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PhD Candidate @Pitt DBMI, using large scale phylogenomics to predict gene function in prokaryotes. Developer for SynExtend and contributor to Biostrings R packages. 


I have a BS in Mathematics from University of Central Florida, and a slight obsession with coffee and building keyboards. 

I blog about my hobby projects, which right now focuses on writing a Forth interpreter from scratch for a 6502-based computer I built. 


All my social/contact links are available from my website! 
(He/him)
Websitehttps://ahl27.com
Tutorialshttps://www.ahl27.com/tutorials/
Bloghttps://www.ahl27.com/blog/
Githubhttps://github.com/ahl27

Excited to announce our article, "EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals" was just published in Nature Communications!

We demonstrate that it's possible to infer how genes work together using only sequencing data by leveraging correlated signals of evolution. Check it out at the link below!

#genomics #bioinformatics #rstats #genetics #evolution #biology

https://www.nature.com/articles/s41467-025-59175-6

EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals - Nature Communications

Despite having structures for most proteins, we still do not know their function. Here, authors introduce EvoWeaver, a de novo method to identify genes working together using evolutionary information. EvoWeaver can help to infer functions for understudied proteins using only genomic sequences.

Nature

I wrote a Forth environment for R! It emulates real Forth implementations, and I’m working on adding more features soon. The package is called froth, and it’s available on CRAN.

If you’ve never heard of Forth, you’re in for a treat—it’s a very cool programming language that people don’t use very often anymore.

I wrote a long tutorial that roughly follows the famous Starting Forth textbook, specifically for doing it all within froth. Check it out at https://www.ahl27.com/froth/index.html.

froth: Forth for R

Emulates a Forth programming environment with added features to interface between R and Forth. Implements most of the functionality described in the original "Starting Forth" textbook <https://www.forth.com/starting-forth/>.

Thanks everyone for the responses! I really appreciate all the feedback; sorry for not responding to each post individually.
As the 4th year panic of doctoral studies comes in, I’m beginning the early stages of probing jobs…seems like a lot of tech research postings are exclusively looking for experience in Python/ML. Any insights on the market for people with expert level #r / #rstats programming and strong knowledge working in #c ? Is it worth going back to Python for some pet projects to make my resume more industry-friendly? #jobs #jobtalk #bioinformatics #compsci #research #industry

🎓 Upcoming #biocsmorgasbord! Learn "Comparative Genomics with DECIPHER and SynExtend" 🧬💻 with Aidan Lakshman @ahl27

📅 May 22-26
➡️ https://gallantries.github.io/video-library/modules/bioconductor
#Bioinformatics #RStats #Bioconductor #Genomics

Bioconductor R analyses

Awesome intro on R in Genomics, talking on sequence alignment and visualization from ~ @ahl27 !!! https://scifind.io/posts/genomics-in-r-part-1-intro-sequence-alignment-and-visualization-5vfasonw71lt4jw ... but also with a continuation on phylogenetic trees featuring–birds! 🐦🦃🦆 https://scifind.io/posts/genomics-in-r-part-2-phylogenetic-reconstruction-ln4dm6r2ybo2azy

#bioinformatics #biology #science #genomics

Genomics in R, Part 1: Intro, Sequence Alignment, and Visualization...

Quick Intro This will be the first of a couple posts I'm planning to make on running some common genomics analyses in R. My advisor develops the DECIPHER package, and I develop the SynExtend pack...

Reminder that the deadline for applications to participate in R Project Sprint 2023 is tomorrow (midnight UTC).

Full details: https://contributor.r-project.org/r-project-sprint-2023/

R Project Sprint 2023

Man, the final stretch of working of a project is just a heck of a slog…how is it that I’ve been doing two years of work and yet the final month feels longer than the rest combined??? I just want to write the damn paper but it seems like there’s always *one* more i to dot or t to cross before I can be done 😅 😅 #research #academia #gradschool
Despite the risk of overloading my anxiety I’ll link the submission here: https://bugs.r-project.org/show_bug.cgi?id=18480
18480 – Suggested enhancements to `dendrapply`

Well, I’ve officially submitted code for review to the R core team…now comes the part where I nervously wait for feedback 😬 😬 #RStats