Ken Koon Wong
@kenkoonwong.bsky.social
data science enthusiast #rstats. infectious disease provider. lazy gardener. tai chi practitioner. life long learner. views are my own. RT or like != endorsement. https://www.kenkoonwong.com/
Pinned
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
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
#IDWeek2025 had the lowest post count since 2022 (1,272 posts). While top posters shifted to Bluesky, X remained on par—the key difference was engagement rates favoring Bluesky. Grateful to learn so much from our SoMe community! 📊💙🙏
#idsky
#idsky
#IDWeek2025 Posts/Tweets Analysis | Everyday Is A School Day
IDWeek2025 had the lowest post count since 2022 (1,272 posts). While top posters shifted to Bluesky, X remained on par—the key difference was engagement rates favoring Bluesky. Grateful to learn so mu...
www.kenkoonwong.com
October 27, 2025 at 1:32 AM
#IDWeek2025 had the lowest post count since 2022 (1,272 posts). While top posters shifted to Bluesky, X remained on par—the key difference was engagement rates favoring Bluesky. Grateful to learn so much from our SoMe community! 📊💙🙏
#idsky
#idsky
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford’s HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But the lesson was worth it
#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
My Attempt To Reproduce Stanford HIVdb Sequence and Mutation Analysis From Scratch | Everyday Is A School Day
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford's HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But th...
www.kenkoonwong.com
October 11, 2025 at 3:51 AM
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford’s HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But the lesson was worth it
#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
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
#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
September 27, 2025 at 9:00 PM
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
#idsky #microsky #rstats #deseq2 #bioconductor
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
#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
September 21, 2025 at 4:50 PM
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
#idsky #tbsky #microsky #bioinformatics
Reposted by Ken Koon Wong
September 16, 2025 at 1:55 AM
Reposted by Ken Koon Wong
Join us this #IDWeek2025 for a SoMe meet-up! One of the highlights every year of the conference is meeting all of you! #IDSky
September 16, 2025 at 2:40 AM
Join us this #IDWeek2025 for a SoMe meet-up! One of the highlights every year of the conference is meeting all of you! #IDSky
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
#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
September 15, 2025 at 11:06 PM
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
#idsky #microsky #rstats
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
#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
September 7, 2025 at 8:00 PM
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
#microsky #idsky #bioconductor #rstats
Reposted by Ken Koon Wong
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...
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
September 4, 2025 at 10:05 PM
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...
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...
🧬🔬 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
#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
August 31, 2025 at 3:07 PM
🧬🔬 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
#microsky #idsky
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
#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
August 15, 2025 at 10:12 PM
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
#idsky #microsky #amr #rstats
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
#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
June 18, 2025 at 6:24 PM
Reposted by Ken Koon Wong
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
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
June 16, 2025 at 1:55 AM
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
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
Enjoyed learning penalized GAM math. Built penalty matrices, optimized λ using GCV, and implement our own GAM function.
Confusing? Yes! Rewarding? Oh yes!
#rstats
Confusing? Yes! Rewarding? Oh yes!
#rstats
From Math to Code: Building GAM with Penalty Functions From Scratch | Everyday Is A School Day
Enjoyed learning penalized GAM math. Built penalty matrices, optimized λ using GCV, and implement our own GAM function. Confusing? Yes! Rewarding? Oh yes!
www.kenkoonwong.com
June 12, 2025 at 1:52 AM
Enjoyed learning penalized GAM math. Built penalty matrices, optimized λ using GCV, and implement our own GAM function.
Confusing? Yes! Rewarding? Oh yes!
#rstats
Confusing? Yes! Rewarding? Oh yes!
#rstats
Wow!!! You can do combo abx too!?!? Amazing!
Congratulations to Matthijs Berends and team for the release of the AMR for R package version 3!
I've been using this package to produce the AGAR Kids reports and can highly recommend.
amr-for-r.org
#Rstats #AMR #IDEpi #MedSky
I've been using this package to produce the AGAR Kids reports and can highly recommend.
amr-for-r.org
#Rstats #AMR #IDEpi #MedSky
June 8, 2025 at 12:53 PM
Wow!!! You can do combo abx too!?!? Amazing!
Just listened to this. Awesome insights!
I'm on a podcast! I had a blast talking with @lucystats.bsky.social and @epiellie.bsky.social on @casualinfer.bsky.social! We cover all sorts of fun things: {marginaleffects}, defining estimands, fixed vs. random effects, & how to teach all this stats stuff in accessible ways #databs #EpiSky #rstats
Casual Inference: The Art of Clarity with Andrew Heiss | Season 6 Episode 6
Andrew Heiss is an assistant professor in the Department of Public Management and Policy at the Andrew Young School of Policy Studies at Georgia State University. Vincent’s “What is your estimand” s...
casualinfer.libsyn.com
June 4, 2025 at 11:47 AM
Just listened to this. Awesome insights!
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
June 4, 2025 at 12:44 AM
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
We learnt to derive the Newton-Raphson algorithm from Taylor series approx. We’ll show how the 2nd-order Taylor expansion leads to the Newton-Raphson update formula, then compare individual parameter updates vs using the full Fisher Information matrix for faster convergence. Fascinating!
#rstats
#rstats
Taylor Series Approximation To Newton Raphson Algorithm - A note for myself of the proof | Everyday Is A School Day
We learnt to derive the Newton-Raphson algorithm from Taylor series approximation and implements it for logistic regression in R. We'll show how the second-order Taylor expansion leads to the Newton-R...
www.kenkoonwong.com
May 25, 2025 at 6:08 PM
We learnt to derive the Newton-Raphson algorithm from Taylor series approx. We’ll show how the 2nd-order Taylor expansion leads to the Newton-Raphson update formula, then compare individual parameter updates vs using the full Fisher Information matrix for faster convergence. Fascinating!
#rstats
#rstats
Refreshed my rusty calculus skills lately! 🤓 Finally understand what happens during complete separation and why those coefficient SE get so extreme. The math behind maximum likelihood estimation makes more sense now! Chain rule, quotient rule, matrix inversion are crucial!
#rstats
#rstats
From Complete Separation To Maximum Likelihood Estimation in Logistic Regresion: A Note To Myself | Everyday Is A School Day
Refreshed my rusty calculus skills lately! 🤓 Finally understand what happens during complete separation and why those coefficient SE get so extreme. The math behind maximum likelihood estimation makes...
www.kenkoonwong.com
May 17, 2025 at 6:55 PM
Refreshed my rusty calculus skills lately! 🤓 Finally understand what happens during complete separation and why those coefficient SE get so extreme. The math behind maximum likelihood estimation makes more sense now! Chain rule, quotient rule, matrix inversion are crucial!
#rstats
#rstats
In my simulations of Response Adaptive Randomization, I discovered it performs comparably to fixed 50-50 allocation in identifying treatment effects. The adaptive approach does appear to work! However, with only 10 trials, I’ve merely scratched the surface. Important limitations exist
#rstats
#rstats
Simulating A Simple Response Adaptive Randomization - I Have To See It To Believe It | Everyday Is A School Day
In my simulations of Response Adaptive Randomization, I discovered it performs comparably to fixed 50-50 allocation in identifying treatment effects. The adaptive approach does appear to work! However...
www.kenkoonwong.com
May 4, 2025 at 9:49 PM
In my simulations of Response Adaptive Randomization, I discovered it performs comparably to fixed 50-50 allocation in identifying treatment effects. The adaptive approach does appear to work! However, with only 10 trials, I’ve merely scratched the surface. Important limitations exist
#rstats
#rstats
Reposted by Ken Koon Wong
Caring for patients with bronchiectasis poses a challenge for both pulmonologists and #AMSky teams.
Standard 14d treatments for exacerbations lack good evidence support.
This small RCT favors shorter durations such as 8d 👉🏻 publications.ersnet.org/content/erj/... #IDsky @bradspellberg.bsky.social
Standard 14d treatments for exacerbations lack good evidence support.
This small RCT favors shorter durations such as 8d 👉🏻 publications.ersnet.org/content/erj/... #IDsky @bradspellberg.bsky.social
May 4, 2025 at 12:43 AM
Caring for patients with bronchiectasis poses a challenge for both pulmonologists and #AMSky teams.
Standard 14d treatments for exacerbations lack good evidence support.
This small RCT favors shorter durations such as 8d 👉🏻 publications.ersnet.org/content/erj/... #IDsky @bradspellberg.bsky.social
Standard 14d treatments for exacerbations lack good evidence support.
This small RCT favors shorter durations such as 8d 👉🏻 publications.ersnet.org/content/erj/... #IDsky @bradspellberg.bsky.social
Reposted by Ken Koon Wong
#IDsky
I did a post on the IDSA community board on the G0545 code. Check it out! I think you will find it interesting! 😊💰
my.idsociety.org/discussion/g...
I did a post on the IDSA community board on the G0545 code. Check it out! I think you will find it interesting! 😊💰
my.idsociety.org/discussion/g...
Note: Since your browser does not support Javascript, you must press the Continue button once to proceed.
my.idsociety.org
May 2, 2025 at 1:28 AM
#IDsky
I did a post on the IDSA community board on the G0545 code. Check it out! I think you will find it interesting! 😊💰
my.idsociety.org/discussion/g...
I did a post on the IDSA community board on the G0545 code. Check it out! I think you will find it interesting! 😊💰
my.idsociety.org/discussion/g...
Reposted by Ken Koon Wong
My latest for @contagionlive.bsky.social on the lastest data about cellulitis epidemiology and how we can use that to update our treatment paradigms! #IDSky
This common skin and soft tissue infection has a high recurrence rate and significant treatment failure. β-Lactams remain effective first-line treatments, though rising resistance to clindamycin and tetracycline, especially in GAS, is a growing concern. #IDsky #Medsky
Shifting Sands in Cellulitis
This common skin and soft tissue infection has a high recurrence rate and significant treatment failure. β-Lactams remain effective first-line treatments, though rising resistance to clindamycin and t...
www.contagionlive.com
April 30, 2025 at 6:47 PM
My latest for @contagionlive.bsky.social on the lastest data about cellulitis epidemiology and how we can use that to update our treatment paradigms! #IDSky
I messed around with DBI and RSQLite and learned it’s actually pretty simple to use in R - just connect, write tables, and use SQL queries without all the complicated server stuff. Thanks to Alec Wong for suggesting this!
#rstats
#rstats
Exploring `RSQLite` With `DBI`: A Note To Myself | Everyday Is A School Day
I messed around with DBI and RSQLite and learned it's actually pretty simple to use in R - just connect, write tables, and use SQL queries without all the complicated server stuff. Thanks to Alec Wong...
www.kenkoonwong.com
April 19, 2025 at 1:15 PM
I messed around with DBI and RSQLite and learned it’s actually pretty simple to use in R - just connect, write tables, and use SQL queries without all the complicated server stuff. Thanks to Alec Wong for suggesting this!
#rstats
#rstats