Noah Reid
@noahreid.bsky.social
Computational Biology Core at the University of Connecticut. Genomics, bioinformatics, evolution. Also nature, natural history. A little too into birding.
https://scholar.google.com/citations?user=IbPpB9sAAAAJ&h
https://scholar.google.com/citations?user=IbPpB9sAAAAJ&h
Reposted by Noah Reid
How the use of AI by colleagues to generate citations or overviews, even if we avoid these “tools” ourselves, may put new pressures on scientific publishing: brianomeara.info/posts/ai_opt...
#AcademicSky
#AcademicSky
November 7, 2025 at 10:16 PM
How the use of AI by colleagues to generate citations or overviews, even if we avoid these “tools” ourselves, may put new pressures on scientific publishing: brianomeara.info/posts/ai_opt...
#AcademicSky
#AcademicSky
Another good bird! A ruff, at Barn Island WMA, Stonington, CT.
November 9, 2025 at 9:57 PM
Another good bird! A ruff, at Barn Island WMA, Stonington, CT.
Grasshopper sparrow in Old Lyme, CT this morning.
November 9, 2025 at 2:24 AM
Grasshopper sparrow in Old Lyme, CT this morning.
Reposted by Noah Reid
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
November 7, 2025 at 3:19 AM
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
to me, a non-ai expert, this gets at one of the most curious things about the hype. it kinda feels like doing ever increasing numbers of matrix multiplications on every text ever written is probably barking up the wrong tree for creating "intelligence".
My favorite comment on the FT story
November 7, 2025 at 2:59 AM
to me, a non-ai expert, this gets at one of the most curious things about the hype. it kinda feels like doing ever increasing numbers of matrix multiplications on every text ever written is probably barking up the wrong tree for creating "intelligence".
Reposted by Noah Reid
Join us Nov 18–20 for a Virtual Genome Annotation Workshop! Learn Linux, genome assembly, evidence-based annotation, & evaluation. No experience needed!
📅 10 AM – 2 PM ET
💻 MS Teams + recording
💰 $500 ($400 UConn)
Register: bioinformatics.uconn.edu/cbc-workshops/
#GenomeAnnotation #Bioinformatics
📅 10 AM – 2 PM ET
💻 MS Teams + recording
💰 $500 ($400 UConn)
Register: bioinformatics.uconn.edu/cbc-workshops/
#GenomeAnnotation #Bioinformatics
November 4, 2025 at 10:26 PM
Join us Nov 18–20 for a Virtual Genome Annotation Workshop! Learn Linux, genome assembly, evidence-based annotation, & evaluation. No experience needed!
📅 10 AM – 2 PM ET
💻 MS Teams + recording
💰 $500 ($400 UConn)
Register: bioinformatics.uconn.edu/cbc-workshops/
#GenomeAnnotation #Bioinformatics
📅 10 AM – 2 PM ET
💻 MS Teams + recording
💰 $500 ($400 UConn)
Register: bioinformatics.uconn.edu/cbc-workshops/
#GenomeAnnotation #Bioinformatics
per the blog post, many of the ideas that inspired this live on in other projects, but still, this site shutting down feels like an emblem of the gap between what everyone thought the internet could be in the 1990s and what it has become.
The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social
subulatepalpomere.com/2025/11/02/t...
subulatepalpomere.com/2025/11/02/t...
The Passing of the Tree of Life Web Project
The Tree of Life Web Project began its journey almost 40 years ago, and was formally announced in early 1996. It has served thousands of pages of information about the evolutionary tree of life and…
subulatepalpomere.com
November 4, 2025 at 9:07 PM
per the blog post, many of the ideas that inspired this live on in other projects, but still, this site shutting down feels like an emblem of the gap between what everyone thought the internet could be in the 1990s and what it has become.
Reposted by Noah Reid
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos
Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...
doi.org
October 30, 2025 at 7:15 PM
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
Tebibytes/Gibibytes/Mebibytes etc are cursed. Maybe I'm just a computational rube, but WTF. I get that computers are working in base 2 so nothing will ever be clean if you count storage in base 10, but the solution is to essentially to MIX base 2 and base 10 in a way that is endlessly confusing?
October 30, 2025 at 1:04 PM
Tebibytes/Gibibytes/Mebibytes etc are cursed. Maybe I'm just a computational rube, but WTF. I get that computers are working in base 2 so nothing will ever be clean if you count storage in base 10, but the solution is to essentially to MIX base 2 and base 10 in a way that is endlessly confusing?
Reposted by Noah Reid
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:33 PM
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
It's a Miyazaki Clouds kind of day.
October 22, 2025 at 4:16 PM
It's a Miyazaki Clouds kind of day.
This workshop is right around the corner. See the link for the rest of our upcoming workshop schedule.
Join us Oct. 28–30 for a Virtual ChIP-Seq / ATAC-Seq Workshop! 🧬
📅 10 AM – 2 PM EST
💻 Live on Zoom + recordings
💰 $500 ($400 UConn affiliates)
Register: bioinformatics.uconn.edu/cbc-workshops/
#ChIPSeq #ATACSeq #Bioinformatics #Workshop
📅 10 AM – 2 PM EST
💻 Live on Zoom + recordings
💰 $500 ($400 UConn affiliates)
Register: bioinformatics.uconn.edu/cbc-workshops/
#ChIPSeq #ATACSeq #Bioinformatics #Workshop
October 21, 2025 at 2:19 PM
This workshop is right around the corner. See the link for the rest of our upcoming workshop schedule.
Maybe time to rewatch The Wire
David Simon, creator of ‘The Wire’, being interviewed by Ari Shapiro (NPR)
October 10, 2025 at 3:08 AM
Maybe time to rewatch The Wire
look, I don't want people going to jail for weed, but is there some compromise position that makes it so I don't have to smell weed 100% of the time in any populated part of the country?
October 10, 2025 at 12:46 AM
look, I don't want people going to jail for weed, but is there some compromise position that makes it so I don't have to smell weed 100% of the time in any populated part of the country?
The number one thing I miss about being 20 is the ability to sleep like the dead for 12 straight hours.
October 10, 2025 at 12:42 AM
The number one thing I miss about being 20 is the ability to sleep like the dead for 12 straight hours.
we started using Starfish to look at data on our HPC. it's pretty amazing. getting a high level view of storage and being able to immediately see problems like, say, 60TB of old nextflow work directories floating around is fantastic.
October 8, 2025 at 7:06 PM
we started using Starfish to look at data on our HPC. it's pretty amazing. getting a high level view of storage and being able to immediately see problems like, say, 60TB of old nextflow work directories floating around is fantastic.
Reminds me of 2020, with then 4yo:
S: we got you a present for your birthday, daddy!
Me: great! I can't wait to see what it is.
S: I'm never going to tell you what it is.
Me: very good. Keep it a surprise.
S: we got you a present for your birthday, daddy!
Me: great! I can't wait to see what it is.
S: I'm never going to tell you what it is.
Me: very good. Keep it a surprise.
I was wondering whether ChatGPT could identify species from drawings, but it said 'no for safety reasons, you can absolutely tell me context (for example: “this jellyfish is small, transparent, and causes Irukandji syndrome”)' -
guess what, I uploaded an Irukandji image
guess what, I uploaded an Irukandji image
October 6, 2025 at 1:18 AM
Reminds me of 2020, with then 4yo:
S: we got you a present for your birthday, daddy!
Me: great! I can't wait to see what it is.
S: I'm never going to tell you what it is.
Me: very good. Keep it a surprise.
S: we got you a present for your birthday, daddy!
Me: great! I can't wait to see what it is.
S: I'm never going to tell you what it is.
Me: very good. Keep it a surprise.
My worst trait as an instructor of online courses is my tendency to start demo videos with "this will be a short video about X" and then the demonstration is absolutely not short.
I console myself with the fact that students can see the progress bar and know that I am lying.
I console myself with the fact that students can see the progress bar and know that I am lying.
October 3, 2025 at 8:30 PM
My worst trait as an instructor of online courses is my tendency to start demo videos with "this will be a short video about X" and then the demonstration is absolutely not short.
I console myself with the fact that students can see the progress bar and know that I am lying.
I console myself with the fact that students can see the progress bar and know that I am lying.
Can someone explain to me what is happening here
October 3, 2025 at 11:44 AM
Can someone explain to me what is happening here
Reposted by Noah Reid
Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)
The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies
Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla
academic.oup.com
October 3, 2025 at 9:54 AM
Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)
RE NCBI and the shutdown: I was able to grab some SRA data I needed last night. Is there any reason to think that NCBI databases might become inaccessible?
October 2, 2025 at 3:24 PM
RE NCBI and the shutdown: I was able to grab some SRA data I needed last night. Is there any reason to think that NCBI databases might become inaccessible?
Reposted by Noah Reid
Okay this one is actually good.
September 29, 2025 at 2:36 PM
Okay this one is actually good.
UConn's CBC is offering a virtual workshop on ChIP and ATAC seq at the end of October.
Join us Oct. 28–30 for a Virtual ChIP-Seq / ATAC-Seq Workshop! 🧬
📅 10 AM – 2 PM EST
💻 Live on Zoom + recordings
💰 $500 ($400 UConn affiliates)
Register: bioinformatics.uconn.edu/cbc-workshops/
#ChIPSeq #ATACSeq #Bioinformatics #Workshop
📅 10 AM – 2 PM EST
💻 Live on Zoom + recordings
💰 $500 ($400 UConn affiliates)
Register: bioinformatics.uconn.edu/cbc-workshops/
#ChIPSeq #ATACSeq #Bioinformatics #Workshop
September 29, 2025 at 6:07 PM
UConn's CBC is offering a virtual workshop on ChIP and ATAC seq at the end of October.