Kerry Cobb
@kerrycobb.bsky.social
Bioinformatics Analyst in the UConn Computational Biology Core. UConn Health Affiliate.
Reposted by Kerry Cobb
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
www.nature.com
February 6, 2026 at 3:15 PM
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Kerry Cobb
New preprint!! 🚨 Did you know that many vertebrate species determine sex based on environmental conditions rather than chromosomes? Some turtles, like Trachemys scripta, rely on temperature. We learned more about how this happen molecularly.👇
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
February 2, 2026 at 11:19 AM
New preprint!! 🚨 Did you know that many vertebrate species determine sex based on environmental conditions rather than chromosomes? Some turtles, like Trachemys scripta, rely on temperature. We learned more about how this happen molecularly.👇
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Kerry Cobb
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
February 2, 2026 at 2:58 PM
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
Reposted by Kerry Cobb
Join us Feb 20–Apr 24 for a 10-week Introduction to R Workshop! 🔢 Learn data import, wrangling, visualization, functions, pipelines, and basic stats with R and the tidyverse. No prior experience needed.
🕐 Fridays, 1–2 PM EST
📍 UConn Storrs (room TBD)
💰 $600 ($500 UConn affiliates)
🕐 Fridays, 1–2 PM EST
📍 UConn Storrs (room TBD)
💰 $600 ($500 UConn affiliates)
January 30, 2026 at 11:53 PM
Join us Feb 20–Apr 24 for a 10-week Introduction to R Workshop! 🔢 Learn data import, wrangling, visualization, functions, pipelines, and basic stats with R and the tidyverse. No prior experience needed.
🕐 Fridays, 1–2 PM EST
📍 UConn Storrs (room TBD)
💰 $600 ($500 UConn affiliates)
🕐 Fridays, 1–2 PM EST
📍 UConn Storrs (room TBD)
💰 $600 ($500 UConn affiliates)
Reposted by Kerry Cobb
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
www.biorxiv.org
January 31, 2026 at 1:13 AM
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
Reposted by Kerry Cobb
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Reposted by Kerry Cobb
Preprint: Genome-Scale Perturb-Seq in Primary Human CD4+ T Cells Maps Context-Specific Regulators of T Cell Programs and Human Immune Traits
papers.ssrn.com/sol3/papers.... @marsonlab.bsky.social @jkpritch.bsky.social
papers.ssrn.com/sol3/papers.... @marsonlab.bsky.social @jkpritch.bsky.social
January 29, 2026 at 4:11 AM
Preprint: Genome-Scale Perturb-Seq in Primary Human CD4+ T Cells Maps Context-Specific Regulators of T Cell Programs and Human Immune Traits
papers.ssrn.com/sol3/papers.... @marsonlab.bsky.social @jkpritch.bsky.social
papers.ssrn.com/sol3/papers.... @marsonlab.bsky.social @jkpritch.bsky.social
Reposted by Kerry Cobb
Join us February 24-26 for a Virtual RNA-seq Analysis Workshop! 🧬Learn QC, alignment, differential expression, and enrichment using a reference genome.
🕙 10 AM – 2 PM ET
💻 MS Teams + recordings
💰 $500 ($400 UConn)
Register: bioinformatics.uconn.edu/cbc-workshops/
#RNAseq #Bioinformatics #Workshop
🕙 10 AM – 2 PM ET
💻 MS Teams + recordings
💰 $500 ($400 UConn)
Register: bioinformatics.uconn.edu/cbc-workshops/
#RNAseq #Bioinformatics #Workshop
January 16, 2026 at 9:23 PM
Join us February 24-26 for a Virtual RNA-seq Analysis Workshop! 🧬Learn QC, alignment, differential expression, and enrichment using a reference genome.
🕙 10 AM – 2 PM ET
💻 MS Teams + recordings
💰 $500 ($400 UConn)
Register: bioinformatics.uconn.edu/cbc-workshops/
#RNAseq #Bioinformatics #Workshop
🕙 10 AM – 2 PM ET
💻 MS Teams + recordings
💰 $500 ($400 UConn)
Register: bioinformatics.uconn.edu/cbc-workshops/
#RNAseq #Bioinformatics #Workshop
We still have space in our variant calling workshop happening next week!
Join us January 27–29, 2026 for a Virtual Variant Detection Workshop! Learn variant detection fundamentals—no experience needed.
📅 10 AM–2 PM EST
💻 MS Teams + recordings
💰 $500 ($400 for University of Connecticut affiliates)
👉 bioinformatics.uconn.edu/cbc-workshops/
#Bioinformatics #Genomics
📅 10 AM–2 PM EST
💻 MS Teams + recordings
💰 $500 ($400 for University of Connecticut affiliates)
👉 bioinformatics.uconn.edu/cbc-workshops/
#Bioinformatics #Genomics
January 23, 2026 at 10:58 PM
We still have space in our variant calling workshop happening next week!
Reposted by Kerry Cobb
Three years ago, we showed ~70% of lifespan variation in yeast traces to rDNA copy number. Ribosomal DNA, encoded as 5S and 45S subunits in hundreds of copies, vary substantially across humans. Does this copy number variation, and sequence variation within these paralogs, matter for humans?
January 22, 2026 at 5:39 PM
Three years ago, we showed ~70% of lifespan variation in yeast traces to rDNA copy number. Ribosomal DNA, encoded as 5S and 45S subunits in hundreds of copies, vary substantially across humans. Does this copy number variation, and sequence variation within these paralogs, matter for humans?
Reposted by Kerry Cobb
New preprint on technologies to scale up CRISPR screens.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
January 20, 2026 at 1:42 PM
New preprint on technologies to scale up CRISPR screens.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
Reposted by Kerry Cobb
🚀 Our new paper on Alignoth just published in Bioinformatics!
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
January 8, 2026 at 1:57 PM
🚀 Our new paper on Alignoth just published in Bioinformatics!
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
Reposted by Kerry Cobb
Reposted by Kerry Cobb
we rescheduled this. it's now about a week out!
Join us Jan 13–16 for a Virtual RAD-seq Workshop! Learn the complete RAD-seq analysis workflow. Beginner-friendly—no experience needed! 📅 10 AM – 2 PM ET 💻 MS Teams + recording 💰 $500 ($400 UConn) Register: bioinformatics.uconn.edu/cbc-workshops/ #RADseq #Bioinformatics #Genomics
January 5, 2026 at 4:49 PM
we rescheduled this. it's now about a week out!
Reposted by Kerry Cobb
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
December 16, 2025 at 4:06 PM
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
Reposted by Kerry Cobb
Virtual workshop on #genomics analysis for #RADSeq - spaces available Jan 13-16th! Live instruction by @noahreid.bsky.social Learn #NGS read QC, #variant detection, and data analysis via common #bioinformatic tools - #Stacks #Freebayes @uconnresearch.bsky.social @cbcuconn.bsky.social
December 27, 2025 at 3:47 PM
Virtual workshop on #genomics analysis for #RADSeq - spaces available Jan 13-16th! Live instruction by @noahreid.bsky.social Learn #NGS read QC, #variant detection, and data analysis via common #bioinformatic tools - #Stacks #Freebayes @uconnresearch.bsky.social @cbcuconn.bsky.social
Reposted by Kerry Cobb
Have you ever wondered: just how strong *is* the evidence for Muller's ratchet on mtDNA?
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
No molecular evidence for Muller's ratchet in mitochondrial genomes
Muller's ratchet predicts that non-recombining genomes can accumulate deleterious mutations, though molecular evidence for it is rare. Previous studies have tried to detect ratchet-like behavior in mi...
www.biorxiv.org
December 17, 2025 at 2:36 PM
Have you ever wondered: just how strong *is* the evidence for Muller's ratchet on mtDNA?
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Reposted by Kerry Cobb
@cademirch.bsky.social @erikenbody.bsky.social TB Sackton & @russcd.bsky.social introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST).
🔗 doi.org/10.1093/molbev/msaf282
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf282
#evobio #molbio #compbio
Efficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More)
Abstract. The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversi
doi.org
December 15, 2025 at 3:08 PM
@cademirch.bsky.social @erikenbody.bsky.social TB Sackton & @russcd.bsky.social introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST).
🔗 doi.org/10.1093/molbev/msaf282
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf282
#evobio #molbio #compbio
Reposted by Kerry Cobb
Virtual workshop on #genomics analysis for #RadSeq - spaces available still for next week - Dec 16-18th! Live instruction by @noahreid.bsky.social Learn QC through data analysis using common #bioinformatic tools - #Stacks #Freebayes @uconnresearch.bsky.social @cbcuconn.bsky.social
December 9, 2025 at 2:00 AM
Virtual workshop on #genomics analysis for #RadSeq - spaces available still for next week - Dec 16-18th! Live instruction by @noahreid.bsky.social Learn QC through data analysis using common #bioinformatic tools - #Stacks #Freebayes @uconnresearch.bsky.social @cbcuconn.bsky.social
Reposted by Kerry Cobb
We are running a RAD-seq workshop in two weeks.
Slowly putting together a page with more details on our workshop series.
cbc-uconn.github.io/workshops/ra...
Slowly putting together a page with more details on our workshop series.
cbc-uconn.github.io/workshops/ra...
December 1, 2025 at 7:16 PM
We are running a RAD-seq workshop in two weeks.
Slowly putting together a page with more details on our workshop series.
cbc-uconn.github.io/workshops/ra...
Slowly putting together a page with more details on our workshop series.
cbc-uconn.github.io/workshops/ra...
Reposted by Kerry Cobb
Excited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)
Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix
Observational studies are commonly used in psychology and epidemiology to identify risk factors correlated with health outcomes. However, these studies are vulnerable to confounding when shared geneti...
www.biorxiv.org
December 1, 2025 at 7:09 PM
Excited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)
Reposted by Kerry Cobb
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
Reposted by Kerry Cobb
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
November 26, 2025 at 4:21 PM
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Reposted by Kerry Cobb
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 8:57 PM
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Reposted by Kerry Cobb
In #GENETICS, @alan-aw.bsky.social et al. introduce models for how individual variant effects in admixed individuals may be influenced by ancestry, contributing to work on the genetic architecture of complex traits and their implications for polygenic prediction. buff.ly/34ZvEil
November 19, 2025 at 11:02 PM
In #GENETICS, @alan-aw.bsky.social et al. introduce models for how individual variant effects in admixed individuals may be influenced by ancestry, contributing to work on the genetic architecture of complex traits and their implications for polygenic prediction. buff.ly/34ZvEil