iiinova — where your digital self keeps evolving

Djoser Genomics @djosergenomics.github.io · 12/01/2026

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! 🚀

djosergenomics.github.io

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

The Silence (And The Grind)

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Djoser Genomics @djosergenomics.github.io · 07/12/2025

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-...

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Nourelden Rihan @noureldenrihan.bsky.social · 23/11/2025

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

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Djoser Genomics @djosergenomics.github.io · 11/11/2025

Part of HTGAA Week 4 is to write a proposal on an In-silico Bacteriophage Engineering. My proposal: 'ArmoredPhage' 🛡️ My goal: Engineer a Thermostable MS2 Bacteriophage Using Protein Design Techniques. Check it out: djosergenomics.github.io/Armored-Phag... #HTGAA #synbio #AlphaFold #proteindesign

A Schematic Showing a Brief Overview of the Proposed Pipeline

PyMOL Visualization showing the full icosahedral 'shell' of the MS2 bacteriophage (PDB: 2MS2).

PyMOL Visualization showing a single 'monomer' or 'building block' of the MS2 capsid protein. (Yellow is Beta Sheets, Red is Alpha helices, Green is in between loops)

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Djoser Genomics @djosergenomics.github.io · 11/11/2025

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

PyMOL Visualization of Structures of Tyrosinase Enzyme (Red Alpha Helices, Yellow Beta Sheets, Green In between Loops) (PDB ID: 3NM8)

PyMOL Visualization of Active Sites of Tyrosinase (Copper (II) ions in Orange) - Transparency = 0.35 (PDB ID: 3NM8)

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Djoser Genomics @djosergenomics.github.io · 31/10/2025

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

Djoser Genomics Step Pyramid Drawn by Opentrons virtual robot

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Djoser Genomics @djosergenomics.github.io · 23/10/2025

I am going to audit the How to Grow Almost Anything (HTGAA) course for my first introduction to my Synthetic Biology journey. I just did the Bio Bootcamp, & i really loved the interactive sessions on Benchling and Opentrons. Super Excited for more! #SyntheticBiology #Bioengineering #MIT #HTGAA

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Djoser Genomics @djosergenomics.github.io · 18/10/2025

I decided to take a deep dive into Synthetic Biology, Bio & Genetic Engineering, something I've wanted to learn for a while. I believe it holds incredible potential & innovation for the future if used correctly Got any tips or resources? :D #SyntheticBiology #Bioengineering

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Djoser Genomics @djosergenomics.github.io · 17/10/2025

Introducing Field Notes from the Step Pyramid! The target is a space where I can document and share my thoughts, experiences, dreams, & struggles as I navigate through bioinformatics & computational biology. I will also share snippets from it here to be able to engage with others and learn more.

djosergenomics.github.io

Field Note 00: Dispatch from the Step Pyramid

Hey everyone 👋 So, something new is happening at Djoser Genomics.

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Djoser Genomics @djosergenomics.github.io · 16/10/2025

Been busy with final exams in med school for the last couple of weeks, still not done! But I'll have some time to get back here :) I've got some new projects and ideas that I'm excited about, so stay tuned! :D

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Djoser Genomics @djosergenomics.github.io · 16/09/2025

🥳 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

djosergenomics.github.io

Djoser Genomics: Year One

Today marks Djoser Genomics’ 1st Birthday.

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Djoser Genomics @djosergenomics.github.io · 20/08/2025

🎉 The Bulk RNAseq Tutorial Codex is now complete! 🎉 From dataset discovery all the way to enrichment analyses Every scroll 📜 is now available, covering alignment, quantification, DEGs, visualization & everything in between The Codex is yours to explore ✨ #RNAseq #Bioinformatics #scicomm

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Rhys White @rhystwhite.bsky.social · 18/08/2025

New Zealand’s prescribing habits likely helped create a homegrown #MRSA 🇳🇿🧬💊 Now ‘AK3’ has been detected overseas Our recent study shows how it evolved & how #Genomics can help reduce the impact of the next ‘superbug’ #AMR is an issue for everyone #SciComm 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠

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Djoser Genomics @djosergenomics.github.io · 15/08/2025

📜 Scroll VIII: Djoser's Discoveries! The Grand Finale, we dive into Gene set Enrichment Analysis (GSEA), why we do it, how we do it and how to visualize and interpret it. Check it out: djosergenomics.github.io/Scroll-8-Djo... #bioinformatics #RNAseq #scicomm

Scroll 8 of Bulk RNAseq Tutorial Codex: Djoser's Discoveries

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Djoser Genomics @djosergenomics.github.io · 15/08/2025

📜 Scroll VII: Thutmose's Trends! Here, We identify Trends among our DEGs using Functional (GO) and Pathway (KEGG) Enrichment Analysis! Check it out: djosergenomics.github.io/Scroll-7-Thu... #bioinformatics #RNAseq #scicomm

Scroll 7 of Bulk RNAseq Tutorial Codex: Thutmose's Trends

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Djoser Genomics @djosergenomics.github.io · 14/08/2025

📜 Scroll VI: Ramses' Plots! We dive into Visualizations! MA, PCA, Volcano Plots and Heatmaps! Check it out: djosergenomics.github.io/Scroll-6-Ram... #bioinformatics #RNAseq #scicomm

Scroll 6 of Bulk RNAseq Tutorial Codex: Ramses' Plots

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Djoser Genomics @djosergenomics.github.io · 12/08/2025

📜 Scroll V: Menkaure's Measures! We dive into Differential expression analysis (DEA), using DESeq2, and how to interpret the findings Check it out: djosergenomics.github.io/Scroll-5-Men... #bioinformatics #RNAseq #scicomm

Scroll 5 of Bulk RNAseq Tutorial Codex: Menkaure's Measures

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Reposted by Djoser Genomics

Fios Genomics @fiosgenomics.bsky.social · 11/08/2025

Q: What can we learn about plants via metabolomics analysis? 🌱🤔 A: Lots of interesting and useful things! Read our blog to find out what they are: www.fiosgenomics.com/plant-metabo... #metabolomics #plantmetabolomics #metabolomicsanalysis #bioinformatics

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Djoser Genomics @djosergenomics.github.io · 09/08/2025

📜 Scroll IV: Khafre’s Connections is here! We step into the next stage of our RNAseq journey! Importing Kallisto results into R, linking them to gene annotations, & building a strong foundation for downstream analysis Here: djosergenomics.github.io/Scroll-4-Kha... #bioinformatics #RNAseq #scicomm

Scroll 4 of Bulk RNAseq Tutorial Codex: Khafre’s Connections

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Djoser Genomics @djosergenomics.github.io · 07/08/2025

🧬 Scroll 3 of the Bulk RNA-seq Tutorial Codex is here! ⚒️ Guided by King Khufu, we pseudoalign our reads using Kallisto — fast, efficient, and accurate. 🌐 Full tutorial + cultural spotlight: 📜 djosergenomics.github.io/Scroll-3-Khu... #RNAseq #bioinformatics #scicomm

Scroll 3 of the Bulk RNA-seq Tutorial Codex: Khufu's Calculations

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Djoser Genomics @djosergenomics.github.io · 05/08/2025

🔍 Scroll 2 of Djoser’s Bulk RNAseq Tutorial Codex is here! We dive into RNA-seq Quality Control with FASTQC — guided by Hesy-Ra, the first known dentist & physician in history. 🧪 Read here: djosergenomics.github.io/Scroll-2-Hes... #bioinformatics #RNAseq #scicomm

Scroll 2 of Djoser’s Bulk RNAseq Tutorial Codex: Hesy-Ra's Diagnostics

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Djoser Genomics @djosergenomics.github.io · 05/08/2025

Did you know? 🧠 The Original Step Pyramid that inspired our logo was designed by Imhotep — the same ancient figure featured in Scroll 1 of our Bulk RNAseq Tutorial Codex. Dive in Now ↓ #RNAseq #Bioinformatics #SciComm

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Djoser Genomics @djosergenomics.github.io · 05/08/2025

🎊 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

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Djoser Genomics @djosergenomics.github.io · 04/08/2025

🧬 Introducing the Bulk RNA-seq Tutorial Codex. A step-by-step series where I guide you through real transcriptomics analysis, one scroll at a time. Check out the blog post and follow the codex 👉 djosergenomics.github.io/Bulk-RNAseq-... #Bioinformatics #RNAseq #scicomm

djosergenomics.github.io

Djoser’s Bulk RNAseq Tutorial Codex

A beginner friendly bulk RNAseq tutorial series told through step by step guides and inspired by ancient Egyptian History.

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Djoser Genomics @djosergenomics.github.io · 02/08/2025

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

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Narita Lab @narita-lab.bsky.social · 29/07/2025

Only a few days left to apply to join our lab and do exciting senescence research at the University of Cambridge Cancer Research UK Cambridge Institute @cruk-ci.bsky.social @cam.ac.uk 🧪🧬 You can also send informal enquiries (info below): www.jobs.cam.ac.uk/job/52026/ www.jobs.cam.ac.uk/job/52027/

media.tenor.com

a cartoon character is surrounded by cats and the caption says when someone asks you what your dream job is

ALT: a cartoon character is surrounded by cats and the caption says when someone asks you what your dream job is

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Narita Lab @narita-lab.bsky.social · 25/07/2025

Spread the news! We are excited to expand our research team, working on cellular senescence, at the Cancer Research UK Cambridge Institute, University of Cambridge. jobs.cam.ac.uk/job/52026/ jobs.cam.ac.uk/job/52027/

media.tenor.com

a yellow sign that says we 're hiring

ALT: a yellow sign that says we 're hiring

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Mallory Freeberg @malloryfreeberg.bsky.social · 26/07/2025

🧬💻 We're hiring a #Software #Developer @emblebi.bsky.social! Join the @deciphergenomics.bsky.social team building tools for global rare disease diagnosis & research. Work that matters, in a collaborative environment. 👉 Apply: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... ⏰ Deadline: 10 August

embl.wd103.myworkdayjobs.com

Software Developer

In this role, you will have the opportunity to develop domain area expertise in human genetics while working with a modern technology stack. You will design, develop and support the DECIPHER platform,...

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Djoser Genomics @djosergenomics.github.io · 23/07/2025

🚀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

djosergenomics.github.io

Discovering Mutations in fisheries-induced Selection of Zebrafish

Zebrafish Variant Calling Training Project

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Djoser Genomics @djosergenomics.github.io · 08/07/2025

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

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Reposted by Djoser Genomics

Gael Cristofari @retrogenomics.bsky.social · 11/07/2025

🦟 Bioinformatics Research Scientist position open in my lab in Nice (FR) to study Aedes mosquito retrotransposons & their interactions with arboviruses collab w/ @salehlabparis.bsky.social & @lambrechtslab.bsky.social Apply: euraxess.ec.europa.eu/jobs/359830 Please boost! #ArboRetro #Bioinformatics

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hsiehyp.bsky.social @hsiehyp.bsky.social · 10/07/2025

Exciting news! I am launching the Lab of Polymicrobial Interaction & Evolution at IPMB at Academia Sinica (ipmb.sinica.edu.tw/en)! 🎉Our brand-new website is live: (www.labofpie.org). Check the lab of PIE out!!🥧🎈

ipmb.sinica.edu.tw

IPMB | 中央研究院植物暨微生物學研究所

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Ming Tommy Tang @tommytang.bsky.social · 09/07/2025

I had a roadmap for biology -> computation. What about the reverse? Many with a computer science background are asking: where should they start to learn biology?

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Djoser Genomics @djosergenomics.github.io · 08/07/2025

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

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Djoser Genomics @djosergenomics.github.io · 29/06/2025

I learned how to read .vcf files, predict mutation effects with VEP, and rank mutation damage using SIFT & PolyPhen. 🥳 Will be diving in real zebrafish datasets soon 🔥 #genomics #bioinformatics #mutations

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Dr. Ali Barry @aliibarry.com · 16/06/2025

Happy preprint day! We have a new transgenic & some sensory neuron compartment proteomics to share #TeamMassSpec www.biorxiv.org/content/10.1...

Schematic of the linked paper. AdvillinCre; TurboIDfl/fl mouse was used to biotylinate proteins in advillin+ cells (ie. sensory neurons), represented by stars in the schema, which were then enriched (eppendorf clipart) and put into a mass spectrometry (DIA-PASEF) to generate a neuronal-enriched proteome

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Djoser Genomics @djosergenomics.github.io · 27/06/2025

I just learned how to navigate the ensemble genome browser, and I am very happy I tackled this, cuz it always looked so complicated from afar :D Now diving into variant calling in Zebrafish (since its quite common), Let’s see what we find! #genomics #bioinformatics #ensembl

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Rachel Ungar @raungar.bsky.social · 02/06/2025

Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪

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Reposted by Djoser Genomics

Jonathan Jacobs @bioinformer.bsky.social · 25/06/2025

🧵🦠🖥️🧬🧪 Please RePost 🙏 We just released reference genomes for another 250 strains to the ATCC Genome Portal (genomes.ATCC.org)! We now have assemblies for _5,750 microbial genomes_ AND all assemblies w/ @nanoporetech.com data will include DNA methylation profiles too (details👇) #genomics 1/

genomes.atcc.org

Home | ATCC Genome Portal

The ATCC Genome Portal is a repository of high-quality, authenticated microbial reference genomes.

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Shrinivas Nandi @shrinivas-nandi.bsky.social · 23/06/2025

🚨 New preprint alert! 🚨 We've just posted our latest work on Stony Coral Tissue Loss Disease. Using metagenomics, we look at microbial dynamics in infected corals 🧬🌊🪸 📄 Read it here: www.biorxiv.org/content/10.1...  #CoralReefs #Microbiome #Metagenomics #ViralEcology #CoralDisease #preprint

biorxiv.org

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Djoser Genomics @djosergenomics.github.io · 23/06/2025

⚙️ 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

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Jonathan Jacobs @bioinformer.bsky.social · 22/06/2025

Hey 👋 #ASMicrobe! If you’re into microbial genomics - stop by during the poster session and chat with Scott Nguyen from my team from ATCC. He’s been working on a whole range of interesting microbial species 🦠many of them have never been sequenced before by anyone. Please RePost🙏 🧪 🧬🖥️

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Abhishek Jha @ajelucidata.bsky.social · 19/06/2025

Automated metadata curation with human-level accuracy, dataset-wide scale, and traceable quality. Our Agentic AI system extracted 23+ metadata fields with 93% recall from GEO, papers, and supplementary files across 211 studies.

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EMBL-EBI @ebi.embl.org · 16/06/2025

If EMBL-EBI managed data resources have ever saved you time & effort, this is your chance to give back! Fill in a 15-minute survey to help us: 🌍Demonstrate the real-world impact of our resources 🤓Understand your needs 🌟Secure continued funding Closes 16 July www.surveymonkey.com/r/QGFMBH8?ch...

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Sanjay Curtis Nagi 🪷 @sanjaycnagi.com · 14/06/2025

Pleased to see this in print! We integrate published transcriptomic and WGS data to identify novel mechanisms of resistance across the major Anopheles vectors. We also present, AnoExpress, a tool that allows users to explore and analyse the transcriptomic dataset 🧬 🖥️ www.nature.com/articles/s42...

nature.com

A multi-omic meta-analysis reveals novel mechanisms of insecticide resistance in malaria vectors - Communications Biology

Multi-omic meta-analysis identifies insecticide resistance mechanisms in Anopheles vectors, highlighting convergent gene expression, purifying selection on highly expressed genes, and offering a tool ...

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Djoser Genomics @djosergenomics.github.io · 23/05/2025

🚀 Introducing DHPTA: Djoser's Host-Pathogen Transcriptomic Atlas! 🧬 A curated collection of reanalyzed RNAseq datasets capturing human responses to microbial infections. ✨ I am excited to build this new project and watch it grow djosergenomics.github.io/Introducing-... #DHPTA #Transcriptomics

djosergenomics.github.io

Introducing DHPTA: A Host-Pathogen Transcriptomic Atlas for Microbial Diseases

Today, I’m proud to announce the launch of DHPTA – Djoser’s Host-Pathogen Transcriptomic Atlas – a curated and reanalyzed collection of public RNAseq datasets capturing host transcriptomic responses t...

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Djoser Genomics @djosergenomics.github.io · 22/05/2025

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

djosergenomics.github.io

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

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Djoser Genomics @djosergenomics.github.io · 21/05/2025

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

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