y ago

🧬 Excited to dive into my next training project! 🖥️ Exploring how melatonin alleviates TNF-α-induced damage in human coronary artery endothelial cells (HCAECs) using RNA-seq. (PRJNA760433) Data from Fudan University. Stay tuned for updates as i process the data 🚀 #Bioinformatics #RNAseq

Excited to announce my next RNAseq project! 🧬🖥️ This time, I'll be analyzing data from a more common organism (humans or mice) to deepen my understanding of transcriptomics If you have suggestions for accessible beginner RNAseq datasets or studies, Please share them! #RNAseq #Bioinformatics

as a kid, i fixed my parent's computer. as an adult I fix my kids's computer. pretty sure we are the only gen that knows how computers work