kenkoonwong.bsky.social
Ken Koon Wong
@kenkoonwong.bsky.social
2.3K followers 6.6K following 910 posts
data science hobbyist #rstats. infectious disease provider. lazy gardener. tai chi practitioner. life long learner. views are my own. RT or like != endorsement. https://www.kenkoonwong.com/
www.kenkoonwong.com
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kenkoonwong.bsky.social
Ken Koon Wong @kenkoonwong.bsky.social · Jun 4
I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they’re just weighted combo of basis functions that make non-linear regression linear. What surprised me is going through Bayesian statistics helped me understand the engine behind the model! #rstats
Understanding Basis Spline (B-spline) By Working Through Cox-deBoor Algorithm | Everyday Is A School Day
I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they're just weighted combinations of basis functions that make non-linear regression linear. What ...
www.kenkoonwong.com
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kenkoonwong.bsky.social
Ken Koon Wong @kenkoonwong.bsky.social · 13h
@jonathanrydermd.bsky.social @josephmarcusid.medsky.social
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Ken Koon Wong @kenkoonwong.bsky.social · 11d
Learned RNA-seq workflow using C. diff data from a study 🧬. Processed raw reads thru fastp → kallisto → DESeq2 pipeline. Results matched the original paper’s findings, with clear differential expression between mucus and control conditions 📊.

#idsky #microsky #rstats #deseq2 #bioconductor
Learning And Exploring The Workflow of RNA-Seq Analysis - A Note To Myself | Everyday Is A School Day
Learned RNA-seq workflow using C. difficile data from a published study 🧬. Processed raw reads through fastp → kallisto → DESeq2 pipeline. Results matched the original paper's findings, with clear dif...
www.kenkoonwong.com
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Ken Koon Wong @kenkoonwong.bsky.social · 14d
This is genius!!!
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Ken Koon Wong @kenkoonwong.bsky.social · 17d
Hands-on with @nanoporetech.com workflow: pod5 → BAM → assembly -> polish! Processed M. tuberculosis from raw signals to complete genome using #dorado + #samtools + #flye. Fascinating how thousands of contigs became one 4M+ bp sequence.

#idsky #tbsky #microsky #bioinformatics
Exploring The Workflow of The Oxford Nanopore Technologies (ONT) from pod5 to Polished Asembly - A Note To Myself | Everyday Is A School Day
Hands-on with Oxford Nanopore workflow: pod5 → BAM → assembly! Processed M. tuberculosis from raw signals to complete genome using dorado + flye. Fascinating how thousands of contigs became one 4M+ bp...
www.kenkoonwong.com
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Reposted by Ken Koon Wong
josephmarcusid.medsky.social
Joseph Marcus @josephmarcusid.medsky.social · 23d
Come join #IDSky at the unofficial @idweek.bsky.social Social Media Meet-Up!

All are welcome.
IDWeek Social Media Meet-Up October 19, 2025 7:30 PM-10:00 PM Lobby Bar at the Signia by Hilton Atlanta Georgia World Congress Center
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Reposted by Ken Koon Wong
jonathanrydermd.bsky.social
Jonathan Ryder, MD @jonathanrydermd.bsky.social · 23d
Join us this #IDWeek2025 for a SoMe meet-up! One of the highlights every year of the conference is meeting all of you! #IDSky
josephmarcusid.medsky.social
Joseph Marcus @josephmarcusid.medsky.social · 23d
Come join #IDSky at the unofficial @idweek.bsky.social Social Media Meet-Up!

All are welcome.
IDWeek Social Media Meet-Up October 19, 2025 7:30 PM-10:00 PM Lobby Bar at the Signia by Hilton Atlanta Georgia World Congress Center
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kenkoonwong.bsky.social
Ken Koon Wong @kenkoonwong.bsky.social · 23d
Thanks to @josephmarcusid.medsky.social and @jonathanrydermd.bsky.social for the motivation and insight!
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Ken Koon Wong @kenkoonwong.bsky.social · 23d
We learnt how to assemble DNA fragments from a recently published N. meningitidis outbreak study www.cdc.gov/mmwr/volumes... using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explored how serogroups are determined!

#idsky #microsky #rstats
Learning About Assemblying DNA, BLAST, and Multiple Loci Sequence Testing (MLST) - A Note To Myself | Everyday Is A School Day
We learnt how to assemble DNA fragments from a recently published *N. meningitidis* outbreak study using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explo...
www.kenkoonwong.com
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kenkoonwong.bsky.social
Ken Koon Wong @kenkoonwong.bsky.social · Sep 7
Ever wondered how DNA alignment actually works under the hood? 🧬 We coded the Needleman-Wunsch algorithm from scratch, working thru scoring matrices w simple examples like "CAT" vs "CT" before testing on E. coli sequences. Pretty neat to see the magic! ✨

#microsky #idsky #bioconductor #rstats
Building DNA Sequence Alignment With Needleman-Wunsch Algorithm From Scratch - A Note To My Self | Everyday Is A School Day
Ever wondered how DNA alignment actually works under the hood? 🧬 We coded the Needleman-Wunsch algorithm from scratch, working through scoring matrices by hand with simple examples like "CAT" vs "CT" ...
www.kenkoonwong.com
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Reposted by Ken Koon Wong
josephmarcusid.medsky.social
Joseph Marcus @josephmarcusid.medsky.social · Sep 4
There have been many documented meningococcal meningitis outbreaks.

Here we describe our investigation and response to the first documented meningococcal conjunctivitis outbreak. 🧫

Contributions by 🌟🌟🌟 fellows @sucroselauren.bsky.social @ogallardo.bsky.social
#IDSky

www.cdc.gov/mmwr/volumes...
Outbreak of Neisseria meningitidis Conjunctivitis ...
This report describes 41 cases of Neisseria meningitidis conjunctivitis among military trainees living in a communal setting in Texas.
www.cdc.gov
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kenkoonwong.bsky.social
Ken Koon Wong @kenkoonwong.bsky.social · Aug 31
Awesome ! Thanks for the tips. Will take a look
kenkoonwong.bsky.social
Ken Koon Wong @kenkoonwong.bsky.social · Aug 31
🧬🔬 Explore phylogenetic analysis from genome to tree! Basic workflow with #rstats #bioconductor. Learnt to work with large genomic data. Extract 16S rRNA from 10K+ E.coli strains using dataset dehydrate, barrnap for extraction, rapidNJ for tree building & FigTree for visualization.

#microsky #idsky
Learning The Basics of Phylogenetic Analysis | Everyday Is A School Day
🧬🔬 Explore phylogenetic analysis from genome to tree! Basic workflow with R/Bioconductor. Learnt to work with large genomic dataset. Extract 16S rRNA from 10K+ E.coli strains using dataset dehydrate, ...
www.kenkoonwong.com
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Ken Koon Wong @kenkoonwong.bsky.social · Aug 26
😱
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Ken Koon Wong @kenkoonwong.bsky.social · Aug 15
Instead of flashcards, we Rube Goldberg’d this with #Bioconductor ! Analyzed 3,280 E. coli genomes from NCBI, detecting ESBL genes in 84.4% of samples. CTX-M-15 was most common. Helped us understand gene nomenclature and sequence analysis! 📊🔬

#idsky #microsky #amr #rstats
Learning Antimicrobial Resistance (AMR) genes with Bioconductor | Everyday Is A School Day
Instead of flashcards, we Rube Goldberg'd this with Bioconductor! Analyzed 3,280 E. coli genomes from NCBI, detecting ESBL genes in 84.4% of samples. CTX-M-15 was most common. Helped us understand gen...
www.kenkoonwong.com
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Ken Koon Wong @kenkoonwong.bsky.social · Jul 30
@jonathanrydermd.bsky.social @josephmarcusid.medsky.social
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Ken Koon Wong @kenkoonwong.bsky.social · Jul 9
Congratulations! Well deserved!
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Ken Koon Wong @kenkoonwong.bsky.social · Jun 28
very thoughtful of you!
kenkoonwong.bsky.social
Ken Koon Wong @kenkoonwong.bsky.social · Jun 27
@apothecarrie.bsky.social
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Ken Koon Wong @kenkoonwong.bsky.social · Jun 26
A but give it 24h for learner to reach out first without prompting.
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Ken Koon Wong @kenkoonwong.bsky.social · Jun 23
#idsky
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Ken Koon Wong @kenkoonwong.bsky.social · Jun 22
E. All of the above. Mentors know best.
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Ken Koon Wong @kenkoonwong.bsky.social · Jun 20
@apothecarrie.bsky.social
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Ken Koon Wong @kenkoonwong.bsky.social · Jun 18
Learn how to build a flash-card style question bank using Google Sheets as storage, #rstats Plumber API, and host it on a Digital Ocean droplet—step-by-step setup, deployment, and tips.

#idsky #medsky #meded
Creating A Question Bank Using Google Sheet, Plumber, and Digital Ocean Droplet | Everyday Is A School Day
Learn how to build a flash-card style question bank using Google Sheets as storage, R’s Plumber API, and host it on a Digital Ocean droplet—step-by-step setup, deployment, and tips.
www.kenkoonwong.com
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Reposted by Ken Koon Wong
seanong.bsky.social
Sean Ong @seanong.bsky.social · Jun 16
Our review on hierarchical composite endpoints (HCEs) has just been published in @cidjournal.bsky.social:
doi.org/10.1093/cid/...

We provide a conceptual overview of HCEs, explain the different associated target parameters and analytic methods.

@steventong.bsky.social @gurujosh.bsky.social
Making sense of hierarchical composite endpoints in randomized clinical trials – a primer for infectious disease clinicians and researchers
Hierarchical composite endpoints (HCEs) are increasingly being used in infectious diseases research. In this review aimed at educating the clinical reader,
doi.org
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kenkoonwong.bsky.social
Ken Koon Wong @kenkoonwong.bsky.social · Jun 16
Is the content similar to… How not to study a disease by karl herrup? a.co/d/1FOpPaR
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